Counterion Effects on the Denaturing Activity of Guanidinium Cation to Protein

The denaturation of a three-α-helix bundle, the B domain of protein A, by guanidinium is studied by molecular dynamics simulations. The simulation results showed that in GdmCl solution, guanidinium cations accumulate around the protein surface, whereas chloride anions are expelled from the protein. In contrast, in GdmSCN solution, both cations and anions accumulate around the protein surface and the degree of Gdm⁺ accumulation is higher than that in GdmCl, suggesting the cooperativity between the cations and anions in preferential binding. Moreover, the accumulation of guanidinium around the protein surface is not uniform, and it prefers to populate near residues with negatively charged or planar side chains. On the other hand, guanidinium participates in direct hydrogen bonding with backbone carbonyl groups. Meanwhile, guanidinium also promotes the hydrogen bonding of water to a backbone carbonyl group by changing the hydrogen bonding network within solvent. Therefore, the attack from both water and guanidinium breaks backbone hydrogen bonds and results in the destruction of secondary structures of the protein. The stronger accumulation of guanidinium and more hydrogen bonding from guanidinium in GdmSCN leads to the increase of its denaturing efficiency compared to GdmCl. In the latter solution, the ion pairing between Cl^– and guanidinium limits the approach of guanidinium to protein and the hydrogen bonding between guanidinium and protein, and the main denaturing contributor is the hydrogen bonding from water.