Monte Carlo Studies Of Oligopeptide Conformation

Monte Carlo studies of short polypeptide chains have been carried out with a view to determining the manner in which the preferred conformations depend on the number and type of residues in the molecule. The constituent atoms and bond dihedral angles are represented in full; short- and long-range interactions, bond torsion and hydrogen bonding energies are incorporated in the study by means of the empirical ECEPP potential (hydration energies are excluded). A number of techniques have been used to analyze the conformations generated by the simulation, including joint distributions of dihedral angles, generalized contact maps, and methods based on concepts of differential geometry which permit classification of sequences of neighbouring residues into distinct conformational states. Particular attention was paid to the problem of a-helix formation, and homopolymers of known helix formers, e.g., poly-L-alanine, were the subject of extensive simulation. The study also Included an assessment of the ability of the Monte Carlo method to sample conformation space adequately for chains of increasing length. The computations were carried out using a minicomputer equipped with a high-speed array processor; special programming methods were required, but these resulted in simulation runs of lengths barely achievable on the fastest of large scientific computers.