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John Allingham PhD
 John Allingham
Position(s)
Associate Professor
Canada Research Chair in Structural Biology
Contact Info
613-533-3137 x33137
Botterell Hall, Room 650

Education:
B.Sc. (Hons.) in Biochemistry (1996) - The University of Western Ontario

Ph.D. in Biochemistry and Molecular Biology (2002) - The University of Western Ontario
CIHR Postdoctoral Fellow in Structural Biology (2002-2006) - Department of Biochemistry, University of Wisconsin

Current Funding:
Canadian Institutes of Health Research
Natural Sciences and Engineering Research Council
Canada Research Chairs Program

Research Interests:    
• Structure-function relationships in kinesin motor proteins
• Roles of kinesins in mitotic spindle function and cell shape changes in human fungal pathogens and cancer cells
• Molecular recognition of protein surfaces and perturbation of protein function by natural toxic small molecules
• Protein engineering and drug design

A primary goal of the research in my lab is to understand the mechanisms of action of biomolecules, and, where possible, to rationally alter or re-purpose their functions in useful ways. To do this, we use X-ray crystallography, high-resolution microscopy, and a number of other biophysical tools to gain detailed descriptions of these molecules in solution and inside cells. Our most intensive areas of focus in recent years has been on: (1) kinesin motor proteins, which form a large superfamily of cytoskeletal motors that are essential for cellular cargo transport, cell division, and cell shape changes; and (2) on natural toxins that possess anti-fungal and anti-tumor properties. The activities these molecules possess have direct relevance for biomedicine. They also provide frameworks for understanding the fundamental underpinnings of biomolecule design.

Research Interests:
 

What we do:

My laboratory studies molecular motors and cytoskeletal proteins that generate pushing and pulling forces required for chromosome segregation, cell morphogenesis, and motility.  These proteins are structurally dynamic. They can associate into complex and beautiful molecular assemblies that are in a constant state of flux in cells.  To gain a complete view of the structure-function relationships of these proteins, we use state-of-the-art X-ray crystallographic, electron and fluorescence microscopic, and protein kinetics measurement instruments, as well as molecular genetics and cell biological approaches.

Research projects:

Structural and molecular biology of kinesin motors in human fungal pathogens

Invasive fungal infections pose a serious threat to human health, particularly for newborn children, immunocompromised individuals and hospitalized patients. Approximately 70–90% of all invasive fungal infections involve Candida fungi. Among these, Candida albicans is the predominant species, with infections involving Candida glabrata becoming more common. In spite of the advances achieved in the diagnosis and treatment of these pathogens, Candida bloodstream infections are associated with a mortality rate of approximately 40%, and millions of otherwise healthy individuals still suffer with serious cutaneous or mucosal Candida infections. These factors place vital importance on learning as much as possible about how these microbes colonize and proliferate in susceptible individuals, and how to target such events with drugs that are safe for patients. Our research has shown that a family of motor proteins, named ‘kinesins’, are required for Candida albicans cells to divide and transition into growth forms that promote host colonization and proliferation. We have also gained information on how some Candida-specific kinesins move and generate forces to drive these biological processes. In the coming years, we will establish fundamental knowledge about the structures, functions, and mechanisms of action of Candida kinesins that have not yet been studied in order to provide a complete picture of the systems that cooperate to organize the internal components of fungal cells during growth and pathogenesis. We have also begun drug-screening assays to look for agents that inhibit relevant kinesin motor functions in these microbes in order to facilitate the development of new therapeutic approaches for treating or preventing Candida infections.

Understanding and targeting actin cytoskeleton-driven cell motility and molecular pathologies
The actin cytoskeleton is the key cellular machinery responsible for the morphological changes in cancer cells that facilitate their ability to metastasize. Actin recruitment and specific actin gene mutations are also involved in the pathogenic mechanisms of many infectious microbes and several cardiovascular diseases and conditions, respectively. Our research on actin-targeting natural products that potently alter actin cytoskeleton dynamics has identified the key bioactive components of these molecules that can be used to guide development of new chemotherapeutic agents to defeat the contribution of actin to the spread of cancer, infections, or other actin-dependent conditions. However, in order to kill malignancy-causing cells exclusively, drugs derived from these natural compounds must be re-engineered in ways that confer cell specificity. This demands an understanding of the common ways in which different forms of these molecules function, and which of their structural features determines their potency. In order to gain such information, we have assembled a collaborative research group to examine the interactions formed between these compounds and their protein targets at an atomic level, and to synthesize potent and cell-specific natural product analogs that structurally and functionally mimic the natural molecules in ways that could slow or prevent disease progression.

