Document Europhys. Lett, 34 (6), pp. 471-476 (1996)
A method for the computer simulation of the free-energy difference in conformational changes of polyelectrolytes. Application to the B- to Z-DNA transition
J. C. Gil Montoro and J. L. F. Abascal
Departamento de Química-Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
(received 11 December 1995; accepted in final form 2 April 1996)
PACS. 87.15By - Structure, bonding, conformation, configuration, and
isomerism ofbiomolecules.
PACS. 87.15He - Molecular dynamics and conformational changes.
PACS. 61.20Ja - Computer simulation.
Abstract:
A method for calculating the free-energy difference between two dissimilar conformational states of a nucleic acid is proposed. The procedure is especially suited for computer simulation. The calculation of the free energy of each conformer is split into two steps; the first one consists in the build-up of the uncharged conformers while the other one ---which leads to the more important contribution--- corresponds to the charging process of such structures. We report preliminary results on the application of the method to evaluate the free-energy difference for the salt-induced conformational change between the B and Z forms of DNA. This is the first rigorous evaluation of the
dependence on the added salt concentration.
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