Group of prof. Mgr. Jiří Damborský, Dr. International Clinical Research Center, St. Anne’s University Hospital Brno. *Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University*
ES-Cat start date; March 2019
Background: I studied Biological Sciences at Forman Christian College, Lahore, and received my BS.c. (Hons.) in 2016. My bachelor’s thesis was focused on “Crystallization of Glutathione Binding Protein gsiB”, which is a transporter protein important in the transmembrane import of glutathione, an important antioxidant. I then joined the iGEM 2016 Peshawar team and conducted research on a synthetic biology device for detection of carbon monoxide and nitrous oxide. Following this, I completed my Masters (M2) in Systems and Synthetic Biology from Université Paris-Saclay, in 2018. My Master’s thesis was focused on a synthetic biology based expression circuit for Alpha-helicoidal HEAT-like Repeat Proteins (αRep). My current interests are interdisciplinary, but mostly focus on protein evolution and design.
Training and Transferable Skills:
- Molecular evolution (Ancestral sequence reconstruction)
- Bioinformatics and computational biology (NCBI/Blast, UCSC Genome Browser, Jalview, Pymol, Autodock, Chimera, working with Linux Bash, and Python)
- Molecular biology (PCR, Site-directed mutagenesis, cloning, sequencing)
- Synthetic biology (Design and construction of biological devices)
- Systems Biology (Metabolic engineering)
- Biochemistry (Recombinant protein expression, purification, crystallization and characterization)
The main focus of the PhD is In silico modelling of biophysical properties of proteins, protein stability prediction, and for generation of thermostable protein candidates especially using a technique called Ancestral Sequence Reconstruction (ASR). ASR is a powerful technique that allows researchers to build an evolutionary history of extant protein sequences. Initially focus will be given to developing the theoretical basis of an online server for ASR. A significant portion of time will then be devoted to validation of this server. The validation will be both in silico, and experimental.
Khan, R. T., Musil, M., Stourac, J., Damborsky, J., & Bednar, D. (2021). Fully Automated Ancestral Sequence Reconstruction using FireProtASR. Current Protocols, 1(2), e30.
Musil, M., Khan, R. T., Beier, A., Stourac, J., Konegger, H., Damborsky, J., & Bednar, D. (2020). FireProtASR: a web server for fully automated ancestral sequence reconstruction. Briefings in Bioinformatics.