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Nuclear magnetic resonance spectroscopy of proteins is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins, and also nucleic acids, and their complexes. The field was pioneered by Richard R. Ernst and Kurt Wüthrich at the ETH, and by Ad Bax, Marius Clore, Angela Gronenborn at the NIH, and Gerhard Wagner at Harvard University, among others. Structure determination by NMR spectroscopy usually consists of several phases, each using a separate set of highly specialized techniques. The sample is prepared, measurements are made, interpretive approaches are applied, and a structure is calculated and validated.
Xplor-NIH is a highly sophisticated and flexible biomolecular structure determination program which includes an interface to the legacy X-PLOR program. The main developers are Charles Schwieters and Marius Clore of the National Institutes of Health. Xplor-NIH is based on a C++ framework with an extensive Python interface enabling very powerful and easy scripting of complex structure determination and refinement protocols. Restraints derived from all current solution and many solid state nuclear magnetic resonance (NMR) and X-ray scattering experiments can be accommodated during structure calculations. Extensive facilities are also available for many types of ensemble calculations where the experimental data cannot be accounted for by a unique structure. Many of the structure calculation protocols involve the use of simulated annealing designed to overcome local minima on the path of the global minimum region of the target function. These calculations can be carried out using any combination of Cartesian, torsion angle and rigid body dynamics and minimization. Currently Xplor-NIH is the most versatile, comprehensive and widely used structure determination/refinement package in NMR structure determination.
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Residual chemical shift anisotropy (RCSA) is the difference between the chemical shift anisotropy (CSA) of aligned and non-aligned molecules. It is normally three orders of magnitude smaller than the static CSA, with values on the order of parts-per-billion (ppb). RCSA is useful for structural determination and it is among the new developments in NMR spectroscopy.
The Journal of Biomolecular NMR publishes research on technical developments and innovative applications of nuclear magnetic resonance spectroscopy for the study of structure and dynamic properties of biopolymers in solution, liquid crystals, solids and mixed environments. Some of the main topics include experimental and computational approaches for the determination of three-dimensional structures of proteins and nucleic acids, advancements in the automated analysis of NMR spectra, and new methods to probe and interpret molecular motions.
Nuclear magnetic resonance crystallography is a method which utilizes primarily NMR spectroscopy to determine the structure of solid materials on the atomic scale. Thus, solid-state NMR spectroscopy would be used primarily, possibly supplemented by quantum chemistry calculations, powder diffraction etc. If suitable crystals can be grown, any crystallographic method would generally be preferred to determine the crystal structure comprising in case of organic compounds the molecular structures and molecular packing. The main interest in NMR crystallography is in microcrystalline materials which are amenable to this method but not to X-ray, neutron and electron diffraction. This is largely because interactions of comparably short range are measured in NMR crystallography.
CS-ROSETTA is a framework for structure calculation of biological macromolecules on the basis of conformational information from NMR, which is built on top of the biomolecular modeling and design software called ROSETTA. The name CS-ROSETTA for this branch of ROSETTA stems from its origin in combining NMR chemical shift (CS) data with ROSETTA structure prediction protocols. The software package was later extended to include additional NMR conformational parameters, such as Residual Dipolar Couplings (RDC), NOE distance restraints, pseudocontact chemical shifts (PCS) and restraints derived from homologous proteins. This software can be used together with other molecular modeling protocols, such as docking to model protein oligomers. In addition, CS-ROSETTA can be combined with chemical shift resonance assignment algorithms to create a fully automated NMR structure determination pipeline. The CS-ROSETTA software is freely available for academic use and can be licensed for commercial use. A software manual and tutorials are provided on the supporting website https://csrosetta.chemistry.ucsc.edu/.
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PREDITOR is a freely available web-server for the prediction of protein torsion angles from chemical shifts. For many years it has been known that protein chemical shifts are sensitive to protein secondary structure, which in turn, is sensitive to backbone torsion angles. torsion angles are internal coordinates that can be used to describe the conformation of a polypeptide chain. They can also be used as constraints to help determine or refine protein structures via NMR spectroscopy. In proteins there are four major torsion angles of interest: phi, psi, omega and chi-1. Traditionally protein NMR spectroscopists have used vicinal J-coupling information and the Karplus relation to determine approximate backbone torsion angle constraints for phi and chi-1 angles. However, several studies in the early 1990s pointed out the strong relationship between 1H and 13C chemical shifts and torsion angles, especially with backbone phi and psi angles. Later a number of other papers pointed out additional chemical shift relationships with chi-1 and even omega angles. PREDITOR was designed to exploit these experimental observations and to help NMR spectroscopists easily predict protein torsion angles from chemical shift assignments. Specifically, PREDITOR accepts protein sequence and/or chemical shift data as input and generates torsion angle predictions for phi, psi, omega and chi-1 angles. The algorithm that PREDITOR uses combines sequence alignment, chemical shift alignment and a number of related chemical shift analysis techniques to predict torsion angles. PREDITOR is unusually fast and exhibits a very high level of accuracy. In a series of tests 88% of PREDITOR’s phi/psi predictions were within 30 degrees of the correct values, 84% of chi-1 predictions were correct and 99.97% of PREDITOR’s predicted omega angles were correct. PREDITOR also estimates the torsion angle errors so that its torsion angle constraints can be used with standard protein structure refinement software, such as CYANA, CNS, XPLOR and AMBER. PREDITOR also supports automated protein chemical shift re-referencing and the prediction of proline cis/trans states. PREDITOR is not the only torsion angle prediction software available. Several other computer programs including TALOS, TALOS+ and DANGLE have also been developed to predict backbone torsion angles from protein chemical shifts. These stand-alone programs exhibit similar prediction performance to PREDITOR but are substantially slower.
