The purpose of this proposal is to gain an understanding of the physical reasons for the unusual stabilization of the alpha-helical conformation observed in short alanine-based copolymers. Despite several experimental studies designed to ascertain the relative helix stability of the naturally occurring amino acids in water, using short alanine-based copolymers that incorporate charged and other highly soluble residues to render them soluble, discrepancies still exist regarding the intrinsic helix propensities of some residues, among which, L-alanine is the most notable. There are two disparate views about these discrepancies. The first view relies on both (a) earlier experimental studies in which the amino acids were incorporated as a central block in a tri-block copolymer, or as guests in a water-soluble host polypeptide, with the resulting propensities inferred from the temperature dependence of the helix content; and (b) on recent experimental studies of alanine-rich sequences N-terminally linked to a synthetic helix-inducing template. Their conclusions, supported by additional theoretical evidence, is that alanine is helix indifferent with a Zimm-Bragg propagation parameter near unity. The second view, relying on studies of short sequence-specific peptides involving an alanine host solubilized by a few charged or polar residues within the alanine block, is that alanine is a strong helix-former with a propagation parameter-near two. Resolution of the discrepancies involving the intrinsic helix-forming tendency of alanine is central to the protein folding problem. To provide a computational resolution of this problem, we have recently considered the coupling between conformation and pH to determine the most probable conformation of a polypeptide in solution. Our new approach combines a robust conformational search method with a fast and stable algorithm to solve the Poisson-Boltzmann equation. Recent applications of this methodology to study a series of short oligopeptides have been very successful, and further development and applications of this technique to the present project is foreseen. Additional experiments to test the computational results will be carried out. The proposed studies attempt to resolve the discrepancies between both disparate views, and provide additional insights into the underlying factors that promote the right-handed alpha-helical conformation in water.
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