Flexibility of prolyl oligopeptidase: molecular dynamics and molecular framework analysis of the potential substrate pathways

Proteins. 2005 Aug 15;60(3):504-12. doi: 10.1002/prot.20508.


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 beta-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 verified by kinetic analysis of the enzyme with a split loop. Catalytic effect of engineered disulfide bridges was rationalized by characterizing the concerted motions of the two domains.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites
  • Catalysis
  • Computer Simulation
  • Crystallography, X-Ray
  • Endopeptidases / chemistry
  • Entropy
  • Escherichia coli / metabolism
  • Hot Temperature
  • Kinetics
  • Models, Molecular
  • Models, Statistical
  • Molecular Conformation
  • Peptide Hydrolases / chemistry
  • Peptides / chemistry
  • Pliability
  • Prolyl Oligopeptidases
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Tertiary
  • Serine Endopeptidases / chemistry*
  • Software
  • Substrate Specificity
  • Swine
  • Thermodynamics
  • Trypsin / chemistry


  • Peptides
  • Endopeptidases
  • Peptide Hydrolases
  • oligopeptidase
  • Serine Endopeptidases
  • Prolyl Oligopeptidases
  • Trypsin