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Microseconds dynamics simulations of the outer-membrane protease T.

Marilisa Neri1, Marc Baaden, Vincenzo Carnevale

  • 1International School for Advanced Studies and CNR National Institute for the Physics of Matter, National Simulation Center, Trieste, Italy.

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Structural Biology

Background:

  • Enzyme conformational dynamics are crucial for substrate recognition and catalysis.
  • Investigating these dynamics is computationally challenging due to the vast degrees of freedom involved in protein function.

Purpose of the Study:

  • To investigate the role of conformational fluctuations in the function of the OmpT protease from Escherichia coli.
  • To explore the catalytic strategy and structure-function relationships of OmpT and its mutants using advanced simulation techniques.

Main Methods:

  • Employed a hybrid molecular mechanics/coarse-grained simulation approach.
  • Treated the OmpT active site with the GROMOS force field and the protein scaffold with a Go-model.
  • Validated the method against all-atom simulations.

Main Results:

  • Identified microsecond-timescale large-scale motions and electric field fluctuations impacting OmpT's biological function.
  • Suggested OmpT shares a catalytic strategy with aspartic proteases, a conclusion not feasible with shorter simulations.
  • Provided structural explanations for reduced catalytic activity in S99A and H212A mutants.

Conclusions:

  • The hybrid coarse-grained approach offers a fast and reliable method for studying enzyme structure-function relationships.
  • Microsecond-timescale dynamics are essential for understanding OmpT's catalytic mechanism and substrate interactions.
  • OmpT's functional dynamics and catalytic strategy are elucidated, offering insights into protease superfamilies.