Dr Tim Knowles BSc(Hons) PhD

Dr Tim Knowles

School of Biosciences
Reader in Structural Biology

Contact details

Address
School of Biosciences
University of Birmingham
Edgbaston
Birmingham
B15 2TT
UK

Tim Knowles is a Reader in Structural Biology whose interest lies in utilising and developing structural and biophysical techniques to elucidate protein function. His research focus spans both prokaryotes and eukaryotes and includes diverse areas of study including resolving the mechanisms of outer membrane biogenesis in Gram-negative bacteria, the development of novel strategies for studying membrane proteins, to the structural biology of rare genetic disorders.

He is also the Birmingham Director of the Midlands Integrative Biosciences Training Partnership (MIBTP) a BBSRC funded Doctoral Training Partnership between the Universities of Birmingham, Warwick, Leicester, Aston and Harper Adams.

Qualifications

  • 2018 – PGCHE – University of Birmimgham. U.K.
  • 2005 – PhD in structural biology, Astbury Centre for Structural Molecular Biology, University of Leeds. U.K.
  • 2000 – B.Sc. (Hons), University of Warwick. U.K.

Biography

Dr Tim Knowles began his interest in biochemisty and structural biology when he undertook a degree in biochemistry at Warwick University, he then began to focus on using nuclear magnetic resonance to probe protein structure when he undertook a Wellcome trust 4 Yr PhD at the Astbury Centre, University of Leeds, where he worked in the labs of Professors Steve Homans and Peter Stockley and focused on elucidating the functional mechanism of the E c.oli methionine repressor, MetJ. In 2005 he moved to the University of Birmingham where he worked within the laboratory of Professor Michael Overduin and focused on novel membrane protein solubilisation techniques, during this time he developed the SMALP method for protein solubilisation, he also began studying his current interest in outer membrane biogenesis in Gram-negative bacteria.

Teaching

Tim teaches on numerous courses including:

  • Undergraduate – Fundamentals of Biosciences, Membranes, energy & Metabolism, Proteins & Enzymes, Chemistry for Biochemists. Structures of Destruction.
  • Postgraduate – MIBTP, Research Techniques in Molecular Biotechnology
  • Module organiser of B.Sc. Biochemistry course “Membranes, Energy & Metabolism”

Postgraduate supervision

If you are interested in studying for a PhD in Tim's lab then please contact him informally using the following email address t.j.knowles@bham.ac.uk.

Funding is available through competition. Both home and international students can apply via the MIBTP scheme, whilst International students by the Darwin scheme – both normally take applications at the end of the calendar year for entry the following year, please email me if you have any questions.

For a full list of available Doctoral Research opportunities, please visit our Doctoral Research Programme pages 

Research

Research Themes

Using structural biology to answer fundamental questions in biology.

Research activity

  1. Outer membrane protein biogenesis


    Gram-negative bacteria contain a double membrane system that acts to protect them from the environment while permitting the selective uptake of nutrients and removal of toxic substances. The outer of these two membranes makes direct contact with the environment and is composed of a lipid inner leaflet, a lipopolysaccharide outer leaflet and harbours two classes of protein, beta-barrel proteins (more commonly known as OMPs for ‘outer membrane protein’) and peripheral lipoproteins (proteins attached to the membrane via a lipid anchor). This membrane make direct contact with the environment and hence is at the frontline of microbial warfare, playing pivotal roles in microbial pathogenesis, virulence and multidrug resistance, mediating many of the lethal processes responsible for infection and disease progression.

    The emergence of bacteria that are resistant to available antibiotics represents an enormous and growing global threat requiring new targets and strategies to combat infection. Multidrug resistance is most serious for Gram-negative bacteria, with essentially few antibiotics under development or likely to be available for clinical use in the near future.

