Long-lived states are particular configurations of nuclear spins which are well-protected against relaxation mechanisms. These configurations appear as particular terms in the spin density operator associated with unusually slow decay rate constants. A seminal example arises in systems of homonuclear spin-1/2 pairs in solution. Singlet order, meaning a population imbalance between the singlet...
Ancient mummies and bones, paintings and violins – what do they have in common? First, they are all highly relevant to cultural heritage, and second, we can use mobile NMR to learn specific details about each of them.
Mobile NMR is a non-destructive technique that uses single-sided mobile NMR sensors capable of recording NMR signals from samples that are exterior to the magnet. The two main...
Intrinsically disordered proteins (IDPs) (or –regions (IDRs)) are functional while existing in broad ensembles of near iso-energetic conformations. Despite their lack of structure, IDPs are involved in molecular communication forming associations ranging from binary, discrete complexes to large multicomponent assemblies. Similar to globular proteins their complexes serve structural,...
GPCRs belong to a family of ca. 850 plasma membrane-embedded proteins, which as molecular signalling switches control a wide range of physiological processes in health and disease. Activation of the individual receptor proteins is initiated via extracellular stimuli, such as photon uptake, or binding of small molecules, peptides, proteins, ions, lipids etc. This initial stimulus leads to...
Computation of conventional NMR parameters has become routine. There remain, however, interesting physics to be explored. I introduce four topics of this kind.
For the first time, measured $J$-coupling over a van der Waals (vdW) bond, between 129Xe and 3He in a gas-phase nuclear spin co-magnetometer, can be directly compared with quantitative calculations [1]. The latter...
Solid-state nuclear magnetic resonance (SSNMR) spectroscopy has emerged as an important technique for structural characterization of solids. Due to the fact that it provides local structural information about the environments of NMR-active nuclei, SSNMR is highly complementary to diffraction techniques whose strength lies in providing information about the long-range periodic structure of a...
The coordinates of a nuclear spin relative to a lanthanide ion can be determined with high accuracy in a system, where a paramagnetic lanthanide tag is attached to a protein of known three-dimensional structure. First, pseudocontact shifts (PCS) of the protein are measured by NMR to determine the coordinate frame of the magnetic susceptibility anisotropy (DeltaChi) tensor associated with the...
Pulse dipolar EPR is widely used to study tertiary structure, dynamics and functional features of biomolecules. Nitroxides are commonly used spin labels. Trityl radicals or TAMs have appeared recently as an alternative source of spin labels using PDEPR[1]. In this presentation we compared functional properties of spin labels based on TAMs and nitroxides.PDEPR in combination with MD were used...
Exchange processes which include conformational change, protonation/deprotonation, binding equilibria etc. are routinely studied by various 2D NMR techniques, e.g. EXSY, ZZ-exchange, CEST. In these techniques the information about exchange of nuclei between environments with different NMR parameters is obtained from the cross-peak development. Cross-peaks due to chemical exchange have been...
Under physiological conditions intrinsically disordered proteins (IDPs) lack a rigid three-dimensional structure; they can be rather described as a large ensemble of possible structures, that are adopted only transiently [1]. Nonetheless, in organisms they play a variety of roles, e.g. related to signaling and regulation. Interestingly, their flexibility is often crucial for fulfilling these...
Pseudocontact shift (PCS) NMR is a powerful tool to gain long-range structural information on protein-protein and protein-ligand interactions. We have shown the localization of three different fluorine containing high affinity ligands within the 30 kDa enzyme human carbonic anhydrase using only 19F PCS NMR [1]. The distances between the 19F atoms and the lanthanide cations ranged...
The GRAPE method of optimal control can attempt to find the maximum overlap between a desired rotation propagator and the effective propagator of the pulse sequence [1], termed the fidelity. In finding optimal rotation pulses, numerical optimisation methods use the gradient of the fidelity to give super-linear convergence to a maximum overlap [2].
Building on past research that creates...
Recently, spin-exchange relaxation free (SERF) alkali-vapor magnetometers have been applied as detectors of nuclear magnetic resonance (NMR) in the zero to ultralow field (ZULF) regime [1]. In ZULF the reduction of spectral line broadening due to field gradients as well as the possible existence of long-lived coherences [2] may lead to spectra with high resolution. These can provide new...
Measuring transverse relaxation rates provides insight into the dynamics of molecules. For example, measurements of relaxation dispersion allow the study of invisible conformations of proteins. Such applications are currently restricted to sparse spin systems in which homonuclear couplings can be neglected, such as 15NH or selectively labelled 13CHD2 groups in proteins. The accurate...
NMR is a powerful tool for studying the structural and electronic properties of paramagnetic solids. However, the interpretation of paramagnetic NMR spectra is often challenging as a result of the interactions of unpaired electrons with the nuclear spins of interest. Recently, we reported a novel protocol to compute and analyze NMR chemical shifts for extended paramagnetic solids, accounting...
The RNA polymerase (RNApol) of respiratory syncytial virus (RSV), the main agent responsible for bronchiolitis infections, is a viral RNA synthesis machinery composed of at least of 2 proteins, a 250 kDa catalytic subunit and a 4x27 kDa phosphoprotein co-factor (RSV P). RNApol associates with the viral nucleocapsid, a ribonucleic complex containing the genomic viral RNA matrix, as well as with...
Tetracene is an archetypal material undergoing singlet fission—the generation of a pair of triplet excitons from one singlet exciton. Here, using time-resolved electron spin resonance, we show how the spin dynamics in tetracene crystals are influenced by temperature and morphology. Upon cooling from 300 to 200 K, we observe a switch between singlet fission and intersystem crossing generated...
The interaction of the N-terminal domain of huntingtin exon-1 with membrane surfaces promotes poly-glutamine mediated aggregation, and is thought to play a role in the etiology of Huntington’s disease. We investigated the kinetics of binding of two huntingtin peptides, comprising the 16-residue N-terminal amphiphilic domain alone (httNT) and with a seven residue poly-glutamine C-terminal tract...
It is demonstrated that deep neural networks (DNN) are a powerful alternative to Tikhonov regularisation methods for the interpretation of double electron-electron resonance (DEER) data. Networks trained using large databases of synthetic DEER traces with carefully modelled distortions and noise are found to process previously unseen experimental data with results comparable to, and...
Methyl groups are privileged probes for the NMR study of large proteins. Methionine is the least abundant of the methyl-containing amino acids but is often directly connected to functionally important sites. While isotopic labeling with 13CH3-methionine is straightforward, assignment of the resulting spectra is challenging and often requires site-specific mutation of each...
The antigenic structure of the HIV-1 envelope spike (Env) is a major consideration for vaccine design to induce effective immune responses. Recent studies suggest that the cytoplasmic tail (CT) of Env influences the antigenic properties of its ectodomain on the opposite side of membrane, but the structural basis of this conformational coupling is still unknown. Using nuclear magnetic resonance...
All-solid-state Li-ion batteries are attracting considerable attention as possible alternatives to conventional liquid electrolyte-based devices as they present a viable opportunity for increased energy density and safety. In recent years, a number of candidate materials have been explored as possible solid electrolytes, including garnets, Li-stuffed garnets, Li-rich anti-perovskites (LiRAPs),...
Metal-organic frameworks (MOFs) are porous crystalline materials with promising applications in molecular adsorption, separation, and catalysis. It has been discovered recently that structural defects introduced unintentionally or by design could have a significant impact on their properties. However, the exact chemical composition and structural evolution under different conditions at the...
Framework flexibility (elasticity), i.e., the ability of a metal-organic framework (MOF) to considerably change its structure as a function of relevant parameters like pressure, temperature, and type of adsorbed molecules is only observed for some special compounds. The MOF compound Ni2(2,6-ndc)2(dabco) [2,6-ndc: 2,6-naphthalenedicarboxylate, dabco:...
Detection of metallic Dirac electron states on the surface of topological insulators${^1}$ is, to date, restricted to a small number of experimental techniques, such as angle resolved photoemission spectroscopy and scanning tunneling microscopy. The encroachment of the Dirac states into the bulk interior of a topological insulator is yet to be illuminated experimentally. Getting insight, is...
Elena Shanina, Sakonwan Kuhaudomlarp‡, Priscila Gomes†, Eike Siebsƒ, Alexander Titzƒ, Didier Rognan†, Anne Imberty‡, and Christoph Rademacher
Max Planck Institute of Colloids and Interfaces, Potsdam, Germany;
‡ Univ. Grenoble Alpes, CNRS, CERMAV, Grenoble,...
Signal Amplification By Reversible Exchange (SABRE) is a method based on the transfer of parahydrogen (p-H2) polarization to the substrate nuclei due to the constant exchange of p-H2 and ligands over metallic Ir center of metal-organic complex. Generated levels of polarization provide the higher signal of the ligand. In the experiments, when SABRE process occurs in high...
In this contribution, we present a simple analytical fitting approach based upon a power-law model of the segmental orientation autocorrelation function (OACF), by the way of which an effective power-law time scaling exponent and the amplitude of the OACF can be estimated from multiple-quantum (MQ) NMR data at any given temperature [1]. This obviates the use of the time-temperature...
Chloride salts have wide applications in pharmaceuticals, whether they are used for isolating and purifying the active pharmaceutical ingredients, or for providing more stability and/or solubility to the drugs. 35Cl nucleus has a 75% natural abundance and it is quadrupolar, with a nuclear spin I=3/2. In many organic compounds where it is covalently bound, the 35Cl nucleus...
Double Quantum NMR is a well-established method to study spatial proximities and local molecular dynamics in solid samples. In many cases, more or less restricted local dynamics of polymer chains has been analyzed. Here we studied the local packing of phosphate groups during the crystallization of precise polyethylene obtained from acrylic diene metathesis (ADMET) polycondensation with...
An unexpected great challenge in dDNP [1] has recently emerged with the use of ultra-shielded DNP magnets; the preservation of hyperpolarization during transfer from one ultra-shielded magnet to the other in ultra-low field regions, as magnetization not only relaxes but can be wiped-out in a non-adiabatic process.
We have recently proposed the design of a fluid path for dDNP [2] based on a...
Short-lived and low-abundance enzyme intermediate complexes represent a mainstream of transient protein complexes in enzyme catalysis and signal transductions. Many transient and unstable protein intermediate complexes are generated in real-time reactions or non-equilibrium conditions, however, resonance assignments of these unstable complexes are a challenge and structural determination of...
The automation of NMR structure determination remains a significant bottleneck towards increasing the throughput and accessibility of NMR as a structural biology tool to study proteins. The chief barrier currently is that obtaining NMR assignments at sufficient levels of completeness to accurately define the structures by conventional methods requires a significant amount of spectrometer time...
It is known that cobalt exhibits polymorphism: it exists in both hcp and fcc phases. Synthesis method and other thermodynamic conditions are known to play a role in determining the phase composition of cobalt nanoparticles. In this work, we have studied the phase composition of the cobalt nanoparticles synthesized using two different solvents (water) and ethanol. XRD measurements confirm the...
Hyperpolarization via dissolution Dynamic Nuclear Polarization (dDNP) is without doubt the most widespread technique to overcome the low sensitivity in the liquid state Magnetic Resonance.1 Hyperpolarized water is a versatile tool with possible applications ranging from biomedicine to chemistry. For instance, it can be used to acquire high resolution angiographic and perfusion...
NMR is a primary method of measurement that provides quantitative results without the need of a standard of the same measurand. Amongst different procedures for quantification of organic compounds by NMR, the International Bureau of Weights and Measures (BIPM) encourages the use of internal standard (IS) NMR as it presents less sources of errors and smaller uncertainties. The use of a...
NMR spectroscopy is an efficient method for obtaining quantitative data on the fractional 13C enrichment of metabolic intermediates or end-products. In biosynthetically directed fractional 13C labelling using uniformly 13C labelled carbon source, the biomass becomes 13C labelled in a metabolic flux distribution dependent manner and the cleavage and...
Exchange processes with the solvent may reveal useful information about intrinsically disordered proteins and their interactions. We introduce a new method to evaluate amide proton exchange rates that relies on the creation of a triple spin order state, i.e. 4CzNzHz. This spin state is left free to evolve in a variable mixing time during which it undergoes...
Introduction
Head and neck cancers (HNC) are mainly located in larynx, pharynx and oral cavity, which play crucial roles in respiratory, nutritional, social and communicative functions. The standard organ preservation treatment method for HNC is sequential and/or concurrent radiotherapy (RT) and chemotherapy (CHT). However, it is associated with significant temporary or permanent toxic side...
Hyperpolarization by dissolution DNP[1] provides a route to enhancing 13C MR sensitivity by more than four orders of magnitude on a wide range of small molecules. However, many potential applications of dDNP (metabolomics, drug discovery, etc.) would highly benefit from a higher efficiency, throughput, and repeatability of the method.
In this context, we had demonstrated in 2016 that high...
Telomeres are specialized structures located at the ends of linear chromosomes essential for cell viability and genome integrity. Their protective function is due to the formation of the Shelterin complex, that caps the end of the DNA. In the mammalian complex, Telomeric Repeat-binding Factor 2 (TRF2) interacts with TRF2-interacting protein 1 (RAP1).
We previously showed by ITC that TRF2-RAP1...
The large diversity of nucleic acid structures can be expanded even further by the introduction of metal-mediated base pairs in which base pairs are generated by coordination to metal ions instead or in addition to hydrogen bonds.[1,2] These metal-mediated base pairs consist of either natural or artificial nucleobases and are frequently used for the programmable and site-specific insertion of...
Direct interaction between intrinsically disordered proteins is often difficult to be characterized hampering the elucidation of their binding mechanism. Particularly challenging are the cases of extreme fuzziness of the complex, which is now appearing as a common interaction mode,requiring new models for their description.1
So far, nuclear magnetic resonance spectroscopy has...
2D J-resolved NMR spectroscopy, separating chemical shifts and J couplings along two independent dimensions, serves as a promising tool for studying molecular structures and compositions. In practice, the classic homo-nuclear 2D J-resolved spectroscopy [1], generally suffers from phase-twist lineshape and field inhomogeneity effects, thus rendering its potential applications limited. Here, a...
NMR spectroscopy is a nondestructive characterization technique that provides detailed information on molecular structures with incomparable specificity. With NMR, it is possible to observe chemical reactions, detect chemical substances, and to determine concentrations.
Commercial NMR devices are usually bulky, expensive and power hungry. To change this situation, our approach uses integrated...
G protein-coupled receptors (GPCRs) are physiologically important transmembrane signaling proteins that elicit intracellular responses upon binding of ligands on the extracellular site. Breakthroughs in crystallography have provided a wealth of static GPCR structures ranging from ligand-bound inactive receptors to fully active receptors in complex with intracellular binding partners such as...
