Turkan Haliloglu

 

Professor in Department of Chemical Engineering

Director of Polymer Research Center

Education

1989 -1992: Ph. D., Chemical Engineering, Bogazici University, Istanbul.

1987-1989: M. S., Chemical Engineering, Bogazici University, Istanbul.

1982-1987: B. S., Chemical Engineering, Bogazici University, Istanbul.

Research Activities

Visiting Scientist at National Cancer Institute /National Instititute of Health (Frederict, USA), short visits, 2002-2008.

Visiting Scientist at Danold Danforth Science Center (St Louis, USA), Department of Bioinformatics and Computational Genomics, summers of 2000, 2001

Visiting Scientist at the University of Akron, Institute of Polymer Science, summers of 1994-1999

Post-Doctorate at the University of Akron, Institute of Polymer Science, 1992-1993

Awards

2012 Selected Member, Science Academy, Turkey

2006 Selected Associate Member, Turkish Academy of Sciences

2001 Distinguished Young Scientist, Turkish Academy of Sciences

2000 Outstanding Achievement in Research Prize, Bogazici University

1996 Chemistry Award (nationwide) for Young Scientists from TUBITAK (Turkish National Science and Technology Foundation)

Research Areas

Theory and computations of biomolecular structure and dynamics; sequence-structure-function relationship. Protein motion and allostery. Physical principles and molecular mechanisms in biochemical/biophysical processes. Binding, communication and regulation/control. Membrane proteins, channels. Design principles for protein engineering and interactions. Sequence variations and diseases. Drug Design. Structural bioinformatics. Computational technologies. Statistical mechanics of polymers, polymer dynamics.

Publications

Onel M, Sumbul F, Liu J, Nussinov R, Haliloglu T, "Cullin neddylation may allosterically tune polyubiquitin chain length and topology", Biochem J., 474 (5): 781-795, 2017.

Soner S, Ozbek P, Garzon JI, Ben-Tal N, Haliloglu T, "DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex's Dynamics", PLoS Comput Biol., 11 (10): e1004461, 2015.

Padan E, Danieli T, Keren Y, Alkoby D, Masrati G, Haliloglu T, Ben-Tal N, Rimon A., "NhaA antiporter functions using 10 helices, and an additional 2 contribute to assembly/stability", Proc Natl Acad Sci U S A., 112 (41): E5575-82, 2015.

Sumbul F, Acuner-Ozbabacan SE, Haliloglu T, "Allosteric Dynamic Control of Binding", Biophys J., 1 109 (6): 1190-201, 2015. 

Yoon SW, Chen N, Ducatez MF, McBride R, Barman S, Fabrizio TP, Webster RG, Haliloglu T, Paulson JC, Russell CJ, Hertz T, Ben-Tal N, Webby RJ, "Changes to the dynamic nature of hemagglutinin and the emergence of the 2009 pandemic H1N1 influenza virus", Sci Rep., 5: 12828, 2015.

Haliloglu T, Bahar I, "Adaptability of protein structures to enable functional interactions and evolutionary implications", Curr Opin Struct Biol., 35: 17-23, 2015.

Ozer N., Ozen A., Schiffer C.A. and Haliloglu1 T. "Drug-resistant HIV-1 protease regains functional dynamics through cleavage site coevolution", Evolutionary Applications, 8 (2), 185-198, 2015.

Gofman Y., Schärfe C., Marks D.S., Haliloglu T., Ben-Tal N. "Structure, Dynamics and Implied Gating Mechanism of a Human Cyclic Nucleotide-Gated Channel", PLOS Computational Biology, 10 (12), e1003976, 2014.

Sahillioglu A.C., Sumbul F., Ozoren N., Haliloglu T. "Structural and Dynamics Aspects of ASC Speck Assembly", Structure, 22, 1722-1734, 2014.

