LONG-TERM MOLECULAR-DYNAMICS SIMULATION OF COPPER PLASTOCYANIN IN WATER

A long molecular dynamics simulation (1.1 ns) of fully hydrated plasto cyanin has been performed and analysed to relate protein dynamics to s tructural elements and functional properties. The solvated structure i s described in detail by the analysis of H-bond network. During all th e simulation, the crystal H-bond network is maintained in the beta-she et regions, while several H-bonds are broken or formed on the external surface of the protein. To evaluate whether such changes could be due to conformational rearrangements or to solvent competition, we have e xamined the average number of H-bonds between protein atoms and water molecules, and the root mean square deviations from crystal structure as a function of protein residues. Protein mobility and flexibility ha ve been examined by positional and dihedral angle rms fluctuations. Fi nally, cross-correlation maps have revealed the existence of correlate d motions among residues connected by hydrogen bonds. (C) 1997 Elsevie r Science B.V.