BIOPHYSICAL THEORY AND MODELING |
Microseconds Dynamics Simulations of the Outer-Membrane Protease T
marilisa neri 1, Marc Baaden 2, Vincenzo Carnevale 3, Claudio Anselmi 3, Amos Maritan 4 and Paolo Carloni 3*
1 Ecole polytechnique fédérale de Lausanne
2 Institut de Biologie Physico-Chimique, Paris
3 International School for Advanced Studies
4 Dipartimento di fisica G. Galilei, Universita' degli studi di Padova, Italy
* To whom correspondence should be addressed. E-mail: carloni{at}sissa.it.
Submitted on June 28, 2007
Revised on August 9, 2007
Accepted on 24 August 2007
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Abstract |
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Conformational fluctuations of enzymes may play an important role for Substrate recognition and/or cayalysis, as it has been suggested in the case of the protease enzymatic superfamily (Carnevale et al. J .Am. Chem. Soc. 128: 9766--9772). 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 E. coli, by hybrid molecular mechanics/coarse-grained approach (MM/CG), in which the active site is treated with the GROMOS force field, whilst 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 µs time scale may impact on the biological function and suggest that OmpT employs the same catalytic strategy as aspartic proteases. Such a conclusion can not be drawn within the 10-100 ns time scale 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 CG approach is a fast and reliable tool for providing structure/function relationships for both wild type OmpT and mutants.
Key Words:
Coarse grained, conformational fluctuations, hybrid model, microseconds, molecular dynamics, omptin
