AN EXTENDED SAMPLING OF THE CONFIGURATIONAL SPACE OF HPR FROM ESCHERICHIA-COLI

Recently, we developed a method (Amadei et al., J. Biomol, Str. Dyn, 1 3: 815-626; de Groot et al., J. Biomol. Str. Dyn. 13: 741-751, 1996) t o obtain an extended sampling of the configurational space of proteins , casing an adapted form of molecular dynamics (MD) simulations, based on the essential dynamics (ED) (Amadei et al,, Proteins 17:412-425, 1 993) method. In the present study, this ED sampling technique is appli ed to the histidine-containing phosphocarrier protein HPr from Escheri chia coli, We find a cluster of conformations that is an order of magn itude larger than that found for a usual MD simulation of comparable l ength. The structures in this cluster are geometrically and energetica lly comparable to NMR structures, Moreover, on average, this large clu ster satisfies nearly all NMR-derived distance restraints. (C) 1996 Wi ley-Liss, Inc.