Kazazić, Saša; Karačić, Zrinka; Sabljić, Igor; Agić, Dejan; Tomin, Marko; Abramić, Marija; Dadlez, Michal; Tomić, Antonija; Tomić, Sanja (2018) Conservation of the conformational dynamics and ligand binding within M49 enzyme family. RSC Advances, 8 (24). pp. 13310-13322. ISSN 2046-2069
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Abstract
The hydrogen deuterium exchange (HDX) mass spectrometry combined with molecular dynamics (MD) simulations was employed to investigate conformational dynamics and ligand binding within the M49 family (dipeptidyl peptidase III family). Six dipeptidyl peptidase III (DPP III) orthologues, human, yeast, three bacterial and one plant (moss) were studied. According to the results, all orthologues seem to be quite compact wherein DPP III from the thermophile Caldithrix abyssi seems to be the most compact. The protected regions are located within the two domains core and the overall flexibility profile consistent with semi-closed conformation as the dominant protein form in solution. Besides conservation of conformational dynamics within the M49 family, we also investigated the ligand, pentapeptide tynorphin, binding. By comparing HDX data obtained for unliganded protein with those obtained for its complex with tynorphin it was found that the ligand binding mode is conserved within the family. Tynorphin binds within inter-domain cleft, close to the lower domain β-core and induces its stabilization in all orthologues. Docking combined with MD simulations revealed details of the protein flexibility as well as of the enzyme–ligand interactions.
| Item Type: | Article | ||||||||||||
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| Additional Information: | Authors thank Dr Bojana Vukelic for her help with the purification of recombinant proteins. This work has been supported by Croatian Science Foundation under the project "7235 Flexibility, activity and structure correlations in the dipeptidyl peptidase III family" and by European Union's Seventh Framework Programme for Research and Technological Development under grant agreement No. 316289 - InnoMol, FP7-REGPOT-2012-2013-1 and Croatian National Grid Infrastructure (CRO NGI, http://www.cro-ngi.hr/). | ||||||||||||
| Uncontrolled Keywords: | dipeptidyl peptidase III ; DPP III ; hydrogen-deuterium exchange ; HDX ; MD simulations ; conformational dynamics | ||||||||||||
| Subjects: | NATURAL SCIENCES > Chemistry | ||||||||||||
| Divisions: | Division of Organic Chemistry and Biochemistry Division of Physical Chemistry |
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| Depositing User: | Marko Tomin | ||||||||||||
| Date Deposited: | 20 Nov 2018 09:12 | ||||||||||||
| URI: | http://fulir.irb.hr/id/eprint/4315 | ||||||||||||
| DOI: | 10.1039/c7ra13059g |
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