Research Outputs

Now showing 1 - 10 of 25

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A genetic approach to reveal determinants of mitochondrial tail-anchorde protein targeting
(Koç University, 2016) Keskin, Abdurrahman; Dunn, Cory David; 0000-0003-2393-5944; Koç University Graduate School of Sciences and Engineering; Molecular Biology and Genetics
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A knowledge-based approach to predict protein torsion angles
(Koç University, 2007) Tunca, Güzin; Erman, Burak; 0000-0002-2496-6059; Koç University Graduate School of Sciences and Engineering; Computational Sciences and Engineering; 179997
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A Two-stage mathematical programming algorithm for predicting secondary structures of proteins
(Koç University, 2003) Yılmaz, Özlem; Savaş, Selçuk; Türkay, Metin; 0000-0003-4769-6714; Koç University Graduate School of Sciences and Engineering; Industrial Engineering; 24956
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Binding and mode coupling of proteins
(Koç University, 2010) Gür, Mert; Erman, Burak; 0000-0002-2496-6059; Koç University Graduate School of Sciences and Engineering; Computational Sciences and Engineering; 179997
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Character-level tagging
(Koç University, 2016) Kuru, Onur; Oğuz, Ceyda; 0000-0003-0994-1758; Koç University Graduate School of Sciences and Engineering; Computer Science and Engineering; 6033
Open Access
Comparative effects of oncogenic mutations G12C, G12V, G13D, and Q61H on local conformations and dynamics of K-Ras
(Elsevier, 2020) Vatansever, Sezen; Gümüş, Zeynep H.; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997
K-Ras is the most frequently mutated protein in human cancers. However, until very recently, its oncogenic mutants were viewed as undruggable. To develop inhibitors that directly target oncogenic K-Ras mutants, we need to understand both their mutant-specific and pan-mutant dynamics and conformations. Recently, we have investigated how the most frequently observed K-Ras mutation in cancer patients, G12D, changes its local dynamics and conformations (Vatansever et al., 2019). Here, we extend our analysis to study and compare the local effects of other frequently observed oncogenic mutations, G12C, G12V, G13D and Q61H. For this purpose, we have performed Molecular Dynamics (MD) simulations of each mutant when active (GTP-bound) and inactive (GDP-bound), analyzed their trajectories, and compared how each mutant changes local residue conformations, inter-protein distance distributions, local flexibility and residue pair correlated motions. Our results reveal that in the four active oncogenic mutants we have studied, the α2 helix moves closer to the C-terminal of the α3 helix. However, P-loop mutations cause α3 helix to move away from Loop7, and only G12 mutations change the local conformational state populations of the protein. Furthermore, the motions of coupled residues are mutant-specific: G12 mutations lead to new negative correlations between residue motions, while Q61H destroys them. Overall, our findings on the local conformational states and protein dynamics of oncogenic K-Ras mutants can provide insights for both mutant-selective and pan-mutant targeted inhibition efforts.
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Computational and experimental investigation of Ras homodimer formation, ras-effector interactions and ras shuttling
(Koç University, 2018) Muratcıoğlu, Serena; Keskin, Özlem; 0000-0002-4202-4049; Koç University Graduate School of Sciences and Engineering; Chemical and Biological Engineering; 26605
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Computational design of a pentapeptide inhibitor for fibroblast growth factor receptor (FGFR3) IIIB
(Koç University, 2011) Öztürk, Mehmet Ali; Erman, Burak; 0000-0002-2496-6059; Koç University Graduate School of Sciences and Engineering; Computational Sciences and Engineering; 179997
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Conformation of peptides in the unfolded state: a coarse-grained model representation
(Koç University, 2007) Engin, Özge; Erman, Burak; Sayar, Mehmet; 0000-0002-2496-6059; 0000-0003-0553-0353; Koç University Graduate School of Sciences and Engineering; Computational Sciences and Engineering; 179997; 109820
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De novo peptide design strategies
(Koç University, 2011) Ünal, Evrim Besray; Erman, Burak; Gürsoy, Attila; 0000-0002-2496-6059; 0000-0002-2297-2113; Koç University Graduate School of Sciences and Engineering; Computational Sciences and Engineering; 179997; 8745

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