Cargando…

Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis

Normal-mode analysis (NMA) can be used to generate multiple structural variants of a given template model, thereby increasing the chance of finding the molecular-replacement solution. Here, it is shown that it is also possible to directly refine the amplitudes of the normal modes against experimenta...

Descripción completa

Detalles Bibliográficos
Autor principal: Delarue, Marc
Formato: Texto
Lenguaje:English
Publicado: International Union of Crystallography 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2394787/
https://www.ncbi.nlm.nih.gov/pubmed/18094466
http://dx.doi.org/10.1107/S0907444907053516
_version_ 1782155449876873216
author Delarue, Marc
author_facet Delarue, Marc
author_sort Delarue, Marc
collection PubMed
description Normal-mode analysis (NMA) can be used to generate multiple structural variants of a given template model, thereby increasing the chance of finding the molecular-replacement solution. Here, it is shown that it is also possible to directly refine the amplitudes of the normal modes against experimental data (X-ray or cryo-EM), generalizing rigid-body refinement methods by adding just a few additional degrees of freedom that sample collective and large-amplitude movements. It is also argued that the situation where several (conformations of) models are present simultaneously in the crystal can be studied with adjustable occupancies using techniques derived from statistical thermodynamics and already used in molecular modelling.
format Text
id pubmed-2394787
institution National Center for Biotechnology Information
language English
publishDate 2008
publisher International Union of Crystallography
record_format MEDLINE/PubMed
spelling pubmed-23947872009-03-05 Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis Delarue, Marc Acta Crystallogr D Biol Crystallogr Research Papers Normal-mode analysis (NMA) can be used to generate multiple structural variants of a given template model, thereby increasing the chance of finding the molecular-replacement solution. Here, it is shown that it is also possible to directly refine the amplitudes of the normal modes against experimental data (X-ray or cryo-EM), generalizing rigid-body refinement methods by adding just a few additional degrees of freedom that sample collective and large-amplitude movements. It is also argued that the situation where several (conformations of) models are present simultaneously in the crystal can be studied with adjustable occupancies using techniques derived from statistical thermodynamics and already used in molecular modelling. International Union of Crystallography 2008-01-01 2007-12-04 /pmc/articles/PMC2394787/ /pubmed/18094466 http://dx.doi.org/10.1107/S0907444907053516 Text en © International Union of Crystallography 2008 http://journals.iucr.org/services/termsofuse.html This is an open-access article distributed under the terms described at http://journals.iucr.org/services/termsofuse.html.
spellingShingle Research Papers
Delarue, Marc
Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis
title Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis
title_full Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis
title_fullStr Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis
title_full_unstemmed Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis
title_short Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis
title_sort dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2394787/
https://www.ncbi.nlm.nih.gov/pubmed/18094466
http://dx.doi.org/10.1107/S0907444907053516
work_keys_str_mv AT delaruemarc dealingwithstructuralvariabilityinmolecularreplacementandcrystallographicrefinementthroughnormalmodeanalysis