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SAR and QSAR in Environmental Research Volume 20, 2009 - Issue 7-8: CMTPI 2009: Computational Methods in Toxicology and Pharmacology Integrating Internet Resources (Istanbul, Turkey, July 4–8, 2009)
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Original Articles

Molecular dynamics study of prolyl oligopeptidase with inhibitor in binding cavity

K. Kaszuba Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland; Department of Physics and Biophysics, University of Warmia and Mazury, ul. Michała Oczapowskiego 4, Olsztyn, Poland
,
T. Róg Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland; Department of Applied Physics, Helsinki University of Technology, P.O. Box 1100, FI-02015 TKK, Finland
,
J.-F. St. Pierre Département de Physique and Regroupement Québécois sur les Matériaux de Pointe, Université de Montréal, C.P. 6128, succursale centre-ville, Montreal (Québec), Canada
,
P.T. Männistö Division of Pharmacology and Toxicology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Finland
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M. Karttunen Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street North, London, Ontario, Canada N6A 5B7
&
A. Bunker Centre for Drug Research, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Finland; Department of Chemistry, Helsinki University of Technology, P.O. Box 6100, FI-02015, TKK, FinlandCorrespondence[email protected]
Pages 595-609 | Received 07 Jul 2009, Accepted 03 Oct 2009, Published online: 17 Dec 2009

Citations (11)

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Dongmei Wang, Hanyong Jin, Junling Wang, Shanshan Guan, Zuoming Zhang & Weiwei Han. (2016) Exploration of the chlorpyrifos escape pathway from acylpeptide hydrolases using steered molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics 34:4, pages 749-761.
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Articles from other publishers (10)

Anna J. Kiss-Szemán, Veronika Harmat & Dóra K. Menyhárd. (2019) Achieving Functionality Through Modular Build-up: Structure and Size Selection of Serine Oligopeptidases. Current Protein & Peptide Science 20:11, pages 1089-1101.
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D.W. Russell, M. Hardison, K.R. Genschmer, T. Szul, P.E. Bratcher, M. Abdul Roda, X. Xu, L. Viera, J.E. Blalock, A. Gaggar & B.D. Noerager. (2019) Benzyloxycarbonyl-proline-prolinal (ZPP): Dual complementary roles for neutrophil inhibition. Biochemical and Biophysical Research Communications 517:4, pages 691-696.
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Alexandra Tsirigotaki, Roos Van Elzen, Pieter Van Der Veken, Anne-Marie Lambeir & Anastassios Economou. (2017) Dynamics and ligand-induced conformational changes in human prolyl oligopeptidase analyzed by hydrogen/deuterium exchange mass spectrometry. Scientific Reports 7:1.
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Peter Canning, Dean Rea, Rory E. Morty & Vilmos Fülöp. (2013) Crystal Structures of Trypanosoma brucei Oligopeptidase B Broaden the Paradigm of Catalytic Regulation in Prolyl Oligopeptidase Family Enzymes. PLoS ONE 8:11, pages e79349.
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Elena Papaleo & Giulia Renzetti. (2012) Coupled motions during dynamics reveal a tunnel toward the active site regulated by the N-terminal α-helix in an acylaminoacyl peptidase. Journal of Molecular Graphics and Modelling 38, pages 226-234.
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Karol Kaszuba, Tomasz Róg, Reinis Danne, Peter Canning, Vilmos Fülöp, Tünde Juhász, Zoltán Szeltner, J.-F. St. Pierre, Arturo García-Horsman, Pekka T. Männistö, Mikko Karttunen, Jyrki Hokkanen & Alex Bunker. (2012) Molecular dynamics, crystallography and mutagenesis studies on the substrate gating mechanism of prolyl oligopeptidase. Biochimie 94:6, pages 1398-1411.
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Adam Orłowski, Jean-François St-Pierre, Aniket Magarkar, Alex Bunker, Marta Pasenkiewicz-Gierula, Ilpo Vattulainen & Tomasz Róg. (2011) Properties of the Membrane Binding Component of Catechol- O -methyltransferase Revealed by Atomistic Molecular Dynamics Simulations . The Journal of Physical Chemistry B 115:46, pages 13541-13550.
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Swati Kaushik & Ramanathan Sowdhamini. (2011) Structural Analysis of Prolyl Oligopeptidases Using Molecular Docking and Dynamics: Insights into Conformational Changes and Ligand Binding. PLoS ONE 6:11, pages e26251.
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Jean-François St-Pierre, Mikko Karttunen, Normand Mousseau, Tomasz Róg & Alex Bunker. (2011) Use of Umbrella Sampling to Calculate the Entrance/Exit Pathway for Z-Pro-Prolinal Inhibitor in Prolyl Oligopeptidase. Journal of Chemical Theory and Computation 7:6, pages 1583-1594.
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Karol Kaszuba, Tomasz Róg, Krzysztof Bryl, Ilpo Vattulainen & Mikko Karttunen. (2010) Molecular Dynamics Simulations Reveal Fundamental Role of Water As Factor Determining Affinity of Binding of β-Blocker Nebivolol to β 2 -Adrenergic Receptor . The Journal of Physical Chemistry B 114:25, pages 8374-8386.
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