Browsing by Author "Tekpinar, Mustafa"

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Flexible Fitting To Cryo-Electron Microscopy Maps With Coarse-Grained Elastic Network Models
(Taylor & Francis Ltd, 2018) Tekpinar, Mustafa
Cryo-electron microscopy has become an important tool for protein structure determination in recent decades. Since proteins may exist in multiple conformational states, combining high resolution X-ray or NMR structures with cryo-electron microscopy maps is a useful approach to obtain proteins in different functional states. Flexible fitting methods used in cryo-electron microscopy aim to obtain an unknown protein conformation from a high resolution structure and a cryo-electron microscopy map. Since all-atom flexible fitting is computationally expensive, many efficient flexible fitting algorithms that utilize coarse-grained elastic network models have been proposed. In this study, we investigated performance of three coarse-grained elastic network model-based flexible fitting methods (EMFF, iModFit, NMFF) using 25 protein pairs at four resolutions. This study shows that the application of coarse-grained elastic network models to flexible fitting of cryo-electron microscopy maps can provide fast and fruitful models of various conformational states of proteins.
High-Resolution Modeling of Protein Structures Based on Flexible Fitting of Low-Resolution Structural Data
(Elsevier Academic Press inc, 2014) Zheng, Wenjun; Tekpinar, Mustafa
To circumvent the difficulty of directly solving high-resolution biomolecular structures, low-resolution structural data from Cryo-electron microscopy (EM) and small angle solution X-ray scattering (SAXS) are increasingly used to explore multiple conformational states of biomolecular assemblies. One promising venue to obtain high-resolution structural models from low-resolution data is via data-constrained flexible fitting. To this end, we have developed a new method based on a coarse-grained Cu-only protein representation, and a modified form of the elastic network model (ENM) that allows large-scale conformational changes while maintaining the integrity of local structures including pseudo-bonds and secondary structures. Our method minimizes a pseudo-energy which linearly combines various terms of the modified ENM energy with an EM/SAXS-fitting score and a collision energy that penalizes steric collisions. Unlike some previous flexible fitting efforts using the lowest few normal modes, our method effectively utilizes all normal modes so that both global and local structural changes can be fully modeled with accuracy. This method is also highly efficient in computing time. We have demonstrated our method using adenylate kinase as a test case which undergoes a large open-to-close conformational change. The EM-fitting method is available at a web server (htt://enm.lobos.nih.gov), and the SAXS-fitting method is available as a pre-compiled executable upon request.
Minactionpath2: Path Generation Between Different Conformations of Large Macromolecular Assemblies by Action Minimization
(Oxford Univ Press, 2024) Koehl, Patrice; Navaza, Rafael; Tekpinar, Mustafa; Delarue, Marc
Recent progress in solving macromolecular structures and assemblies by cryogenic electron microscopy techniques enables sampling of their conformations in different states that are relevant to their biological function. Knowing the transition path between these conformations would provide new avenues for drug discovery. While the experimental study of transition paths is intrinsically difficult, in-silico methods can be used to generate an initial guess for those paths. The Elastic Network Model (ENM), along with a coarse-grained representation (CG) of the structures are among the most popular models to explore such possible paths. Here we propose an update to our software platform MinActionPath that generates non-linear transition paths based on ENM and CG models, using action minimization to solve the equations of motion. The new website enables the study of large structures such as ribosomes or entire virus envelopes. It provides direct visualization of the trajectories along with quantitative analyses of their behaviors at http://dynstr.pasteur.fr/servers/minactionpath/ minactionpath2_submission. Graphical Abstract
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.
Unzipping of Neuronal Snare Protein With Steered Molecular Dynamics Occurs in Three Steps
(Springer, 2014) Tekpinar, Mustafa; Zheng, Wenjun
Soluble NSF-attachment protein receptors (SNAREs) play a crucial role in membrane fusion. Neuronal SNAREs, a four-helix bundle, help synaptic vesicles fuse with plasma membranes. We applied constant velocity pulling forces in silico to C terminal of synaptobrevin, one of the helices in the bundle, to understand unzipping mechanism of neuronal SNAREs. We observed unzipping of snaptobrevin from the other helices in three steps: linker domain unzipping, C terminal unzipping and N terminal unzipping. Our results have good qualitative agreement with a recent optical tweezer experiment that observes this stepwise unzipping. Since we performed 14 different simulations for two large spring force constants, our results are robust and they reveal atomistic details of these distinct unzipping steps.