Canan Atılgan
  • FENS
  • Canan Atılgan

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E-Mail
canansabanciunivedu
Phone
(216) 483 9523
Personal Web
Title
Faculty Member
Jobs
Instructor
Education
B.Sc., M.Sc., and Ph.D. in Chemical Engineering, Bogazici University, 1991, 1993, and 1996, respectively.
Areas of Interest
Polymer and protein dynamics; theoretical and computational investigation of complex molecular systems.
Awards
  • Selected member - Science Academy, Istanbul  2012
  • L'Oréal Turkey For Woman In Science Young Woman Scientist Fellowship -  2005
  • Distinquished Young Scientist Award - urkish Academy of Sciences (TUBA)  2004
  • Encouragement Award - The Scientific and Technical Research Council of Turkey (TUBITAK)  2002
  • Bogazici University Ph.D. Thesis Award - Bogazici University  1996
Memberships
• American Chemical Society (2000 – ) • Biophysical Society (2001 – ) • Protein Society (2001 – 2008) • International Society for Computational Biology (2004 – 2008) • System Dynamics Society (2007) • Complex Systems Society (2007 – 2008)
Publications
  • Article
    Abdizadeh, Haleh and Tamer, Yusuf Talha and Acar, Ömer and Toprak, Erdal and Atılgan, Ali Rana and Atılgan, Canan (2017) "Increased substrate affinity in the escherichia coli L28R dihydrofolate reductase mutant causes trimethoprim resistance", Physical Chemistry Chemical Physics, Vol.19, No.18, 11416-11428 ()
    Furuncuoğlu Özaltın, Tuğba and Aviyente, Viktorya and Atılgan, Canan and Demirel, Levent (2017) "Multiscale modeling of poly(2-isopropyl-2-oxazoline) chains in aqueous solution", European Polymer Journal, Vol.88, 594-604 (SCI)
    Özden-Yenigün, Elif and Atılgan, Canan and Elliott, James A. (2017) "Multi-scale modelling of carbon nanotube reinforced crosslinked interfaces", Computational Materials Science, Vol.129, 279-289 (SCI)
    Şensoy, Özge and Atılgan, Ali Rana and Atılgan, Canan (2017) "FbpA iron storage and release are governed by periplasmic microenvironments", Physical Chemistry Chemical Physics, Vol.19, No.8, 6064-6075 (SCI)
    Abdizadeh, Haleh and Atılgan, Canan (2016) "Predicting long term cooperativity and specific modulators of receptor interactions in human transferrin from dynamics within a single microstate", Physical Chemistry Chemical Physics, Vol.18, No.11, 7916-7926 (SCI)
    Abdizadeh, Haleh and Güven, Gökçe and Atılgan, Ali Rana and Atılgan, Canan (2015) "Perturbation response scanning specifies key regions in subtilisin serine protease for both function and stability", Journal of Enzyme Inhibition and Medicinal Chemistry, Vol.30, No.6, 867-873 (SCI)
    Özbaykal, Gizem and Atılgan, Ali Rana and Atılgan, Canan (2015) "In silico mutational studies of Hsp70 disclose sites with distinct functional attributes", Proteins: Structure, Function and Bioinformatics, Vol.83, No.11, 2077-2090 (SCI)
    Abdizadeh, Haleh and Atılgan, Ali Rana and Atılgan, Canan (2015) "Detailed molecular dynamics simulations of human transferrin provide insights into iron release dynamics at serum and endosomal pH", Journal of Biological Inorganic Chemistry, Vol.20, No.4, 705-718 (SCI)
    Güven, Gökçe and Atılgan, Ali Rana and Atılgan, Canan (2014) "Protonation states of remote residues affect binding-release dynamics of the ligand but not the conformation of apo ferric binding protein", Journal of Physical Chemistry B, Vol.118, No.40, 11677-11687 (SCI)
    Aykut, Ayşe Özlem and Atılgan, Ali Rana and Atılgan, Canan (2013) "Designing molecular dynamics simulations to shift populations of the conformational states of calmodulin", PLoS Computational Biology, Vol.9, No.12 (SCI)