    Gram-negative bacteria are generally more resistant than Gram-positive bacteria to antibiotics, detergents, and other toxic chemicals because of the presence of an additional membrane surrounding the cell, the outer membrane. This membrane contains a sophisticated asymmetry of lipids with Lipopolysaccharide in the outer leaflet and phospholipid in the inner leaflet. It makes for a highly effective permeability barrier, both by acting as a barrier to hydrophilic molecules but also by acting to slow the penetration of small hydrophobic molecules, explaining their increased resistance to hydrophobic antibiotics and detergents. Whilst the proteins present within the outer membrane are the prime instruments of microbial warfare and play key roles in microbial pathogenesis, virulence and multidrug resistance, mediating many of the lethal processes responsible for infection and disease progression. Outer membrane proteins (OMPs) are also essential for cellular homeostasis allowing excretion of toxic substances, such as antibiotics, and uptake of nutrients.

    The research in the laboratory of Dr Tim Knowles is focused on elucidating the mechanisms involved in the fundamental processes of outer membrane biogenesis in Gram-negative bacteria and has several important objectives: (1) to provide fundamental information about how Gram-negative bacteria form. (2) To provide new opportunities to attenuate bacteria in the pursuit of anti-infective strategies. Current antibiotics predominantly target peptidoglycan synthesis and have been very effective in the past. Targeting OM biogenesis offers the potential for a whole new class of antimicrobials urgently required to stay ahead of bacterial resistance. 

     

    Projects within this research area include.

    Phospholipid transport to the outer membrane

    Recently three protein pathways, the Mla, PqiABC and YebST(LetAB) pathways, have been identified that have components in the inner membrane, periplasm and outer membrane and all bind phospholipid suggesting they may be involved in phospholipid transport. How these pathways transport phospholipid and the molecular mechanisms involved in transport still remain to be elucidated however. To answer these questions we are using the latest structural biology techniques including cryo-electron microscopy, X-ray crystallography, nuclear magnetic resonance, neutron reflectometry as well as developing our own novel in house biophysical tools to study these fascinating pathways. Using this approach potential druggable pockets will be identified and allow the identification of compounds that will not only abolish virulence but also impede the restoration of a damaged outer membrane and therefore increase the effectiveness of already available antibiotics.

    The Bam complex

    A single OM complex, the β-Barrel assembly machine (Bam) complex, has been recognized as essential for the efficient insertion of almost all OMPs into the outer membrane.  It is ubiquitous throughout Gram-negative bacteria, however we are only just beginning to understand how it functions. The structure of the complex has been identified but how the components function as part of the complex and how this complex can insert the myriad OMPs targeted to the outer membrane is still to be determined. We are using a multidisciplinary approach, working in both the fields of biophysics and molecular biology to probe the structure of this complex and how it functions. This understanding is critical as the design of compounds that inhibit this process would impede OMP biogenesis and therefore essential physiological, pathogenic and drug resistance functions.

  2. Novel amethods for studying membrane proteins

    Our group focuses on two areas:

    Membrane protein solubilisation

    Working with membrane proteins is technically demanding. The current best technology is the use of detergents which by their very nature often destabilise proteins, inhibit function and decrease sample longevity. Consequently Knowles is developing new technologies to solubilize membrane proteins in the absence of detergents. To date Knowles has developed a styrene maleic acid based system for the solubilisation of membrane proteins, known as SMALP technology, which offers increased stability, longevity and functionality to detergent based systems.

    Membrane protein function

    Knowles is working with colleagues at the ISIS Neutron and Muon source, Rutherford Appleton laboratory, UK, to develop sensor based systems directly utilising membrane proteins within their phospholipid bilayers atop the sensor surface. These allow a “true to nature” approach to studying membrane protein function including drug screening, receptor ligand interactions and viral-membrane interactions amongst other things.

  3. Batten Disease

    Knowles is working with Dr Richard Tuxworth (University of Birmingham) to understand how lysosomal dysfunction contributes to neurodegenerative disease, focusing on the protein Cln3 and the role it plays in the rare but fatal inherited disease, Neuronal Ceroid Lipofuscinosis, or Batten Disease. 

