Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking.
dynamic docking
enhanced conformational sampling
free energy landscape
heat-shock protein 90
multicanonical Molecular Dynamics
Journal
Journal of computational chemistry
ISSN: 1096-987X
Titre abrégé: J Comput Chem
Pays: United States
ID NLM: 9878362
Informations de publication
Date de publication:
30 06 2020
30 06 2020
Historique:
received:
25
01
2020
revised:
18
03
2020
accepted:
25
03
2020
pubmed:
9
4
2020
medline:
25
6
2021
entrez:
9
4
2020
Statut:
ppublish
Résumé
Multicanonical molecular dynamics based dynamic docking was used to exhaustively search the configurational space of an inhibitor binding to the N-terminal domain of heat-shock protein 90 (Hsp90). The obtained structures at 300 K cover a wide structural ensemble, with the top two clusters ranked by their free energy coinciding with the native binding site. The representative structure of the most stable cluster reproduced the experimental binding configuration, but an interesting conformational change in Hsp90 could be observed. The combined effects of solvation and ligand binding shift the equilibrium from a preferred loop-in conformation in the unbound state to an α-helical one in the bound state for the flexible lid region of Hsp90. Thus, our dynamic docking method is effective at predicting the native binding site while exhaustively sampling a wide configurational space, modulating the protein structure upon binding.
Substances chimiques
HSP90 Heat-Shock Proteins
0
Ligands
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1606-1615Informations de copyright
© 2020 Wiley Periodicals, Inc.
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