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Evidence of a Double-Lid Movement in Pseudomonas aeruginosa Lipase: Insights from Molecular Dynamics Simulations

PLoS Computational Biology
Public Library of Science
Publication Date
DOI: 10.1371/journal.pcbi.0010028
  • Research Article
  • Biochemistry
  • Bioinformatics - Computational Biology
  • Molecular Biology - Structural Biology
  • Eubacteria
  • None
  • Biology
  • Computer Science


Synopsis Lipases hydrolyse long-chain fatty acid esters at water-oil interfaces through the mechanism of interfacial activation mediated by the movement of a lid subdomain that covers the active site. Studying lid movement is an area of active research in the field of protein dynamics. The lipase from Pseudomonas aeruginosa is a 29-kDa protein that was previously crystallized in the open conformation, and as expected, an approximately 20-residue lid subdomain was identified. In the present study, the authors report extensive molecular dynamics simulations of the P. aeruginosa lipase. They show that this protein has two lids covering the substrate-binding pocket. The first lid is the one proposed from the known crystal structure. The second lid, a much shorter one, lies over the binding pocket facing the first lid. Furthermore, using position-restrained simulations, these authors show that movement of the second lid may actually be a trigger for the movement of the first, and that this triggering action is driven by hydrophobic contacts between the two lids. This computational study paves a way for experimentalists to study the structure and dynamics of this protein in greater detail in order to understand coupled subdomain movements in a comprehensive fashion.

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