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EnglishThe metadynamics method has been shown to be a valuable tool to study the mechanism of molecular recognition in atomistic detail [Gervasio, F. L.; et al. J. Am. Chem. Soc. 2005, 127, 2600]. However, it requires an a priori knowledge of all slow degrees of freedom relevant to the docking/undocking mechanism. Here we investigate a combination of docking/clustering with metadynamics performed with a subset of the necessary degrees of freedom (coarse metadynamics), and show that it provides a full mechanistic insight on the protein-ligand docking mechanism. Moreover, the proposed protocol is able to clearly distinguish between crystallographic and noncrystallographic poses of protein-ligand complexes, and also to find the transition state of the full undocking mechanism, thus giving an indication on the binding free energy.
| Titolo: | Exploring complex protein-ligand recognition mechanisms with coarse metadynamics |
| Autore/i: | MASETTI, MATTEO; CAVALLI, ANDREA; RECANATINI, MAURIZIO; Gervasio F. L. |
| Autore/i Unibo: | |
| Anno: | 2009 |
| Rivista: | |
| Digital Object Identifier (DOI): | http://dx.doi.org/10.1021/jp803936q |
| Abstract: | The metadynamics method has been shown to be a valuable tool to study the mechanism of molecular recognition in atomistic detail [Gervasio, F. L.; et al. J. Am. Chem. Soc. 2005, 127, 2600]. However, it requires an a priori knowledge of all slow degrees of freedom relevant to the docking/undocking mechanism. Here we investigate a combination of docking/clustering with metadynamics performed with a subset of the necessary degrees of freedom (coarse metadynamics), and show that it provides a full mechanistic insight on the protein-ligand docking mechanism. Moreover, the proposed protocol is able to clearly distinguish between crystallographic and noncrystallographic poses of protein-ligand complexes, and also to find the transition state of the full undocking mechanism, thus giving an indication on the binding free energy. |
| Data prodotto definitivo in UGOV: | 2009-05-14 17:40:35 |
| Appare nelle tipologie: | 1.01 Articolo in rivista |
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