PUBLICATIONS
Journal Articles:
34.Bahar, I., Banerjee, A., Mathew, S.,Naqvi, M. Yilmaz, S., Zachoropoulou,M. Doruker, P. Kumita, J., Yang, S.H., Gur, M., Itzhaki, L., Gordon., R. (2023). Influence of Point Mutations on PR65 Conformational Adaptability: Insights from Nanoaperture Optical Tweezer Experiments and Molecular Simulations, Research Square, 2023.11.16. (Corresponding author)
33. Costa, M. G. S., Gur, M., Krieger, J. M., Bahar, I. (2023). Computational biophysics meets cryo-EM revolution in the search for the functional dynamics of biomolecular systems, WIREs Computational Molecular Science, 2023.06. 10.544469. (Joint First Author) (2022 Impact Factor: 11.4)
32. Salvador-Garcia, D., Jin, L., Hensley, A., Golcuk M. , Gallaud, E., Chaaban, S., Port, F., Vagnoni, A., Planelles-Herrero, V. J., McClintock, M. A., Derivery E., Carter, A. P. , Giet, R., Gur, M., Yildiz, A., Bullock, S. L. (2023). A force-sensitive mutation reveals a spindle assembly checkpoint-independent role for dynein in anaphase progression, bioRxiv, 2023.08. 03.551815. (Preprint)
31. Golcuk, M., Yilmaz, S. Z., Yildiz, A., Gur, M. (2023). The mechanism and energetics of the dynein priming stroke, bioRxiv, 2023.06. 10.544469. (Preprint) (Currently under review) (Corresponding Author)
30. Golcuk, M. , Yildiz A., Gur, M. (2022). Omicron BA.1 and BA.2 variants increase the interactions of SARS-CoV-2 spike glycoprotein with ACE2. Journal of Molecular Graphics & Modelling. 108286.
29. Golcuk M., Hacisuleyman, A., Yilmaz, S. Z., Taka, E. Yildiz A., Gur. M. (2022). SARS-Cov-2 delta variant decreases nanobody binding and ACE2 blocking effectivity. Journal of Chemical Information and Modeling. 62 (10), 2490-2498.
28. Ferro, L. S., Fang, Q.; Eshun-Wilson, L., Fernandes, J., Jack, A., Farrell, D. P., Golcuk, M., Huijben, T., Costa, K., Gur, M., DiMaio, F., Nogales, E., Yildiz, A., (2022). Structural and functional insight into regulation of kinesin-1 by microtubule-associated protein MAP7. Science, 375, 326-331.
27. Gur, M., Yilmaz, S.Z., Taka, E. (2021). The first law of thermodynamics analysis of transporters involved in the Glutamate/Gaba-Glutamine cycle. Journal of Thermal Science and Technology. 41(2), 265-276.
26. Golcuk, M., Hacisuleyman, A., Erman, B., Yildiz, A., Gur, M. (2021). Binding mechanism of neutralizing nanobodies targeting SARS-CoV-2 spike glycoprotein. Journal of Chemical Information and Modeling. 61(10), 5152–5160.
25. Taka, E., Yilmaz, S. Z., Golcuk, M., Kilinc, C., Aktas, U., Yildiz, A., Gur, M. (2021). Critical interactions between the SARS-CoV-2 spike glycoprotein and the human ACE2 receptor. Journal of Physical Chemistry B. 125 (21), 5537-5548.
24. Ferro, L., Eshun-Wilson, L., Golcuk, M., Fernandes, J., Huijben, T., Gerber, E., Jack, A., Costa, K., Gur, M., Fang, Q., Nogales, E. and Yildiz, A. (2020). The mechanism of motor inhibition by microtubule-associated proteins. bioRxiv.(Preprint)
23. Gur, M., Taka, E., Yilmaz, S. Z., Kilinc, C., Aktas, U., Golcuk, M. (2020). Conformational transition of SARS-CoV-2 spike glycoprotein between its closed and open states. Journal of Chemical Physics, 153(7), 075101.
22. Gur, M. (2020). COVID-19 aşı ve ilaç geliştirme çalışmalarında spike glikoproteininin yeri ve önemi. TÜBA Günce, 63.
21. Gur, M., Golcuk, M., Gul, A., Erman, B. (2020). Molecular dynamics simulations provide molecular insights into the role of HLA-B51 in Behçet’s Disease pathogenesis. Chemical Biology & Drug Design, 96(1), 644-658.
20. Zhou, Z., Feng, Z., Hu, D., Yang, P., Gur, M., Bahar, I., Cristofanilli, M., Gradishar, W.J., Xie, X., Wan, Y. (2019). A novel small-molecule antagonizes PRMT5-mediated KLF4 methylation for target therapy. EBioMedicine-The Lancet, 44, 98-111.
