SpyAvidin Hubs Enable Precise and Ultrastable Orthogonal Nanoassembly Fairhead M, Veggiani G, Lever M, Yan J, Mesner D, Robinson CV, Dushek O, van der Merwe PA, Howarth M. Journal of the American Chemical Society 2014 in press Full text   Supporting Info.  Abstract on Medline    Robinson Lab    van der Merwe lab Combining one of the best interactions in nature with our bacterial superglue, to generate nanoassemblies for sensitive activation of cellular signalling. Superglue from Bacteria: Unbreakable Bridges for Protein Nanotechnology Veggiani G., Zakeri B., Howarth M. Trends in Biotechnology 2014 in press Love-Hate ligands for high resolution analysis of strain in ultra-stable protein:small molecule interaction Michael Fairhead, Di Shen, Louis K.M. Chan, Ed D. Lowe, Timothy J. Donohoe, Mark Howarth Bioorganic & Medicinal Chemistry 2014 in press Full text  Supporting Info.  Abstract on Medline  Donohoe lab  PDB entries: SA-LH1, SA-LH3, SA-LH4, A86D-LH4 A novel chemical biology approach to understand how force distorts protein structure. SpyLigase peptide–peptide ligation polymerizes affibodies to enhance magnetic cancer cell capture Fierer J.O.*, Veggiani G.*, Howarth M. PNAS 2014 Apr 1;111(13):E1176-81 PDF+SI      Abstract on Medline    *joint first author  Developing a new way to irreversibly lock two peptides together (via a 3- way split protein), using to assemble tentacle-like polymers of affibodies or antibodies, and applying to improve sensitivity of isolation of cancerous cells. SpyTag/SpyCatcher Cyclization Confers Resilience to Boiling on a Mesophilic Enzyme Schoene C., Fierer J.O., Bennett S.P., Howarth M. Angewandte Chemie 2014 Jun 10;53(24):6101-4. Full text     Supporting Info.    Abstract on Medline      BBSRC News story   Towards a general way to make enzymes that can tolerate tough conditions (e.g. for diagnostics or for biofuels), we found that locking the tails together with our bacterial superglue gave dramatic increases in resilience. Structural Analysis and Optimization of the Covalent Association between SpyCatcher and a Peptide Tag Li L., Fierer J.O., Rapoport T.A., Howarth M. Journal of Molecular Biology 2014 Jan 23;426(2):309-317 PDF    Supporting Info.    Abstract on Medline     PDB entries: SpyTag/SpyCatcher, SpyTag/SpyCatcherΔN1 Crystal structure of the SpyCatcher/SpyTag complex, a genetically encoded peptide forming a spontaneous isopeptide bond to its protein partner, and minimization of the size of SpyCatcher. Plug-And-Play Pairing Via Defined Divalent Streptavidins  Fairhead M, Krndija D, Lowe ED, Howarth M. Journal of Molecular Biology 2014 Jan 9;426(1):199-214 PDF      Abstract on Medline     PDB entries: cis-divalent, trans-divalent, trans-divalent with biotin-fluorescein Streptavidin is one of the most widely used building blocks in biology and also has given promising results for improving delivery of cancer radiotherapy. We developed charged tags to enable isolation of precise tetramers for robust nanoassembly and validated the structures by crystallography. (Plasmids on Addgene.) Cholesterol loading and ultrastable protein interactions determine the level of tumor marker required for optimal isolation of cancer cells. Jain J, Veggiani G, Howarth M. Cancer Research 2013 Apr 1;73(7):2310-21 PDF    Abstract on Medline    Supporting Info. Detecting the circulating tumor cells in blood samples is one of the most promising ways to achieve early cancer diagnosis and rapid feedback on cancer treatment. Here we establish the key factors for magnetic cancer cell isolation and use this insight to enhance the isolation of cells expressing low levels of cancer marker. Described for a general audience on the Oxford University Science Blog. Hydroxy-Terminated Conjugated Polymer Nanoparticles Have Near-Unity Bright Fraction and Reveal Cholesterol-Dependence of IGF1R Nanodomains. Koner AL, Krndija D, Hou Q, Sherratt DJ, Howarth M. ACS Nano 2013 Feb 26;7(2):1137-44 PDF    Abstract on Medline    Supporting