Literature DB >> 17557784

Deciphering protein dynamics from NMR data using explicit structure sampling and selection.

Yiwen Chen1, Sharon L Campbell, Nikolay V Dokholyan.   

Abstract

Perhaps one of the most prominent realizations of recent years is the critical role that protein dynamics plays in many facets of cellular function. While characterization of protein dynamics is fundamental to our understanding of protein function, the ability to explicitly detect an ensemble of protein conformations from dynamics data is a paramount challenge in structural biology. Here, we report a new computational method, Sample and Select, for determining the ensemble of protein conformations consistent with NMR dynamics data. This method can be generalized and extended to different sources of dynamics data, enabling broad applicability in deciphering protein dynamics at different timescales. The structural ensemble derived from Sample and Select will provide structural and dynamic information that should aid us in understanding and manipulating protein function.

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Year:  2007        PMID: 17557784      PMCID: PMC1965439          DOI: 10.1529/biophysj.107.104174

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  37 in total

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Journal:  Nat Struct Biol       Date:  2002-09

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5.  Hydrophobic core fluidity of homologous protein domains: relation of side-chain dynamics to core composition and packing.

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6.  Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution.

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Journal:  Proteins       Date:  2003-02-15

Review 7.  Recent advances in the development and application of implicit solvent models in biomolecule simulations.

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Journal:  Curr Opin Struct Biol       Date:  2004-04       Impact factor: 6.809

8.  Increased rigidity of eglin c at acidic pH: evidence from NMR spin relaxation and MD simulations.

Authors:  Hao Hu; Michael W Clarkson; Jan Hermans; Andrew L Lee
Journal:  Biochemistry       Date:  2003-12-02       Impact factor: 3.162

9.  Dynamics and entropy of a calmodulin-peptide complex studied by NMR and molecular dynamics.

Authors:  Ninad V Prabhu; Andrew L Lee; A Joshua Wand; Kim A Sharp
Journal:  Biochemistry       Date:  2003-01-21       Impact factor: 3.162

10.  Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis.

Authors:  Sagar D Khare; Feng Ding; Nikolay V Dokholyan
Journal:  J Mol Biol       Date:  2003-11-28       Impact factor: 5.469

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  37 in total

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Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2014-11-28       Impact factor: 9.795

2.  Information content of long-range NMR data for the characterization of conformational heterogeneity.

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Journal:  J Biomol NMR       Date:  2015-06-05       Impact factor: 2.835

3.  Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data.

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4.  Recovering a representative conformational ensemble from underdetermined macromolecular structural data.

Authors:  Konstantin Berlin; Carlos A Castañeda; Dina Schneidman-Duhovny; Andrej Sali; Alfredo Nava-Tudela; David Fushman
Journal:  J Am Chem Soc       Date:  2013-11-06       Impact factor: 15.419

5.  Modeling intrinsically disordered proteins with bayesian statistics.

Authors:  Charles K Fisher; Austin Huang; Collin M Stultz
Journal:  J Am Chem Soc       Date:  2010-10-27       Impact factor: 15.419

6.  Approximate reconstruction of continuous spatially complex domain motions by multialignment NMR residual dipolar couplings.

Authors:  Charles K Fisher; Hashim M Al-Hashimi
Journal:  J Phys Chem B       Date:  2009-05-07       Impact factor: 2.991

7.  A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed.

Authors:  Loïc Salmon; Gavin Bascom; Ioan Andricioaei; Hashim M Al-Hashimi
Journal:  J Am Chem Soc       Date:  2013-03-28       Impact factor: 15.419

Review 8.  Advances in the determination of nucleic acid conformational ensembles.

Authors:  Loïc Salmon; Shan Yang; Hashim M Al-Hashimi
Journal:  Annu Rev Phys Chem       Date:  2013-12-16       Impact factor: 12.703

9.  A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.

Authors:  Gregory D Friedland; Nils-Alexander Lakomek; Christian Griesinger; Jens Meiler; Tanja Kortemme
Journal:  PLoS Comput Biol       Date:  2009-05-29       Impact factor: 4.475

10.  Coarse-grained models reveal functional dynamics--I. Elastic network models--theories, comparisons and perspectives.

Authors:  Lee-Wei Yang; Choon-Peng Chng
Journal:  Bioinform Biol Insights       Date:  2008-03-04
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