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PMID: 17535901 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Protein structure determination from NMR chemical shifts.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 104 ·No. 23 ·2007-06-05 ·Pages 9615-20

Cavalli A, Salvatella X, Dobson CM, Vendruscolo M

Abstract

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.

MeSH Terms

Bayes Theorem Biophysical Phenomena Biophysics Computational Biology/methods Models, Molecular Nuclear Magnetic Resonance, Biomolecular/methods Protein Conformation Proteins/chemistry

Chemicals

Proteins

Authors & Affiliations

4 authors, click to expand affiliations / ORCID

Cavalli Andrea

Department of Chemistry, Cambridge University, Cambridge CB2 1EW, United Kingdom.

Salvatella Xavier

Dobson Christopher M

Vendruscolo Michele

References (38)

38 references, click to expand

Bayesian statistical analysis of protein side-chain rotamer preferences.
Protein Sci. 1997 Aug;6(8):1661-81 PMID: 9260279
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions.
J Mol Biol. 1997 Apr 25;268(1):209-25 PMID: 9149153
Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins.
Proteins. 1999 Jan 1;34(1):82-95 PMID: 10336385
Protein backbone angle restraints from searching a database for chemical shift and sequence homology.
J Biomol NMR. 1999 Mar;13(3):289-302 PMID: 10212987
Effective energy function for proteins in solution.
Proteins. 1999 May 1;35(2):133-52 PMID: 10223287
Mapping long-range interactions in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations.
J Am Chem Soc. 2005 Jan 19;127(2):476-7 PMID: 15643843
Simultaneous determination of protein structure and dynamics.
Nature. 2005 Jan 13;433(7022):128-32 PMID: 15650731
Towards complete descriptions of the free-energy landscapes of proteins.
Philos Trans A Math Phys Eng Sci. 2005 Feb 15;363(1827):433-50; discussion 450-2 PMID: 15664892
Intrinsically unstructured proteins and their functions.
Nat Rev Mol Cell Biol. 2005 Mar;6(3):197-208 PMID: 15738986
Toward high-resolution de novo structure prediction for small proteins.
Science. 2005 Sep 16;309(5742):1868-71 PMID: 16166519
Progress in modeling of protein structures and interactions.
Science. 2005 Oct 28;310(5748):638-42 PMID: 16254179
Intrinsic dynamics of an enzyme underlies catalysis.
Nature. 2005 Nov 3;438(7064):117-21 PMID: 16267559
Building native protein conformation from highly approximate backbone torsion angles.
Proc Natl Acad Sci U S A. 2005 Nov 8;102(45):16227-32 PMID: 16251268
Quantitative NMR spectroscopy of supramolecular complexes: dynamic side pores in ClpP are important for product release.
Proc Natl Acad Sci U S A. 2005 Nov 15;102(46):16678-83 PMID: 16263929
Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small alpha/beta protein: a unified picture of high probability, fast atomic motions in proteins.
J Mol Biol. 2006 Feb 3;355(5):879-86 PMID: 16343537
The impact of structural genomics: expectations and outcomes.
Science. 2006 Jan 20;311(5759):347-51 PMID: 16424331
NMR study of the tetrameric KcsA potassium channel in detergent micelles.
Protein Sci. 2006 Apr;15(4):684-98 PMID: 16522799
De novo protein structure determination using sparse NMR data.
J Biomol NMR. 2000 Dec;18(4):311-8 PMID: 11200525
Use of chemical shifts in macromolecular structure determination.
Methods Enzymol. 2001;338:3-34 PMID: 11460554
Dipolar couplings in macromolecular structure determination.
Methods Enzymol. 2001;339:127-74 PMID: 11462810
Automated prediction of 15N, 13Calpha, 13Cbeta and 13C' chemical shifts in proteins using a density functional database.
J Biomol NMR. 2001 Dec;21(4):321-33 PMID: 11824752
De novo determination of protein backbone structure from residual dipolar couplings using Rosetta.
J Am Chem Soc. 2002 Mar 20;124(11):2723-9 PMID: 11890823
NMR analysis of a 900K GroEL GroES complex.
Nature. 2002 Jul 11;418(6894):207-11 PMID: 12110894
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction.
Protein Sci. 2002 Nov;11(11):2714-26 PMID: 12381853
HADDOCK: a protein-protein docking approach based on biochemical or biophysical information.
J Am Chem Soc. 2003 Feb 19;125(7):1731-7 PMID: 12580598
An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes.
J Mol Biol. 2003 Feb 28;326(4):1239-59 PMID: 12589766
A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics.
J Mol Biol. 2003 May 23;329(1):159-74 PMID: 12742025
PROSHIFT: protein chemical shift prediction using artificial neural networks.
J Biomol NMR. 2003 May;26(1):25-37 PMID: 12766400
Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts.
J Biomol NMR. 2003 Jul;26(3):215-40 PMID: 12766419
The ASTRAL Compendium in 2004.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D189-92 PMID: 14681391
Rapid protein fold determination using unassigned NMR data.
Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15404-9 PMID: 14668443
Heteronuclear NMR investigations of dynamic regions of intact Escherichia coli ribosomes.
Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):10949-54 PMID: 15263071
Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR.
Nature. 2004 Jul 29;430(6999):586-90 PMID: 15282609
The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy.
Biochemistry. 1992 Feb 18;31(6):1647-51 PMID: 1737021
Solution structure of carbonmonoxy myoglobin determined from nuclear magnetic resonance distance and chemical shift constraints.
J Mol Biol. 1994 Nov 25;244(2):183-97 PMID: 7966330
Errors in protein structures.
Nature. 1996 May 23;381(6580):272 PMID: 8692262
Knowledge-based protein secondary structure assignment.
Proteins. 1995 Dec;23(4):566-79 PMID: 8749853
New methods of structure refinement for macromolecular structure determination by NMR.
Proc Natl Acad Sci U S A. 1998 May 26;95(11):5891-8 PMID: 9600889

Article Info

Journal

Proceedings of the National Academy of Sciences of the United States of America

Abbr.

Proc Natl Acad Sci U S A

ISSN

0027-8424

DOI

10.1073/pnas.0610313104

Published

2007-06-05

Epub

2007-00-29

Pages

9615-20

Language

English

Region

United States

NLM ID

7505876

PMCID

PMC1887584

Subset

Grants

Wellcome Trust · United Kingdom

External Links

PubMed source DOI: 10.1073/pnas.0610313104 PMC Full Text View journal details

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