Abstract

TORRENS, F.  and  CASTELLANO, G.. Peptide potencial energy surfaces and protein folding. An. Asoc. Quím. Argent. [online]. 2006, vol.94, n.1-3, pp.27-47. ISSN 0365-0375.

This report outlines the utility of a 3D -> 1D transformation of peptide conformation, which leads to a linearized notation of protein secondary and tertiary structures that may be used for an objective description of protein folding. The method is intended to be descriptive and not to be predictive. It is established from first principles that the idealized 2D-y-f map must have nine minima. It is obvious to ask whether all these nine conformations are actually occurring in proteins. The objective is to repeat a previous analysis of 258 proteins determined using program ECEPP2, with the improved ECEPP2 + polarization. An analysis is performed on 258 proteins with known X-ray structure. The proteins contain 56 495 amino-acid residues with well-defined f and y angles. The minima are identified with the aid of the nine ECEPP2 minima of Ac-Ala-NHMe with f and y ± 40° tolerance. ECEPP2 is improved with the inclusion of the interacting induced-dipole polarization model, SIMPLEX-MS 3 geometry optimization and the calculation of the dipole moment from the point distribution of net charges. The analysis of 258 proteins determined using ECEPP2 is repeated with the improved ECEPP2 + polarization. The relative frequency of occurrence of those conformations energetically favoured for enantioners g^-g^-, etc. in the y-f map of the backbone conformations of amino acids decreases as: g^-a/g⁺a > g^-g⁺/g⁺g^- > g^-g^-/g⁺g⁺ >> ag⁺/ag^- > aa. For the amino acids, the same preference diminishes as: Pro >> Ile > Val > Leu > Thr > Met > Ala > Glu > Phe > Trp > Tyr > Gln > Lys > Ser > Cys > Arg > Asp > His > Asn > Gly. The strong preference of Pro is in agreement with its character of a-helix and b sheet breaker, and b turn and random-coil former. The analysis of 258 proteins determined using ECEPP2 is repeated with the improved ECEPP2 + polarization and there is a good agreement between the two. Achiral Gly relative frequencies of occurrence are close to one. Pro is the amino acid with the greatest (g^-g^-, etc.)/(g⁺g⁺, etc.) preference and with the greatest influence on protein conformation. Pro is the amino acid with the largest P_global conformational parameter. The original software used in the investigation is available from the author.