α1-adrenoceptors (α1-ARs) comprise three G protein-coupled receptor (GPCRs) subtypes that stimulate smooth muscle contraction in response to binding adrenaline and noradrenaline. α1A-AR and α1B-AR are clinically targeted for treating hypertension and benign prostatic hyperplasia but are putative drug targets for neurodegenerative diseases. New subtype-selective tool compounds are required to...
Heterochromatin protein 1α (HP1α) plays a central role in the organization of nuclear content and in the regulation of gene expression and chromatin compaction. Recent work has shown that this protein can phase separate into liquid droplets and gels in vitro, properties that have vast implications for the mechanism of heterochromatin formation and regulation in cells. Despite the tremendous...
Fitting a weighted sum of exponentials to a noisy exponential decay is an ill-posed problem. In the T2 relaxation context, it leads to non-unique solutions because different sets of relaxation times and amplitudes give identical least-square distance between the model and the experimental data. Conventional data analysis combine a non-negative least squares (NNLS) algorithm...
In modern organic and medicinal chemistry, fluorine is commonly used to enhance the chemical properties of molecules in many desirable ways: it may delay the metabolism of the molecule, reduce the toxicity of aromatic groups, or increase the bioavailability. As a result, it is estimated that more than 20% of commercial pharmaceutical APIs and 30% of agrochemicals contain at least one fluorine...
The hyperpolarization of biologically relevant molecules for signal-enhanced magnetic resonance detection holds great promise for studying biological processes in vitro and in vivo. Being important metabolites as well as the building blocks of peptides, the canonical amino acids are promising targets for hyperpolarization, and a number of parahydrogen based strategies have been...
Electron Paramagnetic Resonance (EPR) in single crystals is used to study paramagnetic intermediates at the active-site of an enzyme to fully resolve the magnitudes and orientations of the g-, hyperfine, and quadrupole tensors. The electronic structure, when combined with X-ray crystallography, is related to a proposed molecular geometry to gain a better understanding of the catalytic...
NaK and other non-selective channels are able to conduct both sodium (Na+) and potassium (K+) with equally high efficiency. In contrast to previous crystallographic results, we show that the selectivity filter (SF) of NaK in native-like lipid membranes adopts two distinct conformations that are stabilized by either Na+ or K+ ions. The atomic...
Increased dietary consumption of sugar has been implicated in a number of clinical pathologies, including obesity and other metabolic diseases. High fructose corn syrup, a sugar mixture of about 40% glucose and 60% fructose, is a ubiquitous sweetening additive in a number of drinks and food. In this study, we have investigated the metabolism of these two types of sugar in SfXL glioblastoma and...
There exists a number of experimental methods which provide homodecoupled (pure-shift) 1H NMR spectra. Standard techniques (like PSYCHE [2] and TSE-PSYCHE [3]) require to record spectra in a pseudo-2D mode where chunks of data are acquired as separate FIDs. However, this often leads to very time-consuming experiments [1]. The problem with time rises, when a series of pure-shift proton spectra...
Pure-shift NMR [1] is a branch of techniques allowing the suppression of homonuclear J-couplings in an NMR spectrum. This gives a boost in resolution as multiplets in a spectrum collapse into singlets. The techniques rely on echo-type pulse sequences with selective pulses. In between the pulses, a short chunk of an FID is acquired. The whole FID is then constructed from these chunks.
The type...
The combination of a phase-modulated (PM) saturation pulse and symmetry-based dipolar recoupling into a rotational-echo saturation-pulse double-resonance (RESPDOR) sequence has been employed to measure 1H-14N distances. Such a measurement is challenging owing to the quadrupolar interaction of 14N nucleus and the intense 1H-1H homonuclear...
Unambiguous characterization of different acid sites in zeolites is of great importance in heterogeneous catalysis. In addition to various well-characterized extra-framework Al species, tri-coordinated framework aluminum species can also serve as Lewis acid site (LAS) in zeolites, which is however “NMR-invisible” due to its extremely distorted/asymmetrical local environment resulting in the...
Identification of chronic kidney disease patients at risk of progressing to end-stage renal disease (ESRD) is essential for treatment decision-making and clinical trial design. Here, we show that proton nuclear magnetic resonance (NMR) spectroscopy of blood plasma specimens together with techniques from machine learning improves the currently best performing kidney failure risk equation, the...
Ultralow-field (ULF) nuclear magnetic resonance spectroscopy (MRS) and magnetic resonance imaging (MRI) are promising methods allowing for, e.g., the simultaneous detection of multiple nuclei or imaging in the vicinity of metals. To overcome the inherently low signal-to-noise ratio that usually hampers a wider application, we present an alternative approach to prepolarized ULF MRS, employing...
The aggregation of beta-amyloid peptides is closely associated with Alzheimer's disease. We have used different chemical devices such as liposomes and reverse micelles to encapsulate the 40-residue beta-amyloid peptides so that the spatial confinement could lead to the formation of nonfibrillar aggregates of beta-amyloid peptides. These on-pathway beta-sheet intermediates were used to seed the...
The general problem of NMR and MRI is their low sensitivity. The NMR/MRI signal intensity is proportional to the nuclear spin polarization that is on the order of 10−5 or less at a common magnetic field of NMR/MRI. On the other hand, triplet dynamic nuclear polarization (triplet-DNP), a method to enhance NMR/MRI sensitivity using photoexcited triplet electrons, has the great...
Algorithmic cooling is a relatively new method to increase overall spin-polarization in NMR, which is based on manipulations of coupled slow-relaxing and fast-relaxing spins. The method enables increasing the magnetization of slow-relaxing spin by using the ability of fast-relaxing spins to pump entropy into the environment. Here, we suggest a new method to increase spin polarization by using...
Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes and act at the heart of fundamental cellular processes such as cell cycle control and signal transduction. The aberrant function of IDPs is therefore associated with severe diseases such as cancers and neurodegenerative diseases. Protein functions are mediated via motions, therefore a detailed characterization of...
Tc toxins are 1.7 MDa protein complexes that are found in insect- and human-pathogenic bacteria. After endocytosis, Tc penetrates the membrane of the host’s cells and translocates a deadly enzyme into the cytosol. The complex consists of three subunits: the 1.4 MDa TcA pentamer, which mediates target cell association, membrane insertion and toxin translocation, and two smaller subunits, TcB...
The inversion of NMR relaxation time is very important to study object’s molecular dynamics. The inversion is to solve the Fredholm integral equation of the first kind with non-negative constraints, which is known as an ill-posed problem. In this paper, a novel method is presented for NMR inversion based on the regularization method. The proposed objective function can transform the...
EPR is a powerful tool for the investigation of the dynamics of the spin triplet states (STS), i.e. states with the total spin number S=1. A great number of EPR experiments, as well as spin-lattice relaxation (SLR) investigations on STS were made in zero field (ZF). ZF EPR allows studying paramagnetic properties and molecular motion with ultrahigh precision under the action of small...
With the advent of organic solvent compatible orienting media based on either lyotropic liquid crystalline (LLC) phases or swollen gels, the measurement of anisotropic NMR parameters like residual dipolar couplings (RDCs), residual quadrupolar couplings (RQCs) and residual chemical shift anisotropy (RCSA) has become a powerful means to determine the configuration of dissolved molecules. When...
Glycosylation and spontaneous modifications are critical quality attributes of protein therapeutics that can impact drug efficacy and safety. Therefore they need to be tightly monitored during production, formulation and storage. Mass spectrometry and fluorescence-detected chromatography are currently the dominating methods for the analysis of post-translational modifications (PTMs) including...
The functions of lubricant base oil are largely correlated to its structure and composition, which are however very difficult to be measured simultaneously by current analytical methods. Mass spectroscopy could get quantitative group composition of base oil, but it is deficient in characterization of structures with branches. On the other hand, conventional NMR method is not only suffered from...
The aim of a metabolic study is the differentiation of biological populations by their metabolite composition. Even in a simple model the assessment of large numbers of samples is mandatory to produce statistically meaningful data. This requirement becomes even larger in the analysis of metabolite progression, for example in disease development, or mixtures of commodities, for example the...
Hyperpolarized water is a valuable aid in biomolecular NMR. One can utilize it to achieve, under physiologically-like conditions, amide group polarizations that are orders-of-magnitude larger than their thermal counterparts. Suitable experimental procedures can exploit this to deliver 2D 1H-15N NMR correlations, with good resolution and enhanced sensitivity. The resulting...
Pulmonary compliance is an important index for evaluating the function of the lung, which could reflect the pulmonary ability to stretch and expand. Hyperpolarized 129Xe MR is a powerful tool in quantifying the microstructure and function of the lung in vivo, and it has unique advantages in measuring the gas volume in the lung. In this study, a proof-of-concept method was proposed...
The restrictive limits of molecular tumbling have made the study of large proteins and protein complexes a subject ideally suited to the strengths of magic-angle-spinning (MAS) solid-state NMR. Protons form a dense network of strong dipolar interactions and their shifts are sensitive reporters of protein structure and interactions. Higher MAS rates and highly deuterated samples have allowed...
Inorganic materials and compounds with transition metals find numerous applications within catalysis, environmental remediation as well as for energy storage and conversion due to their flexible oxidation states. However, their characterization is challenging due to the absence of long-range order, structural defects and/or the multi-phase nature of such materials. Solid state NMR (SSNMR) is...
The development of improved heterogeneous catalysts can be undertaken in a rational way by a better understanding of their atomic-level structures. Solid-state NMR spectroscopy is very well suited to the study of heterogeneous catalysts because it can give information on the local structure. However, the lack of sensitivity and resolution limits the characterization of surface sites, notably...
Molecular chaperones are necessary for maintaining a functional proteome in the cell by preventing the aggregation of unfolded proteins and/or assisting with their folding. Despite the central importance of the binding of chaperones to unfolded substrates, the structural basis of their interaction remains poorly understood. The scarcity of structural data on complexes between chaperones and...
Benchtop NMR spectrometers are a promising tool for chemical laboratories worldwide because of their moderate price and low handling cost. The easy setup of flow measurements makes them convenient to use for reaction/process monitoring. However, their applications are mainly limited to simple tasks. This is due to the insufficient spectral resolution and sensitivity, which are a consequence of...
Gadolinium is the most promising spin type for in cell studies of spin-labeled proteins. However, the availability of other bioresistant spin labels could aid the development of structural studies of biomolecules in a cellular context. The relatively small and flexible nitroxide label could offer many advantages in this area of research. We characterized iodoacetamide- and...
We have developed experimental methods for initiating nonequilibrium structural conversion processes (e.g., protein folding, peptide self-assembly, ligand/receptor complex formation, etc.) by rapid mixing and for trapping intermediate states by rapid freezing after a defined time interval, on the millisecond time scale. When combined with low-temperature dynamic nuclear polarization,...
Block copolymers (BCP) due to their unique self-assembling properties represent important group among synthetic materials and they are believed to play significant role in future nanolithography. It appears that below certain critical temperature TODT (order-disorder transition temperature) two dissimilar subchains (blocks) become immiscible and tend to separate one from another gathering with...
The recently introduced CLIP-COSY[1] experiment providing homonuclear correlation spectrum with high quality clean in-phase multiplets expedites the assignment of scalar coupled proton spin network, aiding the structure elucidation of small- and medium-sized molecules. The resolution of COSY spectra is, however, limited by the inherently small chemical shift dispersion of proton...
BReast CAncer susceptibility protein 2 (BRCA2) is a 3000 residues long protein that serves as a plateform for proteins involved in genomic stability and mitosis. These functions are regulated by kinases phosphorylating BRCA2 unfolded regions. Among these kinases, Plk1 has the most remarkable impacts on BRCA2. Plk1 is involved in cell cycle progression and mitosis regulation and it is found...
UFM1 is an ubiquitin like protein (UBL), which shares high structural but little sequence similarities to ubiquitin. Like ubiquitin it can be covalently attached to target proteins by specific enzymatic cascade called ufmylation. Ufmylation of target proteins plays a role in central cellular events, such as gene transcription, response to cell stress and differentiation. The process of...
Cancer is a devastating disease that affects the lives of almost everyone, and its effective treatment still remains an important unmet medical need. In order to discover new cancer drugs, we are applying fragment-based methods and structure-based design to identify and optimize small molecules that inhibit highly validated cancer targets. Although many of these targets are technically...
RIP2 is an intracellular protein that is essential for several intracellular reaction cascades. Adaptor protein RIP2 is recruited when the bacterial fragments activate the innate immune pattern recognition receptor NOD2 and NOD1. That leads to interactions with NF-κB and activation of proinflammatory cytokine production. Also, RIP2 is involved when the membrane receptor P75 transduces the...
Among the hyperpolarization (HP) techniques, parahydrogen-based methods are the simplest and technically least demanding. Because such techniques (PHIP, SABRE) rely heavily on catalysis, some of the unsolved problems in both fields are rather similar. One major trend in modern catalysis is a broad search for approaches to combine advantages of homogeneous and heterogeneous catalysts, namely...
The high relevance of G protein-coupled receptors (GPCRs) becomes apparent from their diverse distribution in human tissue and their participation in a variety of physiological functions. This makes them highly interesting molecules for basic research and also a major target for pharmaceutical drugs.
Besides the structural architecture of the seven transmembrane proteins and its interaction...
The physical properties of cement are directly affected by the components of hydrates. NMR T2 experiment using CPMG pulse sequence is a very useful tool to distinguish these components, as the different T2 relaxation values of various states of water. However, CPMG pulse sequence can be constrained by hardware conditions, most notably its echo spacing time (TE). TE always has a minimum value...
Uropathogenic Escherichia coli invades and colonizes hosts by attaching to cells using adhesive pili on the bacterial surface. Although many biophysical techniques have been used to study the structure and mechanical properties of pili, many important details are still unknown. Here we use proton-detected solid-state NMR experiments to investigate solvent accessibility and structural...
Increasing CO2 concentration from anthropogenic sources in the atmosphere is one of the main causes of global climate change and post-combustion CO2 capture is part of the solution to tackle such environmental challenge. Because of their lower regeneration cost, amine-modified porous silicas (AMPS) are the most promising CO2–adsorbents since they are...
RNA is a versatile biomolecule that plays an important role in many cellular processes e.g. translating the genetic information, gene regulation, and reaction catalysis in organisms. NMR spectroscopy can be used to obtain conclusive informations about the structure and dynamics of a system, as well as to investigate interactions of RNA with proteins, ions or ligands. However, long RNAs with...
Interest in RNA structure determination has increased in recent times due to the discovery of many functional RNAs and the existence of a clear structure-function-relationship for RNA. Current approaches of RNA sample preparation for structure investigation with NMR spectroscopy, which has become a useful method for RNA structure-function analysis, are usually time-consuming. Here, we present...
