Mert Gur, Ph.D.
|Ph.D. in Computational Sciences and Engineering, Koc University|
832 Murdoch Building
We specialize in solving problems at the interface of medicine, biology, and engineering, using computational modeling and statistical thermodynamics methods. Our research interests include (i) protein systems including known and potential drug targets and (ii) proteins with complex functional machinery, comparable to macro scaled machines we encounter in daily life. By performing all atom molecular dynamics simulations and elastic network models, we 1) model the transition between protein states, explore the corresponding energetics and make functional inferences, 2) investigate how disease-related mutations affect protein structure, dynamics, and function, and explore novel therapeutic strategies to regulate protein function, and 3) apply protein engineering methods to alter function, machinery and binding mechanisms of proteins. We currently investigate HLA-B51 as potential drug target for Behcet’s disease and design Cell Penetrating Peptide based novel drugs targeting HLA-B51, explore the effect of missense mutations observed in Colon and Breast cancers patients on CHK2 and Mutsα function and contribute to the determination of the cancer association of these mutations for early cancer warning, analyze the effect of SARS-CoV-2 variation on the nanobody effectivity and engineer novel nanobodies targeting variant SARS-CoV-2 Spike proteins, model the functional machinery of the nano scaled biological engines known as motor proteins, how these motors are regulated by microtubule associated proteins, and engineer dynein motor protein based biological nanowalkers. Furthermore, we are closely collaborating with the Ivet Bahar lab on gaining a deeper understanding of allostery and allotargeting by computational approaches, and modifying the structure, dynamics, and mechanical properties of the tandem-repeat proteins to design new functionalities.
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.
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.
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.