Publications

  1. Ratkeviciute, G., B.F. Cooper, and T.J. Knowles, Methods for the solubilisation of membrane proteins: the micelle-aneous world of membrane protein solubilisation. Biochem Soc Trans, 2021. 49(4): p. 1763-1777.
  2. Karunakaran, M.M., C.R. Willcox, M. Salim, D. Paletta, A.S. Fichtner, A. Noll, L. Starick, A. Nohren, C.R. Begley, K.A. Berwick, R.A.G. Chaleil, V. Pitard, J. Dechanet-Merville, P.A. Bates, B. Kimmel, T.J. Knowles, V. Kunzmann, L. Walter, M. Jeeves, F. Mohammed, B.E. Willcox, and T. Herrmann, Butyrophilin-2A1 Directly Binds Germline-Encoded Regions of the Vgamma9Vdelta2 TCR and Is Essential for Phosphoantigen Sensing. Immunity, 2020. 52(3): p. 487-498 e6.
  3. Hall, S.C.L., L.A. Clifton, C. Tognoloni, K.A. Morrison, T.J. Knowles, C.J. Kinane, T.R. Dafforn, K.J. Edler, and T. Arnold, Adsorption of a styrene maleic acid (SMA) copolymer-stabilized phospholipid nanodisc on a solid-supported planar lipid bilayer. J Colloid Interface Sci, 2020. 574: p. 272-284.
  4. Bryant, J.A., F.C. Morris, T.J. Knowles, R. Maderbocus, E. Heinz, G. Boelter, D. Alodaini, A. Colyer, P.J. Wotherspoon, K.A. Staunton, M. Jeeves, D.F. Browning, Y.R. Sevastsyanovich, T.J. Wells, A.E. Rossiter, V.N. Bavro, P. Sridhar, D.G. Ward, Z.S. Chong, E.C. Goodall, C. Icke, A.C. Teo, S.S. Chng, D.I. Roper, T. Lithgow, A.F. Cunningham, M. Banzhaf, M. Overduin, and I.R. Henderson, Structure of dual BON-domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation. Elife, 2020. 9.
  5. Pollock, N.L., M. Rai, K.S. Simon, S.J. Hesketh, A.C.K. Teo, M. Parmar, P. Sridhar, R. Collins, S.C. Lee, Z.N. Stroud, S.E. Bakker, S.P. Muench, C.H. Barton, G. Hurlbut, D.I. Roper, C.J.I. Smith, T.J. Knowles, C.M. Spickett, J.M. East, V.L.G. Postis, and T.R. Dafforn, SMA-PAGE: A new method to examine complexes of membrane proteins using SMALP nano-encapsulation and native gel electrophoresis. Biochim Biophys Acta Biomembr, 2019. 1861(8): p. 1437-1445.
  6. Jamshad, M., T.J. Knowles, S.A. White, D.G. Ward, F. Mohammed, K.F. Rahman, M. Wynne, G.W. Hughes, G. Kramer, B. Bukau, and D. Huber, The C-terminal tail of the bacterial translocation ATPase SecA modulates its activity. Elife, 2019. 8.
  7. Hughes, G.W., S.C.L. Hall, C.S. Laxton, P. Sridhar, A.H. Mahadi, C. Hatton, T.J. Piggot, P.J. Wotherspoon, A.C. Leney, D.G. Ward, M. Jamshad, V. Spana, I.T. Cadby, C. Harding, G.L. Isom, J.A. Bryant, R.J. Parr, Y. Yakub, M. Jeeves, D. Huber, I.R. Henderson, L.A. Clifton, A.L. Lovering, and T.J. Knowles, Evidence for phospholipid export from the bacterial inner membrane by the Mla ABC transport system. Nat Microbiol, 2019. 4(10): p. 1692-1705.
  8. Clifton, L.A., S.C.L. Hall, N. Mahmoudi, T.J. Knowles, F. Heinrich, and J.H. Lakey, Structural Investigations of Protein-Lipid Complexes Using Neutron Scattering. Methods Mol Biol, 2019. 2003: p. 201-251.