Channelrhodopsin-2 (ChR2) is a light-gated ion channel[1] which over the last years has attracted considerable interest due to its unparalleled role in optogenetic applications[2]. However, despite considerable efforts, it has remained elusive how molecular events during the photocycle including the retinal trans-cis isomerization and the de/re-protonation of the Schiff base are coupled to the...
Recently, the proposal and concept development of using chip-integrated voltage-controlled oscillator for electron spin detection has gained significant attention in the research community. Being at the same time highly sensitive and compact in size, these ESR-on-a-chip detectors are ideally suited for next generation portable ESR spectrometer [1]. Moreover, thanks to the fast electronic...
Nitrogen-vacancy color centers (NVs) in diamond can be measured at the single cite level even at room temperature, allowing to perform a variety of fundamental experiments.
Here the recent progress in controlling small nuclear spin ensembles at ambient conditions will be presented. A Dynamic Nuclear spin Polarization (DNP) method was developed to transfer the NV’s high (> 92 %) electron spin...
Acylgermanes are efficient germanium-based photoinitiators (PIs) that are suitable for medical applications such as dental fillings.[1–4] Remarkably, this class of compounds displays electron-transfer properties being comparable with phosphorus-based photoinitiators.[5]
Here we present a combined EPR/DFT/CV approach to characterize the redox properties of acylgermanes....
In view of the world-wide emergence of pathogens being resistant to a large range of commonly used antibiotics finding pharmaceuticals with novel mechanisms of action has become an urgent need. Antimicrobial peptides are abundant in the plant and animal kingdom, have escaped resistance development over millions of years and are therefore considered valuable templates to develop novel drugs. In...
Depletion of helium reserves in the USA as well as unstable political situation around the state of Qatar has caused helium shortages and price increase around the world. Recycling and re-liquefaction of helium provide end users independency on LHe suppliers, simplify logistics and save costs [1]. Environmental aspects are also a strong argument for helium recycling.
Quantum Design Inc. in...
The vast volume of sea oil transport and rise in the number of underwater drilling platforms all around a world creates a great risk for environment. To minimize the ecological impact of possible water spills there is a need for cheap, oil selective materials used for cleaning oil spills from the sea surface.
In the recent years a new branch of aerogel material made up of cellulose...
Neurotensin (NT) is a 13 amino acid peptide expressed in the central nervous, gastro-intestinal and cardiovascular systems where it acts as a neuromodulator of classical neurotransmitters such as dopamine and glutamate, primarily through activation of neurotensin receptor 1 (NTS1), a G Protein-Coupled Receptor (GPCR). Peptide ligands of GPCRs bind through complex, and possibly multiple modes...
Riboswitches are RNA structures that regulate the downstream gene expression upon binding of a small molecule ligand. The guanidine-II riboswitch is a guanidine-binding translational ON switch that is present in many proteobacterial species. The associated genes are usually involved in guanidine detoxification. This riboswitch class is characterized by two hairpins (P1 and P2) with an ACGR...
G protein-coupled receptors (GPCRs) are membrane-integrated signaling proteins that translate extracellular stimuli into an intracellular response for processes ranging from vision, smell and taste to immunologic, neurologic and reproductive functions. Only 16% of the superfamily are clinically targeted – and yet these comprise nearly 35% of all marketed drugs. Despite their obvious...
Conformational ensembles of intrinsically disordered proteins (IDPs) are particularly challenging to characterize. One can obtain information about the entire conformational ensemble of the IDPs by Solid-State NMR in frozen solution. From the experimental side, we have studied the sparsely isotope labelled IDP a-synuclein (α-syn) in frozen solution by Dynamic Nuclear Polarization NMR (DNP-NMR)...
2D NMR spectroscopy is an extremely useful method for analyzing the structure and dynamics of small molecules in liquids and in solid state. Modern 2D NMR approaches allow obtaining direct information about the geometrical configuration of small molecules, which is very important when solving problems of modern physical chemistry of fluids (e.g. micronization of drug substances,...
Abnormal expression of PHF20L1 is closely related to the oncogenesis of breast and ovarian cancer1. Knockdown or mutation of PHF20L1 induces DNMT1 degradation and genome hypomethylation, as PHF20L1 stablizes DNA methyltransferase DNMT1 mono-methylated at lysine 142 (K142me)2. It is bewilderingly that the crystal structure of the homolog PHF20 reveals a closed aromatic...
Several human diseases result from malfunctions of ABC systems. Many ABC exporters contain asymmetric nucleotide-binding sites (NBSs) and some of them are inhibited by the transported substrate.[1] To actively transport diverse chemically substrates across biological membranes, ATP-binding cassette (ABC) transport complexes use the energy of ATP binding and subsequent hydrolysis. In this work,...
The microtubule‐associated protein Tau plays a key role in Alzheimer’s disease (AD). In healthy conditions, Tau binds to tubulin and microtubules, promotes tubulin polymerization and regulates microtubule dynamics in neurons. However, during the course of AD, Tau aggregates into oligomers and amyloid fibrils, which further associate into neurofibrillary tangles in the intracellular space. The...
Conventional nuclear magnetic resonance (NMR) experiments are limited by low sensitivity. Hyperpolarization techniques such as dynamic nuclear polarization (DNP) enhance NMR signals by several orders of magnitude [Larsen et. al. 2003]. Most dissolution-DNP (dDNP) applications involve the use of weakly magnetic isotopes such as 13C, but excessively long...
Copper plays a vital role in fundamental cellular functions, and its concentration in the cell must be tightly regulated, as dysfunction of copper homeostasis is linked to severe neurological diseases and cancer. This talk provides a compendium of current knowledge regarding the mechanism of copper transfer from the blood system to the Golgi apparatus; this mechanism involves the blood carrier...
The dangling bond (db) is the most prominent electronic defect in hydrogenated amorphous silicon (a-Si:H). Acting as recombination centers for charge carriers, dbs crucially determine the electronic material properties. Understanding the mechanism of db-related recombination thus constitutes one of the most fundamental issues concerning a-Si:H.
Since a neutral db is paramagnetic, the ideal...
Some quantum computation schemes rely on having ordered structures of qubits with nano-scale positioning accuracy to perform correctly. One natural candidate for such a system of qubits is an ordered structure of electron spins in a solid-state sample. Such systems (e.g. $\text{NV}^{-}$ centers in diamond, and phosphorus doped $^{28}\text{Si}$) exist in unordered forms, and have been shown to...
Delta subunit of RNA polymerase is exclusively present in Gram positive bacteria. It was proven that it is important for virulence of the bacteria, it ensures the quick and proper response to the changing cell environment conditions, and its role for regulation of RNA polymerase activity was also demonstrated [1]. However, the function of the delta subunit is not fully understood at molecular...
Structure-property relations are essential for designing materials. As many properties are governed by defects and disorder, respectively, elucidating structural details on various length scales is a cornerstone for material science and solid-state chemistry. This lecture will give an overview of our recent progress on using solid-state NMR spectroscopic techniques for studying defects and...
A wide ensemble of protein-protein interaction networks warrants communication and information exchange between cells. These interactions are mainly mediated by protein domains, which could be considered as protein modular building blocks assembled in different fashions. They decode specific signals emerging from post-translational modifications involved in receptor signaling, endocytosis or...
Hyperpolarization by dissolution dynamic nuclear polarization [1] has emerged in the last decade as a powerful tool for boosting the sensitivity of magnetic resonance by orders of magnitude. This has for instance brought metabolic imaging to reality [2]. Unfortunately, hyperpolarization’s lifetimes in all molecules hardly exceed a minute. This means that hyperpolarization needs to be produced...
Paramagnetic restraints have been used in Biomolecular NMR for the last three decades in order to elucidate and refine structures but also to characterize protein/ligand interactions1. Pseudo Contact Shifts (PCS) are the most commonly used restraints, consisting in measuring a shift between a paramagnetic species and a diamagnetic reference, whose magnitude depends on the distance...
The relationship of pancreatic cancer (PC) and diabetes mellitus (DM) is obvious, as more than 2/3rd of the cancer cases are diagnosed with DM. This so-called pancreatogenic diabetes (T3cDM) appears prior to PC within a period of three years and is accompanied by characteristic features such as absence of obesity or frequent infections1. PC belongs to the most lethal...
We have demonstrated 57Fe Zero Field Nuclear Magnetic Resonance (ZFNMR) as a powerful tool in determining the structural composition of nickel-cadmium spinel ferrites of various compositions of Ni1-x CdxxFe2O4 from x = 0 to1, which are synthesized via one-step auto combustion technique. The XRD measurements confirm the phase purity of...
The roster of molecular imaging methods has been recently extended by the introduction of deuterium metabolic imaging (DMI), whereby after administration of a deuterated precursor in rodents or humans, deuterium MRS and MRSI is used to examine metabolic products such as glutamine/glutamate or lactate when applied to brain studies. Here we examine its use for imaging pregnancy-related...
Solid-state dynamic nuclear polarization (DNP) NMR utilizes radical-bearing polarization agents to enhance the signal of nearby nuclei. Consequently, small sample sizes along with insensitive and higher-dimension experiments become feasible on realistic time scales. These sensitivity gains are particularly intriguing for applications to biological systems, where the molecule of interest is...
Heteronuclear-detected NMR experiments are becoming increasingly more common due to the constant development in cryogenic probes. These experiments are particularly beneficial with respect to nucleic acids due to the inherent low proton-density and limited 1H-chemical shift dispersion. Here, we present 15N- and 13C-detected NMR experiments that enable...
We have been developing a millimeter (mm)-wave ESR/NMR double magnetic resonance system in ultra-low temperature and high magnetic field regions aiming for direct detection of diluted nuclear spins.
Increase of nuclear magnetization by using dynamic nuclear polarization (DNP) may enable direct observation of NMR.
One of our targets is a silicon crystal doped lightly with phosphorus...
Fast field cycling (FFC) NMR relaxometry enhanced by DNP [1] has recently been reported to obtain T1 relaxation time dispersion with increased sensitivity and selectivity to study molecular dynamics in various systems. First studies were devoted to the measurement of the DNP spectrum and enhancement as well as DNP-enhanced dispersion curves of polymer systems in the presence of...
Cyclosporin A, well known as an immunosuppressive agent, is one of a family of congeners synthesised in certain soil fungi. Three natural variants of cyclosporin (B, C, D) were studied by high resolution NMR spectroscopy in chloroform and dimethyl formamide. CsB has alanine in position 2 instead of $\alpha$-aminobutyric acid (Abu2) found in CsA, in CsC this residue is replaced by threonine,...
For application of electrolyte materials in energy storage devices their transport properties are essential. Multinuclear (e.g. 1H, 7Li, 19F) Pulsed-Field-Gradient (PFG)-NMR diffusion has become a widely used method in this field. However, to identify the conductivity contribution of specific ion species remains a challenge, since the electrophoretic mobility µ...
Type II collagen is the most abundant macromolecule in articular cartilage. In the tissue collagen forms anisotropic, fibrillous structures. Longitudinal relaxation is generally thought to be isotropic in articular cartilage [1]. We investigate the conditions needed to observe the anisotropy of the collagen network in the longitudinal relaxation time $T_1$.
We have computed longitudinal...
Filamentous supramolecular nanostructures are implicated as pathogenic players in human diseases, such as atherosclerosis, Huntington’s and Alzheimer’s diseases, but are also increasingly seen as powerful frameworks for building functional hydrogels and nanomaterials. In both cases, few methods permit the site-specific determination of structure and motion in the nanoscopic filaments, which...
We apply solid-state MAS NMR-spectroscopy at different temperatures to investigate protein folding and misfolding on a molecular level [1].
On the one hand, we exploit DNP-enhanced MAS NMR spectroscopy at low temperatures (~100K) to investigate conformational ensembles of intrinsically disordered proteins IDPs). Such proteins are not represented by a single well-defined structure but rather by...
Dissolvable 3D-printed templates can be used to produce NMR transceiver coils of a particular geometry. Wire coils such as variable-pitch solenoids are wound on dissolvable 3D printed forms, which are then dissolved away in solvent. The use of high-temperature resin, with the appropriate solvent, enables annealing to be performed before dissolving the template. This approach allows facile,...
MAS DNP is increasingly establishing itself as a powerful technique to boost sensitivity of NMR. It makes it possible to run, in minutes, experiments that would take weeks, or simply would not be possible otherwise because they are too insensitive. At 9.4 T (400 MHz) and 100 K, DNP enhancements of around 250 are now possible with several polarizing agents (PA) (AMUPol1, TEKPol2, and more...
The ability of corals to maintain homeostasis and mineralize has been compromised by ocean acidification and temperature rise causing reefs to recede and even vanish. Therefore, corals have been serving lately as important proxies of environmental impact on marine life. As newborn, corals undergo transformation from a swimming organism (planula) to an benthic immobile one (polyp), that lives...
Enhancement of NMR signals using dynamic nuclear polarization (DNP) enables studying systems that are difficult to tackle with conventional NMR due to low concentrations or low overall quantities of material. One particular example is amyloid-beta peptide, which self-assembly in human brain tissue leads to neurodegeneration in Alzheimer’s disease (AD). Previously, various intermediates along...
Proteorhodopsin (PR) is found in marine bacteria in various ecosystems and is one of the most abundant photoreceptors. It converts light into a transmembrane, electrochemical gradient and forms functionally unresolved higher oligomers. Although the PR monomer is able to undergo a full photocycle, the question arises whether the pentameric complex formed in the membrane via specific...
Domain swapping is a mechanism responsible for existence of alternative folded structures of certain proteins and is indicated in amyloid fibril formation by certain peptides1. A mutant of Immunoglobulin binding domain B1 of Streptococcal Protein G, GB1 HS#124F26A has been known to exist as a domain swapped dimer in equilibrium with its partially folded monomeric...
Proteins are inherently dynamic, exhibiting conformational freedom on many timescales,1 implicating structural rearrangements that play a major role in molecular interaction, thermodynamic stability and biological function. Intrinsically disordered proteins (IDPs) represent extreme examples where flexibility defines molecular function. IDPs exhibit highly heterogeneous local and...
DNP in liquids is driven by electron-nuclear cross-relaxation, known as Overhauser effect (O-DNP). When relaxation is dominated by scalar hyperfine interaction, the enhancements can reach three orders of magnitudes, as recently reported for $^{13}$C-DNP at 3.4 T [1].
Hereby we present a systematic study performed at different magnetic fields on model systems doped with nitroxide radical...
For mechanistic investigation of energy conversion/storage systems such as fuel cells and batteries, integral understanding of not only electrochemical phenomena but also chemical reactions and dynamics of chemical species in the systems is essential. We have employed various NMR techniques to reach the goal and some results will be presented.
The water and proton dynamics in Nafion polymer...
