AN EFFICIENT METHOD FOR SAMPLING THE ESSENTIAL SUBSPACE OF PROTEINS

A method is presented for a more efficient sampling of the configurati onal space of proteins as compared to conventional sampling techniques such as molecular dynamics. The method is based on the large conforma tional changes in proteins revealed by the ''essential dynamics'' anal ysis. A form of constrained dynamics is performed, forcing the system to move along some of the essential coordinates. This results in a bro ader sampling of the essential subspace than in a comparable conventio nal molecular dynamics simulation without constraints. The new samplin g method (essential dynamics sampling) was applied to the histidine-co ntaining phosphocarrier protein HPr. The results indicate that the ess ential dynamics sampling method produces physically allowed structures , as estimated by the evaluation of many geometrical properties. In ad dition, a study of the motions in the essential subspace reveals a dif fusion-like behavior.