In silico Evaluation of Crosslinking Effects on Denaturant m(eq) values and ?Cp upon Protein Unfolding.

Abstract

Important thermodynamic parameters including denaturant equilibrium m values (m(eq)) and heat capacity changes (?Cp) can be predicted based on changes in Solvent Accessible Surface Area (SASA) upon unfolding. Crosslinks such as disulfide bonds influence the stability of the proteins by decreasing the entropy gain as well as reduction of SASA of unfolded state. The aim of the study was to develop mathematical models to predict the effect of crosslinks on ?SASA and ultimately on m(eq) and ?Cp based on in silico methods. Changes of SASA upon computationally simulated unfolding were calculated for a set of 45 proteins with known m(eq) and ?Cp values and the effect of crosslinks on ?SASA of unfolding was investigated. The results were used to predict the m(eq) of denaturation for guanidine hydrochloride and urea, as well as ?Cp for the studied proteins with overall error of 20%, 31% and 17%, respectively. The results of the current study were in close agreement with those obtained from the previous studies.