BiP is the only member of the Hsp70 chaperone family in the human endoplasmic reticulum (1). Its chaperone activity is driven by ATP binding and hydrolysis that trigger the conformational change regulating the docking and undocking of its nucleotide-binding domain (NBD) and substrate-binding domain (SBD). To achieve its many functions, BiP is regulated by several co-chaperones including the...
β-lactamases pose a great threat to our healthcare system, yet may simultaneously present potential solutions. We used CEST, CPMG relaxation dispersion and T1, T2, NOE Lipari-Szabo analyses to characterise the dynamic behaviour of the β-lactamase of Mycobacterium tuberculosis, BlaC, over a wide range of timescales. BlaC is mostly rigid on the fast timescales and shows...
The activities of membrane proteins strongly depend on their dynamics; herein we made use of proton-detected MAS at very high-field and of relaxation violated experiments in liquid state NMR to describe the dynamics of the membrane domain of the Outer Membrane Protein A of Klebsiella pneumoniae (KpOmpA) in liposomes and in micelles.
From 15N relaxation rates and...
We consider the behaviour of precessional phase carried by molecules of a diffusing specimen under magnetic fields typical of magnetic resonance experiments. A time evolution equation for the ensemble of particles is constructed, which treats the phase as well as the position of the molecules as random variables. We refer to the associated probability density function $p ({\vec x}, \phi |t)$...
Oncogenic variants of kras gene are among the most important mutations causing cancer. KRas protein is a membrane-bound small GTPase which acts as a molecular switch and plays a key role in many signal transduction pathways regulating cell proliferation, differentiation, and survival. It alternates between its GTP-bound active and the GDP-bound inactive conformers. The most frequent oncogenic...
Dynamic Nuclear Polarization (DNP) is the most widespread and ubiquitous technique for signal enhancement in Nuclear Magnetic Resonance (NMR). Introduction of the ability to arbitrary modulate the 193 GHz waveform used for excitation of the electron spins at 7 Tesla resulted in up to a factor of 4 improvement in DNP efficiency under varying range of experimental conditions and across different...
Encapsulated atomic hydrogen in silsesquioxane cages is a promising candidate for applications in emerging technologies like spin-based quantum computing, magnetic field sensing, and atomic clock devices. Compared to endohedral fullerenes (N@C$_{60}$ or P@C$_{60}$), which are currently the most used molecular spin systems for demonstrating single-quantum gates and quantum memories, atomic...
So far, we investigated the electronic structure of novel type of organic conductors, ammonium tetrathiafulvalene carboxylate (TTFCOO) and its and tetrathiapentalene derivative (TTPCOO) by high-field ESR and NMR measurements. The pristine TTFCOOH and TTPCOOH molecules are closed-shell. Kobayashi and coworkers (NIMS, Japan) found that self-doped type carrier was generated by substitution of the...
Collagens are the most abundant components of the extracellular matrix (ECM). Due to their diverse structures and compositions, collagens serve many functions, providing structural and mechanical support for surrounding cells, and playing important roles in cell-to-cell communication. Nonetheless, despite being at first glance a simple protein formed by three homologous polypeptide chains of...
We have demonstrated that 1H spin–spin relaxation time (T2), which is measured by using low field NMR techniques, is an effective parameter to elucidate the degradation behavior of poly (urea-urethane). It is difficult to reveal the degradation behavior of poly (urea-urethane), when the degradation proceeds in urea or urethane bond units.
We prepared two types of poly...
β-peptides are important peptidomimetic compounds. Here the formation of ordered backbone conformation of new pentamer β-peptides was studied by NMR (1H, ROESY, TOCSY, COSY NMR techniques) and ECD spectroscopy. The investigated pentamers include trans-[R,R]-2-aminocyclohexanecarboxylic acid (trans-[R,R]-ACHC) building blocks interrupted by different elements in the middle of...
In recent years magic angle spinning - dynamic nuclear polarization (MAS-DNP) developed as an excellent approach for boosting the sensitivity of solid state NMR (ssNMR) spectroscopy, thereby enabling the characterization of challenging systems in biology and chemistry. Most commonly, MAS-DNP is based on the use of nitroxide biradicals as polarizing agents. In materials science, since the use...
Currently, proton nuclear magnetic resonance (1H-NMR) have been combined with electrochemistry (EC) to observe reaction pathways and identify products generated due to its high selectivity, capacity in chemical structure determination [1], and quantitation [2]. We have utilized NMR in our electro-catalysis researches, with a representative example that electro-catalytic performances of...
Nuclear magnetic resonance (NMR) spectroscopy serves as a versatile analytical tool. Resolution is an essential challenge in NMR spectroscopy. Due to the limited range of chemical shifts and extensive signal splittings due to scalar couplings, signal congestion and even overlap are common in NMR spectra, especially in the widely used proton spectra. One major approach to enhance spectral...
The present reports the results of the experimental study of static and dynamical characteristics of the Er3+ ions in the YGa3(BO3)4 crystals. g-factors and the constants of hyperfine interaction are found. The ratio gzAx/ gx*Az is close to unity that is an evidence of insignificant admixing of the excited multiplets. The widening of the absorption lines related to the temperature increase...
Amino acid radicals are involved in essential processes in primary metabolism such as photosynthesis, respiration, and biosynthesis of DNA building blocks. They serve as one-electron redox cofactors in biocatalysis and multistep proton-coupled electron transfer (PCET) reactions. E. coli class Ia ribonucleotide reductase (RNR), which catalyzes the reduction of nucleotides to their...
Hsp90 is a central chaperone performing its activity hydrolyzing ATP with Mg(II) as cofactor. Hsp90 is homo-dimeric and each monomer consists of 3 domains (CTD, MD, NTD). The ATPase site is in the NTDs, while the CTDs are dimerized. In absence of nucleotide Hsp90 is in ‘open’ conformation shifting to an ATP-bound ‘closed’ conformation by dimerization of the NTDs.[1] Yet, there are still open...
Intrinsically disordered proteins (IDPs) are proteins that do not possess a unique well-defined structure, but rather continuously exchange between different conformers. The IDP tau is known to aggregate into amyloid filaments, which are highly ordered protein assemblies, involved in many neurodegenerative diseases including Alzheimer’s disease. Different types of aggregates, called strains,...
Dense metal-formate frameworks of general formula [A][M(HCOO)3]n attracted significant attention of the scientific community due to the indications of the multiferroic behavior [1]. These compounds consist of transition metal ions (M2+) linked by formate groups into porous frameworks, where each pore confines a single molecular cation (An+). The...
Microfluidics is a well-established technique to process, synthesize and analyse small amounts of materials for chemical, biological, medical, and environmental applications. Typically, it involve the use of reagents with volume that is smaller than ~1 microliter – ideally even nano- or pico-liter. Conventional electron spin resonance (ESR), is typically carried out with ~ 1 ml of sample,...
Riboswitches are non-coding RNAs binding a specific second-messenger, modulating transcriptional or translational efficiency of their corresponding genes. These regulatory mechanisms are found in a wide variety of bacteria and are often associated with lifestyle changes like biofilm formation and transition into anaerobic metabolism.[1-3] These lifestyle changes include pathways required for...
Pyrimidine base namely Uracil and its derivatives have immense biological relevance. The Proton Transfer (PT) rate in solution for these molecules determines the nature of solvation, cellular mobility and effect of solution pH on the biological activity. Therefore, quantification of PT rate has attracted attention over the years[1,2]. In the present study, an attempt has been made to avail...
RNA does not only translate the genetic code into proteins, but also carries out important cellular functions. Understanding such functions requires knowledge of the structure and dynamics at atomic resolution. Almost half of the published RNA structures have been solved by NMR, but as a result of severe resonance overlap and low proton density, high-resolution RNA structures are rarely...
The rapid methodology development of sensitivity-enhanced SSNMR spectroscopy has been empowering its success in a broad range of challenging fields in life science. Here I will present a new methyl SSNMR toolkit for exploring the protein structures that offers new types of NMR parameters for decoding the complex molecular systems. These approaches meld DNP-enhancement, heteronuclear NOE, tamed...
A complete description of the pathways and mechanisms of protein folding requires a detailed structural and energetic characterization of the folding energy landscape. Simulations, when corroborated by experimental data yielding global information on the folding process, can provide this level of insight. Molecular Dynamics (MD) has often been combined with force spectroscopy experiments to...
Brevinin-1BYa (FLPILASLAAKFGPKLFCLVTKKC) is a 24-amino acid residue host-defence peptide, first isolated from the skin secretions of the foothill yellow-legged frog Rana boylii. The peptide is of interest as it shows broad-spectrum antimicrobial activity, and is particularly effective against opportunistic yeast pathogens. Its potential for clinical use, however, is hindered by its latent...
Higher magnetic fields lead to higher sensitivity and higher resolution. Reaching higher fields is key to study biomolecular systems of increasing complexity. Yet, higher fields are not optimal for all applications of NMR, neither for all nuclei. For instance, the chemical shift anisotropies of carbon-13 nuclei in many chemical entities, or that of fluorine-19 lead to transverse relaxation...
Smilacis Glabrae Rhizoma is a traditional Chinese medicine used for dissipating stasis, detoxification and diuresis. Astilbin and its three diastereoisomers (neoastilbin, isoastilbin, and neoisoastilbin) and engeletin are the main bioactive components. To quickly conduct the quality control, a proton nuclear magnetic resonance approach was established to simultaneously quantify the absolute...
Because of the hyperfine coupling between unpaired electrons and nuclear spins, NMR signals in paramagnetic systems often experience large shifts and possess short relaxation times, particularly in close proximity to the metal center, rendering observation of active sites in metalloproteins particularly challenging.
Here, we illustrate how, by adapting a set of NMR experiments originally...
NMR is a major tool in metabolomics thanks to its non-destructive and highly reproducible character. NMR metabolomics include untargeted analysis where spectral fingerprints are analyzed with statistical tools to highlight potential biomarkers, and targeted methods which aim at accurately quantifying multiple metabolites. Most studies rely on 1D NMR which suffers from ubiquitous spectral...
We investigate the feasibility of performing functional MRI (fMRI) at ultralow field (ULF) with a Superconducting QUantum Interference Device (SQUID), as used for detecting magnetoencephalography (MEG) signals from the human head. While there is negligible magnetic susceptibility variation to produce blood oxygenation level-dependent (BOLD) contrast at ULF, changes in cerebral blood volume...
Dengue (DENV) and Zika (ZIKV) are major arthropod-borne human viral disease, for which no specific treatment is available. They are a worldwide important health concern, which causes neurological disorders and hemorrhagic syndrome. Although the structure of ZIKV and DENV virion has been determined, information on the nucleocapsid is lacking. The most accepted hypothesis is of a disorganized...
Since the invention of dissolution Dynamic Nuclear Polarization (DDNP)$^{1}$ and the dramatic signal enhancement it provides in solution-state NMR, a wide range of applications have emerged. In particular, this improvement opens new avenues for the study of fast dynamical processes such as chemical reactions, with a time resolution smaller than a second. DDNP has proven of particular interest...
We develop instruments for dynamic nuclear polarization (DNP) nuclear magnetic resonance (NMR) to investigate protein kinase C modulation for HIV cure research. Continuous wave DNP can increase NMR sensitivity, yet intense microwave fields are required to transition magic angle spinning (MAS) DNP to the time domain. We design Teflon lenses for cylindrical and spherical MAS rotors to increase...
NMR spectroscopy provides detailed insight into molecular structures and is capable of quantitation without standards. An area of interest for chemical industry is the possibility to use NMR to rapidly analyze wastewater streams with anomalously high TOC (Total Organic Carbon). A high TOC excursion can lead to regulatory violations and the consequent danger of shutting down an entire...
A fragment screen using ligand detected 19F NMR versus a kinase target will be described. In addition, practicalities of sample preparation and mixture design will be discussed. Furthermore, a TopSpin/Perl script package for automatic analysis of 19F NMR based screening data will be presented.
Among the translated proteins are few validated drug targets. A recent estimate, based on currently approved drug substances, listed 218 validated protein targets. The choice of non-coding RNA as a drug target could be an alternative approach to efficiently control biomolecular signaling pathways. Currently, clinical trials are underway with oligonucleotides and small molecule drug candidates...
The undisputed usefulness in biomedical applications, the high carbon polarization (up to 70%) and the long relaxation time constant after dissolution have made neat [1-13C]pyruvic acid (PA) plus trityl the most studied dissolution DNP sample.
Therefore, sometimes the literature is lacking detailed studies for different trityl-based samples, limiting the potential of other...
Fifteen years after its invention, dissolution dynamic nuclear polarization (dDNP)[1] has become one method of choice to enhance signals in both MRI and liquid state NMR. Despite exciting prospects, this method remains restricted to few research groups as it needs in principle to be performed at the point of use, with specialized equipment and personnel. However, a series of recent advances...
Rapid-scan (RS) electron-spin resonance (ESR) is a technique to boost the signal-to-noise ratio (SNR) in ESR experiments by allowing the use of larger B1 magnitudes without saturating the sample. State-of-the-art rapid-scan setups [1] use fast field sweeps produced by modulation coils in combination with relatively low-Q resonators to achieve a large detection bandwidth. Due to effects of the...
Understanding the physico-chemical basics of protein-membrane interactions are of key importance in functional characterization of the cell membrane. In order to simplify this complex system the best membrane mimetics are bicelles, which at q=0.5 (long chain/short chain lipid) ratio are ideal for solution state NMR studies1,2.
We chose biologically relevant protein fragments: the...
Ionic liquids (ILs) and Deep Eutectic Solvents (DESs) are two strongly related classes of materials of great interest in green chemistry and with enormous potential in several technological and industrial applications.
ILs are well-known low melting salts with unique physicochemical features. To tune properties and structural organization of the final materials, there is nowadays a growing...
Double helix is the most known structure of DNA. It can account for transfer of genetic information. However, DNA can fold into a wide range of structures that are associated with its unique biological roles and functions. G-rich DNA segments adopting to d[G≥3N1–7G≥3N1–7G≥3N1–7G≥3] motif are populated in hundreds of thousands and have the potential to form a G-quadruplex structure. G-rich...
Availability of new materials, precision machining and good design software have facilitated the progress also in NMR probes, a key to successful experiment. Particularly interesting is a possibility to record 1H-MAS spectra at >170 kHz providing a 0.05 ppm homogeneous resolution which may become an alternative to, even supersede, the present “high- resolution” NMR. Despite a very small, ca...
South Africa’s coastline, stretching more than 2500 km from the cold temperate coast west coast to the warm tropical environment of northern Kwazulu-Natal, has an exceptional environment with a high percentage of endemic species. SA’s rich marine biodiversity therefore signifies the production of potent, biologically active, natural products (Davies-Coleman & Beukes, 2004). By 1995, 60% of the...
