Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer: Influence of the crystal environment

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dc.contributorVirginia Techen
dc.contributor.authorBevan, David R.en
dc.contributor.authorLi, L. P.en
dc.contributor.authorPedersen, L. G.en
dc.contributor.authorDarden, T. A.en
dc.contributor.departmentBiochemistryen
dc.date.accessed2014-02-05en
dc.date.accessioned2014-02-26T19:10:04Zen
dc.date.available2014-02-26T19:10:04Zen
dc.date.issued2000-02en
dc.description.abstractMolecular dynamics (MD) simulations of the DNA duplex d(CCAACGTTGG)(2) were used to study the relationship between DNA sequence and structure. Two crystal simulations were carried out; one consisted of one unit cell containing two duplexes, and the other of two unit cells containing four duplexes. Two solution simulations were also carried out, one starting from canonical B-DNA and the other starting from the crystal structure, For many helicoidal parameters, the results from the crystal and solution simulations were essentially identical. However, for other parameters, in particular, alpha, gamma, delta, (epsilon - zeta), phase, and helical twist, differences between crystal and solution simulations were apparent. Notably, during crystal simulations, values of helical twist remained comparable to those in the crystal structure, to include the sequence-dependent differences among base steps, in which values ranged from 20 degrees to 50 degrees per base step, However, in the solution simulations, not only did the average values of helical twist decrease to similar to 30 degrees per base step, but every base step was similar to 30 degrees, suggesting that the sequence-dependent information may be lost. This study reveals that MD simulations of the crystal environment complement solution simulations in validating the applicability of MD to the analysis of DNA structure.en
dc.description.sponsorshipNational Institute of Environmental Health Science (NIEHS)en
dc.description.sponsorshipNorth Carolina Supercomputing Centeren
dc.description.sponsorshipNational Institutes of Health HL-06350en
dc.identifier.citationBevan, DR; Li, LP; Pedersen, LG; et al., "Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer: Influence of the crystal environment," Biophysical Journal 78(2), 668-682 (2000); doi: 10.1016/S0006-3495(00)76625-2en
dc.identifier.doihttps://doi.org/10.1016/S0006-3495(00)76625-2en
dc.identifier.issn0006-3495en
dc.identifier.urihttp://hdl.handle.net/10919/25767en
dc.identifier.urlhttp://www.sciencedirect.com/science/article/pii/S0006349500766252en
dc.language.isoenen
dc.publisherCELL PRESSen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectparticle-mesh-ewalden
dc.subjectb-dnaen
dc.subjectnucleic-acidsen
dc.subjecta-dnaen
dc.subjectminor-grooveen
dc.subjectforce-fielden
dc.subjecthydrationen
dc.subjectsequenceen
dc.subjectWateren
dc.subjectd(cgcgaattcgcg)en
dc.titleMolecular dynamics simulations of the d(CCAACGTTGG)(2) decamer: Influence of the crystal environmenten
dc.title.serialBiophysical Journalen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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