|
rdf:type |
|
|
lifeskim:mentions |
|
|
pubmed:issue |
10
|
|
pubmed:dateCreated |
2007-6-12
|
|
pubmed:abstractText |
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.
|
|
pubmed:commentsCorrections |
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-10222198,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-10496424,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-10600732,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-10688897,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-10891271,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-11031289,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-11124028,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-11416174,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-11721003,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-11746690,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-11754338,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-12657780,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-12930962,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-13054692,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-13054693,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-13072614,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-14659736,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-14671790,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-15107493,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-15465050,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-15562006,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-15749779,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-15869310,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-16287299,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-4427376,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-7604014,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-7918256,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-8676379,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-9275173,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-9342335,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-9631298,
http://linkedlifedata.com/resource/pubmed/commentcorrection/17459891-9736707
|
|
pubmed:language |
eng
|
|
pubmed:journal |
|
|
pubmed:citationSubset |
IM
|
|
pubmed:chemical |
|
|
pubmed:status |
MEDLINE
|
|
pubmed:issn |
1362-4962
|
|
pubmed:author |
|
|
pubmed:issnType |
Electronic
|
|
pubmed:volume |
35
|
|
pubmed:owner |
NLM
|
|
pubmed:authorsComplete |
Y
|
|
pubmed:pagination |
3330-8
|
|
pubmed:dateRevised |
2009-11-18
|
|
pubmed:meshHeading |
|
|
pubmed:year |
2007
|
|
pubmed:articleTitle |
Theoretical study of large conformational transitions in DNA: the B<-->A conformational change in water and ethanol/water.
|
|
pubmed:affiliation |
Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica & Instituto Nacional de Bioinformática, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.
|
|
pubmed:publicationType |
Journal Article,
Research Support, Non-U.S. Gov't
|
