Theoretical evidence for water insertion in .alpha.-helix bending: molecular dynamics of Gly30 and Ala30 in vacuo and in solution

Abstract

In protein crystal structures, ordered water molecules have been frequently observed at instances where a-helices bend or fold. A series of molecular dynamics (MD) simulations have been carried out in order to investigate the possibility that a water-inserted structure may be implicated in the helix-folding process. Both in vacuo and aqueous solution simulations were performed on a variety of canonical right-handed a-helices; these are of various lengths and are comprised entirely of either alanine or glycine. Analysis of the calculations reveals that the polyglycine helices bend due to the intrinsic nature of the constituent amino acids. For alanine helices, bending occurs in a more ordered manner and involves the insertion of a water molecule within the helical hydrogen bond. The calculations indicate a mechanism by which this might occur: in the course of the vibrational motions of the stabilizing N-H...O=C hydrogen bonds, several water molecules hydrogen bond with both the carboxy and amino groups and serve to weaken the intramolecular hydrogen bonds. When the N H 4 = C hydrogen bond is sufficiently extended, one of the hydrogen-bonded water molecules inserts so as to form a bridge; this insertion must occur according to precise orientation requirements. The resulting three-centered hydrogen bond system serves as an intermediate in the breakup (destabilization) of the a-helix at that position, the onset of microfolding. These studies further support the potential role of water insertion in the protein-folding process.