Understanding of ATP-lid conformational dynamics in the N-terminal domain of Hsp90 and its mutants by use of a computational biochemistry approach

Chaperone Hsp90 regulates the activation and maturation of various protein, and is an attractive target for drug discovery. In catalytic cycle of Hsp90, ATP hydrolysis is a key event that drives structural changes, including the interchange of the dimeric Hsp90 structure between open and closed forms. For ATP hydrolysis, ATP-lid closure in the ATP-binding site from the up- to down-conformation is an indispensable co-ordinated structural change. However, the atomistic mechanism underlying lid closure remains unclear. In this study, a computational biochemistry approach was applied to wild-type apo and ATP-complex structures, and the lid-mutants A107N and T101I ATP-complex, to understand lid closure. A total of 15-s molecular dynamic simulation, including the equilibration and production phases, was conducted for every structure starting from the lid up-conformation, but no lid-closures were observed. However, a very early event, i.e., a sign, of lid closure have been captured. In the simulations of wild-type and A107N ATP-complex structures, lid segment showed conformational fluctuations, and helix-7 (H7) segment in lid segment was unwound. This conformational instability of lid segment energetically weakened its interaction with facing region, suggesting the up-to-down transition was triggered by the instability of lid segment, particularly H7 segment. The interaction energy between lid segment and facing region was ranked in the order A107N > wild-type > T101I, which was correlated with experimental results such as the orders of ATP-hydrolytic activity and rapidity of conformational changes of lid segment, measured in ATP-spiking experiments by fluorescence resonance energy transfer method (i.e., A107N > wild-type > T101I).