UnderstandingRamachandranplot for dipeptide: A density functional theory and information‐theoreticapproach study

Abstract

AbstractThe Ramachandran plot in biochemistry visualizes the propensity of amino acid residues to assume different secondary structures. It can be obtained by different approaches such as bioinformatics and molecular dynamics. In this work, we systematically scan the two single bonds around the α‐carbon of a peptide to generate the three‐dimensional potential energy surface and then project it onto the coordinate plane to generate the Ramachandran plot. Using the two schemes of the total energy partition and information‐theoretic approach in density functional theory, we analyze the plot and find out that the dominant contributor to determine the local minima of secondary structures, especially β‐sheets, in the Ramachandran plot is the electrostatic interaction, whereas steric and exchange‐correlation contributions play minor yet indispensable roles, especially for determining α‐helixes. As the generalization of our prior studies for systems with one rotatable bond, our current results confirm what we yielded before from the viewpoint of energetic contributions, and at meanwhile provide an in‐depth understanding about the nature and origin of secondary structure propensities from the Ramachandran plot.