Insights in 17beta-HSD1 enzyme kinetics and ligand binding by dynamic motion investigation.
BACKGROUND
Bisubstrate enzymes, such as 17beta-hydroxysteroid dehydrogenase type 1 (17beta-HSD1), exist in solution as an ensemble of conformations. 17beta-HSD1 catalyzes the last step of the biosynthesis of estradiol and, thus, it is a potentially attractive target for breast cancer treatment.


RESULTS
To elucidate the conformational transitions of its catalytic cycle, a structural analysis of all available crystal structures was performed and representative conformations were assigned to each step of the putative kinetic mechanism. To cover most of the conformational space, all-atom molecular dynamic simulations were performed using the four crystallographic structures best describing apoform, opened, occluded and closed state of 17beta-HSD1 as starting structures. With three of them, binary and ternary complexes were built with NADPH and NADPH-estrone, respectively, while two were investigated as apoform. Free energy calculations were performed in order to judge more accurately which of the MD complexes describes a specific kinetic step.


CONCLUSIONS
Remarkably, the analysis of the eight long range trajectories resulting from this multi-trajectory/-complex approach revealed an essential role played by the backbone and side chain motions, especially of the betaF alphaG'-loop, in cofactor and substrate binding. Thus, a selected-fit mechanism is suggested for 17beta-HSD1, where ligand-binding induced concerted motions of the FG-segment and the C-terminal part guide the enzyme along its preferred catalytic pathway. Overall, we could assign different enzyme conformations to the five steps of the random bi-bi kinetic cycle of 17beta-HSD1 and we could postulate a preferred pathway for it. This study lays the basis for more-targeted biochemical studies on 17beta-HSD1, as well as for the design of specific inhibitors of this enzyme. Moreover, it provides a useful guideline for other enzymes, also characterized by a rigid core and a flexible region directing their catalysis.
Negri
Matthias
M
Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany.
Recanatini
Maurizio
M
Hartmann
Rolf W
RW
D015067:17-Hydroxysteroid Dehydrogenases / Q000737:chemistry / Q000378:metabolism*; D055162:Biocatalysis; D018360:Crystallography, X-Ray; D057075:Enzyme Assays; D004970:Estrone / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D008024:Ligands; D056004:Molecular Dynamics Simulation; D009068:Movement; D009249:NADP / Q000378:metabolism; D011485:Protein Binding; D017433:Protein Structure, Secondary; D015203:Reproducibility of Results; D013816:Thermodynamics
D008024:Ligands; D004970:Estrone; D009249:NADP; D015067:17-Hydroxysteroid Dehydrogenases; C044256:3 (or 17)-beta-hydroxysteroid dehydrogenase