Abstract
The calculation of free energy differences of a system is of great importance as the rate and extent of many if not all chemical and biophysical processes are governed by the nature of underlying free energy landscape. In this study the preferential binding of 3-(5-chloro-2, 4-dihydroxyphenyl)–pyrazole-4-carboxamide (4BC) and Heat shock protein 90(Hsp90) molecular chaperone has been evaluated using molecular dynamics simulation. A soft core potential was used during the mutations to facilitate the creation and deletion of atoms. Trajectory analysis showed a stable equilibrium after energy minimization. Potential energy plot showed equilibrium around -69520 and -183859 kJ/mol for Hsp90 and Hsp90-4BC. Kinetic energy also was calculated for Hsp90 and Hsp90-4BC as 44500 and 65928.29 kJ/mol, respectively.