MODELING THE OPTIMAL SIMULATION PATH IN THE PEPTIDE-CHAIN FOLDING - STUDIES BASED ON GEOMETRY OF ALANINE HEPTAPEPTIDE

The theoretical background of a simple model of polypeptide chain stru cture using two parameters: R (Angstrom) - the radius of curvature for each pentapeptide chain fragment in the protein, and V (deg) - the di hedral angle between two consecutive peptide bond planes, is presented . The mathematical relationship between these two geometrical paramete rs leads to the optimal searching path for low-energy peptide conforma tions. This R versus V relation, corresponding to low-energy structure s in Ramachandran plot, appeared to fit the square function well. Here , the minimum of this function is taken as the optimal starting point for the minimization of all second-order conformations in the peptide chain. The extension, including all structures that satisfy the square function between V and R, showed the Phi, Psi angles that are optimal in searching for the path to low-energy structures. The path is an el lipse connecting the alpha(R)-, beta- and alpha(L)-structures, indicat ing the possible transitions from one to the next. (C) 1995 Academic P ress Limited