Computational elucidation of possible contributors to formation and stabilization of ATP-lid down-conformation in the N-terminal domain of Hsp90

Heat shock protein 90 (Hsp90) controls activation and maturation of various crucial client proteins through a catalytic cycle. In this catalytic cycle, closure of the lid segment from up- to down-conformation in the N-terminal domain (NTD) of Hsp90 through ATP binding is indispensable for coordinated structural changes, including interchange of dimeric Hsp90 structure between open and closed forms. However, the mechanisms underlying lid closure remain unclear. In this study, we investigate structural characteristics of the lid-down conformation in an isolated monomeric NTD structure by two types of molecular-dynamic simulation: a flopping-down simulation for a lid up-conformation using repulsive distance-restraints, and a down-conformation simulation for in-silico H1-mutants of NTD with a lid-down conformation. In the flopping-down simulation, spontaneous formation of a lid-down conformation is observed in multiple times. K98 and K102 in the lid segment are observed to interact with ATP phosphate or D40, suggesting to contribute to formation of the lid-down conformation. In the down-conformation simulation, H1 structure of the chimera H1-model, which only retains a proper down-conformation among the models for the entire simulation period, covers over the lid segment more than that of the X-ray structure. Because stability of the lid-down conformation was influenced by H1 structures, H1 segment is suggested to contribute to stabilization of the lid-down conformation. Although no direct experimental data are currently available to confirm these findings, these simulation results do not show large discrepancies with the experimental data and evidence of structural characteristics of the NTD, deduced from previous X-ray and spectroscopic studies.