Skip to main content
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

Research Interests:

My laboratory studies large, force-generating protein complexes that elicit changes in cell shape, movement, and chromosome segregation in healthy cells, cancerous cells, and fungal pathogens. Our goal is to develop structural models of these huge molecules using experimental tools that include fluorescence microscopy, X-ray crystallography, small-angle X-ray scattering and electron microscopy. We also use molecular genetics and cell biology methods to visualize their actions within cells. These types of observations will provide a deeper understanding of how biomolecular machines evolve to accommodate the specific needs the cell, and will aid development of new medicines to control their activities for therapeutic benefit.

Research projects:

Structural and molecular biology of kinesin motors in human fungal pathogens

Fungi are significant and increasing mediators of pathogenesis in people; causing serious challenges medically and economically. Candida albicans is the most prevalent cause of fungal infections, and can cause life-threatening systemic infections if our immune defenses are compromised. A battery of fitness attributes promote pathogenicity and drug resistance of this fungus, most of which arise by rapid generation of genetic diversity within a fungal population in response to stressful growth conditions, such as exposure to antifungal drugs, as a means of adaptation. Research has shown that aneuploidy (an abnormal number of chromosomes) accounts for much of this diversity, and that this condition often arises from changes in the activity of certain components of the chromosome segregation machinery. Our findings indicate that some of these changes could be induced or enabled by kinesin motor proteins that regulate the structure of the cell’s chromosome segregation apparatus – 'the mitotic spindle'.

In the coming years, we will establish fundamental knowledge about the structures, functions, and mechanisms of action of Candida kinesins that regulate these 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:

2020

Gilet, J. Ivanova, E., Trofimova, D., Rudolf, G., Meziane, H., Broix, L., Drouot, N., Courraud, J., Skory, V., Voulleminot, P., Hinckelmann, M-V., BahiBuisson, N., Yalcin, B., Birling, M-C., Kwok, B.K., Allingham, J.S., Chelly, J. (2020). Conditional switching of KIF2A mutation provides new insights into cortical malformations pathogeny. Human Molecular Genetics. Jan 10. pii: ddz316. doi: 10.1093/hmg/ddz316

2019

Irsa Shoukat, Corey Frazer, and John S. Allingham. (2019). Kinesin-5 is dispensable for bipolar spindle formation and elongation in Candida albicans, but simultaneous loss of kinesin-14 activity is lethal. mSphere. Nov 13;4(6). pii: e00610-19. doi: 10.1128/mSphere.00610-19

Reilly ML , Stokman MF , Magry V , Jeanpierre C , Alves M , Paydar M , Hellinga J , Delous M , Pouly D , Failler M , Martinovic J , Loeuillet L , Leroy B , Tantau J , Roume J , Gregory-Evans CY, Shan X , Filges I , Allingham JS , Kwok BH , Saunier S , Giles RH , Benmerah A. (2019). Loss-of-function mutations in KIF14 cause severe microcephaly and kidney development defects in humans and zebrafish. Human Molecular Genetics. 28(5): 778-795.

Guo S, Campbell R, Davies PL, Allingham JS. (2019). Phasing with calcium at home. Acta Crystallographica. Section F, Structural biology communications. 75(Pt 5): 377-384.

2018

Nersesian, S., Williams, R., Newsted, D., Shah, K., Young, S., Evans, P. A., Allingham, J.S., Craig, A. W. (2018). Effects of Modulating Actin Dynamics on HER2 Cancer Cell Motility and Metastasis. Scientific Reports, 8(1), 17243.

Trofimova, D., Paydar, M., Zara, A., Talje, L., Kwok, B. H., & Allingham, J. S. (2018). Ternary complex of Kif2A-bound tandem tubulin heterodimers represents a kinesin-13-mediated microtubule depolymerization reaction intermediate. Nature Communications, 9(1), 2628.

Loewen, P. C., Switala, J., Wells, J. P., Huang, F., Zara, A. T., Allingham, J. S., & Loewen, M. C. (2018). Structure and function of a lignostilbene-α,β-dioxygenase orthologue from Pseudomonas brassicacearum. BMC Biochemistry, 19(1), 8.

2017

Guo S, Stevens CA , Vance TDR , Olijve LLC , Graham LA , Campbell RL , Yazdi SR , Escobedo C , Bar-Dolev M , Yashunsky V , Braslavsky I , Langelaan DN , Smith SP , Allingham JS , Voets IK , Davies PL. (2017). Structure of a 1.5-MDa adhesin that binds its Antarctic bacterium to diatoms and ice. Science Advances. 3(8): e1701440.

Stevens CA, Semrau J , Chiriac D , Litschko M , Campbell RL , Langelaan DN , Smith SP , Davies PL , Allingham JS. (2017). Peptide backbone circularization enhances antifreeze protein thermostability. Protein Science. Oct;26(10):1932-1941. doi: 10.1002/pro.3228

Grondin, J.M., Duan, D., Kirlin, A.C., Abe, K., Chitayat, S., Furness, H.S., Spencer, H.L., Spencer, C., Campigotto, A., Houliston, S., Arrowsmith, C.H., Allingham, J.S., Boraston, A.B. Smith, S.P. (2017) Diverse modes of galacto-specific carbohydrate recognition by a family 31 glycoside hydrolase from Clostridium perfringens, PLOS ONE. 12(2): e0171606

2016

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.

2015

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.

2014

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.

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.

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.

2013

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.

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.

Lab Members

Dr. Daria (Dasha) Trofimova

(Senior Research Associate / Lab Manager)

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

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

Byron Hunter
(Ph.D. Candidate)
Department of Biomedical and Molecular Sciences 
Queen's University 
Botterell Hall, Rm. 641 
Kingston, ON, K7L 3N6
E-mail: 
12bth@queensu.ca

Pooja Sridhar

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

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

Caitlin Doubleday

(M.Sc. Candidate)

Department of Biomedical and Molecular Sciences 
Queen's University 
Botterell Hall, Rm. 641 
Kingston, ON, K7L 3N6
E-mail:14cjd4@queensu.ca

Kavan Shah

(M.Sc. Candidate)

Department of Biomedical and Molecular Sciences 
Queen's University
Cancer Research Institute, Rm. 315
Kingston, ON, K7L 3N6
E-mail:kavan.shah@queensu.ca