Monoclonal antibodies (mAbs) are among modern bio-therapeutics which are often needed and applied in high concentrations (>100mg/ml), especially for subcutaneous injections. EPR spectroscopy is among the few methods which can be applied directly at such conditions, without making concentration approximations. To the best of our knowledge for the first time, EPR spectroscopy is used to study...
Many limitations of state-of-the-art drug screening by nuclear magnetic resonance (NMR) can be overcome by means of high-throughput hyperpolarization. There is an urgent need for innovative experimental screening techniques to identify new drugs as the resistance of « superbugs » against known drugs, e.g., against mycobacterium tuberculosis and other pathogens. Screening techniques must be...
Electron-nuclear double resonance (ENDOR) and dynamic nuclear polarization (DNP) are two techniques based on polarization transfer between electron and nuclear spins. Despite differences in the experimental realization, their similarities rely on the detailed mechanism of hyperfine interactions. The lecture will give an overview of our recent developments in these two methods in solids (ENDOR)...
Techniques of high-frequency electron paramagnetic resonance (EPR) and electron spin echo (ESE) were applied for investigation of non-Kramers Tb3+ centers in single crystals of yttrium aluminum garnet, Y3Al5O12 (YAG). The EPR-ESE techniques were created on the base of highly stable microwave bridges, quasiresonant system for supplying microwave power...
Water and other polar molecules are known to absorb electromagnetic radiation and the absorption is particularly strong in the mm-Wave (mmW) range. Metal surfaces are also becoming increasingly lossy. These high dielectric losses represent the major challenge for constructing EPR and also DNP NMR probeheads suitable for accommodating samples with the maximum volume. While large samples can...
Huntigton’s disease (HD) is an incurable neurological disorder triggered by the aberrant expansion of the polyglutamine tract present in the huntingtin protein (HTT). The pathological version of HTT (with more than 35 consecutive glutamines) is prone to aggregate and form insoluble fibrils within neurons, affecting their normal functions. However, the precise mechanism by which the expanded...
The alarming rise of drug-resistant bacteria urgently calls for novel antibiotics. A particularly interesting class of antibiotics target essential Lipid II molecules that are present in bacterial membranes, killing even the most refractory bacteria at nanomolecular concentrations. Unfortunately, the native binding modes of these membrane-active antibiotics are unknown due to the enormous...
Among the various alternative DNA structures, G-quadruplexes exhibit a remarkable variety of topologies. In this study, two adjacent guanosine residues adopting syn glycosidic bond conformations in a G-quadruplex of (3+1)-hybrid type were substituted by anti-favoring 2’-F-riboguanosine nucleosides (FrG). Residue-specific 15N labeling along with 2D NOE,...
Geological disposal of high-level radioactive waste usually includes bentonite buffer materials. However, the long-term performance of the bentonites for the containment of the nuclear waste is being increasingly questioned due to specific issues associated with “homogenisation” occurring in these materials. Homogenisation is driven by erosion, variations in density and development of swelling...
Lithium is a leading drug for the treatment of bipolar disorder and affects many biochemical pathways via inhibition of phosphatases and kinases. Lithium can replace magnesium cations in enzymes and small molecules, among them ATP. Yet, despite its fundamental pharmaceutical importance, the mode of binding of lithium to ATP has never been directly observed. Here we present the binding...
Hyperpolarization techniques have the potential to improve the sensitivity of magnetic resonance imaging (MRI) by more than four orders of magnitude.1 Various hyperpolarization techniques have been used to generate hyperpolarized contrast agents to study and diagnose diseases in vivo.2 Amongst the challenges of designing hyperpolarized contrast agents, two are persistent: the need to create...
Magnetic Resonance Imaging (MRI) was proven to be a powerful tool for studying catalytic reactions in operando due to its non-invasive nature and versatility. However, MRI application for gas-phase reactions studies is particularly challenging because of low spin density of reactants and products, and it’s further hampered by inhomogeneity of the magnetic field, associated with the presence...
It has been demonstrated that hyperpolarization using PHIP can be effectively achieved using a ruthenium-based trans-hydrogenation catalyst in contrast to typical cis-hydrogenation reaction [1,2]. This led to a development towards hyperpolarized metabolites such as fumarate, using pairwise trans-hydrogenation of an unsaturated precursor [3]. Aside of the desired reaction to form...
Hyperpolarisation provides the means to dramatically increase the signal-to-noise ratio in an NMR spectrum, however, the useful lifetime of the hyperpolarized state is limited by relaxation processes that lead to the re-establishment of thermal equilibrium over time. In order to make hyperpolarisation useful for experiments requiring lengthy delays for magnetisation transfer, chemical exchange...
Studying intrinsically disordered proteins (IDPs) under physiological conditions may present a great challenge using methods based on HN detection. The main drawback is the signal loss caused by chemical exchange of amide protons with water. Thus, conventional triple-resonance methods such as HNCA, HNCACB and HNCO fail to provide satisfactory information. The alternative way of...
In vivo magnetic resonance spectroscopy has evolved during the last 25 years in terms of localization quality and spatial resolution, acquisition speed, artifact suppression, number of detectable metabolites and quantification precision and has benefited from the significant increase of magnetic field strength that recently became available for in vivo investigations. Today it allows for...
Abelson tyrosine kinase (Abl) is an ubiquitously expressed kinase associated with a number of cellular signaling processes. The regulatory core of Abl consists sequentially of the N-cap, the SH3 and SH2 domains, and the kinase domain (KD) N- and C-lobes. The N-Cap differs between two splice variants, 1a and 1b. Abl 1b is 19 residues longer and N-terminally myristoylated. Under physiological...
DEER on orthogonally spin labeled proteins [1] is a versatile technique that allows to retrieve a much greater information content from a single sample than DEER on proteins spin labeled with just single type of label. The reason behind is that orthogonal spin labels can be addressed independently in DEER experiments due to spectroscopically non-overlapping central transitions and/or distinct...
In recent years Dynamic Nuclear Polarization (DNP), a hyperpolarization technique that boosts the NMR sensitivity, has become a powerful tool for structural studies. DNP applications span from the solid-state NMR studies of proteins, to the development of heterogeneous catalysts. However, its use has been mainly limited to low magnetic fields, due to the unfavourable field dependence of the...
Ultra-low field magnetic resonance imaging (ULF-MRI) obtains images in the static magnetic field with strength ranging from tens to hundreds of microteslas. The introduction of strong prepolarization (Bp) pulse and the use of superconducting quantum interference device (SQUID) improve the signal-to-noise ratio (SNR) in ULF-MRI system. To further enhance the signal amplitude, the Bp coil model...
Magic Angle Spinning Dynamic Nuclear Polarization (MAS-DNP) is becoming a mainstream method to increase the sensitivity of solid-state NMR experiments. By irradiating a sample with a strong microwave ($\mu$w) source, nitroxide biradicals are used to enhance the proton polarization via the cross-effect (CE) mechanism.$^1$
To increase the enhancement factor (the NMR signal ratio with/without...
Acute Respiratory Distress Syndrome (ARDS), as characterized by the onset of clinically significant hypoxemia and diffuse pulmonary infiltrates, has been a challenge to the critical care physicians due to high death toll rate. Categorization of the severity of ARDS is based on degree of hypoxemia enumerated by partial pressure of oxygen to the fraction of inspired oxygen (PaO2/FIO2) ratio and...
Li-ion batteries are considered nowadays as the main source of energy for an electric vehicle application. However, a significantly longer “refueling” time in comparison with the standard vehicles is a substantial disadvantage. Lithium plating on the negative electrode is a drawback of a fast charging. If the current exceeds the intercalation rate at which lithium diffuses into the negative...
Yersinia Adhesin A (YadA) is a protein found in the membrane of Yersinia Enterocolitica, which is involved in a number of food-borne diseases including enterocolitis, acute enteritis, diarrhea, and mesenteric limphadentisis.
YadA plays an important role in the ability of Y. enterocolitica to colonize a host, by aiding in the autotransport of a head domain to the cell surface that can stick to...
Recent breakthroughs in optical and electron microscopy have changed the fields of Cell and Structural Biology in a most profound manner, with ever more detailed information about the inner workings of cells becoming available. Complementary to the advancements, novel in situ methods are beginning to emerge as powerful tools in Cellular Structural Biology. Here, I discuss how recent...
Structural investigation of nucleic acids is usually carried out either in diluted buffered solutions or on crystals of these biomolecules. These environments markedly differ from the native one in which these molecules are found, where effects as macromolecular crowding or intermolecular interactions can play a significant role on the conformation.
Aim of the present study was to investigate...
DNA - the most important intercellular target for UV radiation - can be damaged through the direct absorption by nucleobases, or through photosensitized reactions with endogenous cellular chromophores. Guanine that has the lowest oxidation potential among all DNA components is the main target of one-electron oxidation reactions. Guanine radicals are supposed to be involved in the formation of...
Nanostructured hydrated vanadium oxides (V$_2$O$_5$∙$n$H$_2$O) are actively being researched for applications in energy storage, catalysis, and gas sensors. Recently, a one-step exfoliation technique for fabricating V$_2$O$_5$∙$n$H$_2$O nanosheets in aqueous media was reported. This simple exfoliation process is advantageous in comparison to other synthesis methods based on an ion-exchange or...
Hydrothermal carbon (HTC) materials derived from biomass are of considerable current interest due to low cost, environmentally desirable properties, and a broad range of potential applications, for example as functional materials, catalysts, absorber, or electrode material. Especially nitrogen-doped carbon materials are now playing an important role in energy conversion and storage...
NMR studies of large proteins, over 100 kDa, in solution are technically challenging and thereby of considerable interest in the NMR field. This is primarily due to slowing of molecular tumbling in solution as molecular mass increases. Typical 1H-13C or 1H-15N correlation spectra using 13C- or 15N uniformly labeled proteins show severe line-broadening and signal overlap. It is well known that...
In Nuclear Magnetic Resonance (NMR), magnetic field dependent phenomena attract considerable interest: Paramagnetic relaxation enhancement (PRE) is theoretically, experimentally and from the application point of view an important research area, always looking for new relaxation agents with specific properties especially at high magnetic fields and for improved understanding of the PRE...
1H-detected fast magic-angle-spinning (MAS) solid-state NMR is emerging as an important analysis method for proteins of which only sub-milligram amounts are available. This makes also integral membrane proteins which can be expressed at low yields only accessible for a structural investigation by solid-state NMR.
On the example of the Hepatitis C viral membrane protein NS4B (Non-Structural...
Understanding the function of a protein requires not only knowledge of its tertiary structure but also an understanding of its conformational dynamics. Nuclear magnetic resonance (NMR) spectroscopy, polarization-resolved fluorescence spectroscopy and molecular dynamics (MD) simulations are powerful methods to provide detailed insight into protein dynamics on multiple timescales by monitoring...
Telomerase and 7SK are essential eukaryotic RNA-protein complexes (RNPs) involved in telomeric DNA synthesis and regulation of mRNA transcription, respectively. Each comprises a non-coding RNA and constitutively and/or transiently associated proteins. Telomerase maintains the DNA at the ends of linear chromosomes, thereby preventing genomic instability. Its catalytic core is a non-coding...
Both prion protein (PrP) and amyloid beta (Aβ) play important roles in the pathogenesis of neurodegenerative disorders as they are able to misfold and form toxic assemblies. Aβ oligomers have been identified as neurotoxic agents relevant for the pathogenesis of Alzheimer's disease. Recently, it was shown that human PrP (hPrP) is a receptor for oligomeric Aβ(1-42)1,2. We previously...
Human DNA helicases, BLM (Bloom syndrome protein) and FANCJ (Fanconi Anemia Group J) have a common interaction partner, Replication Protein A (RPA). It has been identified that the interaction of BLM and FANCJ with RPA stimulate their DNA unwinding ability, but binding properties of both proteins to RPA were not investigated. Here, we present interactions of RPA-BLM and RPA-FANCJ by NMR...
Bacterial second messengers regulate a wide range of cellular functions from biofilm formation to growth and survival. Targeting second messenger networks is challenging because the system involves a multitude of components with often overlapping functions. Here, we present a novel strategy to intercept cyclic diguanylate (c-di-GMP) signaling pathways by directly targeting the second...
Iron-based nanoscale metal-organic frameworks (nanoMOFs) have demonstrated their medical applications owing to the versatility of their structural features, low toxicity, stability, and tailored functionality. Among them, nanoMOF MIL-100(Fe) is a promising candidate, which properties can be tailored by coating the particle surface with cyclodextrin phosphate (CD-P) and which can accommodate...
The confinement of materials in nanoporous media greatly affects their thermal and dynamic properties such as melting point, glass transition temperatures etc. Size of the pores and the host-guest interaction at the interfaces play an import role in the confinement effect. Here, we study the effect of the confinement, in particular, surface chemistry on the interfacial structure and the...
Multidimensional NMR is a central tool in many fields but suffers from long experimental durations limiting its use for many applications such as reaction monitoring or high-throughput metabolomics. The duration of 2D NMR experiments can be reduced to less than a second with the "ultrafast" 2D NMR approach introduced in 2002 by Frydman et al. This technique makes it possible to acquire 2D...
Slowly relaxing molecular motions, from nanoseconds up, strongly affect molecular properties, even modifying their chemical functions. Nuclear magnetic relaxation (NMR) data is sensitive to these time-scales and therefore its interpretation provides information on the structural and dynamics characteristics of molecules.
Simple approaches allow extracting information easily for rigid molecules...
If the intracerebral hemorrhage (ICH) rehabilitation animal models studies have included processes related to imaging diagnosis, not only interim evaluation of treatment effects, but also objectification of treatment effects would have been possible. The purpose of this study was to examine the rehabilitate treatment effect bio-marker by Magnetic resonance imaging/spectroscopy in animal intra...
Using Methyl-TROSY HMQC based experiments in selectively labelled proteins is an important strategy for studying large and dynamic systems$^{[1]}$. A key issue faced is the chemical shift assignment of the methyl resonances in proteins where experiments that link side-chains to the backbone are unfeasible. Recent structure-based chemical shift assignment methods obtain the methyl assignment...
Cross-β fibrils (aka amyloid fibrils) are a hallmark of many neurodegenerative diseases. Every mechanism of potential cross-β fibril toxicity will have to be mediated by the (abnormal) interaction of the fibril surface with cellular binding partners. We are studying the firbril surface in the context of huntingtin exon-1 (HTTex1) important in Huntington’s Disease (HD). The core of HTTex1...
Over the last decade, the use of periodic density functional theory (DFT) calculations to aid the assignment and interpretation of NMR spectra of complex solids has become almost mainstream. This new link between bulk crystallographic structure and local NMR interactions via the electron density has given birth to the field of NMR crystallography.
