Kleanthous Group

Welcome to the Kleanthous Research Group


We take a multidisciplinary approach toward the functional, biophysical and structural analysis of protein-protein interactions in a variety of biological settings.  The figure shows some of the structures of protein complexes we have solved and highlights the range of methods we use to understand how and why proteins form complexes with each other.  Our work is driven by specific biological questions where protein-protein recognition is central to function, and by fundamental questions concerning specificity and affinity of protein-protein interactions.

Awards and Distinctions

2018 Elected member of EMBO
2012 Iveagh Chair of Microbial Biochemistry, Oxford
2011-2013 Chair, The Biochemical Society

We take a multidisciplinary approach toward the functional, biophysical and structural analysis of protein-protein interactions in a variety of biological settings.  The figure shows some of the structures of protein complexes we have solved and highlights the range of methods we use to understand how and why proteins form complexes with each other.  Our work is driven by specific biological questions where protein-protein recognition is central to function, and by fundamental questions concerning specificity and affinity of protein-protein interactions.


Colicin Biology

Colicins parasitize E. coli cell envelope proteins

Colicins form one of the major areas of study in the lab.  Colicins are protein antibiotics that are imported into and kill Escherichia coli cells.  Most Gram-negative organisms make equivalent toxins which serve as important agents of competition between microbial populations particularly the Enterobacteriaceae.  We study them as a means of asking fundamental questions as to how folded proteins use protein-protein interactions translocate across membranes.  Colicins contact outer membrane receptors and translocator proteins, the latter helping them to contact periplasmic and inner membrane proteins that are linked to the proton motive force.  Group A colicins translocate into cells via the Tol system whereas Group B colicins utilise the Ton system.  We study the import mechanism of Group A nuclease colicins which bind the vitamin B12 receptor BtuB and OmpF in the outer membrane and Tol proteins in the periplasm; our aim is to understand how contact with these proteins triggers translocation into the cell.  Subsequently, the nuclease domains translocate across the inner membrane to reach their cytoplasmic nucleic acid targets; genomic DNA for ColE9 and 16S ribosomal RNA for ColE3.  Other nuclease colicins (e.g. ColE5) target tRNA molecules.  For a recent review of colicin biology see Papadakos et al (2012), Quarterly Reviews of Biophysics, 45 (01), February 2012, 57-103


Colicins parasitize E. coli cell envelope proteins


Colicins assemble a translocon at the cell surface

The figure shows structures for the group A colicin ColE3/Im3 bound to its receptor BtuB (solved by the Cramer lab; Kurisu et al (2003) Nat. Struct Biol10, 948) and the group B colicin ColIa bound to its receptor Cir, which normally transports iron (solved by the Buchanan lab; Buchanan et al (2007) EMBO J 26, 2594).  Both colicins have intrinsically unstructured translocation domains (IUTDs) which recruit translocator proteins and which have embedded within them signalling epitopes that contact periplasmic proteins.  We have shown that nuclease colicins such as ColE3 and ColE9 recruit OmpF using the IUTD, with the open lumen of the porin being the likely route to the periplasm.  Contact between the colicin’s IUTD and TolB in the periplasm (see slides 4-6) completes formation of a so-called ‘translocon’ formation of which triggers dissociation of the tightly bound immunity protein and initiates cell entry.  See Housden et al (2005) PNAS 102, 13849, Vankemmelbeke et al (2009) J. Biol. Chem284, 18932 and Kleanthous (2010) Mol. Microbiol 75, 529 for further details.




Colicin intrinsically unstructured translocation domain (IUTD) mimics Pal interactions with TolB

The IUTD of enzymatic colicins such as ColE3 and ColE9 contains a 16-residue TolB binding epitope (TBE) within it which folds into a distorted hairpin and hydrogen bonds to TolB residues in a way that precisely mimics interactions made by helical residues in Pal.  See Loftus et al (2006) PNAS 103, 12353 and Bonsor et al (2007) JACS 129, 4800 for further information.


