title: Computational study of protein secondary structure elements: Ramachandran plots revisited.
abstract: Potential energy surface (PES) were built for nineteen amino acids using density functional theory (PW91 and DFT M062X/6-311**). Examining the energy as a function of the φ/ψ dihedral angles in the allowed regions of the Ramachandran plot, amino acid groups that share common patterns on their PES plots and global minima were identified. These patterns show partial correlation with their structural and pharmacophoric features. Differences between these computational results and the experimentally noted permitted conformations of each amino acid are rationalized on the basis of attractive intra- and inter-molecular non-covalent interactions. The present data are focused on the intrinsic properties of an amino acid - an element which to our knowledge is typically ignored, as larger models are always used for the sake of similarity to real biological polypeptides.
authors.affiliation: Department of Chemistry, Faculty of Chemistry and Chemical Engineering, "Babes-Bolyai" University, 11 Arany Janos Str, Cluj-Napoca RO-400028, Romania. Electronic address: franciscocarrascoza@gmail.com.
authors.forename: Francisco
authors.initials: F
authors.lastname: Carrascoza
authors.affiliation: Department of Chemistry, Faculty of Chemistry and Chemical Engineering, "Babes-Bolyai" University, 11 Arany Janos Str, Cluj-Napoca RO-400028, Romania.
authors.forename: Snezana
authors.initials: S
authors.lastname: Zaric
authors.affiliation: Department of Chemistry, Faculty of Chemistry and Chemical Engineering, "Babes-Bolyai" University, 11 Arany Janos Str, Cluj-Napoca RO-400028, Romania.
authors.forename: Radu
authors.initials: R
authors.lastname: Silaghi-Dumitrescu
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary
chemical_list: D000596:Amino Acids
keywords: Amino acid; DFT; Potential energy surface; Ramachandran; Secondary structure