Professor Ramakrishna Vijayacharya Hosur is an Indian biophysical scientist, known for his expertise in the areas of nuclear magnetic resonance and molecular biophysics. The Government of India honoured him, in 2014, by awarding him the Padma Shri, the fourth highest civilian award, for his contributions to the fields of science and technology.
G. Marius Clore MAE, FRSC, FMedSci, FRS is a British-born, Anglo-American molecular biophysicist and structural biologist. He was born in London, U.K. and is a dual U.S./U.K. Citizen. He is a Member of the National Academy of Sciences, a Fellow of the Royal Society, a Fellow of the Academy of Medical Sciences, a Fellow of the American Academy of Arts and Sciences, a NIH Distinguished Investigator, and the Chief of the Molecular and Structural Biophysics Section in the Laboratory of Chemical Physics of the National Institute of Diabetes and Digestive and Kidney Diseases at the U.S. National Institutes of Health. He is known for his foundational work in three-dimensional protein and nucleic acid structure determination by biomolecular NMR spectroscopy, for advancing experimental approaches to the study of large macromolecules and their complexes by NMR, and for developing NMR-based methods to study rare conformational states in protein-nucleic acid and protein-protein recognition. Clore's discovery of previously undetectable, functionally significant, rare transient states of macromolecules has yielded fundamental new insights into the mechanisms of important biological processes, and in particular the significance of weak interactions and the mechanisms whereby the opposing constraints of speed and specificity are optimized. Further, Clore's work opens up a new era of pharmacology and drug design as it is now possible to target structures and conformations that have been heretofore unseen.
Dennis Torchia is an American biophysicist who specialized in NMR spectroscopy. He spent most of his career at the National Institute of Dental and Craniofacial Research (NIDCR), part of the United States National Institutes of Health, where he served as Chief of the Structural Biology Unit before his retirement in 2006.
Marc Baldus is a physicist and professor of NMR spectroscopy at Utrecht University. He is especially known for his work in the field of structural biology using solid-state nuclear magnetic resonance (ssNMR) spectroscopy. He applies ssNMR methods to establish structure-function relationships in complex biomolecular systems including membrane and Amyloid proteins. In addition, he develops cellular NMR methods to study large molecular transport and insertion systems in bacteria as well as signal transduction mechanisms in eukaryotic cells.
James J. Chou (周界文) is a Chinese American scientist and Professor of Biological Chemistry and Molecular Pharmacology at the Harvard Medical School. He is known for pioneering the use of Nuclear Magnetic Resonance (NMR) Spectroscopy to reveal the structural details of the membrane regions of cell surface proteins, particularly those of immune receptors and viral membrane proteins.
Alfred G. Redfield was an American physicist and biochemist. In 1955 he published the Redfield relaxation theory, effectively moving the practice of NMR or Nuclear magnetic resonance from the realm of classical physics to the realm of semiclassical physics. He continued to find novel magnetic resonance applications to solve real-world problems throughout his life.
Eric Oldfield is a British chemist, the Harriet A. Harlin Professor of Chemistry and a professor of Biophysics at the University of Illinois at Urbana-Champaign. He is known for his work in nuclear magnetic resonance spectroscopy of lipids, proteins, and membranes; of inorganic solids; in computational chemistry, and in microbiology and parasitology. He has received a number of recognitions for his work, including the American Chemical Society's Award in Pure Chemistry, the Royal Society of Chemistry's Meldola Medal and the Biochemical Society's Colworth Medal, and he is a member of the American Association for the Advancement of Science, a Fellow of the Royal Society of Chemistry, and a Fellow of the American Physical Society.
Spinach is an open-source magnetic resonance simulation package initially released in 2011 and continuously updated since. The package is written in Matlab and makes use of the built-in parallel computing and GPU interfaces of Matlab.
References
- ↑ "A. Bax". Royal Netherlands Academy of Arts and Sciences. Archived from the original on 21 July 2015. Retrieved 18 July 2015.