  9. Morris, F.C., T.J. Wells, J.A. Bryant, A.E. Schager, Y.R. Sevastsyanovich, D.J.P. Squire, J. Marshall, G.L. Isom, J. Rooke, R. Maderbocus, T.J. Knowles, M. Overduin, A.E. Rossiter, A.F. Cunningham, and I.R. Henderson, YraP Contributes to Cell Envelope Integrity and Virulence of Salmonella enterica Serovar Typhimurium. Infect Immun, 2018. 86(11).
  10. Jain, N., T.J. Knowles, P.A. Lund, and T.K. Chaudhuri, Minichaperone (GroEL191-345) mediated folding of MalZ proceeds by binding and release of native and functional intermediates. Biochim Biophys Acta Proteins Proteom, 2018. 1866(9): p. 941-951.
  11. Hall, S.C.L., C. Tognoloni, J. Charlton, E.C. Bragginton, A.J. Rothnie, P. Sridhar, M. Wheatley, T.J. Knowles, T. Arnold, K.J. Edler, and T.R. Dafforn, An acid-compatible co-polymer for the solubilization of membranes and proteins into lipid bilayer-containing nanoparticles. Nanoscale, 2018. 10(22): p. 10609-10619.
  12. Salim, M., T.J. Knowles, A.T. Baker, M.S. Davey, M. Jeeves, P. Sridhar, J. Wilkie, C.R. Willcox, H. Kadri, T.E. Taher, P. Vantourout, A. Hayday, Y. Mehellou, F. Mohammed, and B.E. Willcox, BTN3A1 Discriminates gammadelta T Cell Phosphoantigens from Nonantigenic Small Molecules via a Conformational Sensor in Its B30.2 Domain. ACS Chem Biol, 2017. 12(10): p. 2631-2643.
  13. Isom, G.L., N.J. Davies, Z.S. Chong, J.A. Bryant, M. Jamshad, M. Sharif, A.F. Cunningham, T.J. Knowles, S.S. Chng, J.A. Cole, and I.R. Henderson, MCE domain proteins: conserved inner membrane lipid-binding proteins required for outer membrane homeostasis. Sci Rep, 2017. 7(1): p. 8608.
  14. Salim, M., C.R. Willcox, F. Mohammed, A.C. Hayday, M. Overduin, B.E. Willcox, and T.J. Knowles, Secondary structure and (1)H, (13)C and (15)N resonance assignments of Skint-1: a selecting ligand for a murine gammadelta T cell subset implicated in tumour suppression. Biomol NMR Assign, 2016. 10(2): p. 357-60.
  15. Salim, M., T.J. Knowles, R. Hart, F. Mohammed, M.J. Woodward, C.R. Willcox, M. Overduin, A.C. Hayday, and B.E. Willcox, Characterization of a Putative Receptor Binding Surface on Skint-1, a Critical Determinant of Dendritic Epidermal T Cell Selection. J Biol Chem, 2016. 291(17): p. 9310-21.
  16. Morrison, K.A., A. Akram, A. Mathews, Z.A. Khan, J.H. Patel, C. Zhou, D.J. Hardy, C. Moore-Kelly, R. Patel, V. Odiba, T.J. Knowles, M.U. Javed, N.P. Chmel, T.R. Dafforn, and A.J. Rothnie, Membrane protein extraction and purification using styrene-maleic acid (SMA) copolymer: effect of variations in polymer structure. Biochem J, 2016. 473(23): p. 4349-4360.
  17. Lee, S.C., T.J. Knowles, V.L. Postis, M. Jamshad, R.A. Parslow, Y.P. Lin, A. Goldman, P. Sridhar, M. Overduin, S.P. Muench, and T.R. Dafforn, A method for detergent-free isolation of membrane proteins in their local lipid environment. Nat Protoc, 2016. 11(7): p. 1149-62.
  18. Lee, S.C., S. Khalid, N.L. Pollock, T.J. Knowles, K. Edler, A.J. Rothnie, R.T.T. O, and T.R. Dafforn, Encapsulated membrane proteins: A simplified system for molecular simulation. Biochim Biophys Acta, 2016. 1858(10): p. 2549-2557.
