Related Research Articles
Kurt Wüthrich is a Swiss chemist/biophysicist and Nobel Chemistry laureate, known for developing nuclear magnetic resonance (NMR) methods for studying biological macromolecules.
Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique based on re-orientation of atomic nuclei with non-zero nuclear spins in an external magnetic field. This re-orientation occurs with absorption of electromagnetic radiation in the radio frequency region from roughly 4 to 900 MHz, which depends on the isotopic nature of the nucleus and increased proportionally to the strength of the external magnetic field. Notably, the resonance frequency of each NMR-active nucleus depends on its chemical environment. As a result, NMR spectra provide information about individual functional groups present in the sample, as well as about connections between nearby nuclei in the same molecule. As the NMR spectra are unique or highly characteristic to individual compounds and functional groups, NMR spectroscopy is one of the most important methods to identify molecular structures, particularly of organic compounds.
Solid-state NMR (ssNMR) spectroscopy is a technique for characterizing atomic level structure in solid materials e.g. powders, single crystals and amorphous samples and tissues using nuclear magnetic resonance (NMR) spectroscopy. The anisotropic part of many spin interactions are present in solid-state NMR, unlike in solution-state NMR where rapid tumbling motion averages out many of the spin interactions. As a result, solid-state NMR spectra are characterised by larger linewidths than in solution state NMR, which can be utilized to give quantitative information on the molecular structure, conformation and dynamics of the material. Solid-state NMR is often combined with magic angle spinning to remove anisotropic interactions and improve the resolution as well as the sensitivity of the technique.
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.
The residual dipolar coupling between two spins in a molecule occurs if the molecules in solution exhibit a partial alignment leading to an incomplete averaging of spatially anisotropic dipolar couplings.
Adriaan "Ad" Bax is a Dutch-American molecular biophysicist. He was born in the Netherlands and is the Chief of the Section on Biophysical NMR Spectroscopy at the National Institutes of Health. He is known for his work on the methodology of biomolecular NMR spectroscopy. He is a corresponding member of the Royal Netherlands Academy of Arts and Sciences, a member of the National Academy of Sciences, a fellow of the American Academy of Arts and Sciences, and a Foreign Member of the Royal Society.
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.
Triple resonance experiments are a set of multi-dimensional nuclear magnetic resonance spectroscopy (NMR) experiments that link three types of atomic nuclei, most typically consisting of 1H, 15N and 13C. These experiments are often used to assign specific resonance signals to specific atoms in an isotopically-enriched protein. The technique was first described in papers by Ad Bax, Mitsuhiko Ikura and Lewis Kay in 1990, and further experiments were then added to the suite of experiments. Many of these experiments have since become the standard set of experiments used for sequential assignment of NMR resonances in the determination of protein structure by NMR. They are now an integral part of solution NMR study of proteins, and they may also be used in solid-state NMR.
The chemical shift index or CSI is a widely employed technique in protein nuclear magnetic resonance spectroscopy that can be used to display and identify the location as well as the type of protein secondary structure found in proteins using only backbone chemical shift data The technique was invented by David S. Wishart in 1992 for analyzing 1Hα chemical shifts and then later extended by him in 1994 to incorporate 13C backbone shifts. The original CSI method makes use of the fact that 1Hα chemical shifts of amino acid residues in helices tends to be shifted upfield relative to their random coil values and downfield in beta strands. Similar kinds of upfield and downfield trends are also detectable in backbone 13C chemical shifts.
Protein chemical shift prediction is a branch of biomolecular nuclear magnetic resonance spectroscopy that aims to accurately calculate protein chemical shifts from protein coordinates. Protein chemical shift prediction was first attempted in the late 1960s using semi-empirical methods applied to protein structures solved by X-ray crystallography. Since that time protein chemical shift prediction has evolved to employ much more sophisticated approaches including quantum mechanics, machine learning and empirically derived chemical shift hypersurfaces. The most recently developed methods exhibit remarkable precision and accuracy.
Nuclear magnetic resonance chemical shift re-referencing is a chemical analysis method for chemical shift referencing in biomolecular nuclear magnetic resonance (NMR). It has been estimated that up to 20% of 13C and up to 35% of 15N shift assignments are improperly referenced. Given that the structural and dynamic information contained within chemical shifts is often quite subtle, it is critical that protein chemical shifts be properly referenced so that these subtle differences can be detected. Fundamentally, the problem with chemical shift referencing comes from the fact that chemical shifts are relative frequency measurements rather than absolute frequency measurements. Because of the historic problems with chemical shift referencing, chemical shifts are perhaps the most precisely measurable but the least accurately measured parameters in all of NMR spectroscopy.
