Mert Gur

Mert Gur, Ph.D.
Associate Professor, Director of Computational Biomedicine & Biotechnology (CoBB) Masters Program

Ph.D. in Computational Sciences and Engineering, Koc University


832 Murdoch Building
3420 Forbes Avenue
Pittsburgh, PA 15213


Twitter: @itugurlab

Research Summary

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.

Recent Publications

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.  


Project Title  Proj Start Date  Proj End Date  Funding Source 
Self-Coordination of Dyneins During Ciliary Beating  07/01/2022  07/01/2025  The Scientific and Technological Research Council of Turkey (TUBITAK) 
Molecular-Scale Modeling of Dynein Microtubule Binding and Power Stroke  07/01/2022  07/01/2025  TUBITAK 
Modeling the Regulation of Motors by Microtubule-Associated Proteins  07/01/2022  07/01/2023  Partnership for Advanced Computing in Europe (PRACE), European Union 
Identification and Reengineering of Effective Nanobodies Against SARS-CoV-2 Omicron Variant   12/08/2021  12/08/2022  COVID-19 High Performance Computing Consortium (COVID-19 HPCC), US 
The Mechanism and Energetics of Dynein’s Powerstroke (EnDy)   06/18/2021  06/18/2022  PRACE DECI-17 (Distributed European Computing Initiative) 
Modeling the Mechanism of the Mechanochemical Cycle of the Cytoplasmic Dynein Motor Protein  03/02/2021  03/02/2022  Istanbul Technical University (ITU) Scientific Research Projects (BAP) 
Designing Cell Penetrating Peptide Based Drug Candidates for Behcet’s Disease  02/01/2020  02/01/2023  TUBITAK 
Development of an Early Detection System for Hereditary Colon and Breast Cancers and its Integration into e-Nabız Personal Health Record System  02/01/2020  08/01/2023  TUBITAK 
Exploring Nanobody Inhibitory Mechanism against SARS-CoV-2 Spike Glycoprotein Using Molecular Dynamics Simulations, (UC Berkeley – ITU Collaboration)  10/26/2020  10/26/2021  COVID-19 HPCC  
Exploring Binding and Fusion Mechanism of SARS-CoV-2 Spike Glycoprotein Using Molecular Dynamics Simulations, (UC Berkeley – ITU Collaboration)  04/02/2020  04/02/2021  COVID-19 HPCC  
Modelling the Mechanochemical Cycle of Cytoplasmic Dynein Machinery  03/27/2020  03/27/2021  PRACE  
Exploring Differences in Binding Characteristics Between HLA-B51 and HLA-B52  02/11/2019  03/11/2019  NVIDIA Hardware Grant Program 
Modeling the Effects of Mutation and Peptide Binding on Thermodynamic Properties of Cyclophilin 40 Enzyme  03/09/2018  03/09/2019  ITU BAP 
Effect of Cell Membrane on the Function of Membrane Proteins Targeted by Therapeutic Drugs Against Neurological Disorders  10/31/2016  10/31/2019  Turkish Academy of Science (TÜBA) 
Insight to LeuT Dynamics Obtained from Multi-Scale Simulations  07/26/2016  09/17/2016  ITU BAP 
Modeling the Mechanics and Energetics of the Cytoplasmic Dynein Motor Protein Mechanochemical Cycle  05/15/2016  05/15/2019  TUBITAK 
Mechanical and Energetic Modeling of the Mechanochemical Cycle of the Cytoplasmic Dynein Motor Protein  05/25/2015  09/05/2015  ITU BAP 
Investigation and Modeling of Functional Mechanisms of Cell Membrane Proteins Targeting Neurological Drugs  03/20/2015  03/16/2017  TUBITAK