Peptides conformational energy

The Empirical Conformational Energy Program for Peptides, ECEPP [63, 64], is one of the first empirical interatomic potentials whose derivation is based both on gas-phase and X-ray crystal data [65], It was developed in 1975 and updated in 1983 and 1992. The actual distribution (dated May, 2000) can be downloaded without charge for academic use. 

D.R. Ripoll, H.A. Scheraga, ECEPP Empirical Conformational Energy Program for Peptides, in The Encyclopedia of Computational Chemistry, Vol. 2,... 

Empirical conformational energy program for peptides (ECEPP) is the name of both a computer program and the force field implemented in that program. This is one of the earlier peptide force fields that has seen less use with the introduction of improved methods. It uses three valence terms that are fixed, a van der Waals term, and an electrostatic term. 

Fig. 1. Conformational energy diagram for the alanine dipeptide (adapted from Ramachandran et al., 1963). Energy contours are drawn at intervals of 1 kcal mol-1. The potential energy minima for p, ofR, and aL are labeled. The dependence of the sequential d (i, i + 1) distance (in A) on the 0 and 0 dihedral angles (Billeter etal., 1982) is shown as a set of contours labeled according to interproton distance at the right of the figure. The da (i, i + 1) distance depends only on 0 for trans peptide bonds (Wright et al., 1988) and is represented as a series of contours parallel to the 0 axis. Reproduced from Dyson and Wright (1991). Ann. Rev. Biophys. Chem. 20, 519-538, with permission from Annual Reviews.

Perczel, A., W. Viviani, and I. G. Csizmadia. 1992. Peptide Conformational Potential Energy Surfaces and Their Relevance to Protein Folding in Molecular Aspects of Biotechnology Computational Models and Theories, Bertran, J., ed., Kluwer Academic Publishers, 39-82. 

Chuman, H., F. A. Momany, and L. Schafer. 1984. Backbone Conformations, Bend Structures, Helix Structures, and Other Tests of an Improved Conformational Energy Program for Peptides ECEPP83. Int. J. Pept. Prot. Res. 24, 233-248. 

Fossey, S. A., Nemethy, G., Gibson, K. D., and Scheraga, H. A. (1991). Conformational energy studies of beta-sheets of model silk fibroin peptides. 1. Sheets of poly(Ala-Gly) chains. Biopolymers 31, 1529-1541. 

ECEPP Empirical conformational energy program for peptides... 

Allowing for rotation about the Ca—C bond (/.e., variation of ijr) and for some degree of freedom about the peptide bond [i.e., small variation of ro), the characteristic ratios of the form / (crs) and form II [trans) poly(L-proline) chain are calculated by a Monte Carlo method in which the conformational energies are used as weighting factors. The Monte Carlo method enabled short-range interactions (beyond those involved in a single residue) to be taken into account. 

Approaches are described in this paper to the deduction of peptide conformation in solution by the use of three techniques 13C nuclear magnetic resonance, conformational energy calculations, and circular dlchroism. Sections of this paper illustrate the types of conformational information that can be derived from each of the individual methods for the synthetic and naturally occurring cyclic peptides. For complete conformational analysis, however, a combination of techniques is usually necessary. 

Some of the parameters that are used in the computer program ecepp (empirical conformational energy program for peptides) of Momany et al. (J. Phys. Chem. 1975, 79, 2361) are updated. The changes are based on experimental information that has become available since 1975,... 

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