Literature DB >> 17535901

Protein structure determination from NMR chemical shifts.

Andrea Cavalli1, Xavier Salvatella, Christopher M Dobson, Michele Vendruscolo.   

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.

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Year:  2007        PMID: 17535901      PMCID: PMC1887584          DOI: 10.1073/pnas.0610313104

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  38 in total

1.  Effective energy function for proteins in solution.

Authors:  T Lazaridis; M Karplus
Journal:  Proteins       Date:  1999-05-01

2.  Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins.

Authors:  K T Simons; I Ruczinski; C Kooperberg; B A Fox; C Bystroff; D Baker
Journal:  Proteins       Date:  1999-01-01

3.  Simultaneous determination of protein structure and dynamics.

Authors:  Kresten Lindorff-Larsen; Robert B Best; Mark A Depristo; Christopher M Dobson; Michele Vendruscolo
Journal:  Nature       Date:  2005-01-13       Impact factor: 49.962

Review 4.  Towards complete descriptions of the free-energy landscapes of proteins.

Authors:  Michele Vendruscolo; Christopher M Dobson
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2005-02-15       Impact factor: 4.226

5.  Toward high-resolution de novo structure prediction for small proteins.

Authors:  Philip Bradley; Kira M S Misura; David Baker
Journal:  Science       Date:  2005-09-16       Impact factor: 47.728

6.  Bayesian statistical analysis of protein side-chain rotamer preferences.

Authors:  R L Dunbrack; F E Cohen
Journal:  Protein Sci       Date:  1997-08       Impact factor: 6.725

7.  Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions.

Authors:  K T Simons; C Kooperberg; E Huang; D Baker
Journal:  J Mol Biol       Date:  1997-04-25       Impact factor: 5.469

8.  Protein backbone angle restraints from searching a database for chemical shift and sequence homology.

Authors:  G Cornilescu; F Delaglio; A Bax
Journal:  J Biomol NMR       Date:  1999-03       Impact factor: 2.835

Review 9.  Intrinsically unstructured proteins and their functions.

Authors:  H Jane Dyson; Peter E Wright
Journal:  Nat Rev Mol Cell Biol       Date:  2005-03       Impact factor: 94.444

10.  Mapping long-range interactions in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations.

Authors:  Matthew M Dedmon; Kresten Lindorff-Larsen; John Christodoulou; Michele Vendruscolo; Christopher M Dobson
Journal:  J Am Chem Soc       Date:  2005-01-19       Impact factor: 15.419

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  183 in total

1.  Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids.

Authors:  Wookyung Yu; Woonghee Lee; Weontae Lee; Suhkmann Kim; Iksoo Chang
Journal:  J Biomol NMR       Date:  2011-10-30       Impact factor: 2.835

2.  Protein structure validation by generalized linear model root-mean-square deviation prediction.

Authors:  Anurag Bagaria; Victor Jaravine; Yuanpeng J Huang; Gaetano T Montelione; Peter Güntert
Journal:  Protein Sci       Date:  2012-01-04       Impact factor: 6.725

3.  A procedure to validate and correct the 13C chemical shift calibration of RNA datasets.

Authors:  Thomas Aeschbacher; Mario Schubert; Frédéric H-T Allain
Journal:  J Biomol NMR       Date:  2012-01-18       Impact factor: 2.835

4.  A Bayesian approach for determining protein side-chain rotamer conformations using unassigned NOE data.

Authors:  Jianyang Zeng; Kyle E Roberts; Pei Zhou; Bruce Randall Donald
Journal:  J Comput Biol       Date:  2011-10-04       Impact factor: 1.479

5.  An improved structural characterisation of reduced French bean plastocyanin based on NMR data and local-elevation molecular dynamics simulation.

Authors:  Denise Steiner; Wilfred F van Gunsteren
Journal:  Eur Biophys J       Date:  2012-06-16       Impact factor: 1.733

6.  Transiently populated intermediate functions as a branching point of the FF domain folding pathway.

Authors:  Dmitry M Korzhnev; Tomasz L Religa; Lewis E Kay
Journal:  Proc Natl Acad Sci U S A       Date:  2012-05-30       Impact factor: 11.205

7.  Accurate protein structure modeling using sparse NMR data and homologous structure information.

Authors:  James M Thompson; Nikolaos G Sgourakis; Gaohua Liu; Paolo Rossi; Yuefeng Tang; Jeffrey L Mills; Thomas Szyperski; Gaetano T Montelione; David Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2012-06-04       Impact factor: 11.205

Review 8.  Chemical shift tensor - the heart of NMR: Insights into biological aspects of proteins.

Authors:  Hazime Saitô; Isao Ando; Ayyalusamy Ramamoorthy
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2010-05-07       Impact factor: 9.795

9.  A low affinity ground state conformation for the Dynein microtubule binding domain.

Authors:  Lynn McNaughton; Irina Tikhonenko; Nilesh K Banavali; David M LeMaster; Michael P Koonce
Journal:  J Biol Chem       Date:  2010-03-29       Impact factor: 5.157

10.  A robust algorithm for optimizing protein structures with NMR chemical shifts.

Authors:  Mark Berjanskii; David Arndt; Yongjie Liang; David S Wishart
Journal:  J Biomol NMR       Date:  2015-09-07       Impact factor: 2.835

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