Uyar A., Kantarci-Carsibasi N., Haliloglu T., Doruker P. "Features of Large Hinge-Bending Conformational Transitions. Prediction of Closed Structure from Open State", Biophysical Journal, 106, 2656–2666, 2014.

Stapleford KA, Coffey LL, Lay S, Borderia AV, Duong V, Isakov O, Rozen-Gagnon K, Arias-Goeta C, Blanc H, Beaucourt S, Haliloglu T, Schmitt C, Bonne I, Ben-Tal N, Shomron N, Failloux AB, Buchy P, Vignuzzi M, "Emergence and transmission of arbovirus evolutionary intermediates with epidemic potential", Cell Host Microbe., 15 (6): 706-16, 2014.

Ozbek P., Soner S., Haliloglu T. "Hot spots in a network of functional sites", PLoS One, 8 (9), e74320, 2013.

Aykac Fas B., Tutar Y., Haliloglu T. "Dynamic Fluctuations Provide the Basis of a Conformational Switch Mechanism in Apo Cyclic AMP Receptor Protein", PLoS Computational Biology, 9 (7), e10031412013, 2013.

Kaya C., Armutlulu A., Ekesan S. and Haliloglu T. "MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues", Nucleic Acids Research, 41, (Web Server Issue), w429-w255, 2013.

Gofman Y, Shats S, Attali B, Haliloglu T, Ben-Tal N. "How does KCNE1 regulate the Kv7.1 potassium channel? Model-structure, mutations, and dynamics of the Kv7.1-KCNE1 complex", Structure, 20 (8): 1343-52, 2012.

King NM, Prabu-Jeyabalan M, Bandaranayake RM, Nalam MN, Nalivaika EA, Ozen A, Haliloglu T, Yilmaz NK, Schiffer CA, "Extreme entropy-enthalpy compensation in a drug-resistant variant of HIV-1 protease", ACS Chem Biol., 7 (9): 1536-46, 2012.

Gofman Y, Haliloglu T, Ben-Tal N, "Monte Carlo simulations of peptide-membrane interactions with the MCPep web server", Nucleic Acids Res.(Web Server issue): W358-63, 2012.

Korkmaz EN, Nussinov R, Haliloglu T, "Conformational control of the binding of the transactivation domain of the MLL protein and c-Myb to the KIX domain of CREB", PLoS Comput Biol., e1002420, 2012.

Schushan M, Rimon A, Haliloglu T, Forrest LR, Padan E, Ben-Tal N, "A model-structure of a periplasm-facing state of the NhaA antiporter suggests the molecular underpinnings of pH-induced conformational changes", J Biol Chem, 287 (22): 18249-61, 2012.

Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Azé J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodríguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D, "Community-wide assessment of protein-interface modeling suggests improvements to design methodology", J Mol Biol., 414 (2): 289-302, 2011.

Ozen A, Haliloglu T, Schiffer CA, "Dynamics of preferential substrate recognition in HIV-1 protease: redefining the substrate envelope", J Mol Biol., 410 (4): 726-44, 2011.

Ma B, Tsai CJ, Haliloglu T, Nussinov R, "Dynamic allostery: linkers are not merely flexible", Structure, 19 (7): 907-17, 2011.

Karaca E, Tozluoglu M, Nussinov R, Haliloglu T, "Alternative allosteric mechanisms can regulate the substrate and E2 in SUMO conjugation", J Mol Biol., 406 (4): 620-30, 2011.

Tozluoglu M, Karaca E, Nussinov R, Haliloglu T, "A mechanistic view of the role of E3 in sumoylation", PLoS Comput Biol., 6 (8), 2010.

Ozer N, Schiffer CA, Haliloglu T, "Rationale for more diverse inhibitors in competition with substrates in HIV-1 protease", Biophys J., 99 (5): 1650-9, 2010.

Haliloglu T, Gul A, Erman B, "Predicting Important Residues and Interaction Pathways in Proteins Using Gaussian Network Model: Binding and Stability of HLA Proteins", PLoS Comput Biol, 6 (7) e1000845, 2010.

