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Issue 41, 2014
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Hunting the human DPP III active conformation: combined thermodynamic and QM/MM calculations

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Abstract

Multiple choices of the protein active conformations in flexible metalloenzymes complicate study of their catalytic mechanism. We used three different conformations of human dipeptidyl-peptidase III (DPP III) to investigate the influence of the protein environment on ligand binding and the Zn2+ coordination. MD simulations followed by calculations of binding free energy components accomplished for a series of DPP III substrates, both synthetic and natural, revealed that binding of the β-strand shaped substrate to the five-stranded β-core of the compact DPP III form (in antiparallel fashion) is the preferred binding mode, in agreement with the experimentally determined structure of the DPP III inactive mutant-tynorphin complex (Bezerra et al., Proc. Natl. Acad. Sci. U. S. A., 2012, 109, 6525). Previously it was proposed that the catalytic mechanism of DPP III is similar to that of thermolysin, which assumes exchange of five and four coordinated Zn2+, and activation of Zn-bound water by a nearby Glu. Our QM/MM calculations, performed for a total of 18 protein structures with different zinc ion environments, revealed that the 5-coordinated metal ion is more favourable than the 6-coordinated one in only the most compact DPP III form. Besides, in this structure E451 is H-bonded to the metal ion coordinating water. Also, our study revealed two constraints for the broad substrate specificity of DPP III. One is the possibility of the substrate adopting the β-strand shape and the other is its charged N-terminus. Altogether, we assume that the human DPP III active conformation would be the most compact form, similar to the “closed X-ray” DPP III structure.

Graphical abstract: Hunting the human DPP III active conformation: combined thermodynamic and QM/MM calculations

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Supplementary files

Article information


Submitted
02 Jul 2014
Accepted
08 Aug 2014
First published
08 Aug 2014

Dalton Trans., 2014,43, 15503-15514
Article type
Paper
Author version available

Hunting the human DPP III active conformation: combined thermodynamic and QM/MM calculations

A. Tomić and S. Tomić, Dalton Trans., 2014, 43, 15503
DOI: 10.1039/C4DT02003K

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