POLYMERS AND BIOMOLECULES IN SOLVENTS: A MOLECULAR DYNAMICS STUDY

Abstract

This study, which is in three parts, uses all-atom Molecular Dynamics (MD) simulations to investigate the behavior of polymers and biomolecules in solvents to enhance the understanding of solvent effects on protein-solvent and polymer-solvent interactions. In the first, the structural, energetic, and dynamical properties of polyacrylamide (PAM) oligomers of different lengths solvated in pure glycerol, glycerol–water, and pure water are investigated. We predict that the oligomers’ globular structure is obtained only when the modeling strategy considers the solvent as a continuous background. Meanwhile, for all-atom modeled solvents, the glycerol solutions display a strong tendency of trapping the oligomers in instantaneous elongated random coiled structures that remain locked-in over tens of nanoseconds. In pure water, the oligomers acquire considerably shorter random coiled structures of increased flexibility. The generalized amber force field is modified by including restrained electrostatic potential atomic charges for glycerol and PAM. Three PAM oligomer lengths monomers are considered in detail by monitoring the structural properties and energetics for several nanoseconds. The density and radial distribution function of glycerol solutions are calculated when modeled with the modified atomic charges and shows very good agreement with experimental results at temperatures around 300 K. Glycerol has multiple applications, including its use in gel formation for PAM gel electrophoresis. Our findings are relevant for the design of sensors based on microfluidics and tailored pharmaceutical buffer solutions.The second part presents a solvation effect of the structure and dynamics of a C-terminal domain of Rift Valley Fever Virus (RVFV) L protein exploration by MD using both explicit and implicit water. The force field parameters of explicit waters were taken from the TIP3P, TIP4P, SPC/E, SPCE/Fw, and OPC water models. The generalized Born (GB) model was employed for the implicit solvent simulation. The results from the study led to the conclusion that the structural conduct and preference of this protein are highly sensitive to the accommodating environment. Also, structural characterization and clustering of the atomic trajectories enable a better understanding of the structural and dynamical behavior of the peptide along time. In the third part of this investigation, the structural dynamics and energetic properties of the C-terminal domain of the RVFV L protein in glycerol and its aqueous solutions at different concentrations by molecular weight are presented. Secondary structure analysis was also performed to examine the extent of conformational drift for the individual alpha-helices and beta-sheets. It is reasonable to predict from the results that the helices and sheets are maintained only when the modeling strategy considers solvents with less glycerol concentration and also, the solvent-peptide becomes more cohesive with decreasing glycerol concentrations.