A method is presented for a more efficient sampling of the configurational space of proteins as compared to conventional sampling techniques such as molecular dynamics. The method is based on the large conformational changes in proteins revealed by the “essential dynamics” analysis. A form of constrained dynamics is performed, forcing the system to move along some of the essential coordinates. This results in a broader sampling of the essential subspace than in a comparable conventional molecular dynamics simulation without constraints. The new sampling method (essential dynamics sampling) was applied to the histidine-containing phosphocarrier protein HPr. The results indicate that the essential dynamics sampling method produces physically allowed structures, as estimated by the evaluation of many geometrical properties. In addition, a study of the motions in the essential subspace reveals a diffusion-like behavior.

The cellular retinol-binding protein (CRBP) is an intracellular retinol carrier protein belonging to a family of hydrophobic ligand–binding proteins. It transports retinol to specific locations in the cell where, for instance, it is esterified for storage. Recently solved crystallographic structures of CRBP homologues with and without bound ligand do not provide evidence for a ligand–induced conformational change. However, it has been shown that there is a difference in binding of holo–CRBP and apo–CRBP to lecithin–retinol acyltransferase. Moreover, proteolysis of holo–CRBP and apo–CRBP yields different products, indicating a difference in structure or dynamics between the two forms. Here, we present the results of molecular dynamics simulations of holo–CRBP and apo–CRBP. The simulations show a significant difference in conformation, in agreement with experimental results. The essential dynamics method was used to study differences in dynamics between the apo and holo forms of CRBP, and showed inhibition of essential motions upon ligand binding. It also revealed large correlated motions of retinol with regions of the protein, pointing to a possible retinol entry/exit site.