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Ligand binding to the flexible metaloenzymes: protein dynamics and the active enzyme conformation

Tomić, Sanja; Tomić, Antonija
Ligand binding to the flexible metaloenzymes: protein dynamics and the active enzyme conformation // European Biophysics Journal 2015, Volume 44, Supplement 1
Dresten, Njemačka: Springer Berlin Heidelberg, 2015. str. 243-243 doi:10.1007/s00249-015-1045-6 (poster, međunarodna recenzija, sažetak, ostalo)

Ligand binding to the flexible metaloenzymes: protein dynamics and the active enzyme conformation

Tomić, Sanja ; Tomić, Antonija

Vrsta, podvrsta i kategorija rada
Sažeci sa skupova, sažetak, ostalo

European Biophysics Journal 2015, Volume 44, Supplement 1 / - : Springer Berlin Heidelberg, 2015, 243-243

10th European Biophysical Congress

Mjesto i datum
Dresten, Njemačka, 18-22.07.2015

Vrsta sudjelovanja

Vrsta recenzije
Međunarodna recenzija

Ključne riječi
Metallopeptidase, enzyme flexibility, molecular dynamics, DPP III

High flexibility of enzymes significantly complicates ligand binding study as well as the study of enzymatic reaction. Besides, in the metalloenzymes protein flexibility complicates study of the metal coordination. Herein we present results of the long range MD simulations of human DPPIII combined with ligand binding study and QM/MM calculations of the metal ion coordination. The DPP III (dipeptidyl-peptidase III) metaloenzyme is present in many human tissues. Besides its role in intracellular protein catabolism, there are significant evidences for its participation in pain modulation and defense against oxidative stress. There are two crystal structures of human DPP III available. The structure of the ligand-free enzyme has a wide cleft (~40 Å wide and ~20 Å high) between the two domains while the structure of the liganded enzyme is more compact. It was assumed that ligand binding induces the closure of DPP III consistently with the induced fit model (Bezerra et al. PNAS 2012). On the other hand, our several hundrends of ns long convential and accelerated MD simulations showed that the ligand-free protein experiences long range conformational changes in solution as well evolving from the open to the compact form. However, the MD simulations showed that the ligand binding influence the mode of protein closure. The transition between the two distinct compact protein forms takes place throught the most populated region at the conformational surface occupied by the semi-closed forms. The steered MD simulations also revealed importance of the semi-closed enzyme form. The fully closed form is too compact to allow the substrate molecule to enter the binding site so to accommodate a substrate in its active site DPP III would need to partially reopen. While the semi-closed forms turned out to be the most potent for the ligand binding the highly compact form of the DPP III – substrate complex is according to the free energy calculations the most stable. Besides, the QM/MM calculations (Tomić et al. Dalton 2014). revealed that only in the most compact DPP III form, the zinc ion coordination is in line with the proposed catalytic mechanisms (5-coordinated Zn2+ and E451 and water ligated to the metal are H-bonded. The results clearly point to importance of combined, multi level approach to study the ligand binding mechanism of the potentially highly flexible enzymes

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Znanstvena područja


Projekt / tema
HRZZ-IP-2013-11-7235 - Povezanost fleksibilnosti, aktivnosti i strukture u porodici dipeptidil-peptidaza III (Sanja Tomić, )

Institut "Ruđer Bošković", Zagreb

Časopis indeksira:

  • Current Contents Connect (CCC)
  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
    • SCI-EXP, SSCI i/ili A&HCI
  • Scopus