Hydrogen bond analysis by MD simulation of copper plastocyanin at different hydration levels

Abstract

Abstract Hydrogen bond interactions in copper plastocyanin aqueous solutions have been investigated in details by computer simulation. Molecular dynamics simulations of the protein in the presence of a different number of water molecules (80, 228, 682, 2516) have been performed for 110 picoseconds. Intraprotein hydrogen bonds occurring on the MD simulations are investigated and compared to the hydrogen bonds detected in the crystal structure as obtained from X-ray data. Protein-water hydrogen bonds are analyzed in terms of the average number of hydrogen bonds formed by each aminoacid residue and in terms of the number of different water molecules forming hydrogen bonds with each amino-acid residue during the simulation time. A strong influence on the protein-solvent interface of the electrical character of the aminoacid residues involved in the protein-water hydrogen bonds is evidenced. The results point out the crucial role played by the hydration level on the organization of the hydrogen bond network surrounding a protein molecule and on the protein-solvent coupling. The behaviour of the protein-solvent hydrogen bonds is discussed in connection with the protein dynamics.