Environmental characteristics of residues in proteins: three-dimensional molecular hydrophobicity potential approach

A new method for quantitative estimation of surrounding hydrophobicity for residues in proteins is proposed. It is based on the formalism of three-dimensional molecular hydrophobicity potential (3D MHP) and includes calculation of 3D MHP created by all atoms in a system "molecule+surrounding water". We calculated 3D MHP in the geometrical centers of residues for 23 proteins (from Protein Data Bank) surrounded by water layers 12-15 A thick. These data, plotted along the protein sequence (1D MHP profiles) contain comprehensive information on protein, water, prosthetic groups and neighbouring domains contributions to residue environment. 1D MHP profiles generated by water molecules strongly correlate with standard accessibility profiles based on calculations of exposed surface areas. The results confirm recently observed interrelation between the resonance Raman cross sections of tryptophan residues and polarity of their microenvironment. 3D MHP contributions (and related 1D MHP profiles) to residue environment from protein atoms, heme in myoglobin, flavin in flavodoxin as well as neighbouring domains in pyruvate kinase were characterized. 3D MHP data for rubredoxin in native and totally extended conformations reveal striking deviations reflecting the influence of long-range interactions between residues far removed in the sequence. Statistical analysis of 3D MHP data yields a new hydrophobicity scale (MHPS) that correlates with several commonly used scales obtained by a variety of complementary techniques.