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Browsing M.S. Theses by Author "Turgut, Pemra Doruker."

Browsing M.S. Theses by Author "Turgut, Pemra Doruker."

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  • A computational approach for analysis of communication in proteins 
    Özel, Sinem. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2007., 2007.)
    Allostery and communication in proteins are crucial for the regulation of protein functions. The binding of a ligand changes the affinity of the protein at a distal ligand binding site and leads to conformational changes ...
  • A computational study on bacterial trigger factor and ribosome dynamics 
    Ezeroğlu, Gökçe. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2014., 2014.)
    Trigger factor (TF), found in bacterial cells and chloroplasts, is the first chaperone that welcomes the newly synthesized nascent polypeptide chains to acquire their native fold. In this thesis, four independent 200 ns ...
  • 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 ...
  • An in silico study on ribosome-binding trigger factor 
    Can, Mehmet Tarık. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2013., 2013.)
    The trigger factor protein (TF), unique to bacterial organisms, binds to ribosome tunnel mouth and works as a chaperone in helping the nascent chains emerging from the ribosome tunnel to acquire their native fold. A 500 ...
  • Analysis of cracking phenomena along conformational transition pathways of proteins 
    Meriçer, Çağlar. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2012., 2012.)
    The weighted ensemble (WE) methodology was incorporated into an iterative ANM-MC (Anisotropic network model- Monte Carlo) simulation algorithm, which has been developed to generating targeted conformational transition ...
  • Analysis of ligand binding effect on enzyme dynamics using elastic network models 
    Fındık, Hüseyin Doğa. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2015., 2015.)
    The objective of this thesis was to investigate the e ect of ligand binding on global vibrational modes of an enzyme, triosphosphate isomerase (TIM). For this aim, mixed coarse-grained elastic network model ENM (MCG ENM) ...
  • Collective dynamics and conformational sampling of triosephosphate isomerase 
    Cansu, Sertan. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    Molecular dynamics simulations (30-60 ns runs) are performed on free/apo triosephosphate isomerase (TIM) to determine any correlation between collective motions and loop 6 dynamics. Native TIM is active only as a homo-dimer ...
  • Conformational transitions of proteins using multi-scale modeling approaches 
    Uyar, Arzu. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2014., 2014.)
    A detailed analysis on a dataset consisting of 30 proteins was performed using a hybrid simulation technique. This iterative technique, named as ANM-MC, generates a targeted pathway between two conformations, where the ...
  • Effect of temperature on collective dynamics of proteins: a time series analysis 
    Türe, Özlem. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    Molecular Dynamics (MD) simulations are used to analyze the internal motions of proteins. In this thesis, the molecular dynamics trajectories of the apo form of dihydrofolate reductase (DHFR), and both apo and holo forms ...
  • Investigation of coupling between collective dynamics and function of enzymes 
    Kocaman, Duygu. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2011., 2011.)
    To bridge the structure and function of an enzyme through dynamics is an important problem in protein science. For this aim, the vibrational dynamics for a set of enzymes with different biological units and fold types are ...
  • Structure-function relationships of type II restriction endonucleases 
    Uyar, Arzu. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    Restriction endonucleases (REs) constitute an enzyme family, which can recognize and cleave specific foreign DNA sequences to protect prokaryotic cells. The vibrational dynamics of Type II REs are investigated by elastic ...
  • Trageted conformational transition pathways of large proteins by integrating elastic network modeling with Monte Carlo simulations 
    Yeşiltepe, Yasemin. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2017., 2017.)
    ANM-MC is a coarse-grained simulation technique, in which the anisotropic network model (ANM) generates the collective modes for deforming the protein structure towards target direction, and Monte Carlo (MC) algorithm ...

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