Literature DB >> 17117856

Simultaneous determination of protein backbone structure and dynamics from residual dipolar couplings.

Guillaume Bouvignies1, Phineus Markwick, Rafael Brüschweiler, Martin Blackledge.   

Abstract

Determination of protein structure classically results in a single average configuration that takes no account of conformational fluctuation. Dynamics are, however, inherently linked to structure and crucial to our understanding of biological function. In this study we have used analytical descriptions of dynamic averaging of residual dipolar couplings (RDCs) to simultaneously determine the backbone structure and dynamics of protein GB3. RDCs alone are used to determine an ultrahigh-resolution structure that compares very closely with a refined X-ray structure (rmsd of 0.34 A overall backbone residues). Dynamic amplitudes reporting on motions up to the millisecond time scale reproduce the main characteristics of dynamics previously determined in conjunction with the crystal structure. The use of RDCs alone allows a bias-free comparison with a purely static approach to structure determination. Extensive cross validation clearly demonstrates that the dynamic description is superior to the static approximation. The demonstration that this level of structural resolution and dynamic detail can be extracted from RDCs supports previous indications that these parameters contain extremely precise information about biomolecular conformational sampling.

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Year:  2006        PMID: 17117856     DOI: 10.1021/ja066704b

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


  31 in total

1.  Residual dipolar couplings: are multiple independent alignments always possible?

Authors:  Victoria A Higman; Jonathan Boyd; Lorna J Smith; Christina Redfield
Journal:  J Biomol NMR       Date:  2010-12-24       Impact factor: 2.835

2.  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

3.  Tilt and azimuthal angles of a transmembrane peptide: a comparison between molecular dynamics calculations and solid-state NMR data of sarcolipin in lipid membranes.

Authors:  Lei Shi; Alessandro Cembran; Jiali Gao; Gianluigi Veglia
Journal:  Biophys J       Date:  2009-05-06       Impact factor: 4.033

4.  Pressure effects on the ensemble dynamics of ubiquitin inspected with molecular dynamics simulations and isotropic reorientational eigenmode dynamics.

Authors:  Nikolaos G Sgourakis; Ryan Day; Scott A McCallum; Angel E Garcia
Journal:  Biophys J       Date:  2008-07-11       Impact factor: 4.033

5.  Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics.

Authors:  Nils-Alexander Lakomek; Korvin F A Walter; Christophe Farès; Oliver F Lange; Bert L de Groot; Helmut Grubmüller; Rafael Brüschweiler; Axel Munk; Stefan Becker; Jens Meiler; Christian Griesinger
Journal:  J Biomol NMR       Date:  2008-06-04       Impact factor: 2.835

6.  An improved algorithm for MFR fragment assembly.

Authors:  Georg Kontaxis
Journal:  J Biomol NMR       Date:  2012-05-13       Impact factor: 2.835

7.  Structural dynamics of protein backbone phi angles: extended molecular dynamics simulations versus experimental (3) J scalar couplings.

Authors:  Phineus R L Markwick; Scott A Showalter; Guillaume Bouvignies; Rafael Brüschweiler; Martin Blackledge
Journal:  J Biomol NMR       Date:  2009-07-24       Impact factor: 2.835

8.  A self-consistent description of the conformational behavior of chemically denatured proteins from NMR and small angle scattering.

Authors:  Pau Bernadó; Martin Blackledge
Journal:  Biophys J       Date:  2009-11-18       Impact factor: 4.033

9.  16-fold degeneracy of peptide plane orientations from residual dipolar couplings: analytical treatment and implications for protein structure determination.

Authors:  Jean-Christophe Hus; Loïc Salmon; Guillaume Bouvignies; Johannes Lotze; Martin Blackledge; Rafael Brüschweiler
Journal:  J Am Chem Soc       Date:  2008-11-26       Impact factor: 15.419

10.  Weak alignment of biomacromolecules in collagen gels: an alternative way to yield residual dipolar couplings for NMR measurements.

Authors:  Junhe Ma; Gregory I Goldberg; Nico Tjandra
Journal:  J Am Chem Soc       Date:  2008-12-03       Impact factor: 15.419

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