Abdessamad Ababou

Dr Abdessamad Ababou

Senior Lecturer

Biochemistry, Infection & Immunity Research Group

Department of Bioscience , School of Health, Sport and Bioscience

Abdessamad Ababou is a senior lecturer in Biochemistry. He is a Bioscientist with expertise in Protein Science (fold, stability, structure, dynamics, binding, design/engineering, kinetic processes, function, drug design, etc) using experimental and computational approaches.

His main research methods/techniques are in the area of Structural Biology (NMR and X-ray crystallography.

Areas Of Interest

  • Protein Science using experimental and computational approaches
  • Structural Biology (NMR and X-ray crystallography
  • Molecular Biology
  • Biochemistry
  • Biophysics
  • Molecular Modeling
  • Bioinformatics
  • The structure, assembly, export activity and drug design of several bacterial efflux pumps
On This Page

OVERVIEW

I am a Bioscientist with expertise in Protein Science (fold, stability, structure, dynamics, binding, design/engineering, kinetic processes, function, drug design, etc) using experimental and computational approaches. My main research methods/techniques are in the area of Structural Biology (NMR and X-ray crystallography. To view my protein structures click here and search my name), Molecular BiologyBiochemistryBiophysicsMolecular Modeling, and Bioinformatics. In my recent/present research projects I am investigating the structure, assembly, export activity and drug design of several bacterial efflux pumps, which are becoming the most frequent drug resistance mechanism in bacteria. Bacterial drug resistance is a serious worldwide problem that causes death, great suffering, and high economic cost.

Note that my research activities include several training aspects (academic and industrial) leading to bioscience/technical jobs for postgraduates (See details in Postgraduate Opportunities). For further details about my research group at UEL see my website.

Postgraduate opportunities

Postgraduate students (MRes and PhD) are welcome to apply and join my research group. All the proposed research projects will be done between UELKing's College London, and Queen Mary University of London. For further details, please contact me for an informal discussion.

At present, I have couple of new research projects in the theme of Bacterial Antibiotics Resistance, which are well imbedded within biomedical and pharmaceutical industries.

These projects consist of several approaches/techniques in:

  • Structural Biology
  • Biochemistry
  • Drug Design (experimental and computational approaches)
  • Cell Biology (in vivo aspects).

External roles

  • Visiting Senior Lecturer at KCL
  • Reviewer for several journals
  • Reviewer for funding agencies

CURRENT RESEARCH

My research interests focus on developing detailed understanding of the interactions between proteins and their ligand(s) in general (ligand = Protein, Peptide, DNA, RNA, small molecules, metals, etc), and in particular Protein-Protein Interactions, for Biomedical and Industrial Applications. My research goals are to design efficient and specific drugs for specific protein targets (Drug Design) and to design novel proteins for therapeutical and/or industrial purposes (Protein Design/Engineering).

For further details about my research group at UEL, see my website.

My present research projects consist of investigating the structure, assembly, export activity and drug design of several bacterial efflux pumps, which are becoming the most frequent drug resistance mechanism in bacteria. Bacterial drug resistance is a serious worldwide problem that causes death, great suffering, and high economic cost.

Overall research themes:

  • Bacterial Multidrug Resistance (Drug Design Strategies)
  • Bacterial Efflux Pumps (Structure, Assembly & Export Mechanism)
  • Type 4 Secretion Systems in Gram-Positive Bacteria (Structure, Assembly & Activity Mechanism)


Overall research work involves:

  • Cellular & Molecular Biology (Cloning, Mutagenesis, Protein Expression/Purification, In-vivo Assays, etc)
  • Protein/Protein-Ligand Structure, Dynamics & Function (Experimental & Computational Approaches)
  • Drug Design Strategies & Applications (Computational & Experimental Approaches)
  • Molecular Modelling (Structure, MD simulation, Binding & Stability Energetics, Biomolecular Interaction)
  • Bioinformatics (Data mining, Databases, scripting/programming)