    Özden-Yenigün, Elif and Şimşek, Eren and Menceloğlu, Yusuf Z. and Atılgan, Canan (2013) "Molecular basis for solvent dependent morphologies observed on electrosprayed surfaces", Physical Chemistry Chemical Physics, Vol.15, No.41, 17862-17872 (SCI)
    Atılgan, Canan and İnanç, İbrahim and Atılgan, Ali Rana (2012) "On modifying properties of polymeric melts by nanoscopic particles", Journal of Polymer Science Part B: Polymer Physics, Vol.50, No.23, 1653-1662 (SCI)
    Atılgan, Ali Rana and Atılgan, Canan (2012) "Local motifs in proteins combine to generate global functional moves", Briefings in Functional Genomics (Sl), Vol.11, No.6, 479-488 (SCI)
    Negi, Sunita and Aykut, Ayşe Özlem and Atılgan, Ali Rana and Atılgan, Canan (2012) "Calmodulin readily switches conformation upon protonating high pK(a) acidic residues", Journal of Physical Chemistry B, Vol.116, No.24, 7145-7153 (SCI)
    Atılgan, Canan and Okan, Osman Burak and Atılgan, Ali Rana (2012) "Network-based models as tools hinting at nonevident protein functionality", Annual Review of Biophysics, Vol.41, 205-225 (SCI)
    Özaltın, Furuncuoğlu T. and Değirmenci, İsa and Aviyente, Viktorya and Atılgan, Canan and De Sterck, B. and Van Speybroeck, V. and Waroquier, M. (2011) "Controlling the tacticity in the polymerization of n-isopropylacrylamide: a computational study", Polymer, Vol.52, No.24, 5503-5512 (SCI)
    Atılgan, Ali Rana and Aykut, Ayşe Özlem and Atılgan, Canan (2011) "Subtle pH differences trigger single residue motions for moderating conformations of calmodulin", Journal of Chemical Physics, Vol.135, No.15 (SCI)
    Atılgan, Canan and Okan, Osman Burak and Atılgan, Ali Rana (2010) "How orientational order governs collectivity of folded proteins", Proteins: Structure, Function, Bioinformatics, Vol.78, No.16, 3363-3375 (SCI)
    Turgut, Deniz and Atılgan, Ali Rana and Atılgan, Canan (2010) "Assortative mixing in close-packed spatial networks", PLoS One, Vol.5, No.12 (SCI)
    Meersman, Filip and Atılgan, Canan and Miles, Andrew J. and Bader, Reto and Shang, Weifeng and Matagne, Andre and Wallace, B. A. and Koch, Michel H. J. (2010) "Consistent picture of the reversible thermal unfolding of hen egg-white lysozyme from experiment and molecular dynamics", Biophysical Journal, Vol.99, No.7, 2255-2263 (SCI)
    Atılgan, Canan and Gerek, Z. N. and Özkan, S. B. and Atılgan, Ali Rana (2010) "Manipulation of conformational change in proteins by single-residue perturbations", Biophysical Journal, Vol.99, No.3, 933-943 (SCI)
    Servantie, James and Atılgan, Canan and Atılgan, Ali Rana (2010) "Depth dependent dynamics in the hydration shell of a protein", Journal of Chemical Physics, Vol.133, No.8 (SCI)
    Kaçar, Gökhan and Atılgan, Canan and Özen, Alimet Sema (2010) "Mapping and reverse-mapping of the morphologies for a molecular understanding of the self-assembly of fluorinated block copolymers", Journal of Physical Chemistry C, Vol.114, No.1, 370-382 (SCI)
    Topal, Kevser Göçmen and Atılgan, Canan and Demir, Ayhan S. and Aviyente, Viktorya (2010) "Understanding the mode of action of ThDP in benzoylformate decarboxylase", Biopolymers, Vol.93, No.1, 32-46 (SCI)
    Atılgan, Canan and Atılgan, Ali Rana (2009) "Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein", PLoS Computational Biology, Vol.5, No.10, 1-14 (SCI)
