Research Interests
Biomolecular interactions
The MCISB's aim is to combine modelling techniques with biological experimentation to investigate how the proteins in our model organism, the yeast Saccharomyces cerevisiae , behave in a coherent fashion. In the first instance, we are focussing on modelling the glycolytic pathway of yeast. I am utilizing a number assay technologies to characterise, quantitatively, the kinetic and binding parameters of enzymes and proteins with their respective ligands. In particular, both homogeneous and solid-phase assays will be utilized. These include solution based absorbance, fluorescence (intensity, polarisation, FRET, TRF and FCS) and luminscence readouts. Other surface-based technologies will be used and evaluated such as surface plasmon resonance (SPR),
isothermal calorimetry (ITC), resonant acoustic profiling (RAP). Expression and subsequent purification of proteins can often give small yields and which can be limiting, therefore, the automation (liquid handling), sensitivity and miniaturation of the assays are important considerations in the configuration of an assay.
New Interaction and Detection Technologies
I am interested in the design and implementation of new technologies for analysis of protein interactions. Previously, I have been involved in the design of novel platforms for constructing protein arrays from DNA arrays and new immobilisation tags with Dr. Mike Taussig that have universal applications for purification and detection of proteins on solid surfaces (ref 1-5). With this group, we have developed novel protein microarray methods and measurement of protein interactions using SPR technology (Biacore). This includes molecular biology techniques and protein purification. Proteins for analysis are synthesized via in vitro transcription / translation and proteins (ref 3-5) are characterized using mass spectrometry, SDS-PAGE and Western blotting. In addition, protein display methods such as ribosome display are being used as powerful tools to find novel interactions using cDNA libraries (ref 6) . I have collaborations which include universities in Sweden (Uppsala) and Germany (Max-Planck) via the Moltools project (Moltools). Recently we have been collaborating with Professor Ulf Landegren in the application of single molecule detection techniques (i.e. proximity ligation) to demonstrate protein interactions in cells (ref 7). My duties also include training laboratory staff on SPR and fluorescence instruments to measure biomolecular interactions, giving seminars (Euroscicon, Biacore), and teaching advanced molecular and protein techniques to graduate students.
Summary of technical expertise and achievements:
- Analysis of His-tagged proteins using SPR, design of a stable His-tag for suface immobilisation and array applications.
- Part of a team to design of a novel DNA array template for printing protein arrays.
- Single molecule detection of the IP3 receptor with Akt complexes in cells
- Production and and 19F-NMR analysis of novel green fluorescent proteins using un-natural amino acid incorporation.
- Structural (NMR and fluorescence spectroscopy) and folding studies of green fluorescent protein (GFP).
- Drug discovery, assay design and high throughput screening technologies (Glaxowelcome)
- Backbone 13C and 15N NMR assignments of GFP
Bio
| 2006 - present |
University of Manchester |
Experimental Officer (Biomolecular Interactions)
at the MCISB, working in the group of Douglas Kell (MCISB director) |
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| 2004 - 2006 |
Babraham Institute, Cambridge |
Scientific Officer
Development of array based technologies (DNA, protein arrays, novel immobilisation methods and ribosome display) for discovery and mapping protein interactions. |
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| 1999-2004 |
University of Cambridge,
Centre for Protein Engineering |
Supervisor Dr. Sophie Jackson
PhD in protein folding kinetics stability and dynamics : Protein engineering studies on the Green Fluorescent protein (GFP) and a four-helical bundle protein (FRB). Biophysical spectroscopy used to study folding:
Studies on the thermodynamics and kinetics (stopped-flow) of folding as measured by fluorescence, Circular Dichroism (CD), Hetero-nuclear NMR (including HSQC, residue assignments) and real-time NMR unfolding and backbone amide dynamics (ref 8).
