Free energy calculation and molecules dynamics simulations of wild-type and variants of the DNA-EcoRI complex

From: Biophysical Journal | Date: October 1, 1999| Author: | Copyright information

ABSTRACT Molecular dynamics simulations and free energy calculations of the wild-type EcoRI-DNA complex and several variants have been performed in aqueous solvent. In general, he theoretical estimations of the free energy differences (AAA) qualitatively agree well with the corresponding experimental data. The modifications which were experimentally found unfavorable compared to the wild-type complex were also found to be so in theoretical estimates. The mutant where the amino group of the base Ade6 was replaced by a hydrogen atom eliminating one H-bond between the DNA and the protein, was ...

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