Computational study of protein secondary structure elements: Ramachandran plots revisited

• DFT PES scan plots for 19 amino acids are provided at DFT PW91 and M06-2x/6-311(d,p) levels of theory.
• Amino acid groups that share common patterns on their PES plots and global minima were identified.
• An analysis is offered to explain the difference between the minima identified for each amino acid, and the statistical preference of them.

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.

Figure optionsDownload high-quality image (181 K)Download as PowerPoint slide