    Okan, Osman Burak and Atılgan, Ali Rana and Atılgan, Canan (2009) "Nanosecond motions in proteins impose bounds on the timescale distributions of local dynamics", Biophysical Journal, Vol.97, No.7, 2080-2088 (SCI)
    Can, Hatice and Kaçar, Gökhan and Atılgan, Canan (2009) "Surfactant formation efficiency of fluorocarbon-hydrocarbon oligomers in supercritical CO2", Journal of Chemical Physics, Vol.131, No.12 (SCI)
    Atılgan, Canan and Demirel, Güven and Atılgan, Ali Rana (2008) "Collective behavior of El Farol attendees", Advances in Complex Systems, Vol.11, No.4, 629-639 (SCI)
    Atılgan, Canan and Aykut, Ayşe Özlem and Atılgan, Ali Rana (2008) "How a vicinal layer of solvent modulates the dynamics of proteins", Biophysical Journal, Vol.94, 79-89 (SCI)
    Özen, Alimet Sema and Atılgan, Canan and Sönmez, Gürsel (2007) "Noncovalent intramolecular interactions in the monomers and oligomers of the acceptor and donor type of low band gap conducting polymers", Journal of Physical Chemistry C, Vol.111, No.44, 16362-16371 (SCI)
    Atılgan, Canan and Aviyente, Viktorya (2007) "Hybrid usage of computational tools in drug synthesis", Current Computer - Aided Drug Design, Vol.3, No.2, 149-159 (SCI)
    Atılgan, Ali Rana and Turgut, Deniz and Atılgan, Canan (2007) "Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication", Biophysical Journal, Vol.92, No.9, 3052-3062 (SCI)
    Atılgan, Ali Rana and Turgut, Deniz and Atılgan, Canan (2007) "A Few designed-in interactions imposed on chain connectivity are sufficient for robust residue communications ", Biophysical Journal , Vol.Suppl S, No.Abstract Issue, 217A-218A (SCI)
    Atılgan, Canan and Sezerman, Ayşe Özlem and Baloğlu, Çetin and Sirer, Irmak and Okan, Osman Burak and Atılgan, Ali Rana (2007) "Solvent mobility and surface group flexibility at the dynamical transition", Biophysical Journal, Vol.Suppl S, No.Abstract issue, 405A-406A (SCI)
    Özen, Alimet Sema and Şen, Ünal and Atılgan, Canan (2006) "Complete mapping of the morphologies of some linear and graft fluorinated co-oligomers in an aprotic solvent by dissipative particle dynamics", The Journal of chemical physics, Vol.124, No.6 (SCI)
    Bilgin, Nalan and Atılgan, Canan and Menceloğlu, Yusuf Z. (2005) "Synthesis of Fluorinated Segment Containing Oligomers for Supercritical CO2 Applications", Polymer, Vol.43, No.21, 5312-5322 (SCI)
    Baloğlu, Çetin and Baysal, Canan and Koch, Michel and Taralp, Alpay (2005) "Influence of Ph on the thermal gelation of food proteins modeled by a variable pD NMR study of lysozyme in D20", Abstracts of Papers of the American Chemical Society, Vol.229, U49-U49 (SCI)
    Baloğlu, Çetin and Baysal, Canan and Koch, Michel and Taralp, Alpay (2005) "Protein gelation impeded in the presence of vitamins: a kinetic study using NMR", Abstracts of Papers of the American Chemical Society, Vol.229, U49-U49 (SCI)
    Baloğlu, Çetin and Baysal, Canan and Koch, Michel H. J. and Taralp, Alpay (2005) "Food stability examined at the level of protein structure: NMR and molecular dynamics study of an egg-white protein", Abstracts of Papers of the American Chemical Society, Vol.229, U62-U62 (SCI)
    Okan, Osman Burak and Atılgan, Ali Rana and Baysal, Canan (2005) "Distribution of relaxation times on the pico-nano time scales for a functional protein (ABSTRACT)", Biophysical Journal, Vol.88, No.1, 16A-16A (SCI)
    Atılgan, Ali Rana and Atılgan, Canan (2004) "Thermodynamics of residue networks in folded proteins", WSEAS Transactions in Biology and Biomedicine, Vol.1, No.2, 205-209
