Literature DB >> 27627888

On the use of time-averaging restraints when deriving biomolecular structure from ³J -coupling values obtained from NMR experiments.

Lorna J Smith1, Wilfred F van Gunsteren2, Niels Hansen3.   

Abstract

Deriving molecular structure from [Formula: see text]-couplings obtained from NMR experiments is a challenge due to (1) the uncertainty in the Karplus relation [Formula: see text] connecting a [Formula: see text]-coupling value to a torsional angle [Formula: see text], (2) the need to account for the averaging inherent to the measurement of [Formula: see text]-couplings, and (3) the sampling road blocks that may emerge due to the multiple-valuedness of the inverse function [Formula: see text] of the function [Formula: see text]. Ways to properly handle these issues in structure refinement of biomolecules are discussed and illustrated using the protein hen egg white lysozyme as example.

Keywords:  Conformational dynamics; Force field; Nuclear magnetic resonance; Statistical mechanics; Structure refinement

Mesh:

Year:  2016        PMID: 27627888     DOI: 10.1007/s10858-016-0058-5

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  30 in total

1.  Self-consistent 3J coupling analysis for the joint calibration of Karplus coefficients and evaluation of torsion angles.

Authors:  J M Schmidt; M Blümel; F Löhr; H Rüterjans
Journal:  J Biomol NMR       Date:  1999-05       Impact factor: 2.835

2.  The GROMOS software for biomolecular simulation: GROMOS05.

Authors:  Markus Christen; Philippe H Hünenberger; Dirk Bakowies; Riccardo Baron; Roland Bürgi; Daan P Geerke; Tim N Heinz; Mika A Kastenholz; Vincent Kräutler; Chris Oostenbrink; Christine Peter; Daniel Trzesniak; Wilfred F van Gunsteren
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

3.  Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics.

Authors:  P Gros; W F van Gunsteren; W G Hol
Journal:  Science       Date:  1990-09-07       Impact factor: 47.728

4.  A reassessment of the structure of chymotrypsin inhibitor 2 (CI-2) using time-averaged NMR restraints.

Authors:  A P Nanzer; F M Poulsen; W F van Gunsteren; A E Torda
Journal:  Biochemistry       Date:  1994-12-06       Impact factor: 3.162

5.  Biomolecular structure refinement using the GROMOS simulation software.

Authors:  Nathan Schmid; Jane R Allison; Jožica Dolenc; Andreas P Eichenberger; Anna-Pitschna E Kunz; Wilfred F van Gunsteren
Journal:  J Biomol NMR       Date:  2011-08-20       Impact factor: 2.835

6.  A method to explore protein side chain conformational variability using experimental data.

Authors:  Jane R Allison; Wilfred F van Gunsteren
Journal:  Chemphyschem       Date:  2009-12-21       Impact factor: 3.102

7.  Parametrisation of time-averaged distance restraints in MD simulations.

Authors:  A P Nanzer; W F van Gunsteren; A E Torda
Journal:  J Biomol NMR       Date:  1995-11       Impact factor: 2.835

8.  How is an NMR structure best defined? An analysis of molecular dynamics distance-based approaches.

Authors:  D A Pearlman
Journal:  J Biomol NMR       Date:  1994-01       Impact factor: 2.835

9.  Molecular dynamics with weighted time-averaged restraints for a DNA octamer. Dynamic interpretation of nuclear magnetic resonance data.

Authors:  U Schmitz; N B Ulyanov; A Kumar; T L James
Journal:  J Mol Biol       Date:  1993-11-20       Impact factor: 5.469

10.  A protein structure from nuclear magnetic resonance data. lac repressor headpiece.

Authors:  R Kaptein; E R Zuiderweg; R M Scheek; R Boelens; W F van Gunsteren
Journal:  J Mol Biol       Date:  1985-03-05       Impact factor: 5.469

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