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Collective‐variable Monte Carlo simulation of DNA
Author(s) -
Gabb H. A.,
Prévost C.,
Bertucat G.,
Robert C. H.,
Lavery R.
Publication year - 1997
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/(sici)1096-987x(199712)18:16<2001::aid-jcc5>3.0.co;2-p
Subject(s) - monte carlo method , molecular dynamics , statistical physics , chemistry , dynamic monte carlo method , computational chemistry , physics , mathematics , statistics
Monte Carlo simulations have been carried out on DNA oligomers using an internal coordinate model associated with a pseudorotational representation of sugar repuckering. It is shown that when this model is combined with the scaled collective variable approach of Noguti and Go, much more efficient simulations are obtained than with simple single variable steps. Application of this method to a DNA oligomer containing a recognition site for the TATA‐box binding protein leads to striking similarities with results recently obtained from a 1‐ns molecular dynamics simulation using explicit solvent and counterions. In particular, large amplitude bending fluctuations are observed directed toward the major groove. Conformational analysis of the Monte Carlo simulation shows clear base sequence effects on conformational fluctuations and also that the DNA energy hypersurface, like that of proteins, is complex with many local, conformational substates. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 2001–2011, 1997