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Flexibility of prolyl oligopeptidase: Molecular dynamics and molecular framework analysis of the potential substrate pathways by Monika Fuxreiter; Csaba Magyar; Tünde Juhász; Zoltán Szeltner; László Polgár; István Simon is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

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## Abstract The flexibility of prolyl oligopeptidase has been investigated using molecular dynamics (MD) and molecular framework approaches to delineate the route of the substrate to the active site. The selectivity of the enzyme is mediated by a seven‐bladed β‐propeller that in the crystal structure does not indicate the possible passage for the substrate to the catalytic center. Its open topology however, could allow the blades to move apart and let the substrate into the large central cavity. Flexibility analysis of prolyl oligopeptidase structure using the FIRST (Floppy Inclusion and Rigid Substructure Topology) approach and the atomic fluctuations derived from MD simulations demonstrated the rigidity of the propeller domain, which does not permit the substrate to approach the active site through this domain. Instead, a smaller tunnel at the inter‐domain region comprising the highly flexible N‐terminal segment of the peptidase domain and a facing hydrophilic loop from the propeller (residues 192–205) was identified by cross‐correlation analysis and essential dynamics as the only potential pathway for the substrate. The functional importance of the flexible loop has been also ve

Who reads Flexibility of prolyl oligopeptidase: Molecular dynamics and molecular framework analysis of the potential substrate pathways?

Author

Monika Fuxreiter; Csaba Magyar; Tünde Juhász; Zoltán Szeltner; László Polgár; István Simon

Publisher

John Wiley and Sons; Wiley (John Wiley & Sons); Wiley-Liss Inc; Wiley (ISSN 0887-3585)

Published

2005

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)