Info. Single molecule imaging is a powerful way to gain insight into receptor function. Here we show that Conjugated Polymer Nanoparticles may be the best nanoparticles for single molecule imaging, because, unlike quantum dots, these particles do not blink and there are almost no "ghost" particles which fail to emit. Quantum Dot Targeting with Lipoic Acid Ligase and HaloTag for Single Molecule Imaging on Living Cells. Liu DS, Phipps WS, Loh KH, Howarth M, Ting AY. ACS Nano 2012 Dec 21;6(12):11080-7. PDF    Abstract on Medline    Supporting Info. Using two re-designed enzymes, a covalent connection can be made between a peptide-tagged cell surface protein and a fluorescent nanoparticle. This enabled two different types of adhesion molecules to be followed at the single molecule level on living cells. Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin. Zakeri B*, Fierer JO*, Celik E, Chittock EC, Schwarz-Linek U, Moy VT, Howarth M. PNAS 2012 Mar 20;109(12):E690-7. PDF     Abstract on Medline    Supporting Info.      *joint first author Graphic design with Myoungshin Kim Peptide interactions with proteins are usually weak. Here we show how to get a genetically encoded peptide to form an irreversible covalent bond when it binds its protein partner (SpyTag with SpyCatcher). This may be useful as a cellular padlock, for imaging and to enable new protein architectures. (Plasmids available from Addgene repository or directly from us.) Described for a general audience on the Oxford University Science Blog. A peptide filtering relation quantifies MHC class I peptide optimization. Dalchau N, Phillips A, Goldstein LD, Howarth M, Cardelli L, Elliott T, Werner JM. PLoS Computational Biology 2011 Oct;7(10):e1002144. PDF     Abstract on Medline    Supporting Info. Collaboration with Microsoft and my previous lab in Southampton to model mathematically all the steps in peptide presentation for T cell recognition. Mechanisms for size-dependent protein segregation at immune synapses assessed with molecular rulers. Alakoskela JM, Koner AL, Rudnicka D, Köhler K, Howarth M, Davis DM. Biophysical Journal 2011 Jun 22;100(12):2865-74. PDF     Abstract on Medline     Supporting Info. The exact intermembrane spacing when a natural killer cell encounters a target cell (virally infected or cancerous) is important in triggering killer cell activation. In collaboration with Dan Davis' lab we developed a controlled size-series of fluorescent proteins and nanoparticles for real-time imaging of how molecules above a certain size are excluded from the synapse. How the biotin-streptavidin interaction was made even stronger: investigation via crystallography and a chimaeric tetramer. Chivers CE, Koner AL, Lowe ED, Howarth M. Biochemical Journal 2011 Apr 1;435(1):55-63. PDF     Abstract on Medline  PDB entries: apo-traptavidin  biotin-traptavidin Our first foray into structural biology, to help determine the origin of one of the strongest non- covalent interactions in nature. The type I IGF receptor translocates to the nucleus of human tumor cells. Aleksic T, Chitnis M, Perestenko O, Gao S, Thomas P, Turner G, Protheroe A, Howarth M, Macaulay V. Cancer Research 2010 Aug 15;70(16):6412-9. PDF   Abstract on Medline  Supporting Info. The classic model of growth factor receptor signaling is that the activated receptor at the plasma membrane/endosomes, activates down-stream pathways. Components of these pathways then enter the nucleus, leading to changes in gene expression. This paper contributes to a new model where the receptor itself moves to the nucleus and has direct effects on transcription. We show that nuclear IGF1R is associated with a more aggressive cancer, suggesting that approaches to block nuclear translocation could improve survival. A streptavidin variant with slower biotin dissociation and increased mechanostability. Chivers CE, Crozat E, Chu C, Moy VT, Sherratt DJ, Howarth M. Nature Methods 2010 May;7(5):391-93. PDF   Abstract on Medline   Supporting Info.   