PUBLICATIONS

Relevant publications

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  • A. Ababou. New insights into the structural and functional involvement of the gate loop in AcrB export activity. Biochem. Biophys. Acta, 1866 (2018) 242-253. 
  • A. Ababou@, M. Zaleska, & M. Pfuhl. On the Ca2+ binding and conformational changes in EF-hand domains: Experimental evidence of Ca2+-saturated intermediates of N-domain of calmodulin. Biochem. Biophys. Acta, 1865 (2017) 640-651. @ Corresponding author
  • A. Ababou@ & V. Koronakis. Structures of gate loop variants of the AcrB drug efflux pump bound by Erythromycin substrate. PLOS ONE, 11 (2016) e0159154. @ Corresponding author
  • M. Zaleska, C. Fogl, A. L. Kho, A. Ababou, E. Ehler, & M. Pfuhl. The Cardiac Stress Response Factor MS1 Can Bind to DNA and Has a Function in the Nucleus. PLOS ONE, 10 (2015) e0144614.
  • A. Ababou@, & M. Zaleska. Electrostatics effects on Ca2+ binding and conformational changes in EF-hand domains: Functional implications for EF-hand proteins. Arch. Biochem. Biophys. 587 (2015) 61-69.  @ Corresponding author
  • N. P. Greene, P. Hinchliffe, A. Crow, A. Ababou, C. Hughes & V. Koronakis. Structure of an atypical periplasmic adaptor from a multidrug efflux pump of the spirochete Borrelia burgdorferi. FEBS Lett. 857 (2013) 2984-2988.
  • P. Didier, A. Ababou, X. Yang, R. Gosh, T. Daviter, J. E. Ladbury & M. Pfuhl. Making ends meet: the importance of the N- and C-terminus for structure, stability and function of the third SH3 domain of CIN85. Biochemistry 50 (2011) 3649-3659. 
  • A. Ababou, M. Pfuhl & J. E. Ladbury. Novel Insights into Binding Mechanisms of CIN85 SH3 Domains to Cbl Proteins: Solution-based Investigations and in vivo Implications. J. Mol. Biol. 387 (2009) 1120-1136.
  • A. Ababou, E. Rostkova, S. Mistry, C. Le Masurier, Gautel, M., & Pfuhl, M. Myosin binding protein C positioned to play a key role in regulation of muscle contraction: structure and interactions of domain C1. J Mol Biol. 384 (2008) 615-630.
  • J. D. Taylor#, A. Ababou#, R. Fawaz, M., C. Hobbs,  A. Williams & J. E. Ladbury. Structure, dynamics, and binding thermodynamics of the v-Src SH2 domain: Implications for drug design. Proteins. 73 (2008) 929-940. # First and second authors contributed equally to this work
  • A. Ababou, M. Pfuhl & J. E. Ladbury. The stoichiometry of binding between CIN85 SH3 domain A and proline-rich motif from Cbl-b in solution. Nat. Struct. Mol. Biol. 15 (2008) 890-891.
  • M. Ritco-Vonsovici, A. Ababou & M. Horton. Molecular plasticity of b-catenin: new insights from single molecule measurements and MD simulation. Protein Sci. 16 (2007) 1984-1998.
  • A. Ababou & J. E. Ladbury. Survey of the year 2005: literature on applications of isothermal titration calorimetry. J. Mol Recognit.20 (2007) 4-14.
  • A. Ababou@, A. van der Vaart, V. Gogonea & K. M. Merz, Jr. Interaction energy decomposition in protein-protein association: A quantum mechanical study of Barnase-Barstar complex. Biophys. Chem. 125 (2007) 221-236. @ Corresponding author
  • A. Ababou, Gautel, M., & Pfuhl, M. Dissecting the N-terminal myosin binding site of human cardiac myosin binding protein C: Structure and myosin binding of domain C2. J. Biol. Chem. 282 (2007) 9204-9215.
  • A. Ababou & J. E. Ladbury. Survey of the year 2004: literature on applications of isothermal titration calorimetry.J Mol Recognit. 19 (2006) 79-89.
  • J. D. Taylor, R. R. Fawaz, A. Ababou, M. A. Williams & J. E. Ladbury. NMR Assignment of the Apo and Peptide-bound SH2 Domain from the Rous Sarcoma Viral Protein Src. J Biomol NMR. 32 (2005) 339.
  • A. Ababou, L. Zhou, M. Gautel & M. Pfuhl. Sequence specific assignment of domain C1 of the N-terminal myosin-binding site of human cardiac myosin binding protein C (MyBP-C). J Biomol NMR. 29 (2004) 431-432.
  • Damblon, C., Jensen, M., Ababou, A., Papamicael, C., Barsukov, I., Schofield, C. J., Bauer, R., & Robert, G. C. K. The inhibitor thiomandelic acid binds to both metal ions in metallo-b-lactamase and induces positive cooperativity in metal binding. J. Biol. Chem. 278 (2003) 29240 - 29251.
  • A. Ababou, R. A. Shenvi & J. R. Desjarlais. Long range calcium binding effect and conformational change in the N-domain of calmodulin. Biochemistry 40 (2001) 12719-12726.
  • A. Ababou & J. R. Desjarlais. Solvation energetics and conformational change in EF-hand proteins. Protein Sci. 10 (2001) 301-312.
  • A. Ababou@ & E. Bombarda. On the involvement of electron transfer reactions in the fluorescence decay kinetics heterogeneity of proteins. Protein Sci. 10 (2001) 2102-2113. @ Corresponding author
  • E. Bombarda, A. Ababou, C. Vuilleumier, D. Gérard, P. Petitjean, E. Piémont & Y. Mély. Time-resolved fluorescence study of two tryptophan residues of the HIV-1 nucleocapsid protein: Influence of the binding of nucleic acids. Biophys. J. 76 (1999) 1561-1570.
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FUNDING

  • UEL Internal Grant (ECR QR funds) - 2018
  • Eric Reid Fund for Methodology Grant - Biochemical Society - 2017-2018