Molecular simulation study to examine the possibility of detecting collective motion in protein by inelastic neutron scattering

The dynamic structure factors in (Q, omega)-space were calculated by using the results of biomolecular simulations at a wide range of temperature from 100 to 300 K. Three types of simulation, normal mode analysis, molecular dynamics in vacuum, and molecular dynamics in water were applied to HEW Lysozyme. The shapes of the three dynamic structure factors in (Q, omega)-space are in good agreement in high-frequency regions (> 10 meV), but considerably different in low-frequency regions (< 10 meV) throughout the temperature range studied here. At cryogenic temperature, the so-called boson peak is observed only in the results of molecular dynamics in water. From these results, we discuss the (Q, omega)-range and the resolution of a detector needed to observe function-related protein dynamics. Proposal of such a detector to be used in J-PARC is made. (C) 2004 Elsevier B.V. All rights reserved.