    Duran, Dilek and Aviyente, Viktorya and Baysal, Canan (2004) "A computational approach to the synthesis of dirithromycin", Journal of molecular modeling, Vol.10, No.2, 94-101 (SCI)
    Yıldız, Burçin and Soydaner, Umut Mehmet Ali and Öztürk, Gözde İpek and Vakos, Helen T. and Baysal, Canan and Taralp, Alpay (2004) "Physico-chemical studies of food proteins facilitated using deuterium-labeled iodomethane and NMR spectroscopic analysis (Abstract)", Abstracts of Papers of the American Chemical Society, Vol.227, U36-U36 (SCI)
    Duran, Dilek and Aviyente, Viktorya and Baysal, Canan (2004) "Theoretical study of selective methylation in the synthesis of azithromycin", Journal of computer-aided molecular design, Vol.18, No.1, 1-11 (SCI)
    Kırmızıaltın, Serdal and Menceloğlu, Yusuf Z. and Baysal, Canan (2003) "New surfactants design for CO2 applications: molecular dynamics simulations of fluorocarbon-hydrocarbon oligomers", The Journal of chemical physics, Vol.119, No.9, 4953-4961 (SCI)
    Kırmızıaltın, Serdal and Baysal, Canan and Erman, Burak (2003) "Conformational properties of the bacterial polyester poly(3-hydroxy-5,8-decadienoate) ", Macromolecules, Vol.36, No.4, 1132-1137 (SCI)
    Doruker, Pemra and Bahar, Ivet and Baysal, Canan and Erman, Burak (2002) "Collective deformations in proteins determined by a mode analysis of molecular dynamics trajectories", Polymer, Vol.43, No.2, 431-439 (SCI)
    Baysal, Canan and Atılgan, Ali Rana (2001) "Coordination topology and stability for the native and binding conformers of chymotrypsin inhibitor 2", Proteins: Structure, Function, and Bioinformatics, Vol.45, No.1, 62-70 (SCI)
    Baysal, Canan and Atılgan, Ali Rana (2001) "Elucidating the structural mechanisms for biological activity of the chemokine family", Proteins: Structure, Function, and Bioinformatics, Vol.43, No.2, 150-160 (SCI)
    Baysal, Canan and Erman, Burak and Chu, Benjamin (2001) "Conformational features of poly(1,1-dihydroperfluorooctyl acrylate) and poly(vinyl acetate) diblock oligomers in supercritical carbon dioxide", Journal of Chemical Physics, Vol.114, No.12, 5444-5449 (SCI)
  • Papers in Conference Proceedings
    Abdizadeh, Haleh and Atılgan, Ali Rana and Atılgan, Canan, "Computational modeling of iron binding and release in human serum transferrin", 41st FEBS Congress on Molecular and Systems Biology for a Better Life, Wiley Online Library, September 2016, 73-73
    Abdizadeh, Haleh and Acar, Ömer and Güçlü, Tandaç Fürkan and Tamer, Yusuf Talha and Altınuşak, Tuğçe and Toprak, Erdal and Atılgan, Ali Rana and Atılgan, Canan, "Computational assessment of trimethoprim resistance in dihydrofolate reductase", 60th Annual Meeting of the Biophysical Society, Cell Press, February 2016, 47A-48A
    Abdizadeh, Haleh and Atılgan, Canan, "Mechanically hot spots correlate with cooperativity and function in human transferrin", 10th European-Biophysical-Societies-Association (EBSA) European Biophysics Congress, Springer, July 2015, S48-S48
    Özden Yenigün, Elif and Atılgan, Canan and Elliott, James, "Tuning interface via multi-scale modeling for superior carbon nanotube-polymer nanocomposites/ Yarns", 20th International Conference on Composite Materials (ICCM20), Copenhagen, Denmark: International Committee on Composite Materials, July 2015
    Özden Yenigün, Elif and Şimşek, Eren and Menceloğlu, Yusuf Z. and Atılgan, Canan, "Theoretical and experimental investigation of dual-scale roughness via electro-spraying", 246th National Meeting of the American-Chemical-Society (ACS), Washington, DC, USA: American Chemical Society, September 2013
