Microseconds dynamics simulations of the outer-membrane protease T

Biophys J. 2008 Jan 1;94(1):71-8. doi: 10.1529/biophysj.107.116301. Epub 2007 Sep 7.


Conformational fluctuations of enzymes may play an important role for substrate recognition and/or catalysis, as it has been suggested in the case of the protease enzymatic superfamily. Unfortunately, theoretically addressing this issue is a problem of formidable complexity, as the number of the involved degrees of freedom is enormous: indeed, the biological function of a protein depends, in principle, on all its atoms and on the surrounding water molecules. Here we investigated a membrane protease enzyme, the OmpT from Escherichia coli, by a hybrid molecular mechanics/coarse-grained approach, in which the active site is treated with the GROMOS force field, whereas the protein scaffold is described with a Go-model. The method has been previously tested against results obtained with all-atom simulations. Our results show that the large-scale motions and fluctuations of the electric field in the microsecond timescale may impact on the biological function and suggest that OmpT employs the same catalytic strategy as aspartic proteases. Such a conclusion cannot be drawn within the 10- to 100-ns timescale typical of current molecular dynamics simulations. In addition, our studies provide a structural explanation for the drop in the catalytic activity of two known mutants (S99A and H212A), suggesting that the coarse-grained approach is a fast and reliable tool for providing structure/function relationships for both wild-type OmpT and mutants.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Outer Membrane Proteins / chemistry*
  • Bacterial Outer Membrane Proteins / ultrastructure*
  • Computer Simulation
  • Enzyme Activation
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / ultrastructure*
  • Models, Chemical*
  • Models, Molecular*
  • Peptide Hydrolases / chemistry*
  • Peptide Hydrolases / ultrastructure*
  • Protein Conformation
  • Protein Folding


  • Bacterial Outer Membrane Proteins
  • Escherichia coli Proteins
  • ompT protein, E coli
  • Peptide Hydrolases