| Faculty of Engineering and Natural Sciences

Ali Rana Atılgan Faculty of Engineering and Natural Sciences Faculty Member (216) 483 9525 aliranaatilgansabanciunivedu

Personal Web

http://people.sabanciuniv.edu/atilgan/

Jobs

Faculty Member

Education

Ph.D. in Aerospace Engineering, September 1989, Georgia Institute of Technology, Atlanta, Georgia, USA. M.S. in Aerospace Engineering, June 1987, Georgia Institute of Technology, Atlanta, Georgia, USA. B.S. in Aeronautical Engineering, June 1984, Istanbul Technical University, Istanbul, Turkey.

Areas of Interest

Physics of proteins • Dynamics of complex systems • Simulation models • Mechanics of materials • Fiber-Reinforced composite structures

Güçlü, Tandaç Fürkan and Atılgan, Ali Rana and Atılgan, Canan (2024) "Deciphering GB1's single mutational landscape: insights from MuMi analysis". Published Online First https://dx.doi.org/10.1021/acs.jpcb.4c04916

Kantarcıoğlu Mazmanoğlu, Işık and Gaszek, Ilona K. and Güçlü, Tandaç Fürkan and Yildiz, M. Sadik and Atılgan, Ali Rana and Toprak, Erdal and Atılgan, Canan (2024) "Structural shifts in TolC facilitate efflux-mediated β-lactam resistance", Communications Biology, Vol.7, No.1 (SCI)

Mesüm, Oğuz and Atılgan, Ali Rana and Kocuk, Burak (2024) "A stochastic programming approach to the antibiotics time machine problem", Mathematical Biosciences, Vol.372 (SCI)

Arlı, Cihan and Atılgan, Ali Rana and Mısırlıoğlu, Burç (2024) "Extended contributions to the pyroelectric effect in ferroelectric thin films", Applied Physics Letters, Vol.124, No.6 (SCI)

Çetin, Ebru and Güçlü, Tandaç Fürkan and Kantarcıoğlu, Işık and Gaszek, Ilona K. and Toprak, Erdal and Atılgan, Ali Rana and Dedeoglu, Burcu and Atılgan, Canan (2023) "Kinetic barrier to enzyme inhibition is manipulated by dynamical local interactions in E. coli DHFR", Journal of Chemical Information and Modeling, Vol.63, No.15, 4839-4849 (SCI)

Liu, Gökşin and Ekmen, Erhan and Jalalypour, Farzaneh and Mertens, Haydyn D. T. and Jeffries, Cy M. and Svergun, Dmitri and Atılgan, Ali Rana and Atılgan, Canan and Sayers, Zehra (2023) "Conformational multiplicity of bacterial ferric binding protein revealed by small angle x-ray scattering and molecular dynamics calculations", Journal of Chemical Physics, Vol.158, No.8 (SCI)

Arlı, Cihan and Atılgan, Ali Rana and Mısırlıoğlu, Burç (2023) "Volumetric effects in electrocaloric response of ferroelectric thin films", Journal of Materials Chemistry C, Vol.11, No.3, 1134-1143 (SCI)

Çetin, Ebru and Atılgan, Ali Rana and Atılgan, Canan (2022) "DHFR mutants modulate their synchronized dynamics with the substrate by shifting hydrogen bond occupancies", Journal of Chemical Information and Modeling, Vol.62, No.24, 6715-6726 (SCI)

Atılgan, Ali Rana and Atılgan, Canan (2022) "Computational strategies for protein conformational ensemble detection", Current Opinion in Structural Biology, Vol.72, 79-87 (SCI)

Burak Okan, Osman and Turgut, Deniz and Atılgan, Canan and Atılgan, Ali Rana and Ozisik, Rahmi (2022) "Could network structures generated with simple rules imposed on a cubic lattice reproduce the structural descriptors of globular proteins?", Journal of Complex Networks, Vol.10, No.1 (SCI)