TolB is an allosteric β-propeller protein which undergoes an order-disorder transition at its N-terminus

The TolB N-terminus is the docking site for TolA, an inner membrane protein which spans the periplasm and is connected to the pmf via its contacts with TolQ and TolR.  In the absence of any binding partners the TolB N-terminus is in conformational exchange.  Pal binding to the β-propeller of TolB results in the opening of a proline gate on TolB revealing a binding site for the TolB N-terminus and blocking its ability to bind TolA.  Conversely, binding of the colicin TBE to the β -propeller promotes TolA binding by closing the proline gate.  Hence, although the colicin mimics Pal it results in a completely different TolB response; this allows the colicin to tap into the pmf-linked Tol system in the inner membrane while still positioned on the outside of the cell.  See Bonsor et al (2009) EMBO J. 28, 2846 for further details.



Nuclease domain electrostatics potentiate cell killing

DNase colicin cell killing is mediated by electrostatic interactions.  Figure shows the relationship between the degree of positive charge on a colicin DNase (using natural and engineered variants) and the efficiency of colicin-mediated cell killing in liquid culture of E. coli HDL11, a strain which is depleted in anionic phospholipids.  Data suggest a direct electrostatically-mediated interaction between colicin nucleases and the bacterial inner membrane.  See  Mosbahi et al (2004) J. Biol. Chem279, 22145, Mosbahi et al (2006) Protein Sci15, 620 and Walker et al (2007) J. Biol. Chem282, 31389 for further details.


All nuclease colicins require FtsH for antibacterial activity

The essential inner membrane AAA+ ATPase/protease FtsH is required for nuclease colicin antibacterial activity.  An FtsH deletion mutant AR3291 is resistant to all Group A and Group B nuclease colicins but is not resistant to pore-forming colicins.  The slide illustrates a speculative model as to how colicins might subvert FtsH, which is involved in degrading misfolded inner membrane proteins, for entry to the cytoplasm.  See Walker et al (2007) J. Biol. Chem282, 31389 for further details



Structure of ColE3 cytotoxic domain bound to the E. coli ribosome

ColE3 kills bacterial cells by blocking protein synthesis which is the result of a single phosphodiester bond being cleaved in the decoding centre of the ribosomal A-site.  Cleavage has a profound effect on the translocation step of protein synthesis, resulting in sequential impaired decoding events until eventually translation halts.  We have been collaborating with the Rodnina (Witten) and Ramakrishnan (LMB) labs to investigate the mechanistic and structural details of this cytotoxic mechanism.  This includes a structure of the E3 rRNase bound to an intact 70S ribosome.  See Lancaster et al (2008) Mol. Microbiol69, 390 and Ng et al (2010) Nat. Struct. Mol. Biol. In Press for further details.


Exosite binding and energetics of Im9 binding the ColE9 DNase

DNase colicins are members of the HNH family of endonucleases, which includes caspase-activated DNases in eukaryotes.  Left-hand figure shows the structure of the E9 DNase bound to dsDNA and a single Mg2+ ion.  Highlighted in blue is the region of the enzyme that is bound by the high affinity immunity protein Im9, an exosite inhibitor.  Immunity proteins protect colicin-producing organisms from suicide and are dissociated from the enzyme during cell entry by an unknown mechanism.  Right-hand figure shows ΔΔG data for alanine mutants of the E9 DNase binding Im9 (only 2 helices of Im9 are shown for clarity).  The hotspot of E9 DNase meets the hotspot of Im9.  See Maté & Kleanthous (2004) J. Biol. Chem279, 34763, Li et al (2004) J. Mol. Biol337, 743 and Keeble et al (2008) J. Mol. Biol379, 745 for further details.


Structural basis for high selectivity in a high affinity protein-protein interaction

Using NMR-based docking as a guide (collaboration with Geoff Moore in Norwich), we deployed a disulfide-trapping strategy on a non-cognate complex between the colicin E9 endonuclease (E9 DNase) and immunity protein 2 (Im2), which is seven orders of magnitude weaker binding than the cognate femtomolar E9 DNase-Im9 interaction.  The 1.77 Å crystal structure of the E9 DNase-Im2 complex reveals an entirely non-covalent interface where the intersubunit disulfide merely supports the crystal lattice.  In combination with computational alanine scanning of interfacial residues (undertaken by the Baker lab in Seattle), the structure reveals that the driving force for binding is so strong that severely unfavourable specificity contacts are tolerated at the interface and as a result the complex becomes weakened through ‘frustration’.  As well as rationalising past mutational and thermodynamic data, comparing our non-cognate structure with previous cognate complexes highlights the importance of loop regions in developing selectivity and accentuates the multiple roles of buried water molecules that stabilise, ameliorate or aggravate interfacial contacts.  See Meenan et al (2010) PNAS 107, 10080 further details.