  19. Fogl, C., F. Mohammed, C. Al-Jassar, M. Jeeves, T.J. Knowles, P. Rodriguez-Zamora, S.A. White, E. Odintsova, M. Overduin, and M. Chidgey, Mechanism of intermediate filament recognition by plakin repeat domains revealed by envoplakin targeting of vimentin. Nat Commun, 2016. 7: p. 10827.
  20. Jeeves, M., P. Sridhar, and T.J. Knowles, Expression, Purification, and Screening of BamE, a Component of the BAM Complex, for Structural Characterization. Methods Mol Biol, 2015. 1329: p. 245-58.
  21. Jeeves, M. and T.J. Knowles, A novel pathway for outer membrane protein biogenesis in Gram-negative bacteria. Mol Microbiol, 2015. 97(4): p. 607-11.
  22. Jamshad, M., V. Grimard, I. Idini, T.J. Knowles, M.R. Dowle, N. Schofield, P. Sridhar, Y.P. Lin, R. Finka, M. Wheatley, O.R. Thomas, R.E. Palmer, M. Overduin, C. Govaerts, J.M. Ruysschaert, K.J. Edler, and T.R. Dafforn, Structural analysis of a nanoparticle containing a lipid bilayer used for detergent-free extraction of membrane proteins. Nano Res, 2015. 8(3): p. 774-789.
  23. Jamshad, M., J. Charlton, Y.P. Lin, S.J. Routledge, Z. Bawa, T.J. Knowles, M. Overduin, N. Dekker, T.R. Dafforn, R.M. Bill, D.R. Poyner, and M. Wheatley, G-protein coupled receptor solubilization and purification for biophysical analysis and functional studies, in the total absence of detergent. Biosci Rep, 2015. 35(2).
  24. Browning, D.F., V.N. Bavro, J.L. Mason, Y.R. Sevastsyanovich, A.E. Rossiter, M. Jeeves, T.J. Wells, T.J. Knowles, A.F. Cunningham, J.W. Donald, T. Palmer, M. Overduin, and I.R. Henderson, Cross-species chimeras reveal BamA POTRA and beta-barrel domains must be fine-tuned for efficient OMP insertion. Mol Microbiol, 2015. 97(4): p. 646-59.
  25. Gulati, S., M. Jamshad, T.J. Knowles, K.A. Morrison, R. Downing, N. Cant, R. Collins, J.B. Koenderink, R.C. Ford, M. Overduin, I.D. Kerr, T.R. Dafforn, and A.J. Rothnie, Detergent-free purification of ABC (ATP-binding-cassette) transporters. Biochem J, 2014. 461(2): p. 269-78.
  26. Browning, D.F., S.A. Matthews, A.E. Rossiter, Y.R. Sevastsyanovich, M. Jeeves, J.L. Mason, T.J. Wells, C.A. Wardius, T.J. Knowles, A.F. Cunningham, V.N. Bavro, M. Overduin, and I.R. Henderson, Mutational and topological analysis of the Escherichia coli BamA protein. PLoS One, 2013. 8(12): p. e84512.
  27. Sevastsyanovich, Y.R., D.L. Leyton, T.J. Wells, C.A. Wardius, K. Tveen-Jensen, F.C. Morris, T.J. Knowles, A.F. Cunningham, J.A. Cole, and I.R. Henderson, A generalised module for the selective extracellular accumulation of recombinant proteins. Microb Cell Fact, 2012. 11: p. 69.
  28. Machado, L.R., R.J. Hardwick, J. Bowdrey, H. Bogle, T.J. Knowles, M. Sironi, and E.J. Hollox, Evolutionary history of copy-number-variable locus for the low-affinity Fcgamma receptor: mutation rate, autoimmune disease, and the legacy of helminth infection. Am J Hum Genet, 2012. 90(6): p. 973-85.
