Modelling Cysteine Disulfide Exchange Reactions by Molecular Dynamics Simulations

Abstract

Disulfide bonds equip many proteins with a stabilizing crosslink. Recently, increasing evidence suggests that many disulfide bonds have a chemically labile, dynamic nature and can easily rearrange upon conformational changes of the proteins.1 Therefore, the computational prediction of disulfide rearrangements would answer highly relevant biological questions such as how proteins fold, how they are activated, or how they assemble. The challenge underlying the answer to those questions lie in the fact that chemical reactions, such as thiol-disulfide exchange, are often coupled to large-scale conformational transitions.We have developed a Molecular Dynamics based framework that allows disulfide rearrangements through a Monte Carlo-based topology swap. We successfully applied this method to study a mutated immunoglobulin I27 domain, for which Alegre-Cebollada et al. were able to characterize the kinetics of spontaneous disulfide bond isomerisation by force-clamp atomic force microscopy.2 Our results show that the force-induced unfolding of I27 leads to an intermediate, in which the free cysteine can, in a minority of unfolding events, get in close proximity to the strained disulfide bond, thus allowing spontaneous swapping.Our approach can handle multiple reactions throughout the molecule, and can access longer time scales than hybrid quantum/molecular mechanics schemes and as such is paradigmatic for the reactivity of other chemical moieties coupled to biomolecular dynamics.(1) Butera D, Cook KM, Chiu J, Wong JW and Hogg PJ. Control of blood proteins by functional disulfide bonds. Blood. 2014:123(13):2000-7.(2) Alegre-Cebollada J, Kosuri P, Rivas-Pardo JA and Fernandez JM. Direct observation of disulfide isomerization in a single protein. Nat Chem. 2011:3(11):882-7.