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Relevant bibliographies by topics / SsNMR spectroscopy

Academic literature on the topic 'SsNMR spectroscopy'

Author: Grafiati

Published: 10 December 2022

Last updated: 29 January 2023

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Journal articles on the topic "SsNMR spectroscopy"

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He, Lichun, Benjamin Bardiaux, Mumdooh Ahmed, Johannes Spehr, Renate König, Heinrich Lünsdorf, Ulfert Rand, Thorsten Lührs, and Christiane Ritter. "Structure determination of helical filaments by solid-state NMR spectroscopy." Proceedings of the National Academy of Sciences 113, no. 3 (January 5, 2016): E272—E281. http://dx.doi.org/10.1073/pnas.1513119113.

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The controlled formation of filamentous protein complexes plays a crucial role in many biological systems and represents an emerging paradigm in signal transduction. The mitochondrial antiviral signaling protein (MAVS) is a central signal transduction hub in innate immunity that is activated by a receptor-induced conversion into helical superstructures (filaments) assembled from its globular caspase activation and recruitment domain. Solid-state NMR (ssNMR) spectroscopy has become one of the most powerful techniques for atomic resolution structures of protein fibrils. However, for helical filaments, the determination of the correct symmetry parameters has remained a significant hurdle for any structural technique and could thus far not be precisely derived from ssNMR data. Here, we solved the atomic resolution structure of helical MAVSCARD filaments exclusively from ssNMR data. We present a generally applicable approach that systematically explores the helical symmetry space by efficient modeling of the helical structure restrained by interprotomer ssNMR distance restraints. Together with classical automated NMR structure calculation, this allowed us to faithfully determine the symmetry that defines the entire assembly. To validate our structure, we probed the protomer arrangement by solvent paramagnetic resonance enhancement, analysis of chemical shift differences relative to the solution NMR structure of the monomer, and mutagenesis. We provide detailed information on the atomic contacts that determine filament stability and describe mechanistic details on the formation of signaling-competent MAVS filaments from inactive monomers.

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van der Wel, Patrick C. A. "New applications of solid-state NMR in structural biology." Emerging Topics in Life Sciences 2, no. 1 (February 23, 2018): 57–67. http://dx.doi.org/10.1042/etls20170088.

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Various recent developments in solid-state nuclear magnetic resonance (ssNMR) spectroscopy have enabled an array of new insights regarding the structure, dynamics, and interactions of biomolecules. In the ever more integrated world of structural biology, ssNMR studies provide structural and dynamic information that is complementary to the data accessible by other means. ssNMR enables the study of samples lacking a crystalline lattice, featuring static as well as dynamic disorder, and does so independent of higher-order symmetry. The present study surveys recent applications of biomolecular ssNMR and examines how this technique is increasingly integrated with other structural biology techniques, such as (cryo) electron microscopy, solution-state NMR, and X-ray crystallography. Traditional ssNMR targets include lipid bilayer membranes and membrane proteins in a lipid bilayer environment. Another classic application has been in the area of protein misfolding and aggregation disorders, where ssNMR has provided essential structural data on oligomers and amyloid fibril aggregates. More recently, the application of ssNMR has expanded to a growing array of biological assemblies, ranging from non-amyloid protein aggregates, protein–protein complexes, viral capsids, and many others. Across these areas, multidimensional magic angle spinning (MAS) ssNMR has, in the last decade, revealed three-dimensional structures, including many that had been inaccessible by other structural biology techniques. Equally important insights in structural and molecular biology derive from the ability of MAS ssNMR to probe information beyond comprehensive protein structures, such as dynamics, solvent exposure, protein–protein interfaces, and substrate–enzyme interactions.

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Robin, Marc, Stanislas Von Euw, Guillaume Renaudin, Sandrine Gomes, Jean-Marc Krafft, Nadine Nassif, Thierry Azaïs, and Guylène Costentin. "Insights into OCP identification and quantification in the context of apatite biomineralization." CrystEngComm 22, no. 16 (2020): 2728–42. http://dx.doi.org/10.1039/c9ce01972c.

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Middleton, D. A. "Solid-state NMR spectroscopy as a tool for drug design: from membrane-embedded targets to amyloid fibrils." Biochemical Society Transactions 35, no. 5 (October 25, 2007): 985–90. http://dx.doi.org/10.1042/bst0350985.

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Structure-based design has gained credibility as a valuable component of the modern drug discovery process. The technique of SSNMR (solid-state NMR) promises to be a useful counterpart to the conventional experimental techniques of X-ray crystallography and solution-state NMR for providing structural features of drug targets that can guide medicinal chemistry towards drug candidates. This article highlights some recent SSNMR approaches from our group for identifying active compounds, such as enzyme inhibitors, receptor antagonists and peptide agents, that prevent the aggregation of amyloid proteins involved in neurodegenerative diseases. It is anticipated that the use of SSNMR in drug discovery will become more widespread in the wake of advances in hardware and methodological developments.