Wainreb G, Ashkenazy H, Bromberg Y, Starovolsky-Shitrit A, Haliloglu T, Ruppin E, Avraham KB, Rost B, Ben-Tal N, "MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data", Nucleic Acids Res (Web Server Issue), W523-8, 2010.

Schushan M, Barkan Y, Haliloglu T, Ben-Tal N, "C (alpha)-trace model of the transmembrane domain of human copper transporter 1, motion and functional implications", Proc Natl Acad Sci U S A, 107 (24), 10908-13, 2010.

Yeheskel A, Haliloglu T, Ben-Tal N, "Independent and cooperative motions of the Kv1.2 channel: voltage sensing and gating", Biophys J, 98 (10) 2179-88, 2010.

Ozbek P, Soner S, Erman B, Haliloglu T, "DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues", Nucleic Acids Res (Web Server Issue), 38, W417-23, 2010.

Yavuzturk, M., Karaca, E., Nussinov, R., Haliloglu, T., "Mechanistic View of the Role of E3 in SumoylationMechanistic View of the Role of E3 in Sumoylation", Plos Comp Biol, in press, 2010.

Ozer, N., Schiffer, C.A., Haliloglu, T. "Rationale for more diverse inhibitors in competition with substrates in HIV-1 protease", Biophysical Journal, in press, 2010.

Ozen, A, Gvnen, M, Alpaydan, E, Haliloglu, T, "Machine learning integration for predicting the effect of single amino acid substitutions on protein stability", BMC Struct Biol, 19 (9): 66, 2009.

Ulutas B, Haliloglu T, Bozma I, "Folding pathways explored with artificial potential functions", Phys Biol, 19 (9), 66, 2009.

Haliloglu, T, Erman, B, "Analysis of Correlations between Energy and Residue Fluctuations in Native Proteins and Determination of Specific Sites for Binding", Physical Review Letters, 102 (8), 0088103, 2009.

Kantarci-Carsibasi N., Haliloglu, T., Doruker, P., "Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes", Biophysical Journal, 95 (12), 5862-73, 2008.

Haliloglu, T., Ben-Tal, N., "Cooperative Transition between Open and Closed Conformations in Potassium Channels", PLoS Computational Biology, 29, 4, 2008.

Tozluoglu M, Karaca E, Haliloglu T, Nussinov R., "Catologing and organizing p73 interactions in cell cycle arrest and apoptosis", Nucleic Acid Res, 36, 5033-49, 2008.

Haliloglu T, Seyrek E, Erman B, "Prediction of Binding Sites in Receptor-Ligand Complex with the Gaussian Network Model", Physical Review Letters, 100 (22), 228102, 2008.

Emekli U, Gunasekaran K, Nussinov R, Haliloglu, T, "What can we learn from highly connected beta-rich structures for structural interface design?", Methods Mol Biol., 474: 235-53, 2008.

Emekli U., Scheidman-Duhovny D., Wolfson H.J., Nussinov R., Haliloglu T., "HingeProt: Automated Prediction of Hinges in Protein Structures", Proteins: Structure, Function, and Bioinformatics, 70, 1219-1227, 2008.

Shental-Bechor D., Haliloglu T., Ben-Tal N., "Interactions of cationic-hydrophobic peptides with lipid bilayers: A Monte Carlo simulation method", Biophysical Journal, 93, 1858-1871, 2007.

Ertekin A., Nussinov R., Haliloglu T., "Association of Putative Protein Binding Sites with the Fluctuation Behavior of Residues", Protein Science, 15, 2265-2277, 2006.

Kantarci N., Doruker P., Haliloglu T., "Cooperative Fluctuations Point to the Dimerization Interface of p53 Core Domain", Biophysical Journal, 91, 421-432, 2006.

