Marcia S. Pottle

Energy of stabilization of the right-handed βαβ crossover in proteins☆

An explanation in terms of conformational energies is provided for the observed nearly exclusive preference of the βαβ structure for forming a right-handed, rather than a left-handed, crossover connection. Conformational energy computations have been carried out on a model βαβ structure, consisting of two six-residue Val β-strands and of a 12-residue Ala α-helix, connected by two flexible four-residue Ala links to the strands. The energy of the most favorable right-handed crossover is 15.51 kcal/mol lower than that of the corresponding left-handed cross-over. The right-handed crossover is a strain-free structure. Its energy of stabilization arises largely from the interactions of the two β-strands with one another and with the α-helix. On the other hand, the left-handed crossover is either disrupted after energy minimization or it remains conformationally strained, as indicated by an energetically unfavorable left twisting of the β-sheet and by the presence of high-energy local residue conformations. In the energetically most favorable right-handed crossover, the right twisting of the β-sheet and its manner of interacting with the α-helix are identical with those computed earlier for isolated β-sheets and for packed αβ structures. This result supports a proposed principle that it is possible to account for the main features of frequently occurring structural arrangements in globular proteins in terms of the properties of their component structural elements.

Implementation of the ECEPP algorithm, the Monte Carlo minimization method, and the electrostatically driven Monte Carlo method on the Kendall square research KSR1 computer

In this article the adaptation of the Empirical Conformational Energy Program for Peptides (ECEPP/3) and two conformational search methods [viz., the Monte Carlo minimization (MCM) method and the electrostatically driven Monte Carlo (EDMC) method] to the Kendall Square Research KSR1 computer is described. The MCM and EDMC methods were developed to surmount the multiple‐minima problem in protein folding. Parallelization of these codes led to substantial speedups (expressed as the ratio between the mean time per energy evaluation in one processor and the mean time per energy evaluation in a set of processors) over the serial versions of these codes. A comparison of the performance of these algorithms on the KSR1 and on the IBM ES9000 computers is presented.

Implementation of ECEPP-Based Programs on the IBM SP2 and the SGI Power Challenge Computers

In this paper, we describe the design and implementation of a message-passing algorithm which enables the Empirical Conformational Energy Program for Peptides (ECEPP/3) and related programs to run efficiently on the IBM RISC System/6000 POWERparallel System (SP2). Either the Message Passing Library (MPL) or the Message Passing Interface (MPI) can be used on the SP2; the MPI version also runs on the SGI Power Challenge computer. Some performance data are presented.