Use of computer simulation in the interpretation of elastic neutron scattering in complex molecular systems: a small protein in various environments

Elastic and quasielastic neutron scattering experiments on complex systems are often difficult to interpret unambiguously directly using analytical dynamical models. In such cases computer simulations can be used to provide information at atomic detail. Here we report on the use of normal mode analysis (NMA) and molecular dynamics (MD) simulations of a small protein, bovine pancreatic trypsin inhibitor (BPTI) in vacuum and in various solvents. The simulations were performed over a range of temperatures (80–300 K). The vacuum simulation data are used to investigate neutron scattering properties. Effects are determined of instrumental energy resolution and of approximations commonly used to extract mean-square displacement data from elastic scattering experiments. Both the presence of a distribution of mean-square displacements in the protein and the use of the Gaussian approximation to the dynamic structure factor lead to quantified underestimation of the mean-square displacement obtained. Variation of the environment of the protein shows that the dry protein has higher fluctuations at lower temperatures than in the solvated protein, in agreement with recent experiments [1 and 2], that the dynamical transition is solvent-independent on short timescales (also in agreement with experiment [3]), and that at longer timescales it is strongly activated by water