Comparison of the dynamics of bovine and human angiogenin: a molecular dynamics study

Abstract

Molecular dynamics simulations have been carried out for 1 ns on human and bovine angiogenin systems in an effort to compare and contrast their dynamics. An analysis of their dynamics is done by examining the rms deviations, following hydrogen-bonding interactions and looking at the role of water in and around the protein. The C-terminus of bovine angiogenin moves appreciably during dynamics suggesting a better structure for ligand binding. However, we do not find any evidence of a conformation where the glutamate residue that obstructs the active site takes on a different conformation. We observe a differential hydrogen-bonding pattern in the active site regions of bovine and human angiogenins, which could have a bearing on the different catalytic activities of the proteins. We also propose that the differential binding of the monoclonal antibody toward the two proteins might be due sequential and not conformational differences. Water molecules might play an important functional role in both proteins given their subtle functional differences. A simple computation on the molecular dynamics data has been carried out to identify locations in and around the protein that are invariably occupied by water. The locations of nearly half the waters we have identified from the simulation as being invariant in bovine angiogenin occupy similar locations in the bovine angiogenin crystal structure. The positions of the waters identified in human angiogenin differ considerably from that of bovine angiogenin.