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Browsing M.S. Theses by Author "Haliloğlu, Türkan."

Browsing M.S. Theses by Author "Haliloğlu, Türkan."

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  • A mechanistic view of cullin neddylation: allosteric conformational control of E3-ring ligases 
    Yıldırım, Melis. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2014., 2014.)
    Cullin-RING E3 ligases (CRLs), which constitute a superfamily of RING type E3 ligases, regulate ~20% of protein degradation by the ubiquitin-proteasome system in the cells. Cullin neddylation activates CRLs by urging a ...
  • A mechanistic view on rRNA - antibiotics binding 
    Güneş, Mehmet Ünal. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2011., 2011.)
    The ribosome, which is the macromolecular machine for protein synthesis, is one of the most striking targets for the antimicrobial drugs. Antibiotics that block the protein synthesis in various ways in ribosome have different ...
  • A study on protein conformational transitions by Monte Carlo simulations 
    Aydın, Bahar. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2010., 2010.)
    Exploration of conformational transitions between two different conformational states of proteins reveals significant information about their action mechanism and function. In this thesis, the recently developed anisotropic ...
  • Allosteric communication in biding domain of nicotinic acetylcholine receptor 
    Tuna, Levent. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2006., 2006.)
    Allosteric interactions have been thought to be of great importance in regulating the gating mechanism of the receptors. The term allostery comes from the Greek words allos, "other," and stereos, "shape”, meaning that ...
  • Collective dynamics of protein complex structures : scoring and prediction 
    Özsezen, Serdar. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2015., 2015.)
    Docking algorithms are widely used in determination of protein complex structures. In order to determine which structure is the most similar to native one, ranking algorithms are used in docking studies. Each year both ...
  • Determination of protein-protein binding sites using machine learning tools 
    Sümbül, Fidan. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    Protein-protein interactions are involved in almost all biological processes. Thus, the understanding of the principles underlying these interactions is of great significance. This is mainly to identify the functional sites ...
  • Dynamic analysis of sumo conjugation cascade by molecular modeling and simulations 
    Karaca, Ezgi. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    Ubiquitin (Ub) and ubiquitin like modifiers (Ubls) are proteins, which facilitate post-translational modification (PTM) of proteins. A PTM involves Ub/Ubl conjugation on to a specific target. In order to modify targets, ...
  • Dynamic nature of H1N1 influenza virus hemagglutinin 
    Erge Akbaş, Zeynep. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2014., 2014.)
    Dynamics of antigenic and host receptor binding behavior of a virus binding protein can be altered via mutations that lead to escape from immune recognition. The main focus of this study is to investigate the dynamic ...
  • Exploring functional motions of muscarinic acetlcholine M2 receptor 
    Yücel, Burcu Özden. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2018., 2018.)
    G-Protein Coupled Receptors (GPCRs) are the largest family of signaling pro teins and a better understanding of dynamics underlying functional mechanism is es sential in drug design. Although many studies have been performed ...
  • Gating mechanism in nicotinic acetylcholine receptor channel 
    Karadağ, Serkan. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2006., 2006.)
    Nicotinic acetylcholine receptor (nAChR) is a ligand gated ion channel. Aberrations of nAChR is the primary reason of many congenital myasthenic syndromes. The mechanism behind the function of nAChRs is still unclear. In ...
  • Hinge prediction using elastic network models 
    Emekli, Uğur. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2006., 2006.)
    The motion and interaction of rigid parts in a protein connected by hingers are important for the function of the protein. This makes identification of the hinge region particularly important. In this work a method and web ...
  • How intrinsic dynamics and allostery in G-protein coupled receptors (GPCRS) define functional selectivity? 
    Duman, Özge. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2020., 2020.)
    G-protein Coupled Receptors (GPCRs) are the largest family of the of sensory proteins which play an important role in many diseases related to signaling pathways. Thus, understanding GPCR activation mechanism is a corner ...
  • Investigation of conformational fluctuations in protein dynamics: torsional Gaussian Network Model 
    Özbakır, Harun Ferit. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2012., 2012.)
    Elastic network models based on Normal Mode Analysis (NMA) are very useful in determining the conformational fluctuations that would affect the functions of proteins. Gaussian Network Model (GNM) is proved to be a very ...
  • Investigation of dynamic allostery in motor proteins 
    Kaya, Cihan. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2013., 2013.)
    Allostery is a key concept in regulation of protein function. The communication pathways which are equivalent of the allosteric signaling or energy propagation pathways are the most significant aspect of allosteric mechanism. ...
  • Investigation of noncanonical Wnt signaling network in C. elegans 
    Alazi, Feras. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2009., 2009.)
    Wnt proteins, a well conserved family of signalling molecules, initiate signalling mechanisms that play important roles in embryonic development of animals. Wnt proteins activate three distinct signalling pathways. ...
  • Ligand docking to proteins undergoing large conformational changes 
    Üçkan, Damla. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2019., 2019.)
    Conformational transitions and ligand binding to the enzyme adenylate kinase were investigated by computational docking. Autodock was used to investigate the dynamics of 92 atomistic conformers, which have been previously ...
  • Molecular dynamics of substrate recognition and co-evolution in HIV-1 protease 
    Özen, Ayşegül. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    Human Immunodeficiency Virus Type 1 (HIV-1) protease recognizes at least ten cleavage sites as its natural substrates. There is little sequence homology between these substrates and they are asymmetric around the cleavage ...
  • Monte Carlo (MC) path generation and small-world network approach to identify functional residues in proteins 
    Armutlulu, Andaç. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2009., 2009.)
    Allosteric mechanism of proteins is crucial for their proper functioning. An important aspect underlying this mechanism is the communication pathways connecting the regulatory and active sites of proteins. Monte Carlo (MC) ...
  • Packing regularities in folded proteins 
    Bağcı, Elife Zerrin. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2001., 2001.)
    Using lattice models of proteins is a common method to reduce conformational space. Despite the suitability of various lattice geometries, the optimal packing geometry of residues in folded structures, or the generic ...
  • Prediction of allosteric key residues and their role in protein folding 
    Ekesan, Şölen. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2009., 2009.)
    Allostery, an aspect of protein dynamics, is crucial in regulation of protein activity. It is believed that allostery is maintained through communication pathways of key residues residing within distant allosteric sites. ...

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