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Sreemantula, Arun Kumar, and Alexander Marchanka. "Solid-state NMR spectroscopy for characterization of RNA and RNP complexes." Biochemical Society Transactions 48, no. 3 (June 23, 2020): 1077–87. http://dx.doi.org/10.1042/bst20191080.

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Ribonucleic acids are driving a multitude of biological processes where they act alone or in complex with proteins (ribonucleoproteins, RNP). To understand these processes both structural and mechanistic information about RNA is necessary. Due to their conformational plasticity RNA pose a challenge for mainstream structural biology methods. Solid-state NMR (ssNMR) spectroscopy is an emerging technique that can be applied to biomolecular complexes of any size in close-to-native conditions. This review outlines recent methodological developments in ssNMR for structural characterization of RNA and protein–RNA complexes and provides relevant examples.

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Ader, C., R. Schneider, K. Seidel, M. Etzkorn, and M. Baldus. "Magic-angle-spinning NMR spectroscopy applied to small molecules and peptides in lipid bilayers." Biochemical Society Transactions 35, no. 5 (October 25, 2007): 991–95. http://dx.doi.org/10.1042/bst0350991.

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ssNMR (solid-state NMR) spectroscopy provides increasing possibilities to study the structural and dynamic aspects of biological membranes. Here, we review recent ssNMR experiments that are based on MAS (magic angle spinning) and that provide insight into the structure and dynamics of membrane systems at the atomic level. Such methods can be used to study membrane architecture, domain formation or molecular complexation in a way that is highly complementary to other biophysical methods such as imaging or calorimetry.

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Zhao, Li, Wei Li, Andreas Plog, Yeping Xu, Gerd Buntkowsky, Torsten Gutmann, and Kai Zhang. "Multi-responsive cellulose nanocrystal–rhodamine conjugates: an advanced structure study by solid-state dynamic nuclear polarization (DNP) NMR." Phys. Chem. Chem. Phys. 16, no. 47 (2014): 26322–29. http://dx.doi.org/10.1039/c4cp04096a.

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Siudem, Paweł, Jarosław Bukowicki, Iwona Wawer, and Katarzyna Paradowska. "Structural studies of two capsaicinoids: dihydrocapsaicin and nonivamide. 13C and 15N MAS NMR supported by genetic algorithm and GIAO DFT calculations." RSC Advances 10, no. 31 (2020): 18082–92. http://dx.doi.org/10.1039/d0ra01320j.

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Zhao, Sha, Yufei Yang, Yujie Zhao, Xinming Li, Yi Xue, and Shenlin Wang. "High-resolution solid-state NMR spectroscopy of hydrated non-crystallized RNA." Chemical Communications 55, no. 93 (2019): 13991–94. http://dx.doi.org/10.1039/c9cc06552k.

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Mandala, Venkata S., Jonathan K. Williams, and Mei Hong. "Structure and Dynamics of Membrane Proteins from Solid-State NMR." Annual Review of Biophysics 47, no. 1 (May 20, 2018): 201–22. http://dx.doi.org/10.1146/annurev-biophys-070816-033712.

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Solid-state nuclear magnetic resonance (SSNMR) spectroscopy elucidates membrane protein structures and dynamics in atomic detail to yield mechanistic insights. By interrogating membrane proteins in phospholipid bilayers that closely resemble biological membranes, SSNMR spectroscopists have revealed ion conduction mechanisms, substrate transport dynamics, and oligomeric interfaces of seven-transmembrane helix proteins. Research has also identified conformational plasticity underlying virus-cell membrane fusions by complex protein machineries, and β-sheet folding and assembly by amyloidogenic proteins bound to lipid membranes. These studies collectively show that membrane proteins exhibit extensive structural plasticity to carry out their functions. Because of the inherent dependence of NMR frequencies on molecular orientations and the sensitivity of NMR frequencies to dynamical processes on timescales from nanoseconds to seconds, SSNMR spectroscopy is ideally suited to elucidate such structural plasticity, local and global conformational dynamics, protein-lipid and protein-ligand interactions, and protonation states of polar residues. New sensitivity-enhancement techniques, resolution enhancement by ultrahigh magnetic fields, and the advent of 3D and 4D correlation NMR techniques are increasingly aiding these mechanistically important structural studies.

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Dissertations / Theses on the topic "SsNMR spectroscopy"

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Shannon, Matthew D. "High Resolution Structural and Dynamic Studies of Biomacromolecular Assemblies using Solid-State NMR Spectroscopy." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1534321838601796.

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Itkin, Anna. "Multidisniplinary study of Alzheimer's disease-related peptides : from amyloid precursor protein (APP) to amyloid β-oligomers and γ-secretase modulators." Thesis, Strasbourg, 2012. http://www.theses.fr/2012STRAF051/document.