Disulphide stress and regulation

Disulfide stress and its regulation by σR-RsrA complex

The sigma factor σRand its inhibitor RsrA regulate the expression of ~30 genes in response to disulfide stress in the soil bacterium Streptomyces coelicolor.  RsrA is a zinc-containing anti-sigma (ZAS) protein, one of a growing list of transcriptional regulators that respond to diverse environmental cues.  During oxidative (disulfide) stress, a trigger disulfide forms in RsrA that causes the expulsion of its single metal ion.  This results in a large structural change that abolishes its ability to bind σR, which is then free to activate transcription of its target genes, including thioredoxin and thioredoxin reductase.  Redox homeostasis is resumed when these cellular reductants re-reduce RsrA via the small molecule reducing agent myothiol.  We found that the trigger disulfide is naturally degenerate, formed between all three of the metal ligands, Cys11, Cys41 and Cys44, which causes substantial changes in protein structure, as deduced by circular dichroism spectroscopy.  See Kang et al EMBO J. (1999) 18, 4292, Li et al (2002) J. Mol. Biol323, 225 and Li et al (2003) J. Mol. Biol333, 461 for further details.


Defining the metal coordination of RsrA

Controversy surrounded the metal ligation chemistry of the single zinc ion in RsrA.  We used a combination of mutagenesis and EXAFS spectroscopy to define this coordination chemistry, which includes the three cysteines known to be involved in forming the degenerate trigger disulfide bond in RsrA.  Three of the ligands to the metal ion (His37xxxCys41xxCys44) are part of a sequence motif which is invariant in ZAS proteins.  See Zdanowski et al (2006) Biochemistry 45, 8294 for further details.


Kleanthous lab publications (Pubmed

External appointments, society memberships and conference organisation

  • 2016- Research Council of Norway

  • 2016- Editor-in-cheif, Emerging Topics in Life Sciences, Portland Press

  • 2014- John Innes Centre Science & Impact Advisory Board

  • 2013 Organising Committee ESF-EMBO conference on 'Molecular Perspectives on Protein-Protein Interactions', Polonia Castle, Pultusk, Poland

  • 2012 Organising Committee, Biochemical Society Focus Meeting 'How bugs kills bugs: Progress and challenges in bacteriocin research', University of Nottingham. 

  • 2011-2012 Chair, Wellcome Trust Basic Science Interview Committee. 

  • 2011-2013 Chairman, The Biochemical Society 

  • 2010 Co-chair, ESF-EMBO conference on Molecular Perspectives on Protein-Protein Interactions, Sant Feliu de Guixols, Spain

  • 2010-2014 Faculty 1000 reviewer-Protein Chemistry & Proteomics

  • 2010-2011 Editorial Advisory Board, Molecular Microbiology

  • 2008 External assessor, Department of Biochemistry, University of Bristol

  • 2008-2009 EPSRC Chemistry International Review Steering Committee

  • 2008-2010 Vice-chair, Biochemical Society

  • 2008 Chair, 2nd international conference on Molecular Perspectives on Protein-Protein Interactions, Dubrovnik, Croatia

  • 2008 Co-chair, Gordon Research Conference on Biomolecular Interactions & Methods, Ventura, CA

  • 2007-2010 Wellcome Trust Basic Science Interview committee

  • 2007 BBSRC REI panel

  • 2006- 2008 External examiner for BSc (Hons) Degree Programmes in Biochemistry, Molecular Biology and Molecular Genetics, University of Dundee

  • 2006 - 2008 External examiner for 1st year MRes of Wellcome Trust 4 year PhD programme at the University of Glasgow

  • 2006 International vice-chair for Gordon Research Conference on Reversible Associations in Structural & Molecular Biology, Ventura, CA

  • 2005 Member of organising scientific committee for the Katzir conference on Molecular Perspectives on Protein-Protein Interactions, Eilat, Israel

