ENERGY-MINIMIZED CONFORMATION OF GRAMICIDIN-LIKE CHANNELS .2. PERIODICITY OF THE LOWEST ENERGY CONFORMATION OF AN INFINITELY LONG POLY-(L,D)-ALANINE BETA(6.3)-HELIX

If an infinitely long polymer has a primary structure characterized by an N-residue periodicity, a minimum energy conformation of the polyme r under the constraint of the conformational N-residue periodicity cor responds to an equilibrium structure (energy minimal or unstable equil ibrium structure) when this constraint is absent. Molecular mechanics calculations showed that with an infinitely long poly-(L,D)-alanine si ngle-stranded beta6.3-helix (which has a 2-residue periodicity with re spect to the primary structure), its lowest energy conformation within the framework of the conformational 2-residue periodicity is also the lowest energy form of this beta6.3-helix even when no conformational periodicity is assumed. In the course of this study, contour maps of h elix parameters and conformation energies for beta structures of poly- (L,D)-alanine were examined. It was also found that beta6.3-, beta4.5- , alpha(L,D)-, and pi(L,D)-helices constitute the global minima in the whole conformational space of this polypeptide. In the present calcul ation, an improved formulation of the conformation energy was introduc ed to estimate the structure and conformation energy of an infinite pe riodic chain from results on a chain of finite length.