Protein engineering and synthetic biology (with Queen's iGEM team)

We have a strong interest in the emerging disciple of synthetic biology, which uses defined pieces of genetic information as building blocks to create biological machines with functions that may be radically different from those found in nature. Through collaborations with other labs at Queen's, and at other universities, we employ protein engineering concepts to understand structure-function relationships for numerous classes of proteins beyond the subjects of motors and cytoskeletal proteins. As the lead advisory group for Queen’s Genetically Engineered Machine Team (QGEM), we also foster opportunities for junior scientists and undergrads to gain expertise in protein engineering and synthetic biology, as well as cell biology techniques, molecular genetics, chemical biology, and advanced techniques for investigating protein structure.

 

Publications:

Brockhausen I, Nair DG, Chen M, Yang X, Allingham JS, Szarek WA, Anastassiades T.  Human acetyl-CoA:glucosamine-6-phosphate N-acetyltransferase 1 has a relaxed donor specificity and transfers acyl groups up to four carbons in length. Biochem Cell Biol. 2016 Apr;94(2):197-204. PMID: 26935656

Frazer, C., Joshi, M., Delorme, C., Davis, D., Bennett, R.J., Allingham, J.S. Candida albicans kinesin Kar3 depends on a Cik1-like regulatory partner protein for its roles in mating, cell morphogenesis and bipolar spindle formation, Eukaryotic Cell, 2015 Aug 14(8):755-74. PMID: 26024903

Arora, K., Talje, L., Asenjo, A.B., Andersen, P., Atchia, K., Joshi, M., Sosa, H., Allingham, J.S., Kwok, B.H. (2014) KIF14 Binds tightly to microtubules and adopts a rigor-like conformation. J. Mol. Biol. 2014 Aug 26;426(17):2997-3015. PMID: 24949858

Partha, S.K., Ravulapalli, R., Allingham, J.S., Campbell, R.L., Davies, P.L. (2014) Crystal structure of calpain-3 penta-EF-hand (PEF) domain - a homodimerized PEF family member. FEBS J. 2014 Jul;281(14):3138-49. PMID: 24846670

Sun, T., Lin, F.H., Campbell, R.L., Allingham, J.S., Davies, P.L. (2014) An antifreeze protein folds with an interior network of more than 400 semi-clathrate waters. Science 2014 Feb 14;343(6172):795-8. PMID: 24531972    

Joshi, M., Duan, D., Drew, D., Jia, Z., Davis, D., Campbell, R.L., Allingham, J.S. (2013) Kar3Vik1 Mechanochemistry Is Inhibited by Mutation or Deletion of the C Terminus of the Vik1 Subunit. J. Biol. Chem. 2013 Dec 27;288(52):36957-70. PMID: 24240171

Guo, S., Garnham, C.P., Karunan Partha, S., Campbell, R.L., Allingham, J.S., Davies, P.L. (2013) Role of Ca²⁺ in folding the tandem β-sandwich extender domains of a bacterial ice-binding adhesin. FEBS J. 2013 Nov;280(22):5919-32. PMID: 24024640

Delorme, C., Joshi, M. & Allingham, J.S. (2012) Crystal structure of the Candida albicans Kar3 kinesin motor domain fused to maltose-binding protein. Biochem. Biophys. Res. Commun2012 Nov 30;428(4):427-32. PMID: 23137538

Duan, D., Jia, Z., Joshi, M., Brunton, J., Chan, M., Drew, D., Davis, D. & Allingham, J.S. (2012) Neck rotation and neck mimic docking in the non-catalytic Kar3-associated protein Vik1J. Biol. Chem. Nov 23;287(48):40292-301. PMID: 23043140   

