engleski

Dipeptidyl peptidase III from a mesophilic and thermophilic bacterium – similarities and differences

Dipeptidyl peptidase III (DPP III) is a two- domain protein, a metallopeptidase from the M49 family which contains a zinc ion within its active site and cleaves dipeptides from N- termini of its substrates. Structure and flexibility of DPP III from the mesophilic bacterium Bacteroides thetaiotaomicron (Bt) and the thermophile Caldithrix abyssi (Ca) as well as their complexes with synthetic substrates and selected inhibitors were studied using computational methods in order to elucidate the differences between DPPs III from a thermophilic and a mesophilic organism. Several force fields have been tested to determine the most suitable one for studying long-range conformational motions within the enzyme. Comparison of results obtained for a termophile with those of a mesophile revealed the structural reasons behind thermal stability of CaDPP III. The biologically relevant binding modes of substrates and inhibitors were identified and correlated with structural characteristics of the respective complexes, as well as with the enzyme flexibility. The identified binding modes qualitatively agree with the kinetic data. These results were used to build a model system of BtDPP III which was used in a quantum mechanics study in order to propose the reaction mechanism behind the peptide bond hydrolysis.

Dipeptidyl peptidase III ; DPP III ; MD simulations

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