HYDROPHOBIC NATURE OF MEMBRANE-SPANNING ALPHA-HELICAL PEPTIDES AS REVEALED BY MONTE-CARLO SIMULATIONS AND MOLECULAR HYDROPHOBICITY POTENTIAL ANALYSIS

We propose an approach to explore the spatial hydrophobic and hydrophilic properties of transmembrane alpha-helical peptides. The computational procedure employs two independent techniques-statistical mechanics Monte Carlo (MC) simulations of nonpolar (propane) and polar (water) solvents around the peptides and three-dimensional molecular hydrophobicity potential (3D MHP) calculations. In the first approach, the polarity of a helix exposure was analyzed in terms of the average peptide-solvent interaction energies, whereas, in the second one, it was assessed using the 3D MHP distribution on the helix surface. The results obtained in the frameworks of both formalisms are in reasonable agreement, compliment each other, and provided a detailed presentation of the spatial hydrophobic nature of the peptides. Particular emphasis was put on testing the validity of simulations, examination of the convergence of energies in the MC runs, and comparison of the hydrophobicity measures obtained using different techniques. The method was applied to several transmembrane alpha-helical peptides from proteins with known structure. Resulting hydrophobic characteristics were compared with experimentally observed lipid- and protein-exposure of these segments in 3D structures of the membrane bundles. The approach was also employed in the hydrophobic mapping of putative channel-forming alpha-helical peptide in epithelial amiloride-sensitive Na+ channel, and the results obtained were used to predict the residues lining the pore as well as exposed to a nonpolar environment. Future applications of the method to spatial arrangement of alpha-helices in membrane protein domains are discussed.