Streptavidin binds to the vitamin biotin with one of the strongest non-covalent interactions in nature. We developed a mutant of streptavidin, termed traptavidin, which binds biotin 10-times better. We tested traptavidin, by setting up a molecular car-crash to investigate a motor protein involved in chromosome segregation. (Traptavidin protein and plasmids available.) Separating speed and ability to displace roadblocks during DNA translocation by FtsK. Crozat E, Meglio A, Allemand JF, Chivers CE, Howarth M, Vénien-Bryan C, Grainge I, Sherratt DJ. EMBO Journal 2010 Apr 21;29(8):1423-33. PDF   Abstract on Medline   Supporting Info.   Sherratt lab   Grainge lab FtsK is a bacterial motor protein that pumps DNA, so that each daughter cell receives one copy of the chromosome. In collaboration with the Sherratt lab we explored through crash-testing how the different active sites in a ring coordinate their firing. Spontaneous Intermolecular Amide Bond Formation between Side Chains for Irreversible Peptide Targeting. Zakeri B & Howarth M. Journal of the American Chemical Society 2010 Apr 7;132(13):4526-7. PDF   Abstract on Medline  Supporting Info. Proof of principle for spontaneous covalent bond formation to a peptide, developed from a pilin and based on Lysine reaction with Asparagine. See also our PNAS 2012 paper. Electrophilic affibodies forming covalent bonds to protein targets. Holm L, Moody P, Howarth M. Journal of Biological Chemistry 2009 Nov;284(47):32906-13 PDF   Abstract on Medline    Supporting Info. Affibodies are like antibodies but smaller and easier to make. We introduced an artificial reactive group next to the target binding site of an affibody. This enabled the affibody to form a specific covalent bond to its target. By preventing affibody dissociation we could improve detection sensitivity and stability. We are working to make this reaction faster and more general, to enable detection of disease markers present in blood at concentrations too low for current tests. Monovalent, reduced-size quantum dots for imaging receptors on living cells. Howarth M, Liu W, Puthenveetil S, Zheng Y, Marshall LF, Schmidt MM, Wittrup KD, Bawendi MG, Ting AY. Nature Methods 2008 May;5(5):397-99. PDF  Abstract on Medline  Supporting Info. Quantum dots are ultra-bright nanoparticles, which make single molecule imaging routine. A major problem in the field is that one nanoparticle can bind several copies of its target receptor. This stops the receptor moving freely and often activates cell signalling. Here we develop a way to purify quantum dots with precisely defined numbers of proteins attached. We use these non-crosslinking high affinity QDs to image the low density lipoprotein receptor and the tumour marker carcinoembryonic antigen. Compact Biocompatible Quantum Dots Functionalized for Cellular Imaging. Liu W, Howarth M, Greytak AB, Zheng Y, Nocera DG, Ting AY, Bawendi MG. Journal of the American Chemical Society 2008 Jan 30;130(4):1274-84. PDF  Abstract on Medline  Supporting Info.   Bawendi lab It has been challenging to reduce quantum dot size at the same time as maintaining high stability and specificity in their targeting. In this paper we engineer the QD passivating layer to address this challenge and apply these QDs to image the epidermal growth factor receptor, an important regulator of cancer cell division. Tapasin shapes immunodominance hierarchies according to the kinetic stability of peptide-MHC class I complexes. Thirdborough SM, Roddick JS, Radcliffe JN, Howarth M, Stevenson FK, Elliott T. European Journal of Immunology 2008 Jan 14;38(2):364-369. PDF   Abstract on Medline A development of work from my DPhil (see PNAS 2004 below), showing that tapasin not only changes how well peptides are displayed by MHC class I at the cell surface, but also how well these peptides activate the immune system from DNA vaccination. Protein imaging in live mammalian cells by site-specific labeling with biotin ligase and monovalent streptavidin. Howarth M, Ting AY. Nature Protocols 2008;3(3):534-45. PDF   Abstract on Medline Step-by-step instructions and trouble-shooting guide, for those applying the approaches we developed for stable cell labeling with biophysical probes and expression of a streptavidin with a single high affinity binding site. (Plasmids for BirA and monovalent streptavidin protein available.) Note in our current protocol we use 5 min with a stir-bar to resuspend inclusion bodies and reduce pipetting effort, while our J Mol Biol paper 2014 describes an easier chromatographic separation.   