Theory of Liquids for Studying the Conformational Flexibility of Biomolecules with Reference Interaction Site Model Approximation

Abstract

The theory of fluids is used to modify the integral equations of the reference interaction site model (RISM) approximation. Its applicability to the study of biomolecules solvation is evaluated. Unlike traditional RISM applications, the new integral equation contains an intramolecular correlation matrix that only needs to be calculated once. This allows us to bypass the effort of repeatedly solving RISM equations and the time-consuming averaging of values obtained for each time point of a molecular trajectory. The new approach allows for the assessment of the conformational transience of dissolved molecules while taking into account the effects of solvation. The free energy of oxytocin, which is a peptide hormone, as well as self-assembled ionic peptide complexes calculated using both the traditional RISM and the new RISM with average matrix (RISM-AM) approach are estimated. The free energy of oxytocin calculated using RISM-AM shows that the statistical error does not exceed the error obtained by standard averaging of solutions in the RISM equation. Despite the somewhat ambiguous results obtained for ionic peptide self-assembly using RISM-AM with Lennard–Jones repulsion correction, this method can still be considered applicable for fast molecular dynamics analysis. Since the required computational power can be reduced by at least two orders of magnitude, the medium-matrix RISM is indeed a highly applicable tool for studying macromolecular conformations as well as corresponding solvation effects.

Keywords

• theory of liquids
• RISM
• solvation energy
• RADA16-I peptide complex
• molecular dynamics
• protofilament