- ↑ "Book of Members, 1780-2010: Chapter B" (PDF). American Academy of Arts and Sciences . Retrieved May 28, 2011.
- ↑ "Welch Award in Chemistry". www.welch1.org.
- ↑ "Outstanding scientists elected as Fellows of the Royal Society | Royal Society". royalsociety.org. Retrieved 2024-05-19.
- ↑ Clore, Marius G (2011). "Adventures in Biomolecular NMR" (PDF). In Harris, Robin K; Wasylishen, Roderick L (eds.). Encyclopedia of Magnetic Resonance. John Wiley & Sons. doi:10.1002/9780470034590. hdl:11693/53364. ISBN 9780470034590.
- ↑ Ikura M; Kay LE; Bax A (1990). "A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin". Biochemistry. 29 (19): 4659–67. doi:10.1021/bi00471a022. PMID 2372549.
- ↑ Lewis E Kay; Mitsuhiko Ikura; Rolf Tschudin, Ad Bax (1990). "Three-dimensional triple-resonance NMR spectroscopy of isotopically enriched proteins". Journal of Magnetic Resonance. 89 (3): 496–514. Bibcode:1990JMagR..89..496K. doi:10.1016/0022-2364(90)90333-5.
- ↑ Tjandra N; Grzesiek S; Bax A (1996). "Magnetic field dependence of nitrogen-proton J splittings in 15N-enriched human ubiquitin resulting from relaxation interference and residual dipolar coupling". Journal of the American Chemical Society. 118 (26): 6264–6272. doi:10.1021/ja960106n.
- ↑ Kontaxis G; Delaglio F; Bax A (2005). "Molecular Fragment Replacement Approach to Protein Structure Determination by Chemical Shift and Dipolar Homology Database Mining". Nuclear Magnetic Resonance of Biological Macromolecules. Methods in Enzymology. Vol. 394. pp. 42–78. doi:10.1016/s0076-6879(05)94003-2. ISBN 9780121827991. PMID 15808217.
- ↑ Boisbouvier A; Delaglio F; Bax A (2003). "Direct observation of dipolar couplings between distant protons in weakly aligned nucleic acids". Proceedings of the National Academy of Sciences of the United States of America. 100 (20): 11333–11338. Bibcode:2003PNAS..10011333B. doi: 10.1073/pnas.1534664100 . PMC 208757 . PMID 12972645.
- ↑ Bax A; Grishaev A (October 2005). "Weak alignment NMR: a hawk-eyed view of biomolecular structure". Curr. Opin. Struct. Biol. 15 (5): 563–70. doi:10.1016/j.sbi.2005.08.006. PMID 16140525.
- ↑ Maltsev AS; Chen J; Levine RL; Bax A (February 2013). "Site-specific interaction between α-synuclein and membranes probed by NMR-observed methionine oxidation rates". J. Am. Chem. Soc. 135 (8): 2943–6. Bibcode:2013JAChS.135.2943M. doi:10.1021/ja312415q. PMC 3585462 . PMID 23398174.
- ↑ Lorieau JL; Louis JM; Bax A (March 2013). "The impact of influenza hemagglutinin fusion peptide length and viral subtype on its structure and dynamics". Biopolymers. 99 (3): 189–95. doi:10.1002/bip.22102. PMC 3532579 . PMID 23015412.
- ↑ Lakomek NA; Kaufman JD; Stahl SJ; Louis JM; Grishaev A; Wingfield PT; Bax A (April 2013). "Internal dynamics of the homotrimeric HIV-1 viral coat protein gp41 on multiple time scales". Angew. Chem. Int. Ed. Engl. 52 (14): 3911–5. doi:10.1002/anie.201207266. PMC 3610801 . PMID 23450638.
- ↑ "Citation Laureates: Chemistry". In Cites. Archived from the original on 2 November 2002.
- ↑ "50 Most Cited Chemists 1981-1997". pcb4122.univ-lemans.fr. Archived from the original on 1 March 2003. Retrieved 12 January 2022.
- ↑ Anfinrud, Philip; Stadnytskyi, Valentyn; Bax, Christina E.; Bax, Adriaan (2020-05-21). "Visualizing Speech-Generated Oral Fluid Droplets with Laser Light Scattering". New England Journal of Medicine. 382 (21): 2061–2063. doi: 10.1056/nejmc2007800 . ISSN 0028-4793. PMC 7179962 . PMID 32294341.
- ↑ Stadnytskyi, Valentyn; Bax, Christina E.; Bax, Adriaan; Anfinrud, Philip (2020-06-02). "The airborne lifetime of small speech droplets and their potential importance in SARS-CoV-2 transmission". Proceedings of the National Academy of Sciences. 117 (22): 11875–11877. Bibcode:2020PNAS..11711875S. doi: 10.1073/pnas.2006874117 . ISSN 0027-8424. PMC 7275719 . PMID 32404416.
