PUBLICATIONS

 

Journal Articles 

21.  Gur, M., Golcuk, M., Gul, A., Erman, B. (2019). Molecular Dynamics Simulations Provide Molecular Insights into the Role of HLA-B51 in Behçet’s Disease Pathogenesis. Chemical Biology & Drug Design. (Accepted)

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 and 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. (Joint first author)

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 

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., Golcuk M., Gul A., Erman B. (2018). Dynamic and Static Differences between Conformations of HLA-B51 and HLA-B52: Implications for the Pathogenic Mechanism of HLA-B51 in Behçet’s Disease. 6th International Bahcesehir University (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. GRC Mechanism of Membrane Transport, Lewiston, ME.

Gur, M., Zomot, E., Cheng, M. H., Bahar, I. (2014). Toward Gaining a Mechanistic Understanding of Substrate Transport by LeuT. 2014 GRC Biopolymers, Newport, RI.

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

Gur, M., Eskici, G. (2013). Computational design of new peptide inhibitors for amyloid beta (Ab) aggregation in Alzheimer's disease: application of a novel methodology. 2013 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., Zomot, E., Bahar, I. (2013). 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.

Gur, M., Madura, J., Bahar, I. (2013). Transition pathways of proteins explored by combining Molecular Dynamics simulations and Monte Carlo sampling of collective modes. Biophysical Society 56th Annual Meeting, 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., Arkun, Y. (2011). Protein folding using coarse-grained optimal control and Molecular Dynamics. 18th 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: 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 (HIBIT), Antalya, Turkey

Gur, M., Erman, B. (2009). Statistical thermodynamics and mode analysis of residue fluctuations in native proteins. Gordon Research Conference: Computer Aided Drug Design, Tilton, NH.

Gur, M., Erman, B. (2009). Statistical thermodynamics of residue fluctuations in native proteins. Biophysical Society 53rdAnnual 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.

 

 

 


Pullara F, Wenzhi M, Gur M, "Why Protein Conformers in Molecular Dynamics Simulations Differ from Their Crystal Structures: A Thermodynamic Insight", Turkish Journal of Chemistry, 2019, Accepted
Pullara F, Wenzhi M, Gur M, "Why Protein Conformers in Molecular Dynamics Simulations Differ from Their Crystal Structures: A Thermodynamic Insight", Turkish Journal of Chemistry, 2019, Accepted
Gur M, Cheng MH, Zomot E, Bahar I, "Effect of Dimerization on the Dynamics of Neurotransmitter:Sodium Symporters", Journal of Physical Chemistry B, 01/2019, ACS, (Accepted)
Gur M, Cheng MH, Zomot E, Bahar I, "Effect of Dimerization on the Dynamics of Neurotransmitter:Sodium Symporters", Journal of Physical Chemistry B, 01/2019, ACS, (Accepted)
Can S, Lacey S, Gur M, Carter A P, Yildiz A, "Dynein’s Directionality is Controlled by the Angle and Length of Its Stalk", Nature, 2019, (Accepted)
Can S, Lacey S, Gur M, Carter A P, Yildiz A, "Dynein’s Directionality is Controlled by the Angle and Length of Its Stalk", Nature, 2019, (Accepted)
Can S, Lacey S, Gur M, Carter A P, Yildiz A, "Dynein’s Directionality is Controlled by the Angle and Length of Its Stalk", Nature, 2019, (Accepted)
Can S, Lacey S, Gur M, Carter A P, Yildiz A, "Dynein’s Directionality is Controlled by the Angle and Length of Its Stalk", Nature, 2019, (Accepted)