Kwok, E., Everingham, S., Zhang, S., Greer, P.A., Allingham. J.S., & Craig, A.W. (2012) FES Kinase Promotes Mast Cell Recruitment to Mammary Tumors Via the Stem Cell Factor/KIT Receptor Signaling Axis. Mol. Cancer Res. 2012 Jul;10(7):881-91. PMID: 22589410

Duan, D., Hnatchuk, D., Brenner, J. Davis, D., & Allingham, J.S. (2012) Crystal structure of the Kar3-like kinesin motor domain from the filamentous fungus Ashbya gossypiiProteins 2012 Apr;80(4):1016-27. PMID: 22493778

Stark, B.C., Wen, K.K., Allingham, J.S., Rubenstein, P.A., & Lord, M. (2011) Functional adaptation between yeast actin and its cognate myosin motors, J. Biol. Chem. 2011 Sep 2;286(35):30384-92. PMID: 21757693

Xu, C., Liu, B., Han, Y., Feng, L. Allingham, J.S., Szarek, W.A., Wang, L., & Brockhausen, I. (2011) Biochemical Characterization of UDP-Gal:GlcNAc-pyrophosphate-lipid Beta-1,4-Galactosyltransferase WfeD, a new enzyme from Shigella boydii type 14 that catalyses the second step in O-antigen repeating-unit synthesis. J. Bacteriol. 2011 Jan;193(2):449-59. PMID: 21057010

Blain, J. C., Mok, Y-F., Kubanek, J. & Allingham, J. S. (2010) Two Molecules of Lobophorolide Cooperate to Stabilize an Actin Dimer Using Both Their 'Ring' and 'Tail' Region. Chem. Biol. 2010 Aug 27;17(8):802-7. PMID: 20797609

Klein, J. C., Svensson, B., Burr, A. R., Kennedy, D. J., Allingham, J. S., Titus, M. A., Rayment, I. & Thomas, D. D. (2008) Actin-binding cleft closure in myosin II probed by site-directed spin labeling and pulsed EPR. Proc. Natl. Acad. Sci. USA 2008 Sep 2;105(35):12867-72. PMID: 18725645

Lucas-lopez, C. Allingham, J. S., Leb, T., Lawson, C. P., Brenk, R. Sellers, J. R., Rayment, I. & Westwood, N. J. (2008) The small molecule tool (s)-(-)-Blebbistatin: novel insights of relevance to myosin inhibitor design. Org. Biomol. Chem. 2008 Jun 21;6(12):2076-84. PMID: 18528569

Tanaka, J. Blain, J. C. & Allingham, J. S. (2008) Actin-binding toxin 'tail' wags the dog. Chem. Biol. 2008 Mar;15(3):205-7. PMID:18355717
  
Allingham, J.S., Miles, C.O., & Rayment, I. (2007) A Structural Basis for Regulation of Actin Polymerization by Pectenotoxins. J. Mol. Biol. 2007 Aug 24;371(4):959-70. PMID: 17599353

Allingham, J.S., Sproul, L.R., Rayment, I. & Gilbert, S.P. (2007) Vik1 Modulates Microtubule-Kar3 Interactions Through a Motor Domain That Lacks an Active Site. Cell  2007 Mar 23;128(6):1161-72. PMID: 17382884  

Rayment, I. & Allingham, J.S. (2007) Myosin Motors: The Chemical Restraints Imposed by ATP. Lecture Notes in Physics  711, 15-40. (Book Chapter)

Allingham, J. S., Klenchin, V. A., & Rayment, I. (2006) Actin-Targeting Natural Products: Structures, Properties and Mechanisms of Action. Cell. Mol. Life Sci. 2006 Sep;63(18):2119-34. PMID: 16909206

Allingham, J. S., Zampella, A., D'Auria,, M. V., & Rayment, I. (2005) Structures of microfilament destabilizing toxins bound to actin provide insight into toxin design and activity. Proc. Natl. Acad. Sci. USA  2005 Oct 11;102(41):14527-32. PMID: 16192358

Allingham, J. S., Smith, R., & Rayment, I. (2005) The structural basis of blebbistatin inhibition and specificity for myosin II. Nat. Struct. Mol. Biol.  2005 Apr;12(4):378-9. PMID: 15750603

