PMID: 8589605Sep 1, 1995Paper

Structure refinement with molecular dynamics and a Boltzmann-weighted ensemble

Journal of Biomolecular NMR
J FennenWilfred van Gunsteren

Abstract

Time-averaging restraints in molecular dynamics simulations were introduced to account for the averaging implicit in spectroscopic data. Space- or molecule-averaging restraints have been used to overcome the fact that not all molecular conformations can be visited during the finite time of a simulation of a single molecule. In this work we address the issue of using the correct Boltzmann weighting for each member of an ensemble, both in time and in space. It is shown that the molecular- or space-averaging method is simple in theory, but requires a priori knowledge of the behaviour of a system. This is illustrated using a five-atom model system and the small cycle peptide analogue somatostatin. When different molecular conformers that are separated by energy barriers insurmountable on the time scale of a simulation contribute significantly to a measured NOE intensity, the use of space- or molecule-averaged distance restraints yields a more appropriate description of the measured data than conventional single-molecule refinement with or without application of time averaging.

Citations

Mar 23, 2010·European Biophysics Journal : EBJ·Vincent KräutlerPhilippe H Hünenberger
Dec 3, 2009·Journal of Chemical Information and Modeling·Janet L Paulsen, Amy C Anderson
Feb 9, 2011·Proceedings of the National Academy of Sciences of the United States of America·Christopher J FennellKen A Dill
Feb 19, 2014·Progress in Nuclear Magnetic Resonance Spectroscopy·Beat Vögeli
Mar 8, 2013·The Journal of Chemical Physics·Benoît Roux, Jonathan Weare
Dec 21, 2006·Journal of Biomolecular NMR·Bettina KellerWilfred F van Gunsteren
Oct 15, 2014·Journal of Biomolecular NMR·Niels HansenWilfred F van Gunsteren
Mar 22, 2015·Current Opinion in Structural Biology·Gunnar F Schröder
Jul 9, 2016·The Journal of Physical Chemistry. B·F VasileG Tiana
Jan 25, 2002·Biopolymers·Thomas P BurghardtKatalin Ajtai
Dec 22, 2009·Molecular BioSystems·Daniela Kruschel, Bojan Zagrovic
Nov 20, 2016·Angewandte Chemie·Wilfred F van GunsterenLorna J Smith
Jan 19, 2019·International Journal of Molecular Sciences·Emanuel K Peter, Jiří Černý
Sep 24, 2020·Pharmaceuticals·Mattia BernettiMatteo Masetti
Nov 5, 2020·Chembiochem : a European Journal of Chemical Biology·Lorna J SmithNiels Hansen
Jun 15, 2021·Frontiers in Molecular Biosciences·Cristina Paissoni, Carlo Camilloni
Oct 9, 2012·Journal of Chemical Theory and Computation·Jane R AllisonJožica Dolenc
Oct 9, 2012·Journal of Chemical Theory and Computation·Jed W Pitera, John D Chodera
Apr 9, 2020·Journal of Chemical Theory and Computation·Bradley W TreeceMathias Lösche
Aug 14, 2019·Journal of Chemical Theory and Computation·Markus R Hermann, Jochen S Hub
Nov 23, 2006·Journal of the American Chemical Society·Joerg GsponerMichele Vendruscolo
Aug 15, 2002·Journal of the American Chemical Society·Adrian J CharltonMichael P Williamson

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