Literature DB >> 15212494

The origin of protein sidechain order parameter distributions.

Robert B Best1, Jane Clarke, Martin Karplus.   

Abstract

Previous work by Wand et al. (Nature 2001, 411, 501-504) showed that the NMR order parameters characterizing the amplitude of motion of protein side chains seemed to form a multimodal distribution. At the time, no detailed explanation of this at the molecular level was offered, yet three "classes" of motion were inferred. We have analyzed a larger published data set and found that, although the distribution is multimodal, the evidence for three classes is weak. More significantly, we have been able to provide a simple physical explanation for the distributions based on the results of molecular dynamics simulations. This result will aid in the interpretation of data from NMR dynamics experiments.

Mesh:

Substances:

Year:  2004        PMID: 15212494     DOI: 10.1021/ja049078w

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


  22 in total

1.  Is a malleable protein necessarily highly dynamic? The hydrophobic core of the nuclear coactivator binding domain is well ordered.

Authors:  Magnus Kjaergaard; Flemming M Poulsen; Kaare Teilum
Journal:  Biophys J       Date:  2012-04-03       Impact factor: 4.033

2.  Relating side-chain mobility in proteins to rotameric transitions: insights from molecular dynamics simulations and NMR.

Authors:  Hao Hu; Jan Hermans; Andrew L Lee
Journal:  J Biomol NMR       Date:  2005-06       Impact factor: 2.835

3.  Relation between native ensembles and experimental structures of proteins.

Authors:  Robert B Best; Kresten Lindorff-Larsen; Mark A DePristo; Michele Vendruscolo
Journal:  Proc Natl Acad Sci U S A       Date:  2006-07-07       Impact factor: 11.205

Review 4.  Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution.

Authors:  Tatyana I Igumenova; Kendra King Frederick; A Joshua Wand
Journal:  Chem Rev       Date:  2006-05       Impact factor: 60.622

5.  Influence of the fluctuations of the alignment tensor on the analysis of the structure and dynamics of proteins using residual dipolar couplings.

Authors:  X Salvatella; B Richter; M Vendruscolo
Journal:  J Biomol NMR       Date:  2007-11-21       Impact factor: 2.835

6.  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

7.  An improved picture of methyl dynamics in proteins from slowly relaxing local structure analysis of 2H spin relaxation.

Authors:  Eva Meirovitch; Yury E Shapiro; Antonino Polimeno; Jack H Freed
Journal:  J Phys Chem B       Date:  2007-10-17       Impact factor: 2.991

8.  Conformational entropy in molecular recognition by proteins.

Authors:  Kendra King Frederick; Michael S Marlow; Kathleen G Valentine; A Joshua Wand
Journal:  Nature       Date:  2007-07-19       Impact factor: 49.962

9.  Comparison of multiple crystal structures with NMR data for engrailed homeodomain.

Authors:  Tomasz L Religa
Journal:  J Biomol NMR       Date:  2008-02-15       Impact factor: 2.835

10.  A simple model of backbone flexibility improves modeling of side-chain conformational variability.

Authors:  Gregory D Friedland; Anthony J Linares; Colin A Smith; Tanja Kortemme
Journal:  J Mol Biol       Date:  2008-05-11       Impact factor: 5.469

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.