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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...
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Formato: | Texto |
Lenguaje: | English |
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International Union of Crystallography
2008
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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 |
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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 |