Protein Engineering and ligand binding studies
Use of molecular biology cloning techniques, including site directed mutagenesis and protein crystal 3D-structures to design the minimal domain and faster folding properties of GFP. Design of novel fluorescent GFP analogues with unnatural amino acids such as fluorine substituted tyrosine, tryptophan and phenylalanine and to probe folded and unfolded structure using 19 F-NMR (including 19 F-residue assignments) (ref 9,10). Folding studies on a GFP- cytochrome b562 chimera protein as an artificial light-harvesting complex and ligand binding studies. Measurement of Heam binding by fluorescence quenching assays. Identification of a partially folded intermediate state populated as detected by kinetic analysis and ANS binding during the folding of FRB (ref 11) . Analysis of protein structure after reductive alkylation of lipase using CD and molecular modelling techniques (ref 12) .
Former Treasurer of Biology in Business
An organisation which bridges academia and business in order to facilitate the transfer of people and ideas between commercial and academic life science. In so doing we hope to increase understanding of how the two can synergise to increase innovation and productivity in an increasingly important part of the UK economy. |
1997- 1999
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GlaxoSmithKline (formerly Smithkline Beecham) |
Drug Discovery Scientist -Molecular Screening Technologies
New Assay Technologies for HTS and Target Characterisation Development of highly sensitive fluorescence based assays and assessment of new technologies for HTS and SAR for a wide range of therapeutic targets (enzymatic and binding assays i.e. peptide-protein, protein-protein, DNA/RNA-protein and carbohydrate-protein interactions). These include assay design, optimisation of assays, robustness, miniaturisation and in-house synthesis of assay reagents to be used as a molecular tool-box. |
1993-1994 |
University of Salford , Manchester |
| MSc. Biochemical and Molecular Parasitology. |
1989-1993
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University of Salford , Manchester |
BSc. Joint Honours in Biochemistry and Chemistry |
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Publications
(1) Khan F., He M. and TaussigM. J. (2006) Double-hexahistidine tag with high affinity binding for protein immobilisation, purification and detection on Ni-Nitrolotriacetic Acid surfaces, Analytical Chemistry (2006) 1;78(9):3072-9.
(2) Steinhauer C., Wingren C., Khan F., He M., Taussig M.J and Borrebaeck, C. (2006) Improved affinity coupling for antibody microarrays: Engineering of double-(His)6-tagged single framework recombinant antibody fragments Proteomics 6:4227-34.
(3) He M., Khan F. and Taussig M. J. (2007) Printing protein arrays from DNA arrays (submitted).
(4) He M., Khan F., Palmer E., Wang M., and Taussig M. J, (2007) Book Chapter: Predki, P. (Ed) Functional Protein Microarrays: Pathways to Discovery (in press) Protein In Situ Arrays Through Cell-Free Protein Synthesis.
(5) Palmer E., Lui H., Khan F., Taussig M. J. and He M. (2006) Enhanced cell-free protein expression by fusion with immunoglobulin Ck domain.
Protein Science 15(12):2842-6.
(6) He M. and Khan F. (2005) Ribosome Display: Next generation of display technologies for production of antibodies in vitro . Expert Review in Proteomics 2(3):421-30.
(7) Szado T., Khan F., Sodenberg, O., Bootman, M. and Roderick, L. (2007) Cellular interaction studies of the IP3 receptor with Akt (submitted).
(8) Khan F., Stott K., Jackson S.E. (2003) 1H, 15N and 13C backbone assignment of the green fluorescent protein (GFP). Journal of Biomolecular NMR. 26(3):281-2
(9) Khan F, Kuprov I, Craggs TD, Hore P, Jackson SE (2006) 19F-NMR studies on the native and denatured states of green fluorescent protein Journal of American Chemical Society, 128, 10729-10737 9 10729
(10) Khan, F. & Jackson, S.E, (2007) Novel fluorinated analogues of the Green Fluorescent Protein (in manuscript).
(11) Marianayagam N.J., Khan F., Male L., Jackson S.E. (2002) Fast folding of a four-helical bundle protein. Journal of American Chemical Society 21;124(33):9744-50 .
(12) Rahman. R. N. Z., Tejo, B.A, Basri M., Rahman. M.B.A., Khan, F., Zain S.M, Siahaan T. J., Salleh A.B. (2004) Reductive alkylation of lipase: Experimental and molecular modelling approaches. Special ICB issue of Applied Biochemistry and Biotechnology 118 (1-3) 11-20.
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