Papila, Melih and Atılgan, Ali Rana (2022) "All-composite honeycomb core sandwich structures: master curves for stiffness-based design", Forces in Mechanics, Vol.6 (NA)

Manna, Madhu Sudan and Tamer, Yusuf Talha and Gaszek, Ilona and Poulides, Nicole and Ahmed, Ayesha and Wang, Xiaoyu and Toprak, Furkan C.R. and Woodard, Da Nae R. and Koh, Andrew Y. and Williams, Noelle S. and Borek, Dominika and Atılgan, Ali Rana and Hulleman, John D. and Atılgan, Canan and Tambar, Uttam and Toprak, Erdal (2021) "A trimethoprim derivative impedes antibiotic resistance evolution", Nature Communications, Vol.12, No.1 (SCI)

Güçlü, Tandaç Fürkan and Atılgan, Ali Rana and Atılgan, Canan (2021) "Dynamic community composition unravels allosteric communication in pdz3", Journal of Physical Chemistry B, Vol.125, No.9, 2266-2276 (SCI)

Güçlü, Tandaç Fürkan and Kocatuğ, Nazlı and Atılgan, Ali Rana and Atılgan, Canan (2021) "N-terminus of the third PDZ domain of PSD-95 orchestrates allosteric communication for selective ligand binding", Journal of Chemical Information and Modeling, Vol.61, No.1, 347-357 (SCI)

Abdizadeh, Haleh and Jalalypour, Farzaneh and Atılgan, Ali Rana and Atılgan, Canan (2020) "A coarse-grained methodology identifies intrinsic mechanisms that dissociate interacting protein pairs", Frontiers in Molecular Biosciences, Vol.7 (SCI)

Tamer, Yusuf Talha and Gazsek, Ilona K. and Abdizadeh, Haleh and Batur, Tuğçe and Reynolds, Kimberly and Atılgan, Ali Rana and Atılgan, Canan and Toprak, Erdal (2019) "High-order epistasis in catalytic power of dihydrofolate reductase gives rise to a rugged fitness landscape in the presence of trimethoprim selection", Molecular Biology and Evolution, Vol.36, No.7, 1533-1550 (SCI)

Ross, Caroline and Nizami, Bilal and Glenister, Michael and Amamuddy, Olivier Sheik and Atılgan, Ali Rana and Atılgan, Canan and Bishop, Özlem Tastan (2018) "MODE-TASK: large-scale protein motion tools", Bioinformatics, Vol.34, No.21, 3759-3763 (SCI)

Ross, Caroline Jane and Atılgan, Ali Rana and Taştan Bishop, Özlem and Atılgan, Canan (2018) "Unraveling the motions behind Enterovirus 71 uncoating", Biophysical Journal, Vol.114, No.4, 822-838 (SCI)

Abdizadeh, Haleh and Atılgan, Ali Rana and Atılgan, Canan and Dedeoğlu, Burcu (2017) "Computational approaches for deciphering the equilibrium and kinetic properties of iron transport proteins", Metallomics, Vol.9, No.11, 1513-1533 (SCI)

Brown, David K. and Penkler, David L. and Amamuddy, Olivier Sheik and Ross, Caroline and Atılgan, Ali Rana and Atılgan, Canan and Bishop, Özlem Taştan (2017) "MD-TASK: a software suite for analyzing molecular dynamics trajectories", Bioinformatics, Vol.33, No.17, 2768-2771 (SCI)

Abdizadeh, Haleh and Atılgan, Ali Rana and Atılgan, Canan (2017) "Mechanisms by which salt concentration moderates the dynamics of human serum transferrin", Journal of Physical Chemistry B, Vol.121, No.18, 4778-4789 (SCI)

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 (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 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)

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)

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)

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)

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)

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)

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 , No.Abstra, 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 , No.Abstra, 405A-406A (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 (NA)