A COLLECTIVE MOTION DESCRIPTION OF THE 3(10-)/ALPHA-HELIX TRANSITION - IMPLICATIONS FOR A NATURAL REACTION COORDINATE

The 3(10)-/alpha-helical transitions in an eight-residue Aib homopeptide is investigated using the methods of normal mode (NM) and principal component (PC) analysis. Energy minimization is followed by a NM analysis of the two (3(10)- and alpha-helix) minimized conformations. From the analysis of the NMs it is shown that the 3(10)-helix is entropically favored over the alpha-helix. A 2 ns molecular dynamics (MD) simulation run is then analyzed by the method of PC analysis-a quasi-harmonic method for delineating collective motions of the peptide from the raw MD data. Important information about the mechanism of transition at the molecular level is then extracted by projecting the MD trajectory onto the first few PC axes. The first PC axis, representing about two-thirds of the total fluctuation, is shown to corroborate well with the helical states of the peptide and is a natural pathway in one dimension. Addition of contributions from four more PC axes was sufficient to accurately reproduce the peptide dynamics during the transition. A description of the transition, almost in its entirety, in a conformational subspace spanned by only the first few PCs, is significant, and the general implications for simulations of conformational transitions are discussed.