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rdf:type |
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lifeskim:mentions |
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pubmed:issue |
4 Pt 1
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pubmed:dateCreated |
2009-6-12
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pubmed:abstractText |
We test a hypothesis that the closed form of the C2 domain of coagulation factor V is more stable than the open form in an aqueous environment using a two-dimensional free-energy calculation with a simple dielectric solvent model. Our result shows that while the free-energy difference between two forms is small, favoring the closed form, a two-dimensional free-energy surface (FES) reveals that a transition state (1.53 kcal/mol) exists between the two conformations. By mapping the one-dimensional order parameter DeltaQ onto the two-dimensional FES, we search the conformational change path with the highest Boltzmann weighting factor between the closed and open form of the factor V C2 domain. The predicted transition path from the closed to open form is not that of simple side chain movements, but instead concerted movements of several loops. We also present a one-dimensional free-energy profile using a collective order parameter, which in a coarse manner locates the energy barriers found on the two-dimensional FES.
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pubmed:grant |
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pubmed:commentsCorrections |
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-10586886,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-10586887,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-11444970,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-11557887,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-12947041,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-14695293,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-15184653,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-15291524,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-15869310,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-16529932,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-16680712,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-16785435,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-17583728,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-17783020,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-18000050,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-18075575,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-18083096,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-18805918,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-2914947,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-500617,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-762106,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19518258-7724609
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pubmed:language |
eng
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pubmed:journal |
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pubmed:citationSubset |
IM
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pubmed:chemical |
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pubmed:status |
MEDLINE
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pubmed:month |
Apr
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pubmed:issn |
1539-3755
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pubmed:author |
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pubmed:issnType |
Print
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pubmed:volume |
79
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
041909
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pubmed:dateRevised |
2010-9-27
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pubmed:meshHeading |
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pubmed:year |
2009
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pubmed:articleTitle |
Conformational change path between closed and open forms of C2 domain of coagulation factor V on a two-dimensional free-energy surface.
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pubmed:affiliation |
Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA.
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pubmed:publicationType |
Journal Article,
Research Support, N.I.H., Extramural
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