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Browsing by Author "Wassenaar, Tsjerk A."

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    Article
    Molecular Dynamics Investigation of Helicobacter Pylori Chemotactic Protein Chey1 and Two Mutants
    (Springer, 2014) Yildirim, Ahmet; Tekpinar, Mustafa; Wassenaar, Tsjerk A.
    CheY is a chemotactic response regulator protein modulating the rotation direction of bacterial flagellar motors. It plays an important role in the colonization and infection of Helicobacter pylori (H. pylori), which is a common pathogen. Recently, the structure of CheY1 of H. pylori (HpCheY1) was solved, showing similarities and differences with CheY from E. coli. Here, we report 200 ns atomistic molecular dynamics (MD) simulations of HpCheY1 and two mutants. The results suggest that the surface of HpCheY1 has regions with increased affinity for Mg2+. In addition, wildtype HpCheY1 (WT HpCheY1) shows characteristic dynamics in helix 4, which is involved in FliM binding. This dynamics is altered in the D53A mutant and completely suppressed in the T84A mutant. The results are discussed in relation to the binding and function of HpCheY1.
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    Article
    Molecular Dynamics Study of the Effect of Active Site Protonation on Helicobacter Pylori 5'-methylthioadenosine/s-adenosylhomocysteine Nucleosidase
    (Springer, 2015) Tekpinar, Mustafa; Yildirim, Ahmet; Wassenaar, Tsjerk A.
    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 K-2 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.