Effects of Concentration on Like-Charge Pairing of Guanidinium Ions and on the Structure of Water: An All-Atom Molecular Dynamics Simulation Study
journal contributionposted on 27.08.2015, 00:00 by Dibyendu Bandyopadhyay, K. Bhanja, Sadhana Mohan, Swapan K. Ghosh, Niharendu Choudhury
Like-charge ion-pair formation in an aqueous solution of guanidinium chloride (GdmCl) has two important facets. On one hand, it describes the role of the arginine (ARG) side chain in aggregation and dimer formation in proteins, and on the other hand, it lends support for the direct mechanism of protein denaturation by GdmCl. We employ all-atom molecular dynamics simulations to investigate the effect of GdmCl concentration on the like-charge ion-pair formation of guanidinium ions (Gdm+). From analyses of the radial distribution function (RDF) between the carbon atoms of two guanidinium moieties, the existence of both contact pairs and solvent-separated pairs has been observed. Although the peak height corresponding to the contact-pair state decreases, the number of Gdm+ ions in the contact-pair state actually increases with increasing GdmCl concentration. We have also investigated the effect of the concentration of Gdm+ on the structure of water. The effect of GdmCl concentration on the radial and tetrahedral structures of water is found to be negligibly small; however, GdmCl concentration has a considerable effect on the hydrogen-bonding structure of water. It is demonstrated that the presence of chloride ions, not Gdm+, in the first solvation shell of water causes the distortion in the hydrogen-bonding network of water. In order to establish that Gdm+ not only stacks against another Gdm+ but also directly attacks the ARG residue of a protein or peptide, simulation of an ARG-rich peptide in 6 M aqueous solution of GdmCl has been performed. The analyses of RDFs and orientation distributions reveal that the Gdm+ moiety of the GdmCl attacks the same moiety in the ARG side chain with a parallel stacking orientation.