M.S. Theses
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Browsing M.S. Theses by Author "Akdoğan, Demet Akten."
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Item Blind docking simulations of benzothiazoles on triosephosphate isomerase(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2011., 2011.) Ural, Gülgün.; Turgut, Pemra Doruker.; Akdoğan, Demet Akten.Selective inhibition of the activity of the glycolytic enzyme triosephosphate isomerase from Trypanosoma cruzi (TcTIM) as opposed to human TIM (hTIM) has been critical for drug design studies on Chagas disease. The aim of this docking study is to uncover the binding modes of benzothiazoles, reported as effective inhibitors of TcTIM. Blind dockings of five benzothiazoles are performed on both TcTIM and hTIM by using the Lamarckian genetic algorithm of AutoDock v4.0. Protein flexibility is incorporated via docking to multiple, distinct conformations that are obtained from extended molecular dynamics simulations. The clusters that fall within 1 kcal/mol of the lowest energy poses from docking are analyzed for determination of alternative binding sites. The inhibitors mostly bind to the tunnel-shaped region formed at the interface of the subunits in TcTIM, whereas other sites are preferred by the non-inhibitors. Moreover, blind dockings to equilibrated conformers of TcTIM monomer indicate no distinct tendency of inhibitors for binding to the interface region that becomes solvent accessible upon dissociation to monomers. Thus, the tunnel-shaped cavity on the TcTIM dimer interface is the most distinct site for the action of inhibitors, consistent with previous studies. Interactions of strong inhibitors at the interface at the TcTIM interface include interactions with aromatic residues (Phe75, Tyr102 and Tyr103) and cation-interactions (with Arg71, Arg99 and Lys113). In addition, multiple hydrogen bonds between the sulfonate group (present only in inhibitors) and residues Asn67, Thr70, Arg99 and Lys113 are found to be specific in the case of the strong inhibitors. Further blind dockings of sulfonate-free derivatives of inhibitors and a sulfonate-added derivative of a non-inhibitor on TcTIM have indicated that the sulfonate group aids the correct positioning of benzothiazoles in the tunnel-shaped cavity. The inhibitors docked on hTIM conformers show a non-selective behavior for the interface of hTIM dimer, which does not present an accessible tunnel-shaped cavity as TcTIM. Binding sites other than the interface region are also reported for TcTIM and hTIM.Item Exploring the intrinsic dynamics of human beta-2 adrenergic G-protein coupled receptor(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2011., 2011.) Özcan, Özer.; Turgut, Pemra Doruker.; Akdoğan, Demet Akten.G protein-coupled receptors (GPCRs) represent the single largest family of cell surface receptors involved in signal transduction. It is estimated that several hundred distinct members of this receptor family in humans direct responses to a wide variety of chemical transmitters, including biogenic amines, amino acids, peptides, lipids, nucleosides, and large polypeptides. These transmembrane receptors are key controllers of such diverse physiological processes as neurotransmission, cellular metabolism, secretion, cellular differentiation, and growth as well as inflammatory and immune responses. GPCRs therefore represent major targets for the development of new drug candidates with potential application in all clinical fields. In this thesis, the crystal structure of a human β2- adrenergic receptor (β2AR) complexed with a partial inverse agonist carazolol was used as a starting conformation (PDB ID: 2rh1). The missing intracellular loop III (ICL3), which plays an essential role in G protein recognition, was estimated via homology modelling. An alternative model of the receptor with missing loop, which called as "clipped" model, was also used in order to understand the effect of the loop on the dynamics. The purpose of this study is to explore the dynamics of the receptor and the effect of the generated loop on the whole structure the shed light on the results of MD simulations. Here we characterize 0.8 μs and 0.5 μs all-atom MD simulation of an apo-β2AR for looped and clipped model respectively. Also Asn187 residue has been replaced with Glu187 to facilitate crystallization for the clipped model. Though it is estimated that a single residue will not affect the dynamics of the system significantly, to obtain a definite outcome, the system, undergoing no mutation, has been formed with its natural contents, and being placed within cell membrane, it has been exposed to a 0.5 μs all-atom MD simulation of an apo- β2AR. From MD studies, it was shown that the global orientation of the loop region (ICL3) changed considerably with respect to the core structure. The maximum mobility was observed for ICL3 and short loops ICL2, ECL2 and ECL3 connecting the transmembrane helices.Item Investigation of allosteric coupling in beta-2 adrenergic receptor through molecular dynamics simulations(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2014., 2014.) Özgür, Canan.; Turgut, Pemra Doruker.; Akdoğan, Demet Akten.The purpose of this thesis is to investigate the allosteric coupling between intra- and extracellular parts of G-protein coupled human β2 adrenergic receptor (β2AR) in the presence of intracellular loop ICL3, which is missing in all crystallographic structures. In a recent study, a 1 μs MD run showed that closure of the G-protein binding site due to tight packing and closure of ICL3 under the receptor was coupled with the expansion of the ligand binding site. In this study, two independent 500 ns runs, which started from the final snapshot of the original 1 μs MD run with closed ICL3, showed that ICL3 stayed mostly in closed position, pointing out that it is a stable state blocking the binding cavity of G-protein. This allosteric coupling between ICL3 opening/closure and ligand binding site compression/expansion was further investigated by imposing specific distance constraints on the ligand binding site of the receptor. A total of seven constraints were applied between the residues on helices 3, 5, 6 and 7 that form the binding pocket. Specifically, these constraints were between residue couples Ser203Oγ-Asp113Cγ, Ser204Oγ-Asp113Cγ, Ser207Oγ-Asp113Cγ, Asn293Cβ-Asp113Cβ, Phe289Cβ-Asp113Cβ, Asn312Cβ-Asp113Cβ, and Phe289Cβ-Asp312Cβ. Constraining the binding site to an open position forced ICL3 to close from its fully open position. Constraining the binding site to a relatively closed position kept ICL3 around its open form. Using one extra constraint on backbone atoms (between residues Ser207Cα-Asp113Cα of helices 5 and 3) facilitated the opening of the binding site, and thus accelerated the closure of ICL3 from a relatively open position. However, attempting to compress the binding pocket did not lead to a fully open ICL3. Through this work, the allosteric coupling between the ligand binding regions in the extracellular parts of H5 and H6 and the intracellular part of the receptor including ICL3