  29. Rossiter, A.E., D.L. Leyton, K. Tveen-Jensen, D.F. Browning, Y. Sevastsyanovich, T.J. Knowles, K.B. Nichols, A.F. Cunningham, M. Overduin, M.A. Schembri, and I.R. Henderson, The essential beta-barrel assembly machinery complex components BamD and BamA are required for autotransporter biogenesis. J Bacteriol, 2011. 193(16): p. 4250-3.
  30. Knowles, T.J., D.F. Browning, M. Jeeves, R. Maderbocus, S. Rajesh, P. Sridhar, E. Manoli, D. Emery, U. Sommer, A. Spencer, D.L. Leyton, D. Squire, R.R. Chaudhuri, M.R. Viant, A.F. Cunningham, I.R. Henderson, and M. Overduin, Structure and function of BamE within the outer membrane and the beta-barrel assembly machine. EMBO Rep, 2011. 12(2): p. 123-8.
  31. Jamshad, M., Y.P. Lin, T.J. Knowles, R.A. Parslow, C. Harris, M. Wheatley, D.R. Poyner, R.M. Bill, O.R. Thomas, M. Overduin, and T.R. Dafforn, Surfactant-free purification of membrane proteins with intact native membrane environment. Biochem Soc Trans, 2011. 39(3): p. 813-8.
  32. Knowles, T.J., P. Sridhar, S. Rajesh, E. Manoli, M. Overduin, and I.R. Henderson, Secondary structure and 1H, 13C and 15N resonance assignments of BamE, a component of the outer membrane protein assembly machinery in Escherichia coli. Biomol NMR Assign, 2010. 4(2): p. 179-81.
  33. Knowles, T.J., A. Scott-Tucker, M. Overduin, and I.R. Henderson, Membrane protein architects: the role of the BAM complex in outer membrane protein assembly. Nat Rev Microbiol, 2009. 7(3): p. 206-14.
  34. Knowles, T.J., D.M. McClelland, S. Rajesh, I.R. Henderson, and M. Overduin, Secondary structure and (1)H, (13)C and (15)N backbone resonance assignments of BamC, a component of the outer membrane protein assembly machinery in Escherichia coli. Biomol NMR Assign, 2009. 3(2): p. 203-6.
  35. Knowles, T.J., R. Finka, C. Smith, Y.P. Lin, T. Dafforn, and M. Overduin, Membrane proteins solubilized intact in lipid containing nanoparticles bounded by styrene maleic acid copolymer. J Am Chem Soc, 2009. 131(22): p. 7484-5.
  36. Knowles, T.J., M. Jeeves, S. Bobat, F. Dancea, D. McClelland, T. Palmer, M. Overduin, and I.R. Henderson, Fold and function of polypeptide transport-associated domains responsible for delivering unfolded proteins to membranes. Mol Microbiol, 2008. 68(5): p. 1216-27.
  37. Conner, M., M.R. Hicks, T. Dafforn, T.J. Knowles, C. Ludwig, S. Staddon, M. Overduin, U.L. Gunther, J. Thome, M. Wheatley, D.R. Poyner, and A.C. Conner, Functional and biophysical analysis of the C-terminus of the CGRP-receptor; a family B GPCR. Biochemistry, 2008. 47(32): p. 8434-44.
  38. Knowles, T.J., S. Bobat, M. Jeeves, I.R. Henderson, and M. Overduin, Secondary structure and 1H, 13C and 15N resonance assignments of the Escherichia coli YaeT POTRA domain. Biomol NMR Assign, 2007. 1(1): p. 113-5.

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