title: Molecular dynamics study of the effect of active site protonation on Helicobacter pylori 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase.
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.
authors.affiliation: Department of Physics, Faculty of Science, Yüzüncü Yıl University, 65100, Van, Turkey. tekpinar@buffalo.edu.
authors.forename: Mustafa
authors.initials: M
authors.lastname: Tekpinar
authors.affiliation: Department of Physics, Faculty of Science and Art, Siirt University, 56100, Siirt, Turkey.
authors.forename: Ahmet
authors.initials: A
authors.lastname: Yildirim
authors.affiliation: Department of Biology, University of Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany.
authors.forename: Tsjerk A
authors.initials: TA
authors.lastname: Wassenaar
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D020134:Catalytic Domain; D016480:Helicobacter pylori / Q000201:enzymology; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009699:N-Glycosyl Hydrolases / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011522:Protons
chemical_list: D001426:Bacterial Proteins; D011522:Protons; D009699:N-Glycosyl Hydrolases; C019606:adenosylhomocysteine nucleosidase
keywords: D198 protonation; Helicobacter pylori; MTAN; Molecular dynamics simulation