Browsing by Author "Yildirim, Ahmet"

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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.
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.
Opening Mechanism of Adenylate Kinase Can Vary According To Selected Molecular Dynamics Force Field
(Springer, 2015) Unan, Hulya; Yildirim, Ahmet; Tekpinar, Mustafa
Adenylate kinase is a widely used test case for many conformational transition studies. It performs a large conformational transition between closed and open conformations while performing its catalytic function. To understand conformational transition mechanism and impact of force field choice on E. Coli adenylate kinase, we performed all-atom explicit solvent classical molecular dynamics simulations starting from the closed conformation with four commonly used force fields, namely, Amber99, Charmm27, Gromos53a6, Opls-aa. We carried out 40 simulations, each one 200 ns. We analyzed completely 12 of them that show full conformational transition from the closed state to the open one. Our study shows that different force fields can have a bias toward different transition pathways. Transition time scales, frequency of conformational transitions, order of domain motions and free energy landscapes of each force field may also vary. In general, Amber99 and Charmm27 behave similarly while Gromos53a6 results have a resemblance to the Opls-aa force field results.
Variational Iteration Method for the Time-Fractional Fornberg-Whitham Equation
(Pergamon-elsevier Science Ltd, 2012) Sakar, Mehmet Giyas; Erdogan, Fevzi; Yildirim, Ahmet
This paper presents the approximate analytical solutions to solve the nonlinear Fornberg-Whitham equation with fractional time derivative. By using initial values, explicit solutions of the equations are solved by using a reliable algorithm like the variational iteration method. The fractional derivatives are taken in the Caputo sense. The present method performs extremely well in terms of efficiency and simplicity. Numerical results for different particular cases of a are presented graphically. (c) 2012 Elsevier Ltd. All rights reserved.