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OmpT: molecular dynamics simulations of an outer membrane enzyme
1Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
Biophysical Journal
|August 19, 2004
Summary
Molecular dynamics simulations reveal Escherichia coli OmpT protease stability and flexibility. Key active site residues and water interactions support a catalytic mechanism, with lipid interactions also identified.
Area of Science:
- Biochemistry
- Structural Biology
- Computational Biology
Background:
- The outer membrane protease OmpT from Escherichia coli plays a crucial role in bacterial outer membrane protein processing.
- Understanding OmpT's structure-function relationship is vital for deciphering bacterial envelope biology and potential therapeutic targets.
Purpose of the Study:
- To investigate the conformational stability and dynamics of OmpT within a lipid bilayer using molecular dynamics simulations.
- To elucidate the catalytic mechanism of OmpT, focusing on active site residue interactions and water molecule involvement.
- To explore potential protein-lipid interactions at the OmpT surface.
Main Methods:
- Five molecular dynamics (MD) simulations totaling over 25 ns were performed on OmpT in a dimyristoylphosphatidylcholine lipid bilayer.
- Docking calculations were used to model substrate binding to OmpT.
- Extended Huckel calculations were employed to analyze the electronic properties of the docked substrate.
Main Results:
- OmpT exhibited overall conformational stability, with some tilt of its beta-barrel relative to the bilayer.
- Extracellular loops displayed the highest degree of flexibility.
- A network of hydrogen bonds involving active site residues (Asp210, His212, Asp83) and water molecules was observed, supporting a catalytic mechanism involving water activation.
- Docking and electronic structure calculations indicated that the lowest unoccupied molecular orbital localized on the scissile peptide bond, favoring nucleophilic attack by activated water.
- Water molecules accessed the active site from the intracellular side, suggesting a role for the central pore.
- Specific lipid interaction sites on the OmpT surface were identified.
Conclusions:
- Extended MD simulations provide valuable insights into OmpT's structural dynamics, catalytic mechanism, and protein-lipid interactions.
- The identified catalytic mechanism involving Asp83, His212, and water molecules is consistent with OmpT's function.
- OmpT's interaction with lipids may influence its stability and function within the outer membrane.