PROTEINS IN-VACUO - DENATURING OF DISULFIDE-INTACT AND DISULFIDE-BROKEN LYSOZYME PROBED BY MOLECULAR-DYNAMICS SIMULATIONS

Proteins in vacuo are the subject of a number of experimental techniqu es 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 (D I) and disulfide-reduced (DR) lysozyme (LYZ) molecules at 293 K in vac uo 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 bo th DI- and DR-LYZ, inducing large conformational transitions. Denatura tion followed a pathway eliciting the existence of two well-defined su bdomains involving the alpha helixes (designated here as alpha(1) and alpha(2)) while the beta sheet appeared to comprise a full domain (bet a). The domain unfolding differed markedly for DI- and DR-LYZ. The unu sual structures found in this type of simulation for DI-LYZ were compa red with related unfolding simulations in water and were found to be s imilar to those obtained using radial unfolding forces. Furthermore, t he transient structures were compatible with a three state model used to describe unfolding. The present simulation of DI-LYZ would be partl y compatible with the results of an experiment, on nonequilibrium refo lding of DI-LYZ (Miranker, A.; et al. Science 1993, 262, 896) if the u nfolded structures were to belong to a putative refolding pathway. Mod eling 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 t he extended conformers observed experimentally by energetic surface im printing.