MODEL PROTEIN CONFORMATIONS VIA PAIR CORRELATION-FUNCTIONS, DISTANCE MATRIX, AND EMBEDDING ALGORITHM

A method of constructing three-dimensional structures of model protein conformations is presented, The method consists of self-consistent fi eld integral equations for pair correlation functions of constituent u nits in a heteropolymer chain and the use of the distance matrix and t he embedding algorithm for constructing conformations. The pair correl ation functions obey integral equations that are derived from the Kirk wood hierarchy by applying closure approximations; they appear as a ge neralized form of the liquid-state Percus-Yevick integral equation. Mo del protein sequences that exhibit the formation of secondary-like pat terns and tertiary-like structures are examined, These structural feat ures are formed at low temperatures and they are stabilized by strong hydrogen bonding forces, To obtain the structure in three dimensions, the method of distance geometry is used to refine the distance matrix of a folded structure which is then embedded in the three-dimensional space by an embedding algorithm. (C) 1998 American Institute of Physic s. [S0021-9606(98)51704-7].