Protein chemical shift re-referencing is a post-assignment process of adjusting the assigned NMR chemical shifts to match IUPAC and BMRB recommended standards in protein chemical shift referencing. In NMR chemical shifts are normally referenced to an internal standard that is dissolved in the NMR sample. These internal standards include tetramethylsilane (TMS), 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS) and trimethylsilyl propionate (TSP). For protein NMR spectroscopy the recommended standard is DSS, which is insensitive to pH variations. Furthermore, the DSS 1H signal may be used to indirectly reference 13C and 15N shifts using a simple ratio calculation [1]. Unfortunately, many biomolecular NMR spectroscopy labs use non-standard methods for determining the 1H, 13C or 15N “zero-point” chemical shift position. This lack of standardization makes it difficult to compare chemical shifts for the same protein between different laboratories. It also makes it difficult to use chemical shifts to properly identify or assign secondary structures or to improve their 3D structures via chemical shift refinement. Chemical shift re-referencing offers a means to correct these referencing errors and to standardize the reporting of protein chemical shifts across laboratories.
Gareth Alun Morris FRS is a Professor of Physical Chemistry, in the School of Chemistry at the University of Manchester.
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.
Geoffrey Bodenhausen is a French chemist specializing in nuclear magnetic resonance, being highly cited in his field. He is a Corresponding member of the Royal Netherlands Academy of Arts and Sciences and a Fellow of the American Physical Society. He is professeur émérite at the Department of Chemistry at the École Normale Supérieure (ENS) in Paris and professeur honoraire at the Laboratory of Biomolecular Magnetic Resonance of the École Polytechnique Fédérale de Lausanne (EPFL). He is a member of the editorial board of the journal Progress in Nuclear Magnetic Resonance Spectroscopy. He is the chair of the editorial board of the journal Magnetic Resonance.
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.
Hartmut Oschkinat is a German structural biologist and professor for chemistry at the Free University of Berlin. His research focuses on the study of biological systems with solid-state nuclear magnetic resonance.
Lucio Frydman is an Israeli chemist whose research focuses on magnetic resonance imaging (MRI), nuclear magnetic resonance (NMR) and solid-state NMR. He was awarded the 2000 Günther Laukien Prize, the 2013 Russell Varian Prize and the 2021 Ernst Prize. He is Professor and Head of the Department of Chemical and Biological Physics at the Weizmann Institute of Science in Israel and Chief Scientist in Chemistry and Biology at the US National High Magnetic Field Laboratory in Tallahassee, Florida. He is a fellow of the International Society of Magnetic Resonance and of the International Society of Magnetic Resonance in Medicine. He was the Editor-in-Chief of the Journal of Magnetic Resonance (2011-2021).
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.
References
- ↑ "Director's Report to Council: May 2006". National Institute of Dental and Craniofacial Research. National Institutes of Health. Retrieved 14 March 2015.
- 1 2 "2013 EAS Award for Outstanding Achievements in Nuclear Magnetic Resonance". Eastern Analytical Symposium. Retrieved 14 March 2015.
- ↑ Clore, Marius G. (2011). "Adventures in Biomolecular NMR". In Harris, Robin K.; Wasylishen, Roderick L. (eds.). Encyclopedia of Magnetic Resonance (PDF). John Wiley & Sons. doi:10.1002/9780470034590. ISBN 9780470034590. Archived from the original (PDF) on 2016-03-05. Retrieved 2015-03-14.
- ↑ Bax, Ad (December 2011). "Triple resonance three-dimensional protein NMR: Before it became a black box". Journal of Magnetic Resonance. 213 (2): 442–445. Bibcode:2011JMagR.213..442B. doi:10.1016/j.jmr.2011.08.003. PMC 3235243 . PMID 21885307.
- ↑ Kay, LE; Torchia, DA; Bax, A (14 November 1989). "Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease". Biochemistry. 28 (23): 8972–9. doi:10.1021/bi00449a003. PMID 2690953.
- ↑ Torchia, Dennis A. (February 2015). "NMR studies of dynamic biomolecular conformational ensembles". Progress in Nuclear Magnetic Resonance Spectroscopy. 84–85: 14–32. Bibcode:2015PNMRS..84...14T. doi:10.1016/j.pnmrs.2014.11.001. PMC 4325279 . PMID 25669739.
- ↑ Torchia, Dennis A. (2012). "Adventures in Biomolecular NMR". Encyclopedia of Magnetic Resonance. John Wiley & Sons. doi:10.1002/9780470034590.emrhp1081. ISBN 9780470034590.
   | This article about an American biochemist is a stub. You can help Wikipedia by expanding it. |