19. Gur, M., Golcuk, M., Yilmaz, S. Z., Taka, E. (2019). Thermodynamic first law efficiency of membrane proteins. Journal of Biomolecular Structure & Dynamics, 1-11.
18. Can, S., Lacey, S., Gur, M., Carter, A. P., Yildiz, A. (2019). Directionality of dynein is controlled by the angle and length of its stalk. Nature, 566(7744), 407.
17. Pullara, F., Wenzhi, M., Gur, M. (2019). Why protein conformers in molecular dynamics simulations differ from their crystal structures: a thermodynamic insight. Turkish Journal of Chemistry, 43(2), 394-403.
16. Gur, M., Blackburn, E. A., Ning, J., Narayan, V., Ball, K. L., Walkinshaw, M. D., Erman, B. (2018). Molecular dynamics simulations of site point mutations in the TPR domain of cyclophilin 40 identify conformational states with distinct dynamic and enzymatic properties. Journal of Chemical Physics, 148(14), 145101.
15. Gur, M., Cheng, M. H., Zomot, E., Bahar, I. (2017). Effect of dimerization on the dynamics of neurotransmitter: Sodium symporters. Journal of Physical Chemistry B, 121(15), 3657-3666. (Joint corresponding author)
14. Gur, M. (2016). Balkabağının akışkan yataklı kurutucuda kurutulmasının deneysel ve teorik incelenmesi. Uludağ University Journal of The Faculty of Engineering, 21(2), 145-158.
13. Gur, M., Zomot, E., Cheng, M. H., Bahar, I. (2015). Energy landscape of LeuT from molecular simulations. Journal of Chemical Physics, 143 (24), 243134.
12. Hu, D., Gur, M., Zhou, Z., Gamper, A., Hung, M. C., Fujita, N., Lan L , Bahar I., Wan, Y. (2015). Interplay between arginine methylation and ubiquitylation regulates KLF4-mediated genome stability and carcinogenesis. Nature Communications, 6, 8419. (Joint corresponding author)
11. Zomot, E., Gur, M., Bahar, I. (2015). Microseconds simulations reveal a new sodium-binding site and the mechanism of sodium-coupled substrate uptake by LeuT. Journal of Biological Chemistry, 290(1), 544-555.
10. Das, A., Gur, M., Cheng, M. H., Jo, S., Bahar, I., Roux, B. (2014). Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model. PLOS Computational Biology, 10(4), e1003521.
9. Gur, M., Madura, J. D., Bahar, I. (2013). Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase. Biophysical Journal, 105(7), 1643-1652.
8. Gur, M., Zomot, E., Bahar, I. (2013). Global motions exhibited by proteins in micro-to milliseconds simulations concur with anisotropic network model predictions. Journal of Chemical Physics, 139(12), 121912.
7. Eskici, G., Gur, M. (2013). Computational design of new peptide inhibitors for amyloid beta (Aβ) aggregation in alzheimer's disease: application of a novel methodology. PLOS One, 8(6), e66178.
6. Gur, M., Erman, B. (2012). Quasi‐harmonic fluctuations of two bound peptides. Proteins: Structure, Function, and Bioinformatics, 80(12), 2769-2779.
5. Arkun, Y., Gur, M. (2012). Combining optimal control theory and molecular dynamics for protein folding. PLOS One, 7(1), e29628.
4. Meireles, L., Gur, M., Bakan, A., Bahar, I. (2011). Pre‐existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins. Protein Science, 20(10), 1645-1658. ()
3. Kabakçıoğlu, A., Yuret, D., Gur, M., Erman, B. (2010). Anharmonicity, mode-coupling and entropy in a fluctuating native protein. Physical Biology, 7(4), 046005.
2. Gur, M., Erman, B. (2010). Quasi-harmonic analysis of mode coupling in fluctuating native proteins. Physical Biology, 7(4), 046006.
1. Yogurtcu, O. N., Gur, M., Erman, B. (2009). Statistical thermodynamics of residue fluctuations in native proteins. Journal of Chemical Physics, 130(9), 03B607.