Ozer N., Haliloglu T., Schiffer C.A., "Substrate Specificity in HIV-1 Protease by a Biased Sequence Search Method", Proteins-Structure Function And Bioinformatics, 64, 444-456, 2006.

Kantarci N, Tamerler C, Sarikaya M, et al. "Molecular dynamics simulations on constraint metal binding peptides", Polymer, 46 (12), 4307-4313, 2005.

Konuklar FAS, Aviyente V, Haliloglu T, "Coupling of Structural Fluctuations to Deamidation Reaction in Triosephosphate Isomerase by Gaussian Network Modelj, Proteins, 62, 715-727, 2006.

Shental-Bechor D, Kirca S, Ben-Tal N, Haliloglu T, "Monte Carlo Studies of Folding, Dynamic and Stability in alpha-Helices", Biophysical Journal, 88 (4): 2391-2402, 2005.

Haliloglu T, Keskin O, Ma B, Nussinov R, "How similar are protein folding and protein binding nuclei? Examination of fluctuations of energy hot spots and conserved residues", Biophysical Journal, 88, 3, 1552-1559, 2005.

Kessel, A., Haliloglu, T., Ben-Tal, N, "Interaction of M2d Segment of the Acetylcholine Receptor with Lipid Bilayers: A Continuum Solvent Model Study", Biophysical Journal, 85, 3687-3695, 2003.

Kessel, A., Haliloglu, T., Ben-Tal, N, "Interaction of Hydrophobic Peptides with Lipid Bilayers: Monte Carlo Simulations with M2d", Biophysical Journal, 85, 3431-3444, 2003.

Haliloglu, T, Kolinski, A, Skolnick, J, "Use of NMR Residual Dipolar Coupling (RDCs) as Restraints in ab initio Structure Prediction", Biopolymers, 70, 548-562, 2003.

Kurt, N., Halilogu, T, Schiffer, C, "Structure-Based Prediction of Potential Binding and Non-Binding Peptides to HIV-1 Protease", Biophysical Journal, 864-863, 2003.

Ozkan SB, Dalgyn GS, Haliloglu T, "Unfolding events of Chymotrypsin Inhibitor 2 (CI2)revealed by Monte Carlo (MC) simulations and their consistency from structure-based analysis of conformations", POLYMER 45 (2): 581-595 JAN 15, 2004.

Kurt, N., Walter, R. P. S., Schiffer, C.A., Haliloglu T., "Vibrational dynamics of unliganded and substrate-bound HIV-1 protease: A structure-based analysis on a variety of conformations from chrystallography and molecular dynamics simulations", Proteins, 51, 409-422, 2003.

Kurt, N., Haliloglu, T., "Distribution of Cooperative Interactions in Barnase at Different Time Windows by Coarse-grained simulations", Polymer, 43, 403-408, 2002.

Kurt, N, Haliloglu, T., "Conformational Dynamics of Subtilisin-Chymotrypsin Inhibitor 2 Complex by Coarse-Grained Simulations", Journal of Biomolecular Stucture and Dynamics, 18 (5), 713-731, 2001.

Haliloglu, T., Bahar, I., Jernigan, R. L., "Collective dynamics of class I MHC/peptide complexes and binding to T cell receptors", Biophys. J., 78, 34A, 2000.

Jang, J. J., Haliloglu, T., von Meerwall, E. D., and Mattice W. L., "Effect of Vinyl Content on Self-Diffusion in Polybutadiene Melts", Macromolecules, 33 (11), 4271-4277, 2000.

Haliloglu, T., Mattice, W. L., "Simulation of Rotational Isomeric State Models for Polypropylene Melts in a High Coordination Lattice", Reviews in Chemical Engineering, 15, No: 4, 1999.

Haliloglu, T., Bahar, I., "Structure-Based Characterization of Protein Dynamics. Results for Hen Lysozyme in Comparison with X-ray Diffraction and NMR Relaxation Data", Proteins: Structure, Function and Genetics, 37, 654-667, 1999.