Giving cells a new sugar-coating. Howarth M, and Ting AY. Nature Chemical Biology 2006 Mar;2(3):127-8 PDF   Abstract on Medline    News and Views article on a paper by Kevin Yarema feeding cells a thiol sugar. This enables them to redecorate the cell surface with sialic acids bearing thiols, which changed adhesion of stem cells. We explain how this method works and discuss the importance of manipulating protein glycosylation. A monovalent streptavidin with a single femtomolar biotin binding site. Howarth M, Chinnapen DJ-F, Gerrow K., Dorrestein PC, Grandy MR, Kelleher NL, El-Husseini A, Ting AY. Nature Methods 2006, Apr;3(4):267-73 PDF   Abstract on Medline     News and Views   Supp. Info.   Dorrestein lab Streptavidin is used in almost every biology lab and also by many physicists and engineering seeking to manipulate molecules on the nanometre scale. Streptavidin is used so much in biotechnology because of its rapid, selective and stable binding to anything modified with biotin. However, streptavidin has 4 binding sites. This can cross-link proteins on the surface of cells and limit one's control in nanotechnology applications. We made a version where one can control the number of binding sites from 0-4 but keep the tight binding. Our J Mol Biol paper 2014 describes an easier chromatographic separation of the monovalent and divalent forms. (Monovalent streptavidin protein and plasmids available.) Targeting quantum dots to surface proteins in living cells with biotin ligase. Howarth M, Takao K, Hayashi Y, and Ting AY. PNAS 2005, May;102(21):7583-8 PDF  Abstract on Medline  Supp. Info./Movie       Hayashi Lab     Quantum dots are inorganic nanoparticles that are so bright that they make it routine to image single proteins moving in living cells. Here we develop the use of biotin ligase to add biotin to neurotransmitter receptors on the neuron surface and then track the receptors with quantum dots. Site-Specific Labeling of Cell Surface Proteins with Biophysical Probes using Biotin Ligase.  Chen I, Howarth M, Lin W, Ting AY. Nature Methods 2005 Feb;2(2):99-104 PDF  Abstract on Medline   Supp. Info. It is a great challenge to label proteins with new tags that will probe their function. Biotin ligase recognizes a 15 amino acid tag specifically over other cytosolic and cell surface proteins. We get Biotin ligase to add a ketone analog of biotin to a tagged cell-surface protein. Since there are no ketones on the cell- surface, this enables us to react the ketone with any hydrazide-labeled biophysical probe. DNA Transfection Screening from Single Beads.  Yingyongnarongkul BE, Howarth M, Elliott T, Bradley M. Journal of Combinatorial Chemistry 2004 Sep-Oct;6(5):753-60. PDF  Supporting info.  Abstract on Medline  Solid-phase synthesis of 89 polyamine-based cationic lipids for DNA delivery to mammalian cells. Yingyongnarongkul BE, Howarth M, Elliott T, Bradley M.  Chemistry 2004 Jan 23;10(2):463-73. PDF  Supporting info.  Abstract on Medline   One of the greatest challenges in medicine is to get DNA expressed long term in a wide number of cells, for gene therapy. Even in the laboratory it is still a challenge to get DNA into many cell-types. However, it is hard to predict which compound will be best at introducing DNA into cells, known as DNA transfection. Mark Bradley's group are experts in combinatorial synthesis, where new compounds are made in a highly parallel fashion, rather than one at a time. They turned their attention to combinatorial synthesis of transfection reagents and we helped them in the testing and design of these reagents.  