Book Chapters:
2. Gur, M. (2020) Exploring conformational transition of 2019 novel coronavirus spike glycoprotein between its closed and open states using molecular dynamics simulations. In M., Şeker, A., Özer, Z., Tosun, C., Korkut, M., Doğrul (Ed.). TÜBA Assessment Report on COVID-19 Global Outbreak (pp. 161). Ankara, Turkey: Turkish Academy of Sciences Publications
1. Gur, M., Gur, M. (2014). Comparing corn drying in fluidized bed dryer and convective tray dryer. In I., Dincer, A., Midilli, H., Kucuk (Ed.). Progress in Exergy Energy and the Environment (pp. 1085). Springer International Publishing.(Corresponding author)
Conferences, Symposia and Meetings:
37. Golcuk, M., Yilmaz, S. Z., Yildiz A. Gur M. (2022) The mechanism and energetics of the dynein priming stroke. 8th International BAU-Drug Design Congress. Istanbul, Turkey
36. Buran C. H., Taka, E., Gur M. (2022) Investigation of the structural differences between wild-type and mutant forms of mutsa Heterodimer with Molecular Dynamic Simulations. 8th International BAU-Drug Design Congress. Istanbul, Turkey
35. Yilmaz, S. Z., Golcuk, M., Erman, B., Gur, M. (2022). Modelling cell membrane passing mechanism and energetics of cell penetrating peptides comprising HLA-B*51 binding motifs. International Congress of the Molecular Biology Association of Turkey (MolBiyoKon22). Istanbul, Turkey
34. Dingiloglu, B., Basturk, E., Turk M., Golcuk M., Eyupoglu, A. E., Karakus, B. Z., Can O., Erman B., Gur M., Dinler-Doğanay, G. (2022). Developing novel peptide-based inhibitor candidates against receptor binding domain (RBD) of SARS-CoV-2 spike protein. International Congress of the Molecular Biology Association of Turkey (MolBiyoKon22). Istanbul, Turkey
33. Gur, M. (2021). Exploring conformational transitions during the CHK2 activation via Molecular Dynamics Simulations. 3rd International Cancer and Ion Channels Congress (CANCERION-2021). (Invited Speaker)
32. Gur, M., Yilmaz, S.Z., Taka, E. (2021). Thermodynamic first law analysis of transporters involved in the Glutamate/GABA-Glutamine cycle. 23rd Congress on Thermal Science and Technology.
31. Golcuk M., Hacisuleyman A., Erman B., Yildiz A., Gur M. (2021). Exploring the binding mechanisms of nanobodies targeting SARS-CoV-2 spike glycoprotein using Molecular Dynamics Simulations. 2021 ACS Fall Meeting. (Atlanta, GA) (Invited Speaker)
30. Taka, E., Yilmaz, S.Z., Golcuk, M., Kilinc, C., Aktas, U., Yildiz, A., Gur, M. (2021). Critical interactions between the SARS-CoV-2 spike glycoprotein and the human ACE2 receptor. 2021 ACS Spring Meeting. (Invited Speaker
29. Gur, M. (2021). Molecular Dynamics Simulations of large biomolecular systems. High Performance Computing Technologies in Drug Design Workshop. (Invited Speaker
28. Taka, E., Yilmaz, S.Z., Golcuk, M., Kilinc, C., Aktas, U., Yildiz, A., Gur, M. (2021). Critical interactions between the SARS-CoV-2 spike glycoprotein and the human ACE2 receptor. ITU Department of Chemical Engineering 2nd Graduate Symposium. (Invited Speaker) Istanbul, Turkey
27. Gur, M., Can, S., Lacey, S., Carter, A. P., Yıldız, A. (2019). Modelling plus-end-directed dyneins. 7th International Congress of the Molecular Biology Association of Turkey (MolBiyoKon19). Istanbul, Turkey
26. Gur, M., Golcuk, M., Gul, A., Erman, B. (2019). Molecular overview of the role of HLA-B51 in Behçet’s disease. 7th International Congress of the Molecular Biology Association of Turkey (MolBiyoKon19). Istanbul, Turkey
25. Gur, M. (2019). Insight into the mechanochemical cycle of cytoplasmic dynein from molecular dynamics simulations. 7th International BAU Drug Design Congress. (Invited Speaker) Istanbul, Turkey
24. Golcuk, M., Taka, E., Yilmaz, S.Z., Gur, M. (2019). Molecular Dynamics Simulations of the dynein linker movement. The 12th International Symposium on Health Informatics and Bioinformatics. Izmır, Turkey
23 Can, S., Lacey, S., Gur, M., Carter, A. P., Yildiz, A. (2019). Dynein's directionality is controlled by the angle and length of its stalk. 63rd Annual Meeting of the Biophysical-Society. Baltimore, MD
22. Gur, M., Can, S., Lacey, S., Carter, A. P., Yildiz, A. (2018). Engineering plus-end directed dyneins. 6th International BAU Drug Design Congress. Istanbul, Turkey
21. Gur, M., Gul, A., Erman, B. (2018) Dynamic and static differences between conformations of HLA-B51 and HLA-B52: implications for the pathogenic mechanisms of HLA-B51 in Behçet’s disease. 6th International BAU Drug Design Congress. Istanbul, Turkey
20. Gur, M., Golcuk, M., Yilmaz, S. Z., Taka, E. (2018). Thermodynamic first law analysis of proteins. 6th International BAU Drug Design Congress. Istanbul, Turkey
19. Gur, M., Cheng, M. H., Zomot, E.,Bahar, I. (2017). Importance of dimerization in facilitating the functional dynamics of neurotransmitter: Sodium symporters. 61st Annual Meeting of the Biophysical-Society.New Orleans, LA
18. Gur, M., Cheng, M. H., Zomot, E., Bahar, I. (2017). Investigation of the effect of dimerization on the functional dynamics of neurotransmitter: Sodium symporters. 5th International BAU-Drug Design Congress. Istanbul, Turkey
17. Gur, M., Zomot, E., Cheng, M. H., Bahar, I. (2015). Insight into the dynamics of LeuT from multiscale simulations. Gordon Research Conferences (GRC) Mechanism of Membrane Transport. Lewiston, ME.
