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Molecular Dynamics Studies of Caspase-3

M. Sulpizi^*, U. Rothlisberger^* and P. Carloni^,

^* Laboratory of Computational Chemistry and Biochemistry, Federal Institute of Technology (EPFL) CH-1015 Lausanne, Switzerland; SISSA, International School for Advanced Studies, via Beirut 2-4, 34013 Trieste, Italy; and INFM DEMOCRITOS Center for Numerical Simulation, Italy

Correspondence: Address reprint requests to U. Rothlisberger, Laboratory of Computational Chemistry and Biochemistry, Federal Institute of Technology (EPFL) CH-1015 Lausanne, Switzerland. Tel.: +41-21-693 0321; Fax: +41-21-693 0320; E-mail: ursula.roethlisberger{at}epfl.ch.

Caspase-3 is a fundamental target for pharmaceutical interventions against a variety of diseases involving disregulated apoptosis. The enzyme is active as a dimer with two symmetry-related active sites, each featuring a Cys-His catalytic dyad and a selectivity loop, which recognizes the characteristic DEVD pattern of the substrate. Here, a molecular dynamics study of the enzyme in complex with two pentapeptide substrates DEVDG is presented, which provides a characterization of the dynamic properties of the active form in aqueous solution. The mobility of the substrate and that of the catalytic residues are rather low indicating a distinct preorganization effect of the Michaelis complex. An essential mode analysis permits us to identify coupled motions between the two monomers. In particular, it is found that the motions of the two active site loops are correlated and tend to steer the substrate toward the reactive center, suggesting that dimerization has a distinct effect on the dynamic properties of the active site regions. The selectivity loop of one monomer turns out to be correlated with the N-terminal region of the p12 subunit of the other monomer, an interaction that is also found to play a fundamental role in the electrostatic stabilization of the quaternary structure. To further characterize the specific influence of dimerization on the enzyme essential motions, a molecular dynamics analysis is also performed on the isolated monomer.