ISSN:
0192-8651
Keywords:
molecular simulation
;
nucleic acids
;
internal coordinates
;
substates
;
curvature
;
TATA-box
;
Chemistry
;
Theoretical, Physical and Computational Chemistry
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Chemistry and Pharmacology
,
Computer Science
Notes:
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
Additional Material:
8 Ill.
Type of Medium:
Electronic Resource
Permalink
