PhD student
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*
Contact email:491474@mail.muni.cz
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)

Research Projects:

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.

Publications:

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.

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