BIOMAT Database Logo BIOMAT Database Logo

Protein structure determination from NMR chemical shifts. 2007

Andrea Cavalli, and Xavier Salvatella, and Christopher M Dobson, and Michele Vendruscolo
Department of Chemistry, Cambridge University, Cambridge CB2 1EW, United Kingdom.

NMR spectroscopy plays a major role in the determination of the structures and dynamics of proteins and other biological macromolecules. Chemical shifts are the most readily and accurately measurable NMR parameters, and they reflect with great specificity the conformations of native and nonnative states of proteins. We show, using 11 examples of proteins representative of the major structural classes and containing up to 123 residues, that it is possible to use chemical shifts as structural restraints in combination with a conventional molecular mechanics force field to determine the conformations of proteins at a resolution of 2 angstroms or better. This strategy should be widely applicable and, subject to further development, will enable quantitative structural analysis to be carried out to address a range of complex biological problems not accessible to current structural techniques.

UI MeSH Term Description Entries
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D011487 Protein Conformation The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). Conformation, Protein,Conformations, Protein,Protein Conformations
D011506 Proteins Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein. Gene Products, Protein,Gene Proteins,Protein,Protein Gene Products,Proteins, Gene
D001499 Bayes Theorem A theorem in probability theory named for Thomas Bayes (1702-1761). In epidemiology, it is used to obtain the probability of disease in a group of people with some characteristic on the basis of the overall rate of that disease and of the likelihood of that characteristic in healthy and diseased individuals. The most familiar application is in clinical decision analysis where it is used for estimating the probability of a particular diagnosis given the appearance of some symptoms or test result. Bayesian Analysis,Bayesian Estimation,Bayesian Forecast,Bayesian Method,Bayesian Prediction,Analysis, Bayesian,Bayesian Approach,Approach, Bayesian,Approachs, Bayesian,Bayesian Approachs,Estimation, Bayesian,Forecast, Bayesian,Method, Bayesian,Prediction, Bayesian,Theorem, Bayes
D001703 Biophysics The study of PHYSICAL PHENOMENA and PHYSICAL PROCESSES as applied to living things. Mechanobiology
D055592 Biophysical Phenomena The physical characteristics and processes of biological systems. Biophysical Concepts,Biophysical Processes,Biophysical Phenomenon,Biophysical Process,Biophysical Concept,Concept, Biophysical,Concepts, Biophysical,Phenomena, Biophysical,Phenomenon, Biophysical,Process, Biophysical,Processes, Biophysical
D019295 Computational Biology A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets. Bioinformatics,Molecular Biology, Computational,Bio-Informatics,Biology, Computational,Computational Molecular Biology,Bio Informatics,Bio-Informatic,Bioinformatic,Biologies, Computational Molecular,Biology, Computational Molecular,Computational Molecular Biologies,Molecular Biologies, Computational
D019906 Nuclear Magnetic Resonance, Biomolecular NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope. Biomolecular Nuclear Magnetic Resonance,Heteronuclear Nuclear Magnetic Resonance,NMR Spectroscopy, Protein,NMR, Biomolecular,NMR, Heteronuclear,NMR, Multinuclear,Nuclear Magnetic Resonance, Heteronuclear,Protein NMR Spectroscopy,Biomolecular NMR,Heteronuclear NMR,Multinuclear NMR,NMR Spectroscopies, Protein,Protein NMR Spectroscopies,Spectroscopies, Protein NMR,Spectroscopy, Protein NMR

Related Publications

Andrea Cavalli, and Xavier Salvatella, and Christopher M Dobson, and Michele Vendruscolo
Characterization of protein secondary structure from NMR chemical shifts.
April 2009, Progress in nuclear magnetic resonance spectroscopy,
Andrea Cavalli, and Xavier Salvatella, and Christopher M Dobson, and Michele Vendruscolo
Nucleic acid helix structure determination from NMR proton chemical shifts.
June 2013, Journal of biomolecular NMR,
Andrea Cavalli, and Xavier Salvatella, and Christopher M Dobson, and Michele Vendruscolo
Determination of protein structures in the solid state from NMR chemical shifts.
December 2008, Structure (London, England : 1993),
Andrea Cavalli, and Xavier Salvatella, and Christopher M Dobson, and Michele Vendruscolo
Interpreting protein structural dynamics from NMR chemical shifts.
April 2012, Journal of the American Chemical Society,
Andrea Cavalli, and Xavier Salvatella, and Christopher M Dobson, and Michele Vendruscolo
The impact of direct refinement against proton chemical shifts on protein structure determination by NMR.
June 1995, Journal of magnetic resonance. Series B,
Andrea Cavalli, and Xavier Salvatella, and Christopher M Dobson, and Michele Vendruscolo
Use of 13Calpha chemical shifts in protein structure determination.
June 2007, The journal of physical chemistry. B,
Andrea Cavalli, and Xavier Salvatella, and Christopher M Dobson, and Michele Vendruscolo
Structure determination of noncanonical RNA motifs guided by ¹H NMR chemical shifts.
April 2014, Nature methods,
Andrea Cavalli, and Xavier Salvatella, and Christopher M Dobson, and Michele Vendruscolo
Probing structure in invisible protein states with anisotropic NMR chemical shifts.
March 2008, Journal of the American Chemical Society,
Andrea Cavalli, and Xavier Salvatella, and Christopher M Dobson, and Michele Vendruscolo
NMR chemical shifts and structure refinement in proteins.
September 1993, Journal of biomolecular NMR,
Andrea Cavalli, and Xavier Salvatella, and Christopher M Dobson, and Michele Vendruscolo
Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings.
April 2011, Journal of the American Chemical Society,
Copied contents to your clipboard!