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Theoretical study of large conformational transitions in DNA: the B↔A conformational change in water and ethanol/water
We explore here the possibility of determining theoretically the free energy change associated with large conformational transitions in DNA, like the solvent-induced B⇔A conformational change. We find that a combination of targeted molecular dynamics (tMD) and the weighted histogram analysis method...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2007
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1904281/ https://www.ncbi.nlm.nih.gov/pubmed/17459891 http://dx.doi.org/10.1093/nar/gkl1135 |
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author | Noy, Agnes Pérez, Alberto Laughton, Charles A. Orozco, Modesto |
author_facet | Noy, Agnes Pérez, Alberto Laughton, Charles A. Orozco, Modesto |
author_sort | Noy, Agnes |
collection | PubMed |
description | We explore here the possibility of determining theoretically the free energy change associated with large conformational transitions in DNA, like the solvent-induced B⇔A conformational change. We find that a combination of targeted molecular dynamics (tMD) and the weighted histogram analysis method (WHAM) can be used to trace this transition in both water and ethanol/water mixture. The pathway of the transition in the A→B direction mirrors the B→A pathway, and is dominated by two processes that occur somewhat independently: local changes in sugar puckering and global rearrangements (particularly twist and roll) in the structure. The B→A transition is found to be a quasi-harmonic process, which follows closely the first spontaneous deformation mode of B-DNA, showing that a physiologically-relevant deformation is in coded in the flexibility pattern of DNA. |
format | Text |
id | pubmed-1904281 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-19042812007-07-03 Theoretical study of large conformational transitions in DNA: the B↔A conformational change in water and ethanol/water Noy, Agnes Pérez, Alberto Laughton, Charles A. Orozco, Modesto Nucleic Acids Res Structural Biology We explore here the possibility of determining theoretically the free energy change associated with large conformational transitions in DNA, like the solvent-induced B⇔A conformational change. We find that a combination of targeted molecular dynamics (tMD) and the weighted histogram analysis method (WHAM) can be used to trace this transition in both water and ethanol/water mixture. The pathway of the transition in the A→B direction mirrors the B→A pathway, and is dominated by two processes that occur somewhat independently: local changes in sugar puckering and global rearrangements (particularly twist and roll) in the structure. The B→A transition is found to be a quasi-harmonic process, which follows closely the first spontaneous deformation mode of B-DNA, showing that a physiologically-relevant deformation is in coded in the flexibility pattern of DNA. Oxford University Press 2007-05 2007-04-25 /pmc/articles/PMC1904281/ /pubmed/17459891 http://dx.doi.org/10.1093/nar/gkl1135 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Structural Biology Noy, Agnes Pérez, Alberto Laughton, Charles A. Orozco, Modesto Theoretical study of large conformational transitions in DNA: the B↔A conformational change in water and ethanol/water |
title | Theoretical study of large conformational transitions in DNA: the B↔A conformational change in water and ethanol/water |
title_full | Theoretical study of large conformational transitions in DNA: the B↔A conformational change in water and ethanol/water |
title_fullStr | Theoretical study of large conformational transitions in DNA: the B↔A conformational change in water and ethanol/water |
title_full_unstemmed | Theoretical study of large conformational transitions in DNA: the B↔A conformational change in water and ethanol/water |
title_short | Theoretical study of large conformational transitions in DNA: the B↔A conformational change in water and ethanol/water |
title_sort | theoretical study of large conformational transitions in dna: the b↔a conformational change in water and ethanol/water |
topic | Structural Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1904281/ https://www.ncbi.nlm.nih.gov/pubmed/17459891 http://dx.doi.org/10.1093/nar/gkl1135 |
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