Proteins in Vacuo. Denaturing of Disulfide-Intact and Disulfide-Broken Lysozyme Probed by Molecular Dynamics Simulations

Abstract

Proteins in vacuo are the subject of a number of experimental techniques where unfolding has been shown to be an important feature. In this paper we report on a detailed structural study of protein denaturation modeled in molecular dynamics (MD) simulations of disulfide-intact (DI) and disulfide-reduced (DR) lysozyme (LYZ) molecules at 293 K in vacuo with the GROMOS force field. The trajectories were carried out over at least 1.0 ns in the absence of water molecules, starting from an X-ray structure. A repulsive centrifugal potential was generated for both DI- and DR-LYZ, inducing large conformational transitions. Denaturation followed a pathway eliciting the existence of two well-defined subdomains involving the alpha helixes (designated here as α1 and α2) while the beta sheet appeared to comprise a full domain (β). The domain unfolding differed markedly for DI- and DR-LYZ. The unusual structures found in this type of simulation for DI-LYZ were compared with related unfolding simulations in water and were found to be similar to those obtained using radial unfolding forces. Furthermore, the transient structures were compatible with a three state model used to describe unfolding. The present simulation of DI-LYZ would be partly compatible with the results of an experiment on nonequilibrium refolding of DI-LYZ (Miranker, A.; et al. Science 1993, 262, 896) if the unfolded structures were to belong to a putative refolding pathway. Modeling of structures of protein ions, stored and manipulated in vacuo, is initiated using the information herein presented. The most extended conformer of DI-LYZ derived computationally resembles qualitatively the extended conformers observed experimentally by energetic surface imprinting.