We look at an uncommon class of transfection agent with only one lipid tail and show that the amount of compound made on a single polymer bead is sufficient to test transfection activity. Tapasin enhances MHC class I antigen presentation according to peptide half-life. Howarth M, Williams A, Tolstrup AB, Elliott T. PNAS 2004 Aug;101(32):11737-11742  PDF   Abstract on Medline   Elliott lab  MHC class I presents peptides that are seen by killer T cells and controls their activation and killing. Tapasin is an ER chaperone that associates with newly synthesized MHC class I. Here we show that the interaction with tapasin changes the repertoire of peptides that MHC class I presents, to favour stable peptides, with consequences for autoimmune disease and vaccine design. The processing of antigens delivered as DNA vaccines. Howarth M, Elliott T. Immunological Reviews 2004 199:27-39 PDF   Abstract on Medline  DNA vaccination involves stimulating an immune response with DNA encoding pathogenic genes or gene fragments, rather than immunizing with protein or attenuated virus, as is more conventional. Trials of DNA vaccination are taking place for many diseases, including skin cancer and HIV. This review discusses how our basic knowledge of MHC class I and II antigen presentation may explain DNA vaccination results and guide future strategies. Assembly and antigen-presenting function of MHC class I molecules in cells lacking the ER chaperone calreticulin. Gao B, Adhikari R, Howarth M, Nakamura K, Gold MC, Hill AB, Knee R, Michalak M, Elliott T. Immunity 2002 Jan;16(1):99-109 PDF  Abstract on Medline   Bin Gao lab Calreticulin is a multi-talented protein, involved in calcium homeostasis, gene regulation, and folding of secretory proteins. Here we tested how the presence of calreticulin changed the loading of MHC class I with peptide and its exit from the endoplasmic reticulum. Processing and presentation of glycoproteins in the MHC class I and II antigen presentation pathways.  Golgher DB, Elliott T, Howarth M. Chapter in "Immunobiology of Carbohydrates", Landes Biosciences, 2002. Link on Google books  (can click through the pages) MHC class I presents peptides to killer T cells and MHC class II presents peptides to helper T cells. Many cellular proteins are glycosylated, yet how this affects what peptides are presented by MHC is little understood and challenging to study. It may have relevance to immune responses in conditions such as allergy and cancer. We also point out many of the key questions still unanswered. The quantity of naturally processed peptides stably bound by HLA-A*0201 is significantly reduced in the absence of tapasin. Barber LD, Howarth M, Bowness P, Elliott T.  Tissue Antigens 2001 Dec;58(6):363-8 PDF  Abstract on Medline  MHC class I presents a sample of peptides derived from cellular proteins, allowing killer T cells to monitor what is going on inside the cell. It is possible to profile these peptides by eluting them with acid and then HPLC analysis. Here we see the effect of the ER chaperone tapasin on the abundance and nature of peptides eluted from the most common HLA allele in Western populations.   Peptide tag systems that spontaneously form an irreversible link to protein partners via isopeptide bonds. Howarth M, Zakeri B. 2010, United Kingdom Patent Application (described by Isis Innovation) for PDF High Stability Streptavidin Mutant Proteins. Howarth M, Chivers C. 2009, United Kingdom Patent Application (described by Isis Innovation) PDF Controlled modification of semiconductor nanocrystals. Ting AY, Bawendi MG, Howarth M, Liu W. 2007, US Patent and Trademark Office. for PDF Monovalent Streptavidin compositions. Ting AY, Howarth M. 2006, US Patent and Trademark Office. for PDF
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