Here, we investigate the NMR crystallography...
Dynamic nuclear polarization (DNP) provides a significant sensitivity gain for solid-state NMR under magic-angle spinning (MAS). However, both resolution and selectivity are of high importance as well, and may be compromised under DNP conditions. Particularly, this applies towards biomolecular applications where inhomogeneous line broadening under cryogenic conditions often prevents...
Lanthanide-doped yttrium aluminum garnet (YAG) is a widely used class of materials in solid-state lasers as well as other optical applications. The analysis of the dilute substituent species requires powerful state of the art experimental techniques that focus on the local structures and how they interact with the YAG host lattice [1]. 27Al solid-state Nuclear Magnetic Resonance (NMR) is a...
A large ribonucleoprotein complex called the ribosome is responsible for several steps of protein synthesis in all organisms. In bacteria, regulation of translation begins at initiation. Despite the availability of structural information, we still lack a clear understanding of how the ribosome encounters folded mRNA structures during translation initiation.
A general mechanism for initiation...
RNA helicases are enzymes that unwind double stranded RNA in an ATP dependent reaction. They have shown to be important players in RNA metabolism in both eukaryotes and prokaryotes. RhlB is a DEAD-Box RNA helicase from E.coli. It constitutes an essential part of the RNA catabolizing enzyme complex degradosome. Its ATP dependent unwinding reaction, which features a strong bend in the RNA, is...
Dengue is the most widely spread mosquito-borne viral disease affecting the human population. It is estimated that about 390-million dengue infection occur each year, of which 96 million shown signs of severity. Dengue virus (DENV) is a single-stranded positive-sense RNA virus featuring an icosahedral, ordered envelope and a nucleocapsid of unknown structure.
The structure of the Dengue...
The aberrant folding of certain proteins results in toxic oligomers and aggregates involved in a plethora of diseases. Alzheimer’s disease, the most prevalent debilitating and fatal neurodegenerative disorder is linked to misfolding of the protein amyloid beta. Pathological indicators which confirm AD include brain shrinkage, plaques and neurofibrillary tangles, whereby the plaques are mainly...
The hepatitis C virus (HCV) causes acute and chronic hepatitis with approximately 70 million infected people worldwide. HCV life cycle in infected cells is functionally linked to membrane structures and lipid metabolism. Transmembrane protein NS4B is one of major contributors to formation of membranous replication organelles and thus playing a crucial role in viral genome replication and...
The ability to convert quantum states from microwave photons to optical photons is important for the hybrid system approaches to quantum information processing. The inverse transformation allows one to implement quantum memory of photon states based on electron and nuclear spins with a very long coherence storage time. The problem of quantum state conversion of microwave photons into optical...
Ubiquitination is a pivotal, multi-step, enzymatic post-translational modification that conjugates ubiquitin into chains onto protein substrates. Ubiquitination triggers a plethora of biological signals, and our focus is on protein homeostasis achieved through degradation of misfolded, unassembled, and highly regulated proteins in the ER. The specificity and mechanism of interaction between...
Understanding the function of a protein relies on the precise knowledge of its structure, dynamics and interactions. Pseudocontact shifts (PCS) have proven to be a valuable source of distance and angle-dependent restraints to monitor structural changes. DOTA-based lanthanide chelating tags (LCTs) have found numerous applications for the measurement of PCS on cysteine mutant proteins. A major...
Spin-diffusion (SD) was amongst the first methods proposed to spatially transfer polarization between dipolar-coupled nuclear spins. Lab-frame proton spin-diffusion (PSD) has proved particularly useful in structural characterization of a large variety of molecules. Perturbation theory treatment of the SD phenomenon states that during SD, the rate constant of magnetization exchange between two...
Paramagnetic NMR using lanthanide binding tags has proven to be very useful for structural characterization of proteins and strongly bound ligands in slow exchange. This is based on the distance and orientation dependence of pseudocontact shifts (PCS) induced by the paramagnetic center. A combination of NMR titrations and binding kinetics from other techniques such as AlphaScreenTM can be used...
Sensitivity and resolution have been the two important traits in NMR of biomolecules. With the advent of cryogenically cooled probed and non-uniform sampling methods, the battle of sensitivity and resolution has to be revisited. 1H has long enjoyed the limelight due to its inherent sensitivity. The large gyromagnetic ratio of 1H it is nemesis when dealing high molecular weight systems since...
Two- or multicomponent systems allow bacteria to turn various environmental stimuli into specific cellular responses including but not limited to development, cell division, metabolism and even antibiotic resistance. A typical two-component system consists of a sensory histidine kinase, which autophosphorylates a histidine in response to the input signal, and a transcription factor termed...
Rhodopsin belongs to the largest GPCRs (G-protein coupled receptor) membrane protein family in the human genome. Light absorption by rhodopsin is the initiation point for photoactivated signaling cascade in retinal rods. Point mutations in the protein sequence cause the disruption of the phototransduction resulting in the impaired visual cycle. G90 is a unique position, depending on the nature...
Reversibly photo-switchable fluorescent proteins (RSFPs) are important tools for microscopy and other biotechnological applications. They are currently routinely used for Near-Field Super Resolution Microscopy techniques, e.g. RESOLFT (1). Their characteristic switching between a fluorescent “on” state and a non-fluorescent “off” state, combined with signal processing algorithms has allowed to...
Long-lived nuclear spin state of the 15N pair in doubly 15N labelled trans-azobenzene have been studied. The singlet state of the two 15N spins is accessible due to magnetic non-equivalence1. It is possible to convert 1H or 15N magnetization to the long-lived state and backwards2. The lifetime of the singlet order...
Adding nanosized fillers into a polymer matrix alters its mechanical properties from the behavior of the pure state [1]. We used static low-resolution $^1$H NMR spectroscopy to study model nanocomposites consisting of poly(ethylene oxide), mixed with spherical silica nanoparticles. Attractive interactions lead to slowing down of segmental motion and formation of an interfacial layer around the...
Magnetic resonance spectroscopies can provide unique contributions to describe cellular processes. Magnetic resonance is indeed suitable not only for characterizing the structural and dynamical properties of biomolecules but, even more importantly, for describing transient interactions and functional events with atomic resolution possibly in a cellular context. This requires the development of...
Magnetic resonance (MR) is one of the most important techniques for characterizing compositions, structure and dynamics of molecules. Over the past several years, quantum sensing with Nitrogen-Vacancy (NV) center has opened a new door for magnetic resonance spectroscopy of a single molecule. In my talk, I will mainly introduce several new experimental results on both of methods and biology...
Temperature monitoring is critical in MRI guided ablations to deliver necessary thermal energy to kill tumor cells while preventing damage to healthy adjacent organ tissue. The most popular tMRI technique, proton resonance frequency (PRF) based on the 0.01 ppm/oC change in chemical shift of protons in water, fails in areas near or within adipose tissue. A minimally invasive MRI...
Manatee is a program written in Matlab that facilitates various types of statistical analyses of 2D NMR data by transforming a set of 2D spectra (or a selected region thereof) into a data matrix suitable for various analyses such as multivariate analyses (PCA, OPLS etc.) or a built-in peak correlation analysis. These types of analyses have several different applications when studying complex...
The smaller chemical shift dispersion and the pairwise interaction among all the abundant nuclear spins of the molecule renders 1H NMR spectrum highly complex, severely hindering the straightforward analysis and the accurate determination of homo- and hetero- nuclear scalar couplings. The inherent insentitivy of NMR technique poses additional challenge. We have manipulated the spin dynamics...
Human thioredoxin (Trx) is a major player in signal transduction that involves the post-translational modification S-nitrosation (SNO). The mechanism for Trx disulfide reduction activity is well-known and it occurs though the redox-active cysteines, Cys32 and Cys35. S-nitrosation activity is a gain of function in mammalians, which involves 3 redox-inactive cysteines, Cys62, Cys69 and Cys73,...
Although Fischer-Tropsch synthesis (FTS) has become a core technology of coal-to-liquid (CTL) and gas-to-liquid (GTL) processes since it was invented almost a century ago, to bring the product selectivity beyond the Anderson-Schultz-Flory (ASF) distribution remains a significant challenge. Recently, an increasing number of studies have demonstrated that the bifunctional catalyst concept of...
Intrinsically disordered presynaptic neuronal protein, α-Synuclein plays a critical role in synaptic vesicle trafficking, though the exact mechanism still remains unknown. It is also amyloidogenic in nature and deposits of higher aggregates of α-Synuclein in the Lewy bodies are the histopathological hallmark of second most prevalent neurodegenerative disorder, Parkinson’s disease....
NMR is a powerful tool in early stage drug discovery. Its most prominent roles in the pharmaceutical industry are as a sensitive screening method for finding de novo hit matter or as an orthogonal biophysical method for confirming hits. Primary hit finding, and validation is most efficiently performed using ligand-observed experiments. The corollary of this approach is protein-observed NMR,...
An integrated microfluidic perfusion system that allows in-situ metabolomic observation by NMR of liver tissue has been developed. Ex-vivo culture of the precision-cut liver slice (PCLS) can be a preferable alternative to animal models to study the effect of external factors like drugs and toxicity on living systems due to the requirement of significantly less resources [1]. Recent advances...
Nuclear magnetic resonance (NMR), one of the most powerful analytical techniques in chemistry and life science, is typically limited to macroscopic volumes due to its inherent low sensitivity. This excludes NMR spectroscopy from analysis of microscopic samples sizes such as in single-cell biology or in microfluidic applications. In recent years, it has been shown that NMR signals can be...
Glycosylation brings chemical heterogenity and can add functionality to a protein. Such modificatoins on a large protein can present challenges for intact chemical structure characterization. For example, glycosylation of 150-kDa monoclonal antibodies (mAbs) is a critical quality attribute that impacts protein drug efficacy and safety. In demonstrating glycan structure and composition...
The function of a protein depends on both its structure and the internal dynamics of the peptide chain. Solid-state NMR is a one of the few techniques to determine ps to ms dynamics of large biomolecule complexes with atomic-resolution at physiologically relevant conditions. The development of fast MAS (>60 kHz spinning) has contributed to the ability to constrain the protein dynamics in at...
Over the last few years, the use of ionic liquids as co-solutes to modulate protein activity/stability or amyloidogenesis has attracted considerable attention. This is due to the large amount of possible cation/anion combinations that allow to develop tailor-made ILs with properties matched for specific applications - the control of protein stability or folding landscapes (Weingartner et al....
One of the main application fields of EPR in biological samples is the investigation of paramagnetic centers (like metal ions or amino acid radicals) in proteins. Electron-nuclear double resonance (ENDOR) allows obtaining information about naturally occurring, nuclear spins (1H, 14N, …) in the immediate neighborhood of such electron spin centers. Interactions with remote...
Molecular dynamics of imidazolium-based ionic liquids (ILs) with Br anion [1] combined with poly(vinyl alcohol) (PVOH), as well as structural features and conductivity in these gels is investigated using relaxation, diffusion and double quantum low field NMR.
The combination of ILs solvents with polymers offers the possibility of new applications in the field of material science in particular...
Protein and lipid components in biological membranes act as a dynamic network of subtle molecular interactions segregating the membrane into particular highly dynamic regions called nanodomains. Nanodomains constitute functional platforms enriched in specific lipids (such as sterols and phosphoinositides) and proteins to perform their diverse activities. Remorins (REMs) are plant proteins and...
With the advent of site-specific isotope labeling and deuteration, the study of local dynamics in biological macromolecules, has reached levels of unprecedented accuracy. There are, however, many cases in e.g. soft materials science, where such strategies are not feasible. While classical carbon-13-based solid-state NMR techniques are often possible, they nevertheless suffer from low...
Molecular orientation distributions of polymeric fibers and films are known to be responsible for mechanical and electro-chemical properties. A quantitative interpretation of the molecular orientation distribution can be made by analyzing rotor phase separated CSA sideband intensities during slow rotation rates. The 2D rotor synchronized spectrum is matched with a theoretical model of the same...
Microalgae are increasingly studied in both academy and industry owing to their broad applicative potential. Indeed, they are able to create biomass with significant productivities compared to traditional crops. Besides, several microalgae species present the ability to produce lipids thanks to a metabolic shift provoked by nitrogen starvation conditions. In order to better understand this...
We report an in-situ, non-invasive approach to quantify oxygen partial pressure
in microfluidic lab-on-a-chip (LoC) devices. LoC systems provide a versatile
platform to culture biological systems. As they allow a detailed control over
the growth conditions, LoC devices are finding increasing applications in the
culture of cells, tissues and other biological systems [1]. ...
The molecular mechanisms that regulate genome organization in the mammalian interphase nucleus are largely unclear. At the interface between the nuclear membrane and chromatin, the inner nuclear envelope contains both nucleoskeleton filaments (lamins) and transmembrane proteins (NETs). Lamins tether heterochromatin to the nuclear envelope and modulate chromosome territory positions. Tissue...
Introduction: Modern clinical MRI systems are able to offer sub-millimetre imaging of the human body. However, the high up-front and maintenance cost of these systems means that much of the world lacks access to this technology. For clinical conditions such as hydrocephalus where very high resolution images are not required, low-field MRI systems can offer a low-cost approach towards...
A key goal in biopharmaceutical development is to reduce costs and accelerate cell culture process development. Disposable single use bioreactors have aided the rapid development and manufacturing of drug products, but to further reduce costs and timescales, scale-down bioreactor systems have become popular. The ambrTM system has gained much attention in recent years through the...
The development of the rapid scan technique was historically connected to the problem of the enhancement of the signal-to-noise ratio in NMR but it did not find wide application in NMR or EPR due to the rapid development of high power radio-frequency and microwave sources for pulse methods. However, the past decade is marked by the intense development of solid-state THz instruments, which has...
Surfactants are a group of chemicals, which lower the surface tension of liquids [1]. They may be completely unnoticeable, but we come across them in multiple different ways. They are used extensively in industry and science as detergents, wetting agents, emulsifiers, foaming agents and dispersants. However, these substances can also be found directly in our day-to-day life as they are used in...
RNA viruses tend to concentrate their replication machinery within so called “viral factories”. This membraneless compartment, formed by phase separation, has liquid properties and has been shown for several viruses in vivo [1,2]. Measles virus (MeV) is the cause of measles, it infects T-cells and macrophage cells, belongs to Paramyxoviridae family. Its genome consists of non-segmented...
Mussel glue-proteins undergo distinct structural responses during adhesion processes at the material interface by optimizing binding kinetics and multivalent surface contacts (Waite et al., Science 2015). Aspects of this intriguing behavior are mimicked by a mussel-glue mimetic peptide (HSYSGWSPYRSG (Y*=L-Dopa)) that has been previously selected by phage-display to adhere to Al2O3 after...
