Ct. Reimann et al., PROTEINS IN-VACUO - DENATURING OF DISULFIDE-INTACT AND DISULFIDE-BROKEN LYSOZYME PROBED BY MOLECULAR-DYNAMICS SIMULATIONS, JOURNAL OF PHYSICAL CHEMISTRY B, 102(12), 1998, pp. 2277-2283
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.