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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...

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Detalles Bibliográficos
Autores principales: Noy, Agnes, Pérez, Alberto, Laughton, Charles A., Orozco, Modesto
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2007
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.
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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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