engleski

Conformational study of Bacteroides thetaiotaomicron dipeptidyl peptidase III

Bacteroides thetaiotaomicron, a Gram-negative anaerobe, is a dominant member of human intenstinal microbiota. As such, it is of great importance in understanding the symbiotic host-bacterial relationship within the human intestine. Dipeptidyl peptidase III isolated from Bacteroides thetaiotaomicron(Bt.DPP III) is a two-domain zinc exopeptidase from the M49 family. Members of this family, characterized by their HEXXGH motive, cleave dipeptidyl residues from the N-terminus of their substrates. This conserved region contains two His residues that coordinate the Zn ion along with Glu449 and Glu476. The crystal structure of Bt.DPP III reveals a two-domain molecule, with a cleft inbetween, strongly resembling the human DPP III, despite their low sequence identity (~23%). In this work we used classical and accelerated molecular dynamics simulations (MD)to examine the long-range conformational changes of the enzyme over the course of 200 ns and compared them to its human counterpart. In order to determine the best method for the enzyme and complex description severa force fields, ff03, ff12SB andff14SB were utilized. We identified twodistinctBt.DPP III conformers, open and closed. Special emphasis has been placed on the zinc ion coordination flexibility, since the existing data for human DPP III suggests the high plasticity of the Zn2+ coordination. The syntetic substrates Arg-Arg-2-naphtylamide and Lys-Ala-2-naphtylamide were docked into the active siteof the wild type protein and ofthe C450S mutant and the solvated complexes were simulated for at least 200ns at room temperature. In order to understand the enzyme-ligand interactions the results of simulation were compared with the experimental data.

DPP III ; molecular dynamics ; simulation

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