Kurt, N., Haliloglu, T., "Conformational Dynamics of Chymotrypsin Inhibitor 2 by Coarse-Grained Simulations", Proteins: Structure, Function and Genetics, 37, 454-464, 1999.

Haliloglu, T., "Conformational Dynamics of Cytochrome c by Coarse-Grained Simulations", Polymer Preprints, 81, 155, 1999.

Haliloglu, T., Mattice, W. L., "Detection of the onset of demixing in simulations of polypropylene melts in which the chains differ only in stereochemical composition", J. Chem. Phys., 111 (9), 4327-4333, 1999.

Haliloglu, T., "Coarse-Grained Simulations of Conformational Dynamics of Proteins", Theoretical and Computational Polymer Science, 9/3-4, 255-260, 1999.

Haliloglu, T., "Characterization of Internal Motions of Escherichia coli Ribonuclease H by Monte Carlo Simulation", Proteins: Structure, Function and Genetics, 34, 533-539, 1999.

Haliloglu, T., Cho, J., Mattice, W. L., "Simulation of Rotational Isomeric State Chains with Asymmetric Torsional Potential Energy Functions on a High Coordination Lattice in Bulk State", Macromolecular Theory and Simulations, 7, 613-617, 1998.

Haliloglu, T., Cho, J., Mattice, W. L., "Simulation of Rotational Isomeric State Models for Polypropylene Melts on a High Coordination Lattice", Polymer Preprints, 78, 259-260, 1998.

Atilgan, A., Haliloglu, T., Bahar, I., Erman, B., "Correlated Fluctuations in Polymer Networks", Theoretical and Computational Polymer Science, 8, 55-59, 1998.

Haliloglu, T., Mattice, W. L., "Mapping of Rotational Isomeric State Chains with Asymmetric Torsional Potential Energy Functions on a High Coordination Lattice", Application to Polyproplylene, J. Chem. Phys., 108, 6989-6995, 1998.

Haliloglu, T., Bahar, I., "Coarse-Grained Simulations of Conformational Dynamics of Proteins: Application to Apomyoglobin", Proteins: Structure, Function and Genetics, 31, 271-281, 1998.

Bahar, I., Erman, B., Haliloglu, T., Jernigan, R. L., "Coarse-Grained Simulations of Collective Motions in Protein. T4 Lysozyme", Biochemistry, 36, 3512-3513, 1997.

Haliloglu, T., Bahar, I., Erman, B., "Relative Contributions of Coupled Rotations and Small Amplitude Torsion to Conformational Relaxation in Polymers", Polymer Preprints, 213, 292-COMP, 1997.

Haliloglu. T., Bahar, I., Erman, B., "Gaussian Dynamics of Folded Proteins", Pysical Review Letters, 79, 3090-3093, 1997.

Haliloglu, T., Mattice, W. L., "Conformational Transitions of End-Adsorbed triblock Copolymers in a nonselective Solvent", Macromolecular Theory and Simulations, 6, 667-677, 1997.

Bahar, I., Doruker, P., Erman, B., Haliloglu, T., Kim, Eung-Gun, Mattice, W. L., Monnerie, L., Rapold, R. F., "Three aproaches that may permit more efficient simulation of the dynamics of atomistic models of polymers", Trends in Polymer Science, 5, 155-160, 1997.

Haliloglu, T., Stevenson, D., Mattice, W. L., "Adsorption of Triblocks in nonselective solvent", J. Chem. Phys., 106, 3365-3369, 1997.

Haliloglu, T. , Bahar, I., Erman, B. Mattice, W. L., "Relative Contributions of Coupled Rotations and Small Amplitude Torsions to Conformational Relaxation in Polymers", Macromolecules, 29, 8942-8947, 1996.

Haliloglu, T., Mattice, W. L., "Monte Carlo Simulation of Self-Assembly in Macromolecular Systems", in NATO ASI, vol. 327, p.167-196, ed: S. Webber, Kluwer, 1996.

