Conformational transitions in eosinophil cationic protein: a molecular dynamics study in aqueous environment.
Extensive molecular dynamics simulations have been performed on eosinophil cationic protein (ECP). The two structures found in the crystallographic dimer (ECPA and ECPB) have been independently simulated. A small difference in the pattern of the sidechain hydrogen bonds in the starting structure has resulted in interesting differences in the conformations accessed during the simulations. In one simulation (ECPB), a stable equilibrium conformation was obtained and in the other (ECPA), conformational transitions at the level of sidechain interactions were observed. The conformational transitions exhibit the involvement of the solvent (water) molecules with a pore-like construct in the equilibrium conformation and an opening for a large number of water molecules during the transition phase. The details of these transitions are examined in terms of intra-protein hydrogen bonds, protein-water networks and the residence times of water molecules on the polar atoms of the protein. These properties show some significant differences in the region between the N-terminal helix and the loop before the C-terminal strand as a function of different conformations accessed during the simulations. However, the stable hydrogen bonds, the protein-water networks, and the hydration patterns in most part of the protein including the active site are very much similar in both the simulations, indicating the fact that these are intrinsic properties of proteins.
Sanjeev
B S
BS
Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.
Vishveshwara
S
S
D019281:Dimerization; D047150:Eosinophil Cationic Protein / Q000737:chemistry*; D006801:Humans; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011487:Protein Conformation; D020836:Protein Structure, Quaternary; D012997:Solvents; D013816:Thermodynamics; D014867:Water
D012997:Solvents; D014867:Water; D047150:Eosinophil Cationic Protein; C479220:RNASE3 protein, human