(1980). Reverse Turns in Peptides and Protein. Critical Reviews in Biochemistry: Vol. 8, No. 4, pp. 315-399.

Reverse turns in peptides and proteins.

A procedure, CONGEN, for uniformly sampling the conformational spaceof short polypeptide segments in proteins has been implemented. Because thetime required for this sampling grows exponentially with the number of residues, parameters are introduced to limit the conformational space that has to be explored. This is done by the use of the empirical energy function ofCHARMM [B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan and M. Karplus (1983) J. Comput. Chem.4, 187-217] and truncating the search when conformations of grossly unfavorable energy are sampled. Tests are made to determine control parameters that optimize the search without excluding important configurations. When applied to known protein structures, the resulting procedure is generally capable of generating conformations where the lowest energy conformation matches the known structure within a rms deviation of 1 A.

Prediction of the folding of short polypeptide segments by uniform conformational sampling.

https://link.springer.com/content/pdf/10.1007/BF02459652.pdf

The theory and practice of distance geometry

(1980). Intramolecularly Hydrogen-Bonded Peptide Conformation. Critical Reviews in Biochemistry: Vol. 9, No. 1, pp. 1-44.

Intramolecularly hydrogen-bonded peptide conformations.

Conformational energy calculations using an Empirical Conformational Energy Program for Peptides (ECEPP) were carried out on the N-acetyl-N′-methylamides of Pro-X, where X = Ala, Asn, Asp, Gly, Leu, Phe, Ser, and Val, and of X-Pro, where X = Ala, Asn, Gly, and Pro. The conformational energy was minimized from starting conformations which included all combinations of low-energy single-residue minima and several standard bend structures. It was found that almost all resulting minima are combinations of low-energy single-residue minima, suggesting that intra residue interactions predominate in determining conformation. The calculations also indicate, however, that inter residue interactions can be important. In addition, librational entropy was found to influence the relative stabilities of some minima. Because of the existence of 10–100 low-energy minima for each dipeptide, the normalized statistical weight of an individual minimum rarely exceeds 0.3, suggesting that these dipeptides have considerable conformational flexibility and exist as statistical ensembles of low-energy structures. The propensity of each dipeptide to form bend conformations was calculated, and the results were compared with available experimental data. It was found that bends are favored in Pro-X dipeptides because ϕPro is fixed by the pyrrolidine ring in a conformation which is frequently found in bends, but that bends are not favored in X-Pro dipeptides because interactions between the X residue and the pyrrolidine ring restrict the X residue to conformations which are not usually found in bends.

Influence of local interactions on protein structure. I. Conformational energy studies of N‐acetyl‐N′‐methylamides of pro‐X and X‐pro dipeptides

Using an improved method for computing conformations of closed rings with symmetry, in conjunction with an improved empirical energy function, the conformational space of Gramicidin S is reexamined. The search for minimum energy conformations is confined to the subspace containing closed symmetric rings. A large number of initial conformations selected from that subspace is subjected to energy minimization or is eliminated in a sequence of steps designed to locate the global minimum-energy conformation. One conformation having distinctly low energy is found and is judged to be the global minimum-energy conformation. This conformation is of the beta-pleated sheet type and is in complete agreement with experimental data. Similar structures with beta-pleated sheet-type conformations have been proposed previously on the basis of less extensive examiniations of the conformational space; the condition of exact ring closure, and the extensive examination of conformational space, used here, establish this structure on a firm basis.

Mary Dygert

Papers

Use of a Symmetry Condition to Compute the Conformation of Gramicidin S