  • 2005 Contributor to Faculty of 1000 Biology - Protein Chemistry & Proteomics

  • 2005 BBSRC Integrative & Systems Biology Strategy panel

  • 2005 External RAE adviser to the School of Biological Sciences, University of East Anglia

  • 2002 - 2006 Biochemistry and Cell Biology panel of the BBSRC

  • 2004-2007 External ‘critical friend’ for RAE08 Department of Biochemistry, University of Sussex

  • 2002 Co-opted panel member for Wellcome Trust Functional Genomics Development Initiative

  • 1995 - 1997 Molecular Enzymology Group of the Biochemical Society

  • 1994 - 1997 Editorial Board of the Biochemical Journal

  • 1994 - 1997 Molecular and Cell Panel of The Wellcome Trust

  • Member of the Biophysical Society

  • Member of the Biochemical Society

Recent invited lectures


  • Keynote, Mechanisms of bacterial toxin delivery symposium, UC Santa Barbara, USA
  • Department of Infectious Diseases, Genetech, USA


  • 40th Lourne conference on Protein Function and Sctructure, Lourne, Australia
  • i3 Institute University of Technology Sydney, Australia
  • School of Chemistry and Molecular Biosciences, University of Brisbane, Australia
  • Department of Biological Chemistry, Weizmann Institute of Science, Israel
  • 5th International conference on Molecular Perspectives on Protein-Protein interactions, Toronto, Canada
  • Gordon Research Conference on Proteins, Holderness College, NH, USA
  • Leibniz Institute of Molecular Pharmacology, FMP Berlin, Germany


  • Gordon Research Conference on Bacterial Cell Surfaces, Mount Snow, VT, USA
  • Gordon Research Conference on Intrinsically Disordered Proteins, Stonehill College, MA, USA
  • Protein Society, San Diego, California, USA


  • Randall Institute, King’s College London
  • Microbes in Norwich symposium & JIC open seminar, John Innes Centre, Norwich
  • Department of Biochemistry annual recess, Oxford
  • ESF-EMBO conference on Molecular Perspectives on Protein-Protein Interactions, Pultusk, Poland
  • Marie Curie TRANSPOL network summer school, Pultusk, Poland
  • Keynote speaker, Inaugural South West Doctoral Training Partnership Conference
  • 10th annual EIMID meeting, Couvent Royal de Saint-Maximin, France
  • AFMB, FRISBI workshop, Marseille, France
  • School of Life Sciences, University of Warwick


  • Biochemical Society Focus Meeting, How bugs kill bugs: Progress & challenges in bacteriocin research.  University of Nottingham, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
  • Biochemical Society lecture, Queenstown Molecular Biology 2012 meeting, New Zealand
  • Young Microbiologists Symposium, University College Cork, Ireland


  • 103rd meeting of the Scottish Protein Structure Group, University of Edinburgh
  • 50th Anniversary of the University of Leicester Biochemistry Department
  • Society of General Microbiology, Cell Envelope: Architecture, University of York
  • Institute for Cell & Molecular Biosciences, University of Newcastle
  • Biochemical Society sponsored seminar, John Innes Centre, Norwich
  • British Crystallography Association, winter meeting, Harwell, Didcot


  • Gordon Research Conference on Ligand Recognition & Molecular Gating, Il Ciocco, Lucca, Italy      
  • Speaker and Session chair, Advances in Biophysical Methods, Gordon Research Conference on Biomolecular Interactions & Methods, Galveston, Tx, USA
  • Division of Infection and Immunity and Wellcome Centre for Molecular Parasitology, University of Glasgow


  • Department of Pathology, University of Cambridge
  • Department of Crystallography, Birkbeck College, University of London
  • Conway Institute of Biomolecular and Biomedical Research, University College Dublin
  • National Institute of Medical Research, Mill Hill, London
  • Division of Molecular Biosciences, Imperial College, London
  • Dahlem Lecture, Max Planck Institute for Molecular Genetics, Berlin
  • Division of Molecular Microbiology, University of Dundee
  • Faculty of Biological Sciences, University of Leeds
  • School of Biological Sciences, Queen’s University Belfast


