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Report No.
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Neutron scattering and molecular simulation studies of protein structure and dynamics

Nakagawa, Hiroshi   ; Saio, Tomohide*; Nagao, Michihiro*; Inoue, Rintaro*; Sugiyama, Masaaki*; Tominaga, Taiki*; Kawakita, Yukinobu  

The flexible conformation of a multidomain protein is responsible for its biological function. 3-domain protein: MurD (47kDa) changes its domain conformation sequentially from open to semi-closed to closed conformation during enzymatic reactions. However, the dynamics of the domains in each conformation is unknown. In this study, we combined small-angle X-ray and neutron scattering (SAXS and SANS), dynamic light scattering (DLS), neutron back scattering (NBS), neutron spin echo (NSE), and molecular dynamics (MD) simulations to investigate the conformational dynamics of MurD in the three corresponding states (apo and ATP, inhibitor-bound state). The analysis showed that the conformational dynamics of MurD during the enzymatic reaction was not affected. The analysis suggests that the changes in domain dynamics during enzymatic reactions are related to the affinity and reaction efficiency with ligands that bind specifically to each reaction state.

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