THz ESR under multi-extreme conditions, which covers the frequency region between 0.03 and 7 THz1, the temperature region between 1.8 and 300 K1, the magnetic field region up to 55 T1, and the pressure up to 1.5 GPa2, has been developed in Kobe. Firstly, we will show our recent developments of the torque magnetometry3 and mechanically...
The self-assembly of organic molecules onto the surface of gold nanoparticles (AuNPs) provides a simple way to generate protecting monolayers that can incorporate molecular receptors. By exploiting different kinds of non-covalent interactions (namely hydrophobic, ion pairing, and metal−ligand coordination) such receptors can in turn provide tailored host sites for virtually any class of guest...
The nitrogen-vacancy (NV) centre in diamond is an optically addressable single spin-1 electronic system with relatively long coherence persisting at room temperature, making it ideal for a range of nanoscale quantum sensing applications. The NV system is sensitive to local magnetic and electric fields, as well as material properties such as strain and temperature. An exciting direction is the...
For any conformational analysis based on spectroscopic data, both the amount of data extracted and the accuracy of the theoretical relation between data and conformation are key. In this presentation, new developments for both the measurement of 1H-1H J-couplings and their use for conformational analysis of five-membered rings will be discussed.
Measuring...
Hyperpolarization allows one to increase the NMR sensitivity by several orders of magnitude. The main drivers behind the development of hyperpolarization techniques are their biomedical applications. For example, the inhalation of hyperpolarized noble gases, such as 129Xe and 3He, enables functional imaging of lung diseases. However, highly specialized 129Xe...
Hepatitis B Virus (HBV) is a double stranded DNA virus and belongs to hepadnavirdae family. HBV infection causes a severe liver infectious disease and has become a global problem affecting human health. At least 250 million people are chronically infected with HBV, with an estimated 650,000 deaths per year from HBV associated hepatocellular carcinoma, mainly in Asia. Current clinical strategy...
Dynamic Nuclear Polarization (DNP) has recently established itself as a valuable technique to enhance the sensitivity of solid-state NMR spectroscopy. Over the years, sample formulations have been carefully optimized for intermediate magnetic fields (9.4 T), where DNP equipment is commercially and readily available to scientists in the field. An extensive list of polarizing agents has been...
Spin labels are intrinsically required for many applications of EPR to biological systems. Tuning their properties is therefore essential for both increasing the efficiency of the EPR experiment and/or labelling chemistry and broadening the scope of the systems that can be investigated. One aspect of these improvements is to label a wider range of proteins by overcoming issues associated with...
The measurement of residual dipolar couplings (RDCs) in orienting media has become an important tool for solving conformational and configurational problems in structural analysis of small molecules[1,2].
The model-free analysis of configurational problems using the recently developed software ConArch+[3] benefits from measurements in as many as possible independent alignment media. Beyond...
In general, structure and function of biomolecules can be strongly influenced by their environment. This is in particular true for membrane (associated) proteins and soluble proteins inside a densely-packed cell. Modern structural biology therefore requires advanced biochemical tools to generate adequate complex environments as well as techniques that can be used in these environments and...
Transportation of cellular cargo towards the minus end of microtubules is mediated by specific adaptors that engage with dynein to recruit and activate the motor. Malfunction of this machinery is known to cause diseases such as tumors and spinal muscular atrophy, but the molecular mechanisms remain incompletely understood.
Here, we use structural and dynamics nuclear magnetic resonance (NMR)...
Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
Naturally occurring as well as ‘designer’ cyclic peptides offer great potential as leads for drug design or crop protection agents in agriculture. This talk will focus on one class of cyclic peptides known as cyclotides, which are topologically unique in that they have a head-to-tail cyclized...
NMR spectroscopy and molecular dynamics are ideal tools to investigate intrinsically disordered proteins (IDPs), difficult to study by other structural methods. Recent literature documents that force-fields developed for well ordered proteins fail to simulate molecular dynamics of intrinsically disordered proteins (IDPs) realistically. In particular, parameters of the water model need to be...
Solid-state NMR enables atomic resolution characterization of molecular structure and dynamics within complex heterogeneous samples, but it is typically insensitive. Dynamic nuclear polarization (DNP) increases NMR signal intensity by orders of magnitude and can be performed in combination with magic angle spinning (MAS) for sensitive, high-resolution spectroscopy. We are interested in...
Glycans serve as recognition elements for glycan binding proteins at the surface of most cells and mediate key biological processes such as cell-cell adhesion, migration and other events critical for the development and function of complex multicellular organisms. At the heart of important living processes, protein-glycan interactions are also linked with several diseases, including infection,...
Nuclear Magnetic Resonance (NMR) Spectroscopy is a unique tool to study complex systems such as biological macromolecules due to its ability to probe molecular structure and dynamics at atomic resolution and on a wide range of timescales. During the last decades major progresses have been made towards the description of biomolecular dynamics and protein folding. However, fundamental questions...
Tuberculosis is one of the deadliest diseases, affecting approximately 10 million people in 2017. This classifies tuberculosis as epidemic in several countries and lead to an increasing number of multidrug-resistant strains. Thereby, the development of new drugs is essential to effective treatments. The ribose 5-phosphate isomerase (Rpi) catalyzes the interconversion of D-ribulose-5-phosphate...
Current NMR methods for studying proteins are primarily focused on backbone resonances and on methyl bearing side chains. In contrast, NMR of aromatic side chains has been less pursued although these moieties form a large portion of the hydrophobic protein cores. This is in part due to the complexity of aromatic side-chain spectra, which appear in a narrow and crowded spectral region....
Riboswitches are a class of RNA regulatory elements that are located in the 5´-UTR (untranslated region) of genes. Upon binding of small molecules, riboswitches undergo a structural rearrangement preventing the formation of terminator or antiterminator elements regulating the transcription of the downstream genes. The secondary messengers c-di-GMP (3′,5′) enables terminator formation off the...
The availability of antibiotics has allowed for the successful treatment of many bacterial infections as well as the ability to perform invasive medical procedures including surgery and chemotherapy. However, their wide use has led to pathogens' increased drug resistance and the need to find novel classes of antimicrobial peptides as alternatives to antibiotics. Lactophoricin (LPcin), a...
TGF-β stimulates the proliferation and differentiation of regulatory T-cells (Tregs) to promote peripheral immune tolerance. The mouse parasite Heligmosomoides polygyrus manipulates the host immune system through the induction of Fox3p+ Tregs using the five-domain complement control protein (CCP) protein, TGM. Though lacking any homology to the TGF-βs, TGM binds directly...
Biological membranes are made up of phospholipids, which form a bilayer structure along with proteins and carbohydrates. In order to study the behaviour of these membranes, phospholipid vesicles have long been used as models. Whilst they may be a far cry from the complexity of a cellular membrane, their simplicity allows researchers to study individual biophysical effects in isolation....
Synthetic polymeric hydrogel have attracted huge attention due to their unique properties as a 3D crosslinked network as well as their various applications in tissue engineering scaffolds and bio-sensors. Among all the synthetic polymeric hydrogels, polypeptides shows excellent suitability for hydrogelating materials as they possess a number of desirable properties. Besides their side chain...
Historical and cultural-heritage buildings were mainly built of stone or a mixture of stone and brick, using lime-based mortars. Because of poor quality of the used mortar and the presence of voids in the walls, the load bearing capacity of such walls is mostly insufficient and the buildings deteriorate in the course of time. An efficient technique for the repair and/or strengthening of the...
Peroxiredoxins (PRDXs) are thiol active peroxidases responsible for the regulation of peroxides in the cell thanks to the presence of a peroxidatic cysteine within their active site. Upon elevated peroxides levels, they are subject to catalytic inactivation by hyperoxidation, which involves structural modifications and leads to the exhibition of chaperone function.
Recently, the major...
The metabolism of plants has evolved several different strategies to cope with different types of abiotic stresses, ranging from reconfiguration of central metabolic pathways such as carbon, nitrogen and energy metabolism, to biosynthesis of specialized secondary metabolites. The plant circadian clock is intimately connected with plant response and tolerance to abiotic stress. We performed...
Under static-conditions, broadband $\mu w$-irradiation using arbitrary-waveform-generator (AWG) can create large polarization difference between electron-spins, leading to large DNP enhancement ($\varepsilon_{DNP}$) via the Cross-Effect-DNP mechanism. Here, we focus on AWG-DNP under MAS- that induces significant electron-spins energy-modulations.
We found that, unlike under static-conditions,...
Nuclear Magnetic Resonance is widely used for qualitative as well as quantitative evaluation of chemical compounds. For chemists, it is particularly valuable tool providing an insight into reactions and allowing to study their mechanisms. An interesting case is the observation of intermediate products that can not be observed in the post-reaction mixture. Often, changes in their chemical...
Laplace NMR (LNMR), comprising of relaxation and diffusion experiments, provides detailed information about molecular rotational and translational motion. The resolution and information content of LNMR can be increased substantially by a multidimensional approach. However, the approach leads to very long experiment times due to need for repetitions with an incremented evolution time or...
Residual dipolar couplings (RDCs) have proven to be an invaluable anisotropic NMR parameter for the structural elucidation of complex biomolecules and organic molecules. However, a remaining bottleneck limiting its wider use by organic and natural product chemists is the lack of a range of easily applicable aligning media for diverse organic solvents. In recent years, we have developed three...
Riboswitches belong to the group of sensory RNA motifs that are able to form two different conformations in response to physiological signals like differing metabolite concentrations. While the RNA adopting one conformation will encourage expression of the associated genes, adopting the other one leads to termination of either transcription or translation. Until today, various metabolites...
Nuclear spin singlet states consist of two spin-½ nuclei and form a spin 0 which can only be probed indirectly[1]. The equilibration time (TS) between the triplet and singlet state often exceeds the longitudinal relaxation time T1[1].
We are going to present our recent investigations on using the singlet phenomenon as contrast mechanism. In initial experiments we have...
NMR is a very powerful tool to study weak protein-ligand interactions exhibiting dissociation constants in the 1 µM – 1 mM range. This weak binding is usually associated with fast ligand off-rates. One of the most widely used NMR technique to study such complexes is the measurement of chemical shift perturbation upon binding. This is being used to map the residues in the binding protein...
Organic electrolytes, such as tetraethylammonium tetrafluoroborate in acetonitrile (TEA-BF4/ACN) are used in most commercial supercapacitors [1]. Studies on the aqueous electrolytes reported the presence of hydration cages around the ions and provided the evidence for the interaction of ions beyond their first hydration shell [2, 3]. This work is aimed at the investigation of ion...
The 91Zr SSNMR has become a useful tool for structural studies of crystalline systems, for example zirconocenes and zirconium-containing metal–organic frameworks, despite of a low natural abundance (11.2%) and receptivity (1.07E–3 relative to 1H), and a quite high quadrupole moment (–0.176E–28 m2), of the 91Zr(I=5/2) nucleus. However, the...
Recently, Magnetic Resonance Imaging (MRI) has strongly advanced its performance by Dynamic Nuclear Polarization (DNP) methods. One of them is a continuous flow of hyperpolarized substrate produced by a DNP polarizer placed directly inside the bore of a 1.5 T MRI scanner [1,2]. Here we present a new open Fabry-Perot resonance structure with a 4-fold increased flow rate of hyperpolarized...
Solid-liquid heterogeneous catalysis reactions play key roles in industrial catalytic reactions, throughout pollution control, fuel cell, methanol reforming and so on. The routes and dynamics of the reaction products dictate the whole efficiency. Hence, tracking the products generation trajectories deep into the realistic reaction becomes particularly significant. But, few operando techniques...
NMR signal is usually measured using induction in a coil around the sample. However, it has been shown that nuclear magnetization can also be detected using optical methods sensitive to the polarization of light [1]. Such methods might, for example, employ nuclear spin-induced circular dichroism (NSCD), one of new theoretically predicted nuclear magneto-optic effects [2].
In its essence, NSCD...
The method of optically detected magnetic resonance (ODMR) was used to observe spin transfer processes from the paramagnetic Gd3+ and Tb3+ ions to Ce3+ emitters in garnet crystals. The intensity of photoluminescence excited by circularly polarized light into Ce3+ absorption bands can be used for selective monitoring the population of the...
Overhauser Dynamic Nuclear Polarization (DNP) is a powerful technique for improving the signal-to-noise ratio of liquid state NMR. It usually uses microwaves to saturate the EPR transitions in radicals, which, owing to cross-relaxation, results in polarization transfer to nuclear spins. An alternative approach has recently been demonstrated, using visible light to generate triplet states of a...
A broad effort is underway to improve the sensitivity of nuclear magnetic resonance through the use of dynamic nuclear polarization (DNP). Nitrogen-vacancy (NV) centers in diamond offer an appealing platform because these paramagnetic defects show efficient optical pumping at room temperature. This presentation focuses on the spin dynamics of NVs coupled to substitutional nitrogen (the so...
Pyruvate is a hub metabolite of glucose and its metabolic flux is highly sensitive to tumor microenvironment. Success in clinical trials of hyperpolarized 13C MRI of pyruvate metabolism using dissolution dynamic nuclear polarization (dDNP) have reignited interest in parahydrogen induced polarization (PHIP) as a low-cost alternative means to prepare hyperpolarized...
Overhauser Dynamic Nuclear Polarization (ODNP) is employed to solve the premagnetization issue in continuous flow Nuclear Magnetic Resonance (NMR) spectroscopy. This might enable monitoring of very fast chemical reactions and processes, which is important in chemical engineering. NMR detection is performed with a mobile, medium-field NMR spectrometer (benchtop, 43 MHz proton frequency) due to...
Chemical activation of parahydrogen molecules plays a key role in parahydrogen-based hyperpolarization techniques. Commonly, metal-containing activators/catalysts (complexes, nanoparticles, oxides) are employed to mediate such activations and produce hyperpolarization in parahydrogen-induced polarization (PHIP) as well as in signal amplification by reversible exchange (SABRE). Signal...
Paramagnetic NMR is a direct probe of electronic structure in many coordination compounds and organometallic systems. Unpaired electrons alter the NMR spectrum of the surrounding nuclei causing paramagnetic shifts and relaxation enhancements which report in a direct way on the structure of the compounds and configuration of the chemically active molecular orbitals. Such effects can nowadays be...
High-field magnetic resonance is an extremely powerful characterization technique, which cannot however be trivially adapted to perform in in operando studies in technological materials like porous solids. Limitations with space, radio-frequency compatibility, transportability and maintenance are some of the difficulties one has to fight against. On the other hand, low-field magnetic resonance...
The increasing demand for high capacity yet safe storage of renewable energy calls for the development of all-solid-state batteries. To utilize these solid-state batteries to their full potential, a new type of electrolyte has to be developed. Nanoconfined lithium borohydride is a candidate solid-state electrolyte due to its high lithium mobility at ambient temperatures. The origin of the high...