  • School of Biological Sciences, University of East Anglia, Norwich
  • Department of Molecular Biology & Biotechnology, University of Sheffield
  • 2nd International Conference on Molecular Perspectives on Protein-Protein Interactions, Dubrovnik, Croatia
  • ESF-EMBO Bacterial Networks meeting (BacNet08), Barcelona, Spain
  • Strategies for intrinsically unfolded proteins, International Conference on Structural Genomics, Oxford
  • Inaugural lecture, University of York
  • Boston Biomedical Research Institute, Boston, MA, USA
  • NIDDK, NIH, Bethesda, USA


  • Department of Biochemistry, University of Bristol
  • Department of Biochemistry, University of Birmingham
  • Laboratory of Molecular Biology, Cambridge
  • Society for General Microbiology, Cells and Cell Surfaces, University of Manchester
  • Department of Chemistry, University of Edinburgh
  • Department of Biology, University of York
  • 6th European Biophysics Congress, session on Disordered and Aggregated Proteins, Imperial College London
  • Institute of Chemistry, University of Leiden, The Netherlands
  • School of Biosciences, University of Nottingham


  • Department of Biosciences, University of Kent
  • Department of Protein Engineering, Genentech, South San Francisco, USA
  • FASEB Summer Research Conference, Nucleic Acid Enzymes, Vermont, USA
  • 1st UK Bacterial Cell Wall Biosynthesis Network meeting, University of Warwick
  • ProSA Marie-Curie Network workshop, MPI, Berlin, Germany
  • John Innes Centre, Norwich Research Park, Norwich


  • Biomolecular Dynamics & Interactions Symposium, Bio21 Institute, University of Melbourne, Australia
  • 30th Annual Lorne Conference on Protein Structure & Function, Phillip Island, Australia
  • School of Molecular and Microbial Sciences, University of Brisbane, Australia
  • Bioinformatics Institute, Biopolis, Singapore
  • York Biology Cell Signalling minisymposium
  • Head of Department Seminar series, York
  • Speaker and session chair at the Katzir conference on Molecular Perspectives on Protein-Protein Interactions, Eilat, Israel


  • Speaker and session chair, Gordon Research Conference on Reversible Associations in Structural & Molecular Biology, Ventura, CA
  • Department of Biomolecular Sciences, University of St. Andrews
  • Protein Structure & Folding minisymposium, Faculties of Pharmacy & Chemistry, University of Utrecht, The Netherlands
  • 5th International Conference on ‘Zinc Signals’, University of Aarhus, Denmark
  • Invited speaker at EMBO Workshop on Transient kinetics applied to biological macromolecules, University of Kent, Canterbury


  • Department of Biological Sciences, University of Southampton
  • Department of Biochemistry, University of Glasgow
  • Society of General Microbiology sponsored seminar, Department of Microbiology, Moyne Institute for Preventative Medicine, Trinity College, Dublin
  • Department of Biological Sciences, University of Hull


  • 40th Anniversary Celebrations, Department of Biochemistry, University of Leicester


  • Norwich Research Park Symposium on ‘Proteins: Cells, Systems & Applications’
  • Department of Biochemistry and Genetics, University of Newcastle
  • Cambridge Centre for Molecular Recognition, University of Cambridge
  • Biochemical Society (Bristol), symposium on Molecular Communications
  • Departments of Chemistry and Biology Joint Seminar, University of York
  • Department of Microbiology & Immunology, Queen’s University of Belfast
  • Department of Biosciences, University of Birmingham


  • Speaker and Session Chair, Gordon Research Conference on Bacterial Cell Surfaces, Colby-Sawyer College, NH
  • Plenary speaker, Macromolecules in Chemistry and Biology symposium, University of Lancaster
  • Bijvoet Centre, University of Utrecht, The Netherlands

Current Collaborators

Post Doctoral Research Associates


PhD students

  • 2013-17 Patrice Rassam*
  • 2015-17 Katarina Jansen
  • 2014-15 Amar Joshi
  • 2011-15 Karthik Rajasekar
  • 2010-14 Greg Papadakos
  • 2010-14 Justyna Wojdyla
  • 2009-11 James Pullen
  • 2007-09 Nicola Meenan
  • 2007-09 Amit Sharma
  • 2007-08 Nikki Copeland*
                 Danielle Smith
  • 2005-07 Irina Grishkovskaya
                 Afua Nyarko
  • 2004-07 Khédidja Mosbahi
  • 2003-08 Konrad Zdanowski
  • 2002-05 Maria Maté*
  • 2002-07 Daniel Walker*
  • 2002-05 Anthony Keeble
  • 2000-02 Cecile Le Duff
  • 2000-02 Chris Law*
  • 1999-02 Wei Li*
  • 1998-04 Theonie Georgiou
  • 1997-00 Ryan Bingham
  • 1997-99 Christelle Lemaitre
  • 1996-97 Catriona Giffard
  • 1992-95 Russell Wallis*
  • 1992-95 Andrew Leech



