Thermodynamics and transport properties of valine and cysteine peptides in water

Abstract

The study of thermodynamic and transport properties of amino acids gives access to knowledge about interactions between distinct molecules necessary to understand a variety of biological processes. In this work, we have performed molecular dynamics simulations of valine and cysteine peptides with lengths of (n) = 1, 2, 4, 8 & 16 monomers in an aqueous environment to estimate the solvation free energy and diffusion coefficients. We modeled our system using OPLS-AA parameter sets and TIP3P water at 310 K temperature. Solvation free energy of both the peptides have been reported using two thermodynamic integration (TI) based methods: TI and TI-CUBIC. The solvation free energy of both the peptides increases with the chain length. The estimated values using both methods are in good agreement with a statistical error of < 3%. The solvent accessible surface area (SASA) of solutes and hydrogen bonds between solute and solvent have also been presented to get more insights on solvation processes. The increase in solvation energy of both peptides with chain length is further corroborated by increase in the number of hydrogen bond (between peptide and water) and SASA with the chain length. In addition, the self diffusion coefficient of both solute and solvent along with their binary diffusion coefficient have been estimated for both the peptides. Furthermore, the effect of chain length on solvation free energy as well as diffusion coefficients have been studied.