Paper Citing NAMD - Abstract
Favia, Angelo D.; Masetti, Matteo; Recanatini, Maurizio; Cavalli, Andrea
Substrate Binding Process and Mechanistic Functioning of Type 1 11 beta-Hydroxysteroid Dehydrogenase from Enhanced Sampling Methods
PLOS ONE, 6 Art. No. e25375, SEP 23 2011
In humans, type 1 11 beta-hydroxysteroid dehydrogenase (11 beta-HSD-1) plays a key role in the regulation of the glucocorticoids balance by converting the inactive hormone cortisone into cortisol. Numerous functional aspects of 11 beta-HSD-1 have been understood thanks to the availability at the Worldwide Protein Data Bank of a number of X-ray structures of the enzyme either alone or in complex with inhibitors, and to several experimental data. However at present, a complete description of the dynamic behaviour of 11 beta-HSD-1 upon substrate binding is missing. To this aim we firstly docked cortisone into the catalytic site of 11 beta-HSD-1 (both wild type and Y177A mutant), and then we used steered molecular dynamics and metadynamics to simulate its undocking. This methodology helped shedding light at molecular level on the complex relationship between the enzyme and its natural substrate. In particular, the work highlights a) the reason behind the functional dimerisation of 11 beta-HSD-1, b) the key role of Y177 in the cortisone binding event, c) the fine tuning of the active site degree of solvation, and d) the role of the S228-P237 loop in ligand recognition.