16. Gur, M., Zomot, E., Cheng, M. H., Bahar I. (2014). Toward gaining a mechanistic understanding of substrate transport by LeuT. Gordon research Conferences (GRC) Biopolymers. Newport, RI.
15. Gur, M., Zomot, E., Bahar, I. (2014). Global motions of proteins observed in micro to milliseconds simulations concur with Anisotropic Network Model predictions. Membrane Protein Structural Dynamics Consortium’s Annual Meeting. Chicago, IL
14. Das, A., Gur, M., Bahar, I., Roux, B. (2013). A simple coarse-grained model to map the transition pathway between two stable conformations using the Anisotropic Elastic Network model. 57th Annual Meeting of the Biophysical-Society. Philadelphia, PA
13. Gur, M., Eskici, G. (2013). Computational design of new peptide inhibitors for amyloid beta aggregation in Alzheimer's disease application of a novel methodology. American Institute of Chemical Engineers (AIChE) Annual Meeting. San Francisco, CA.
12. Gur, M., Zomot, E., Bahar, I. (2013). Multiscale investigation of biomolecular systems dynamics. American Institute of Chemical Engineers (AIChE) Annual Meeting. San Francisco, CA.
11. Gur, M., Gur, M. (2013). Comparing corn drying in fluidized bed dryer and convective tray dryer. The Sixth International Exergy, Energy and Environment Symposium. Rize, Turkey
10. Gur, M., Madura, J., Bahar, I. (2013). Global transitions or proteins explored by a multiscale hybrid methodology: Application to dopamine transporter. 57th Annual Meeting of the Biophysical-Society. Philadelphia, PA
9. Gur, M., Madura, J., Bahar, I. (2012). Transition pathways of Dopamine transporters explored by combining Molecular Dynamics simulations and Monte Carlo sampling of collective modes. Membrane Protein Structural Dynamics Consortium’s Annual Meeting. Chicago, IL.
8. Gur, M., Madura, J., Bahar, I. (2012). Transition pathways of proteins explored by combining Molecular Dynamics simulations and Monte Carlo sampling of collective modes. Biophysical Society 56th Annual Meeting. Philadelphia, PA.
7. Arkun, Z.Y., Gur, M. (2011). Protein folding using coarse grained optimal control and Molecular Dynamics. 18th International Federation of Automatic Control (IFAC) World Congress. Milano, Italy.
6. Gur, M., Bahar, I. (2011). Transition pathways of enzymes explored by combining the Anisotropic Network Model, Molecular Dynamics Simulations and a Monte Carlo sampling of conformational space. Albany 2011: Conversation 17. Albany, NY.
5. Gur, M., Erman, B. (2010). Harmonic fluctuations of two bound peptides. Gordon Research Conference (GRC) Biopolymers. Newport, RI.
4. Gur, M., Erman, B. (2010). Coupling between energy and residue position fluctuations in native proteins. 5th International Symposium on Health Informatics and Bioinformatics. Antalya, Turkey
3. Gur, M., Erman, B. (2009). Statistical thermodynamics and mode analysis of residue fluctuations in native proteins. Gordon Research Conference (GRC) Computer Aided Drug Design. Tilton, NH.
2. Gur, M., Erman, B. (2009). Statistical thermodynamics of residue fluctuations in native proteins. Biophysical Society 53rd Annual Meeting. Boston, MS.
1. Gur, M., Erman, B. (2008). Determining binding forces between two peptides using the Gaussian Network Model. XXI Sitges Conference-Statistical Mechanics of Biopyhsics. Sitges, Spain