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Une des caractéristiques histopathologiques de la maladie d'Alzheimer (AD) est la présence de plaques amyloïdes formées par les peptides amyloïdes β (Aβ) de 40 et 42 résidus, qui sont les produits de clivage par des protéases de l'APP. Afin de comprendre le rôle des variations structurelles du TM dans le traitement de l'APP, les peptides APP_TM4K ont été étudiés dans la bicouche lipidique en utilisant l’ATR-FTIR et ssNMR. Tandis que la structure secondaire globale du peptide APP_TM4K est hélicoidale, hétérogénéité de conformation et d'orientation a été observée pour le site de clivage γ et , que peuvent avoir des implications dans le mécanisme de clivage et donc dans la production d’Aβ. Les peptides Aβ s'agrègent pour produire des fibrilles et aussi de manière transitoire d'oligomères neurotoxiques. Nous avons constaté qu'en présence de Ca2+, l’Aβ (1-40) forme de préférence des oligomères, tandis qu'en absence de Ca2+ l'Aβ (1-40) s’agrège sous forme de fibrilles. Dans les échantillons sans Ca2+, l’ATR-FTIR révèle la conversion des oligomères en feuillets β antiparallèles en la conformation caractéristique des fibrilles en feuillets β parallèles. Ces résultats nous ont amené à conclure que les Ca2+ stimulent la formation d'oligomères d'Aβ (1-40), qui sont impliqués dans l’AD. Les positions et une orientation précise de deux nouveaux médicaments puissants modulateurs de la γ-sécrétase - le benzyl-carprofen et le sulfonyl-carprofen  dans la bicouche lipidique, ont été obtenus à partir des expériences des ssNMR. Ces résultats indiquent que le mécanisme probable de modulation du clivage par la y-sécrétase est une interaction directe avec le domaine TM de l’APP
A histopathological characteristic of Alzheimer’s disease (AD) is the presence of amyloid plaques formed by amyloid β(A) peptides of 40 and 42 residues-long, which are the cleavage products of APP by proteases. To understand the role of structural changes in the TM domain of APP, APP_TM4K peptides were studied in the lipid bilayer using ATR-FTIR and ssNMR. While the overall secondary structure of the APP_TM4K peptide is helical, conformational and orientational heterogeneity was observed for the y- and for the -cleavage sites, which may have implications for the cleavage mechanism and therefore the production of Aβ. Starting from its monomeric form, Aβ peptides aggregate into fibrils and / or oligomers, the latter being the most neurotoxic. We found that in the presence of Ca2 +, Aβ (1-40) preferably forms oligomers, whereas in the absence of a2 + Aβ (1-40) aggregates into fibrils. In samples without Ca2 +, ATR-FTIR shows conversion from antiparallel β sheet conformation of oligomers into parallel β sheets, characteristic of fibrils. These results led us to conclude that Ca2 +stimulates the formation of oligomers of Aβ (1-40), that have been implicated in the pathogenesis of AD. Position and precise orientation of two new drugs  powerful modulators of γ-secretase  benzyl-carprofen and carprofen sulfonyl  in the lipid bilayer were obtained from neutron scattering and ssNMR experiments. These results indicate that carprofen-derivatives can directly interact with APP. Such interaction would interfere with proper APP-dimer formation, which is necessary for the sequential cleavage by β -secretase, diminishing or greatly reducing Aβ42 production

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Stevens, J. S., S. J. Byard, Colin C. Seaton, G. Sadiq, R. J. Davey, and S. L. M. Schroeder. "Proton transfer and hydrogen bonding in the organic solid state: a combined XRD/XPS/ssNMR study of 17 organic acid–base complexes." 2013. http://hdl.handle.net/10454/10190.

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Yes
The properties of nitrogen centres acting either as hydrogen-bond or Brønsted acceptors in solid molecular acid–base complexes have been probed by N 1s X-ray photoelectron spectroscopy (XPS) as well as 15N solid-state nuclear magnetic resonance (ssNMR) spectroscopy and are interpreted with reference to local crystallographic structure information provided by X-ray diffraction (XRD). We have previously shown that the strong chemical shift of the N 1s binding energy associated with the protonation of nitrogen centres unequivocally distinguishes protonated (salt) from hydrogen-bonded (co-crystal) nitrogen species. This result is further supported by significant ssNMR shifts to low frequency, which occur with proton transfer from the acid to the base component. Generally, only minor chemical shifts occur upon co-crystal formation, unless a strong hydrogen bond is formed. CASTEP density functional theory (DFT) calculations of 15N ssNMR isotropic chemical shifts correlate well with the experimental data, confirming that computational predictions of H-bond strengths and associated ssNMR chemical shifts allow the identification of salt and co-crystal structures (NMR crystallography). The excellent agreement between the conclusions drawn by XPS and the combined CASTEP/ssNMR investigations opens up a reliable avenue for local structure characterization in molecular systems even in the absence of crystal structure information, for example for non-crystalline or amorphous matter. The range of 17 different systems investigated in this study demonstrates the generic nature of this approach, which will be applicable to many other molecular materials in organic, physical, and materials chemistry.
EPSRC, Sanofi-Aventis

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Book chapters on the topic "SsNMR spectroscopy"

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Paul, Subhradip, Hiroki Takahashi, Sabine Hediger, and Gaël De Paëpe. "Third Spin-Assisted Recoupling in SSNMR." In Annual Reports on NMR Spectroscopy, 93–142. Elsevier, 2015. http://dx.doi.org/10.1016/bs.arnmr.2014.12.003.

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