PUBLICATIONS

Journal Articles:

30. 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 EffectivityJournal of Chemical Information and Modeling​. (Accepted for publication)

29. 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.

28. Golcuk M., Yildiz A., Gur. M. (2021). The Omicron Variant Increases the Interactions of SARS-CoV-2 Spike Glycoprotein with ACE2bioRxiv. (Preprint).

27. Gur, M., Yilmaz, S.Z., Taka, E. (2021) The First Law of Thermodynamics Analysis of Transporters Involved in the Glutamate/Gaba-Glutamine CycleJournal 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 ReceptorThe 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 proteinsbioRxiv.(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. The 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. The 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. The Journal of Physical Chemistry B, 121(15), 3657-3666. (Joint corresponding author)

14. Gur, M. (2016). Balkabağının Akışkan Yataklı Kurutucuda Kurutulmasının Deneysel Ve Teorik İncelenmesi. Uludağ Üniversitesi Mühendislik Fakültesi Dergisi, 21(2), 145-158.

13. Gur, M., Zomot, E., Cheng, M. H., Bahar, I. (2015). Energy landscape of LeuT from molecular simulations. The 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. The 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. The 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. (p. 155), TÜBA Assessment Report on COVID19 Global Outbreak.

1. Gur M., Gur M. (2014) Comparing Corn Drying in Fluidized Bed Dryer and Convective Tray Dryer. Dincer I., Midilli A., Kucuk H. Progress in Exergy, Energy, and the Environment. (pp. 687-694), Springer, Cham

 

Conferences, Symposia and Meetings

Gur, M. (2021). Exploring conformational transitions during the CHK2 activation via molecular dynamics simulations. 3rd International Cancer and Ion Channels Congress (CANCERION-2021).

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.

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)

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)

Gur, M. (2021). Molecular Dynamics Simulations of Large Biomolecular Systems. High Performance Computing Technologies in Drug Design Workshop.  

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

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

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

Gur, M. (2019). Insight into the mechanochemical cycle of cytoplasmic dynein from molecular dynamics simulations. 7th International BAU Drug Design Congress. Istanbul, Turkey

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

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

Gur, M., Can, S., Lacey, S., Carter, A. P., Yildiz, A. (2019). Modelling plusend-directed dyneins. 7th International Congress of the Molecular Biology Association of Turkey. Istanbul, Turkey

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

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

Gur, M., Golcuk, M., Yilmaz, S. Z., Taka, E. (2018). Thermodynamic First Law Analysis of Proteins. 6th International BAU Drug Design Congress. Istanbul, Turkey

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

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

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.

Gur, M. (2015). Coupling Between Energy and Residue Position Fluctuations in Native Proteins. Health Informatics and 5th International Symposium on Health Informatics And Bioinformatics (HIBIT). Antalya, Turkey

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.

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

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 

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.

Gur, M., Zomot, E., Bahar, I. (2013). Multiscale investigation of biomolecular systems dynamics. American Institute of Chemical Engineers (AIChE) Annual Meeting. San Francisco, CA.

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

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

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.

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.

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.

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.

Gur, M., Erman, B. (2010). Harmonic fluctuations of two bound peptides. Gordon Research Conference (GRC) Biopolymers. Newport, RI.

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

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.

Gur, M., Erman, B. (2009). Statistical thermodynamics of residue fluctuations in native proteins. Biophysical Society 53rd Annual Meeting. Boston, MS.

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