    Atılgan, Ali Rana and Aykut, Ayşe Özlem and Atılgan, Canan, "Non-equilibrium fluctuation theorems, redundant paths in proteins, and elucidating conformational changes by single-residue perturbations", 57th Annual Meeting of the Biophysical-Society, Cambridge, MA, USA: Biophysical Society, January 2013, 70A-70A
    Atılgan, Canan and Güven, Gökçe and Atılgan, Ali Rana, "Structural basis of how ferric binding proteins utilize pH differences for controlled release of iron", 57th Annual Meeting of the Biophysical-Society, Cambridge, MA, USA: Biophysical Society, January 2013, 212A-212A
    Negi, Sunita and Atılgan, Ali Rana and Atılgan, Canan, "Driving calmodulin protein towards conformational shift by changing ionization states of select residues", Stocks, G. M. and Troparevsky, M. C. (eds.), 23rd IUPAP C20 Conference on Computational Physics (CCP 2011), Bristol, England: Institute of Physics, December 2012
    Atılgan, Canan and İnanç, İbrahim and Atılgan, Ali Rana, "Effect of van der Waals interaction strength and nanocluster size on the dynamical and mechanical properties of 1,4-cis-polybutadiene melts", Materials Research Society Fall Meeting 2011 , Boston: Materials Research Society, February 2012
    Özden Yenigün, Elif and Atılgan, Canan and Menceloğlu, Yusuf Z. and Papila, Melih, "Tracing the superior thermo-mechanical properties in nanocomposites of crosslinked fillers at the interface: molecular point of view", 15th European Conference on Composite Materials (ECCM15), Venice, Italy: European Society for Composite Materials 2012
    Aykut, Ayşe Özlem and Atılgan, Ali Rana and Atılgan, Canan, "Molecular recognition mechanisms of calmodulin examined by perturbation-response scanning", 2010 MRS Fall Meeting, UK: Cambridge University Press Academic and Professional Books 2011
    Özden Yenigün, Elif and Atılgan, Ali Rana and Bilge, Kaan and Menceloğlu, Yusuf Z. and Atılgan, Canan and Papila, Melih, "Designed-in molecular interactions lead to superior thermo-mechanical properties in nanocomposites", 2010 MRS Fall Meeting, UK: Cambridge University Press Academic and Professional Books 2011
    Atılgan, Canan and İnanç, İbrahim and Atılgan, Ali Rana, "Long-range structural regularities and collectivity of folded proteins", Levitz, P. and Metzler, R. and Reichman, D. (eds.), 2009 MRS Fall Meeting, Warrendale, PA: MRS (Materials Research Society) 2010
    Atılgan, Canan and Demirel, Güven and Atılgan, Ali Rana, "Landscape Dynamics of El Farol Attendees", The 2007 International Conference of the System Dynamics Society, Boston, Massachusetts, USA: System Dynamics Society, October 2007
  • Before SU Publications

    (selected; please see the personal web site for full list) C. Baysal, A. R. Atilgan, B. Erman, I. Bahar, "Molecular Dynamics Analysis of Coupling between Librational Motions and Isomeric Jumps in Chain Molecules," Macromolecules, 29, 2510-2514 (1996). C. Baysal, A. R. Atilgan, "Coordination Topology and Stability for the Native and Binding Conformers of Chymotrypsin Inhibitor 2," Proteins, 45, 62-70 (2001). C. Baysal, B. Erman, I. Bahar, F. Lauprêtre, L. Monnerie, "Local Dynamics of Bulk Polybutadienes of Various Microstructures: Comparison of Theory with NMR Measurements," Macromolecules, 30, 2058-2066 (1997). C. Baysal, H. Meirovitch, "Determination of the Stable Microstates of a Peptide from NOE Distance Constraints and Optimization of Atomic Solvation Parameters," J. Am. Chem. Soc., 120, 800-812 (1998).