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Molecular dynamics study of the effect of active site protonation on Helicobacter pylori 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase

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Abstract

The protein 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) is involved in the quorum sensing of several bacterial species, including Helicobacter pylori. In particular, these bacteria depend on MTAN for synthesis of vitamin K2 homologs. The residue D198 in the active site of MTAN seems to be of crucial importance, by acting as a hydrogen-bond acceptor for the ligand. In this study, we investigated the conformation and dynamics of apo and holo H. pylori MTAN (HpMTAN), and assessed the effect of protonation of D198 by use of molecular dynamics simulations. Our results show that protonation of the active site of HpMTAN can cause a conformational transition from a closed state to an open state even in the absence of substrate, via inter-chain mechanical coupling.

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Acknowledgments

All calculations reported in this paper were performed at TUBITAK (Turkish Scientific and Technical Research Counsel) ULAKBIM (National Academic Information Center), High Performance and Grid Computing Center (TRUBA Resources). We would like to thank TUBITAK for providing us with these excellent computational resources and service.

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Authors and Affiliations

  1. Department of Physics, Faculty of Science, Yüzüncü Yıl University, 65100, Van, Turkey

    Mustafa Tekpinar

  2. Department of Physics, Faculty of Science and Art, Siirt University, 56100, Siirt, Turkey

    Ahmet Yildirim

  3. Department of Biology, University of Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany

    Tsjerk A. Wassenaar

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  1. Mustafa Tekpinar
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  2. Ahmet Yildirim
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Correspondence to Mustafa Tekpinar.

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Tekpinar, M., Yildirim, A. & Wassenaar, T.A. Molecular dynamics study of the effect of active site protonation on Helicobacter pylori 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase. Eur Biophys J 44, 685–696 (2015). https://doi.org/10.1007/s00249-015-1067-0

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