Solvent accessibilities in glycyl, alanyl and seryl dipeptides

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Abstract
Theoretical studies on glycyl, alanyl and seryl dipeptides were performed to determine the probable backbone and side-group conformations that are preferred for solvent interaction. By following the method of Lee et Richards, a solute molecule is represented by a set of interlocking spheres of appropriate van der Waals radii assigned to each atom, and a solvent (water) molecule is rolled along the envelope of the van der Waals surface, and the surface accessible to the solvent molecule, and hence the solvent accessibility for a particular conformation of the solute molecule, is computed. From the calculated solvent accessibilities for various conformations, solvation maps for dipeptides were constructed. These solvation maps suggest that the backbone polar atoms could interact with solvent molecules selectively, depending on the backbone conformation. A conformation in the right-handed bridge (.zeta.R) region is favored for solvent interaction and intrachain H-bonding. Also the backbone side-chain H-bonding within the same dipeptide fragment in proteins is less favored than H-bonding between side chain and water and between side chain and atoms of other residues. Solvent accessibilities suggest that very short distorted .alpha.R-helical and extended-structural parts may be stabilized via solvent interaction, and this could easily be possible at the surface of the protein molecules, in agreement with protein-crystal data.