• Faridoon Yousafzai's Research

• Martin Trick

Related links

• AT JIC:
• Computational and Systems Biology

Curriculum Vitae

• 1973 BSc, University of Peshawar, Pakistan.
• 1973-1975 MSc, Chemistry, University of Peshawar, Pakistan.
• 1975-1977 Teaching/Research Fellow, University of P.eshawar, Pakistan
• 1978-1986 Lecturer in Chemistry, Govt. College Karak and Post Graduate Jahanzeb Govt College, Swat, Pakistan
• 1986-1988 PhD, University College Cork, Ireland
• 1989-1991 Postdoctoral Fellow, University of Newcastle-upon-Tyne, UK.
• 1992-1994 Postdoctoral Fellow, Nitrogen Fixation Lab, University of Sussex, UK.
• 1995-2000 Research Scientist, Dept of Biological Chemistry, John Innes Centre, UK
• 2000-2005 Senior Research Scientist, Dept of Biological Chemistry, John Innes Centre, UK
• 2005-present Biomolecular Modelling Scientist, Dept of Computational and Systems Biology, John Innes Centre, UK

Faridoon Yousafzai

Senior Scientist

Computational and Systems Biology

Contact details

Tel: +44 (0)1603 450723
faridoon.yousafzai@bbsrc.ac.uk

Research interests

I am interested in Macromolecular Modelling and Dynamic Simulations and work with the JIC scientists, on a collaborative basis, to resolve relevant biological problems at molecular level using macromolecular structures and in silico experimentations such as homology modelling, dynamic simulations, protein-protein interaction and protein-ligand docking.

Macromolecular Modelling: Why and How?

One of the major problems in understanding the chemical basis of life is to unfold the protein folding puzzle. Proteins emerging from the mRNA translational factory are generally featureless chains of amino acids with no specific 3-dimensional (3D) structure or protein fold. It is the lack of this fold which makes a protein not only featureless but mostly functionless as well. However, as soon as a peptide chain of amino acid residues undergoes a protein folding process, the mechanism of which is not understood at the moment, the peptide chain acquires not only a specific 3D structure but the entire array of its activity and functionality come into play. In other words it is largely the amino acid sequence of a protein that determines its 3D configuration or folded state but it is the 3D structure of the protein that determines its function. Hence, to understand and analyse the mechanism of function of a protein and to devise a methodology for enhancing, abolishing or regulating that function, it is very helpful to have a 3D structure of the protein. In general, if the protein folding problem is solved, it will greatly enhance our ability to interpret the huge amount of data collected by the various genome projects. It will also help to understand the mechanisms of various biological processes that have immense importance for mankind such as the development of cancer, hereditary and other infectious diseases; the mechanism by which pathogens attack plants and plants develops or fail to develop resistance to such attacks; and the mechanism by which various regulatory and signalling processes operate. It will also enhance our ability to design molecules with specific biological properties such as personalised drugs, drugs with specific therapeutic actions, molecular switches that will turn on/off specific biological processes, molecular timers that will control biological cycles and many more.

The significance of 3D structures of macromolecules is massive but the methods available to determine them are not that many. At the moment X-ray crystallography and NMR (Nuclear Magnetic Resonance) spectroscopy are the only two experimental techniques that are available to determine molecular structures of proteins and other macromolecules such as RNA and DNA. The two techniques are very effective but both require isolation and purification of proteins in relatively large amounts while X-ray crystallography additionally requires the growth of suitable and stable crystals. Although, NMR requires pure proteins only (no need of suitable crystals) and techniques such as isotope labelling and Transverse Relaxation Optimised Spectroscopy (TROSY) have been developed to study large proteins, traditionally the NMR spectroscopy has been limited to relatively small proteins or protein domains. It is these time consuming processes of protein isolation, purification, crystallisation and limited application of NMR that renders the output of proteins 3D structures compared to proteins sequencing data very low.

In order to tackle the problem, a number of initiatives, both experimental and theoretical (or combination of the two) have been undertaken by the scientific community.

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