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Browsing Kimya Mühendisliği by Author "Haliloğlu, Türkan."

Browsing Kimya Mühendisliği by Author "Haliloğlu, Türkan."

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  • 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. ...
  • Protein dynamics in deleterious and compensatory mutations 
    Kutlu, Yiğit. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2020., 2020.)
    Mutations are associated with many diseases (cancer, Alzheimer’s disease etc.). These disease-causing mutations are called deleterious mutations and their effects can be corrected by other mutations, i.e. compensatory ...
  • Recognition and binding processes in HIV-1 protease 
    Özer, Asuman Nevra. (Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    HIV-1 protease is a drug target against AIDS and understanding its molecu- lar recognition processes is important in development of drugs. Here, the combined computational methodologies used put three different perspectives ...
  • Segmental orientation and conformational dynamics of polymer chains 
    Haliloğlu, Türkan. (Thesis (Ph.D)- Bogazici University. Institute for Graduate Studies in Science and Engineering, 1992., 1992.)
    Various remarkable features of polymers, as compared with metallic and inorganic materials, arise from the fact that macromolecules can take up various conformations. The study of macromolecular conformations and dynamics ...
  • Structural dynamics of ABC transporters 
    Ersoy, Akarun Ayça. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022)
    The ATP-binding cassette transporters (ABC transporters) translocate sub strates across membranes by ATP binding and hydrolysis. To understand the com plex structural dynamics, transporters were investigated on three case ...
  • Structural dynamics of proteins in functional control 
    Özgüney, Rümeysa Büşra. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2020., 2020.)
    Manipulation of protein conformational ensembles are well-known phenomenon yielding the development of rational drug design strategies. As a novel contribution, the aim of this thesis is to mechanistically identify and ...
  • Structure and dynamics of catabolite gene activator protein by molecular modeling and simulations 
    Fas, Ayşe Burcu Aykaç. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    The activities of proteins are regulated by interactions with other molecules through various types of local to global motions. Such internal motions may occur at different time scales and involve complex correlations ...
  • Study of protein-protein interfaces using Gaussian network model 
    Soner, Seren. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2009., 2009.)
    The interface type of the proteins are useful in determining the functioning mechanism of proteins. The interface type may either be obligatory, non-obligatory or crystal (non biological). Previous studies have tried to ...
  • Subsets of slow dynamic modes reveal global information sources as allosteric sites 
    Altıntel, Bengi. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022)
    Allostery is a crucial biological regulation mechanism, and dynamic information flow offers a framework to characterize allosteric interactions in causal links. Here, using a novel application of the Transfer Entropy (TE) ...
  • Systems-level understanding of copper effect in Saccharomyces cerevisiae 
    Öç, Şebnem. (Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2019., 2019.)
    Copper is a crucial trace element for all living systems as it is required for the proper functioning of several biological processes. Copper homeostasis, which governs the mechanisms of copper uptake, delivery, utilization, ...
  • Tagging proteins: sumoylation mechanism by molecular modeling and molecular dynamics simulations 
    Korkmaz, Elif Nihal. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2010., 2010.)
    Sumoylation, the covalent attachment of SUMO (Small Ubiquitin Like Modifier) to target proteins is a posttranslational modification that can alter intracellular localization, interactions with other proteins or result in ...
  • The dynamics underlying enhancement of E2 ligase activity by E3 ligases in sumoylation 
    Tozluoğlu, Melda. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    Covalent attachment of SUMO (Small Ubiquitin Like Modifier) to proteins, sumoylation, is a posttranslational modification that can alter intracellular localization, interactions with other proteins or lead to modifications ...
  • 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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