 

Lab Members

 
Principal Investigator

Dr. John S. Allingham, Ph.D.
Department of Biomedical and Molecular Sciences 
Queen's University 
Botterell Hall, Rm. 652 
Kingston, ON, K7L 3N6
Phone: (613) 533-3137
E-mail: allinghj@queensu.ca

Senior Research Associate / Lab Manager

Dr.  Daria (Dasha) Trofimova
Department of Biomedical and Molecular Sciences 
Queen's University 
Botterell Hall, Rm. 637 
Kingston, ON, K7L 3N6
Phone: (613) 533-6000 x 79033
E-mail: daria.trofimova@queensu.ca

Ms. Jacqueline Hellinga 
(Ph.D. Candidate)
Department of Biomedical and Molecular Sciences 
Queen's University 
Botterell Hall, Rm. 641 
Kingston, ON, K7L 3N6
E-mail: 14jrh1@queensu.ca
 

Ms. Rodette Williams 
(M.Sc. Candidate)
Department of Biomedical and Molecular Sciences 
Queen's University 
Botterell Hall, Rm. 641 
Kingston, ON, K7L 3N6
E-mail: rodette.williams@queensu.ca

Ms. Irsa Shoukat 
(M.Sc. Candidate)
Department of Biomedical and Molecular Sciences 
Queen's University 
Botterell Hall, Rm. 641 
Kingston, ON, K7L 3N6
E-mail: irsa.shoukat@queensu.ca

Ms. Sarah Nersesian
(M.Sc. Candidate)
Department of Biomedical and Molecular Sciences Queen's University 
Botterell Hall, Rm. 641 
Kingston, ON, K7L 3N6
E-mail: sn57@queensu.ca

Mr. Byron Hunter
(Honours B.Sc. Candidate)
(NSERC Summer Student)
Department of Biomedical and Molecular Sciences 
Queen's University 
Botterell Hall, Rm. 641 
Kingston, ON, K7L 3N6
E-mail: 12bth@queensu.ca

 

LAB ALUMNI

Ms. Chloe Mitchell - B.Sc. (2016)
Dr.  Corey Frazer - Postdoctoral Fellow (2011-2016)
Mr. Ian Downie - B.Sc. (2015)
(Fomer NSERC Summer Student and Pepitos Connoisseur)
Ms. Kritica Arora  - M.Sc. (2014) 
Dr.  Monika Joshi  - Postdoctoral Fellow (2011-2014)
Mrs. Darlene Davis  - Lab Manager (2007-2014)
Dr. Da Duan - Ph.D. (2013)
Mr.  Doran Drew - B.Sc. (2013)
Mr. Dylan Valleau - B.Sc. (2013)
Ms.  Caroline Delorme - M.Sc. (2012)
Mr.  Dan Hnatchuk - M.Sc. (2012)
Mr. Dong Yan - Research Technician (2011)
Ms. Shannon Smith Research Technician (2011-2012)
Mr. Craig Spencer - Research Technician (2010)
Dr. Y-F Mok - Postdoc (2009-2010)
Mr. Zhi Jia - B.Sc. (2012)
Ms. Cailtin Miron - B.Sc. (2012)
Mr. Paul Atkins - B.Sc. (2011)
Ms. Jackie Brunton - B.Sc. (2011)
Ms. Laura Mechefske - B.Sc. (2010)
Ms. Michelle Chan - B.Sc. (2010)
Ms. Jill Brenner - B.Sc. (2009)
Mr. Craig Blain - B.Sc. (2008)
Ms. Heather O'Shea - B.Sc. (2008)
Ms. Eleasa Sieh - B.Sc. (2008)

 

 

 

SUMMER STUDENTS (Past and Present)

Ian Downie (NSERC-USRA)
Amr Omer (NSERC-USRA)
Paul Beamish (NSERC-USRA)
Zhi Jia (NSERC-USRA)
Adrian McNeely
Doran Drew
Aditya Varambally
Paul Atkins
Justin Godbout
Bengi Turegun
Nicholas Hou
Leah O'Shea