Haliloglu, T., Bahar, I., Erman, B., "The response of a single Grafted Chain to Shear Flow. A Brownian Dynamics Simulation Study", J. Chem. Phys., 105, 2919-2926, 1996.

Haliloglu, T., Bahar, I., Erman, B., Mattice, W. L., "Mechanisms of the Exchange of Diblock Copolymers between Micelles at Dynamic Equilibrium", Macromolecules, 29, 4764-4771, 1996.

Haliloglu, T., Bahar, I., Erman, B., Kim E. -G., "A Dynamic Rotational Isomeric State Approach for Extension of the Time Scale of the Local Dynamics Observed in Fully Atomostic Molecular Dynamics Simulations", J. Chem. Phys., 104, 4828-4834, 1996.

Haliloglu, T., Mattice, W. L., R "The Molecular Dynamics of poly (1, 4‐trans‐butadiene) in the amorphous state and in an inclusion complex", Macromolecular Symposia, 101, 435-442, 1995.

Haliloglu, T., Bahar, I., Erman B., "Dependence of Segmental Orientation on Polymer Conformational Characteristics", Polymer, 36, 4131-4134, 1995.

Haliloglu, T., Mattice, W. L., "The Roles of c and N on the Dynamics of the Exchange of Chains between Micelles Formed by Diblock Copolymers in Selective Solvents at Concentrations Slightly Above the Critical Micelle Concentration", Computational Polymer Science, 5, 65-70, 1995.

Haliloglu, T., Mattice, W. L., "Exchange of Chains between Micelles formed by Diblock Copolymers", ACS Polym. Prepr., 35 (1), 572-573, 1994.

Bahar, I., Erman, B., Haliloglu, T., "Role of Structural Heterogeneities on Segmental Orientation in Deformed Chains: Applications to Alternating Copolymers", Macromolecules, 27, 1703-1709, 1994.

Haliloglu, T., Mattice, W. L., "Monte Carlo Lattice Simulation of the Interchange of Chains between Micelles of Diblock CopolymersS", Journal of Chemical Engineering Science, 49, 2851-2857, 1994.

Haliloglu, T., Balaji, R., Mattice, W. L., "Mobility of Free Ends and Junction Points in a Lamellar Block CopolymerS", Macromolecules, 27, 1473-1476, 1994.

Haliloglu, T., Mattice, W. L., "Monte Carlo Lattice Simulation of the Exchange Chains between Micelles of Diblock Copolymerss", ACS Polym. Prepr., 34 (2), 460-461, 1993.

Haliloglu, T., Mattice, W. L., "Analysis of Orientation Auto- and Cross-Correlation Functions for Polyethylene in Inclusion Complex with PerhydrotriphenyleneS", Macromolecules, 26, 3137-3142, 1993.

Haliloglu, T., Erman, B., Bahar, I., "Orientational Mobility in Uniaxially Deformed Polymer Chains: A Brownian Dynamics Simulation Study", Polymer, 34, 440-442, 1993.

Haliloglu, T., Erman, B., Bahar, I., "Time Dependent Probability Distribution Functions for Orientational Motions of Segments in Polymer Chains", J. Chem. Phys., 97, 4438-4444, 1992.

Haliloglu, T., Bahar, I., Erman, B., "Orientational and Conformational Correlations in Deformed Polymer Chains with Fixed End-to-End Separation: A Brownian Dynamics Simulation Study", J. Chem. Phys., 97, 4428-4437, 1992.

Haliloglu, T., Bahar, I., Erman, B., "Segmental Orientation in Polyoxyethylene Chains", Computational Polymer Science, 1, 151-156, 1991.

Erman, B., Haliloglu, T., Bahar I., and Mark, James E., "Segmental Orientation in Uniaxially Deformed Networks", Macromolecules, 24, 901-907, 1991.
Last Updated: May 2017