  • 2003-10 Nadine Kirkpatrick
  • 1991-02 Ann Reilly
  • 1997-02 Christine Moore
  • 2011-12 Judith Hawkhead
  • 2012-13 Colin Seepersad
  • 2014-17 Connor Sharp
  • 2014-17 Paul White
  • 2012-16 Peter Holmes
  • 2008-12 Eoin Cassells
  • 2006-10 Anne Marie Krachler* 
  • 2005-09 Dan Bonsor
                 Katie Lilly
  • 2003-07 Charles Heise
  • 2002-06 Steven Loftus
  • 2001-05 Lorna Lancaster
  • 2000-04 Nikki Copeland*
                 Khédidja Mosbahi
  • 1998-02 Anthony Keeble
  • 1998-01 Daniel Walker
  • 1995-99 Wei Li*          
  • 1994-98 Theonie Georgiou
                 Caitriona A. Dennis           
  • 1993-97 Ansgar J. Pommer
                 Kit-Yi Leung*
  • 1992-96 Hortense Videler
  • 1991-95 Joanna R. Bottomle

Masters students

  • 2015-16 Yana Deniyanenko
  • 2013-14 Marie-Louise Francis
  • 1993-94 Debbie Flanagan
  • 1991-92 Greg Dean

Part II & Summer Students

  • 2018 Martin Weber (intern)
  • 2017-18 Martin Vesely (Part II)
  • 2017-18 Mariam Diauet (Summer)
  • 2017-18 Sabet Gilani (Summer)
  • 2016-17 Duke Quinton (Part II)
  • 2016-17 Orr Chinthaumit (Part II)
  • 2016-17 Sarah Pommer (Summer)
  • 2015-16 Sam Rodenberg (Summer)
  • 2015-16 Piotr Tokarz (Summer)
  • 2015-16 Grace Seagall (Part II)
  • 2015-16 Sophie Jolliffe (Part II)
  • 2014-15 Jonathan Goult (Part II)
  • 2014-15 Harry Scholes (Part II)
  • 2015 Piotr Tokarz (Summer)
  • 2015 Sam Rodenberg (Summer)
  • 2013-14 Tom Rowntree (Part II)
  • 2013-14 Emma Elliston (Part II)
  • 2013 John Snape (Summer)


* Have established their own labs

No current vacancies.


    All graduate student enquires should be directed to Prof. Colin Kleanthous.

The 5th International Conference on Molecular Perspectives on Protein-Protein Interactions

29 May - 2 June 2015




The 40th Lorne Conference on Protein Structure and Function

Lorne Proteins 2015

The 40th Lorne Conference on Protein Structure and Function

8-12 Feb 2015

Mantra Lorne, Victoria, Australia




Intrinsically disordered proteins

Gordon Research Conferences

Understanding Intrinsically Disordered Regions (IDRs) at Different Scales: From Single Molecules to Complex Systems

6-11 July 2014

Stonehill College Easton, MA




Bacterial cell surfaces

Gordon Research Conferences

Building, Splitting, and Traversing the Cell Surface

22-27 June 2014

Mount Snow West Dover, VT




The Protein Society Symposium

The 28th Annual Symposium of the Protein society

27-30 July 2013

San Diego United States




European Science Foundation

ESF-EMBO Symposium

Molecular Perspectives On Protein-Protein Interactions

25-30 May 2013

Polonia Castle in Pultusk, Poland

Chaired by: Prof. Marcellus UbbinkUniversity of Leiden
Co-chaired by: Gideon SchreiberWeizmann Institute of ScienceColin KleanthousOxford University


How bugs kill bugs: progress and challenges in bacteriocin research 

16—18 July 2012

University of Nottingham, UK

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