Literature DB >> 15225030

Determination of protein structures consistent with NMR order parameters.

Robert B Best1, Michele Vendruscolo.   

Abstract

Order parameters obtained from NMR experiments characterize distributions of bond vector orientations. Their interpretation, however, usually requires the assumption of a particular motional model. We propose a multiple-copy simulation method in which the experimental order parameters are used as restraints in conjunction with a standard molecular force field. The latter effectively acts as a sophisticated motional model, allowing ensembles of structures consistent with the experimental order parameters to be determined.

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Year:  2004        PMID: 15225030     DOI: 10.1021/ja0396955

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  41 in total

1.  Interpreting dynamically-averaged scalar couplings in proteins.

Authors:  Kresten Lindorff-Larsen; Robert B Best; Michele Vendruscolo
Journal:  J Biomol NMR       Date:  2005-08       Impact factor: 2.835

2.  Structural comparison of the two alternative transition states for folding of TI I27.

Authors:  Christian D Geierhaas; Robert B Best; Emanuele Paci; Michele Vendruscolo; Jane Clarke
Journal:  Biophys J       Date:  2006-04-07       Impact factor: 4.033

3.  On the characterization of protein native state ensembles.

Authors:  Amarda Shehu; Lydia E Kavraki; Cecilia Clementi
Journal:  Biophys J       Date:  2006-12-08       Impact factor: 4.033

4.  Distinguishing among structural ensembles of the GB1 peptide: REMD simulations and NMR experiments.

Authors:  Daniel S Weinstock; Chitra Narayanan; Anthony K Felts; Michael Andrec; Ronald M Levy; Kuen-Phon Wu; Jean Baum
Journal:  J Am Chem Soc       Date:  2007-04-03       Impact factor: 15.419

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

Authors:  Yiwen Chen; Sharon L Campbell; Nikolay V Dokholyan
Journal:  Biophys J       Date:  2007-06-08       Impact factor: 4.033

6.  Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins.

Authors:  Paul Maragakis; Kresten Lindorff-Larsen; Michael P Eastwood; Ron O Dror; John L Klepeis; Isaiah T Arkin; Morten Ø Jensen; Huafeng Xu; Nikola Trbovic; Richard A Friesner; Arthur G Palmer; David E Shaw
Journal:  J Phys Chem B       Date:  2008-03-01       Impact factor: 2.991

7.  An experimentally guided umbrella sampling protocol for biomolecules.

Authors:  Maria Mills; Ioan Andricioaei
Journal:  J Chem Phys       Date:  2008-09-21       Impact factor: 3.488

8.  Structure-based protein NMR assignments using native structural ensembles.

Authors:  Mehmet Serkan Apaydin; Vincent Conitzer; Bruce Randall Donald
Journal:  J Biomol NMR       Date:  2008-03-26       Impact factor: 2.835

9.  Solid-state NMR ensemble dynamics as a mediator between experiment and simulation.

Authors:  Taehoon Kim; Sunhwan Jo; Wonpil Im
Journal:  Biophys J       Date:  2011-06-22       Impact factor: 4.033

10.  CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data.

Authors:  Annamária F Angyán; Balázs Szappanos; András Perczel; Zoltán Gáspári
Journal:  BMC Struct Biol       Date:  2010-10-29
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