The nuclear factor of activated T-cells (NFAT1) is arguably the most important transcription factor in the immune system. NFAT initiates immune response by up-regulating the production of several cytokines (IL-4, TNF-alpha, IFN-gamma, etc.). Besides its prominent role in infectious disease response as well as e.g. organ transplant rejection, NFAT has been linked to a number of mechanisms...
The ubiquitin-ligase Mdm2 is the principal regulator of the tumor suppressor p53. Mdm2 activity is driven to a great part by phosphorylation states of dozens of phosphosites in its large disordered regions. The underlying mechanisms are still to be elucidated. The kinases responsible of these phosphorylation states are either consitutively active, either stimulated by various stress...
High Mobility Group Protein A1a (HMGA1a) is a highly abundant nuclear protein, which plays a crucial role during embryogenesis, cell differentiation, and neoplasia. Here, we present the first ever NMR-based structural ensemble of full length HMGA1a. Our results show that the protein is not completely random coil but adopts a compact structure consisting of transient long-range contacts, which...
Photoirradiation solid-state NMR spectroscopy is a powerful means to study photoreceptor retinal-binding membrane proteins by the detection of short-lived photointermediates to elucidate the photoreaction pathways and photoactivated intermediates. An in situ photoirradiation solid-state NMR apparatus has been developed for the irradiation of samples from inside a sample tube with extremely...
Much work in the field of parahydrogen-enhanced NMR involves the transfer of proton polarization to heteronuclei using the molecular J-coupling network. Techniques such as magnetic field cycling [1] and ‘SABRE-SHEATH’ [2] have emerged for this purpose. We recently presented a new technique: a molecule containing a heteronuclear spin is hydrogenated with parahydrogen at some magnetic field to...
Misfolding and aggregation of the presynaptic protein α-synuclein is linked to sporadic and genetic forms of Parkinson’s disease. Because α-synuclein is intrinsically disordered in solution, many protein partners can bind to α-synuclein and modulate its aggregation and neurotoxicity. However, little is known about the molecular determinants of these interactions. Here we show that the...
G protein-coupled receptors (GPCRs) are versatile chemical sensors, which transmit the signal of an extracellular binding event across the plasma membrane to the intracellular side, leading to the activation of downstream effector proteins.1 This function is achieved via the modulation of a highly dynamical equilibrium of various conformational receptor states.2,3...
High-pressure NMR spectroscopy (HPNMR) represents a powerful method for characterizing conformational equilibria in biological macromolecules thermodynamically in solution [1]. High-pressure x-ray crystallography (HPX) is an alternative method to observe pressure induced conformational changes with high structural precision [2]. Ras protein is a central element of the cellular signal...
Host−guest interactions between adsorbed molecules and active sites on catalyst strongly influence catalytic performances (activity and selectivity) because they play essential roles in the reactant adsorption, intermediate formation, and product desorption. The methanol-to-olefins (MTO) conversion on acidic zeolite catalysts provides an alternative to produce lower olefins from decreasing...
α-synuclein aggregates are a hallmark of Parkinson’s Disease (PD). Modulation and understanding of the toxic species is, therefore, a key goal in disease treatment. The small molecule anle138b, a 3,5-diphenyl-pyrazole derivative, has shown efficacy in PD animal models.[1] Here we report the interaction of anle138b embedded in phospholipid membranes, with α-synuclein aggregates. We used...
The interrelation of physical and chemical properties of graphene oxide (GO) makes it a very interesting material for several practical applications. We synthesized an array of GO samples by oxidizing ballmilled graphite. The GO samples exhibited varying oxidation level. Through NMR and MRI investigations, we observed that GO samples have different effects on the relaxation of water which...
ATP-binding cassette (ABC) transporters regulate the human biological systems through the trafficking of endogenous components (e.g. lipids, vitamins, steroids, and metabolites) and exogenous compounds (e.g. drugs). They are known for their critical role in multidrug resistance (MDR) in human cell derivatives and diseases (e.g. cancer, Alzheimer’s disease, atherosclerosis), as well as in the...
Methodological and technological advances in EPR spectroscopy have enabled novel insight into the structural and dynamic aspects of spin-labeled integral membrane proteins. In addition to an extensive toolkit of EPR methods, multiple spin labels have been developed and utilized, among them Gd(III)-chelates which offer high sensitivity at high magnetic fields. Here, we applied a dual labeling...
A protein’s environment is often key to understanding its structure and function. However determining the environment of a membrane protein at atomic resolution is difficult by most techniques used in structural biology. We present a method to site-specifically probe water- and lipid proximities in membrane proteins at a resolution of ~3 Å using magic-angle spinning (MAS) NMR spectroscopy...
Low-field NMR relaxometers are powerful instruments as they can be moved outside the laboratory to be closer to the sample (in fields or next to a production line), for on-line quality control for example. Open-magnets present the advantages of (i) being slice selective and (ii) able to record 1D NMR profile if the magnet is mounted on a high-precision lift. The NMR-MOUSE is an example of a...
We have previously shown that bullet-dynamic nuclear polarization (bullet-DNP) can achieve liquid-state 13C polarization levels of 30% at less than 10-fold dilution with sub-mL solvent volumes as used in NMR spectroscopy [1].
Low-field thermal mixing [2] has the potential to rapidly polarize low-gamma nuclei, without the need for strong B1 fields at cryogenic temperatures....
The accessible free energy landscape is a generic property of proteins, which determines both their protein folding pathways and their biological function. This landscape can be explored by determining the thermodynamic stability of proteins at different pressures and temperatures. We combine these variations with NMR spectroscopy to gain molecular resolution. For two proteins (apoKti11 [1]...
The difficulty to automate data acquisition and analysis of complex protein spectra has been one of the major bottlenecks for the widespread use of NMR spectroscopy in structural biology. A promising approach are spectra of high dimensionality (>3) which yield multiple nuclear correlations within fewer experiments, provide high resolution and unambigouos sequential resonance assignment, thus...
The M2 protein from influenza is a membrane protein that forms a tetramer and acts as a proton channel. M2 inhibitors cause large conformational changes upon binding.1 A histidine cluster (His 37) localized in the middle of the pore has been identified as a main component of the proton shuttle mechanism. However, the histidine cluster has been reported as structured in either a box...
We here use the hepatitis B virus capsid made from the core protein as a model to establish approaches allowing to investigate conformation, assembly and interactions in large protein complexes. We have previously demonstrated that HBV capsids produced in E. coli can be studied by solid-state NMR at high resolution and sensitivity using 13C-detection experiments1,2.
We...
In the highest-field NMR magnets (currently 23.5 T, 1 GHz proton NMR frequency), the Larmor precession frequency for spin-1/2 electrons is 660 GHz. The recently-demonstrated 32 T superconducting magnet at MagLab in Tallahassee pushes the Larmor frequency to nearly 900 GHz. However, at the present time, it is difficult to generate a programmable sequence of phase-coherent narrow-band pulses...
Despite breakthroughs in MAS NMR hardware and experimental methodologies making large biological systems accessible for atomic-level characterization, sensitivity remains a major challenge. Here, we report dramatic, 3-4 fold, sensitivity enhancements, in heteronuclear-detected experiments using a novel CPMAS probe, where the sample coil and the electronics operate at cryogenic temperatures,...
NMR line shapes have long been analyzed to study coupling constants and multiplicities, molecular structure and mobility, chemical exchange and other molecular properties. Line shape narrowing by complex shim procedures, sample spinning and/or other techniques has been extremely important for optimal suppression of line shape contributions not related to molecular properties. In biomedical...
Fine particulate matter with an aerodynamic diameter less than 2.5 μM (PM2.5) is one of the most important air contaminants. The exposure to PM2.5 could cause pulmonary oxidative stress, inflammation, and thickening of the alveolar wall. The conventional methods including bronchoalveolar lavage fluid (BALF), synchrotron radiation X-ray fluorescence, and histopathological...
We propose a solution to the matrix dimension problem in quantum mechanical simulations of MRI experiments on complex molecules. This problem is very old; it arises when Kronecker products of spin operators and spatial dynamics generators are taken – the resulting matrices are far too large. However, spin and spatial operators individually have manageable dimensions, and the action by their...
Electron paramagnetic resonance (EPR) is the method of choice to investigate and quantify paramagnetic states in e.g. semiconductor devices, proteins, catalysts and molecular nanomagnets. Common EPR spectrometers use microwave (mw) resonators, where the sample is inserted. This design, however, limits the versatility for in situ / operando measurements. Here, we present an improved design of a...
SPatiotemporal ENcoding (SPEN) is an ultrafast technique that relies on frequency swept pulses combined with readout gradients to collect 2D images of a sample in a single scan with fewer distortions than EPI. SPEN achieves this at the expense of a higher SAR (power deposition) associated to the use of the widely swept RF pulses. The present study presents a way to extend 2D SPEN scans to 3D...
Over the years Dynamic Nuclear Polarization (DNP) has developed into a powerful method for sensitivity enhancement of NMR. At high magnetic fields, DNP in the solid-state is particularly effective. This has led to the successful implementation of cryo-MAS DNP for studying proteins and materials and dissolution DNPin a clinical setting. However, the application of DNP to chemical analysis of...
CO2 absorption in a series of choline-based ionic liquids is investigated using solid-state 13C and 15N MAS NMR spectroscopy [1]. Natural abundance and 13C enriched CO2 gas was purged through 50 wt % aqueous solutions of alkyldimethyl(2-hydroxyethyl)ammonium threonine, [N1,1,n,2OH][Threo], (alkyl = butyl, pentyl and hexyl) and pentyldimethyl(2-hydroxyethyl)ammonium taurine [N1,1,5,2OH][Tau]....
NMR spectroscopy is a powerful tool for the monitoring of organic chemical reactions. Multidimensional experiments have the potential to bring more information on reacting mixtures, but the duration required for classic experiments (several minutes) limits the accessible timescales. Ultrafast 2D NMR, originally proposed by Frydman in 2002 (1), makes it possible to collect 2D spectra in less...
A key feature of NMR is that information is accessible at atomic resolution. However, ambiguities arise if signals overlap and, therefore, great effort has been made to increase either signal dispersion (e.g. high magnetic fields, n-dimensional NMR, detection of heteronuclei) or to reduce signal width (e.g. pure shift NMR, TROSY). Despite the fact that individual homonuclear couplings might...
The encapsulation of active ingredients in liposomes is used in several domains such as food, pharmaceutical and cosmetic industries. Liposomes are drug delivery systems (DDS) used both for lipophilic cargos and for hydrophilic cargos. Such encapsulation allows a controlled release of active ingredients over time [1].
To increase the efficiency of peptide drugs, we aim at designing optimized...
Potential building blocks for multi-level qubits or qudits are intensively investigated because of the multi-dimensional Hilbert space (d >2) for encoding several bits per unit, reduced number of units and hardware size, and robustness against noise and error rates. These advantages over simple qubits could lead to novel scalabale and downsized quantum computer architectures.
Although this...
Anisotropic NMR parameters become increasingly important in organic structure elucidation for the determination of conformations and relative configuration of natural products, synthesized compounds and catalysts.[1]
For anisotropic NMR parameters to be obtained suitable alignment media are necessary. The use of lyotropic liquid crystals from helically chiral polymers is especially...
Speeding-up NMR molecular analysis is an important research field which has been continuously advancing since NMR early days. The relevant benefits are clear and evident:
- Reduce the time per analysis directly reduce its cost
- Gaining spectrometer time to analyze new samples
Many interesting tools and concepts have been appearing in last decades. Concretely, our experience focuses on the...
Fluorine-19 seems to be an ideal target for site-specific studies of biomolecules: it has a gyromagnetic just below the one of proton, 100% natural abundance, a large chemical shift dispersion and offers a background-free signal in biomolecules. However, its large chemical shift anisotropy (CSA) leads to transverse relaxation rates too high for standard multi-dimensional NMR (transverse...
Objective of the study was to compare relaxation properties of theranostic paramagnetic liposomes prepared by two distinct preparation methods, that is thin lipid hydration (TLH) and microfluidic method (MM). Liposomal formulations were prepared with Zn-Phthalocyanine (ZnPc) a highly hydrophobic model photosensitizer, incorporated within lipid membrane with or without PEG moieties, composed of...
Rheo-NMR involves the use of rheometers together with NMR instruments to study complex fluids such as polymer melts, liquid crystals, or colloidal suspensions under flow.1,2 This methodology is well suited to investigate the molecular origins of the macroscopic behavior of such fluids. Recent Rheo-NMR setups are based on microimaging probes, which enable spectroscopic and imaging...
Rheo NMR has been applied to investigate the effect of external shear on the aggregation and on the chain dynamics of polymers. A Couette cell with the polymer melt or solution in the gap is applied. To get further insight, oscillating rotation in addition to continuous rotation has been applied.
An in-house built rheo NMR system using a servo motor, avoiding any vibrations has been used on a...
Alternate structural conformers are the foundation of “protein evolvability”, which refers to the aptitude of proteins to rapidly adopt new functions within existing folds or even adopt entirely new folds. The understanding of protein evolution depends on the ability to relate the impact of mutations on molecular traits to organismal fitness. Antibiotic resistance mediated by β-lactamases...
The mixed alkali metal effect is a long-standing problem in glasses.
Electron paramagnetic resonance (EPR) is used by several researchers to study the
mixed alkali metal effect, but a detailed analysis of the nearest neighbor environment
of the glass former using spin-Hamiltonian parameters was elusive. In this study we
have prepared a series of vanadate glasses having general formula (mol %)...
A nitroxide spin label has been covalently attached to the weak polyelectrolyte poly(ethylene-alt-maleic acid) (P(E-alt-MA)) to study the rotational dynamics of the polyacid backbone in swollen polyelectrolyte multilayers (PEMs) formed by P(E-alt-MA) and the oppositely charged weak polycation poly(allylamine hydrochloide) (PAH) by continuous wave (CW) electron paramagnetic resonance (EPR)...
SABRE (Signal Aplification By Reversible Exchange) allows for rapid, affordable and repeated hyperpolarization of molecules directly in room temperature solutions. SABRE has many applications, ranging from biomedical to high precision measurements. To achieve the full potential, we investigated key steps in spin physics, chemistry, and engineering. Specifically, we (1) engineered membrane...
Diffusion NMR (D-NMR) is a broad term that includes all NMR techniques which measure or exploit molecular diffusion. D-NMR applications span from diffusion ordered spectroscopy, where the complex NMR spectra of molecular mixtures are resolved exploiting the diffusion coefficients of each component, to q-space imaging, where diffusion in a confined medium produces diffraction-like patterns...