Allingham | Biomedical and Molecular Sciences | School of Medicine

John Allingham PhD Biochemistry and Molecular Biology

Position(s)

Professor

Contact Info

allinghj@queensu.ca

613-533-3137 x33137

Botterell Hall, Room 642

Lab website: www.allinghamlab.com

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:

Research in the Allingham laboratory focuses on understanding the mechanical properties of the cytoskeleton and cytoskeleton-binding motor proteins, which generate piconewton-scale forces that produce changes in cell shape and whole-cell movement. Our goal is to understand: (1) the force-generating mechanisms of these proteins and (2) the roles they play in cellular processes like mitotic spindle assembly and chromosome movements in mitosis, and establishment of cell polarity, migration, and invasion into new environments. We develop and use biochemical, molecular genetics, and cell biological methods to observe, measure and manipulate these proteins, in combination with X-ray crystallography and cryo-electron microscopy to obtain detailed 3D information about their dynamic structures.

Research projects:

Design and development of actin-targeting compounds

Cancer is responsible for approximately 10 million deaths annually. Cancer metastasis accounts for over ninety percent of these deaths and is one of the most significant challenges in cancer treatment because, in many patients, metastasis has already occurred by the time they are diagnosed with primary cancer. Current cancer therapies fail to prevent metastasis in many patients with advanced cancers. Allingham lab scientists and our collaborators are developing simplified analogs of actin-targeting natural products that inhibit cancer cell metastasis (e.g., Mycalolide B). We are also exploring strategies for targeting these analogs to cancer cells, beginning with conjugation to clinical-grade oncology antibodies. At the same time, we have initiated studies to define the impact of multivalency of these synthetic toxins toward enhancing their anti-metastatic activities.

Molecular mechanisms of kinesins that control cytoskeleton structure

Eukaryotic cells contain a dense array of microtubules and actin filaments that serve as the cell's cytoskeleton and as substrates against which molecular motor proteins generate force. Microtubules are used for intracellular transport, cell motility, cell signaling, and chromosome segregation. Actin filaments control the cell cortex's architectures and mediate cell motility, cell division, and endocytosis. When cells transition through each cell cycle, or change morphology, they disassemble these arrays and reconstruct them into new configurations according to their functions. This process is also highly regulated in cells by many microtubule- and actin-binding proteins and cofactors, a major one being kinesins. Our short-term aims are to: (1) determine how subtle tweaks and edits within the amino acid sequence of kinesin-3, kinesin-8, and kinesin-13 family members has diversified their mechanism of cytoskeleton regulation, and to (2) construct structural models of each kinesin’s mechanism that explain the fundamental differences in their cellular functions. Our long-term aim is to understand how unique segments of amino acids from kinesins, and other cytoskeleton regulatory systems, can be recombined to create new biomolecular machines that work with engineered cytoskeleton tracks.

Roles and regulation of kinesins in pathogenic fungi

Fungi are significant and increasing mediators of pathogenesis, causing severe challenges medically and economically. Candida albicans is the most prevalent cause of fungal infections in people and can cause life-threatening systemic infections if our immune defenses are compromised. A battery of fitness attributes enables drug resistance of this fungus, most of which arise by the rapid generation of genetic diversity within a population as a means of adaptation. Research has shown that aneuploidy (an abnormal number of chromosomes) accounts for much of this diversity. This condition often arises from changes in components of the chromosome segregation machinery. Allingham lab researchers have discovered that some of these changes could be induced or enabled by altered activity of kinesin motor proteins that regulate the mitotic spindle. A goal of our research program is to understand how kinesins regulate the structure and function of the mitotic spindle in Candida albicans. Our specific aims are to: (1) determine the three-dimensional structures of kinesins that drive mitotic spindle assembly and chromosome aggregation in C. albicans, (2) to identify which of these kinesins are critical parts of stress-adaption mechanisms that promote mitotic errors leading to beneficial aneuploidy, and (3) to identify kinesin binding partners that regulate kinesin function under stress.

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

Dr. Allingham has 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, his lab members learn to 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 advisors 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.

Representative Publications:

*co-corresponding authors

2022

Hunter, B., Benoit, M.P.M.H, Doubleday, C., Asenjo, A., Trofimova, D., Sosa, H.,* Allingham, J.S.* (2022) Kinesin-8-specific loop-2 controls the dual activities of the motor domain according to tubulin protofilament shape. bioRxiv 2022.02.28.480783

2021

Pipaliya, B., Trofimova, D., Grange, R., Aeluri, M., Deng, X., Shah, K., Craig, A.W., Allingham, J.S.,* Evans, PA.* (2021) Truncated actin-targeting macrolide derivative blocks cancer cell motility and invasion of extracellular matrix. Journal of the American Chemical Society, May 12;143(18):6847-6854

2020

Sridhar, P.S., Trofimova, D., Subramaniam, R., González-Peña Fundora, D., Foroud, N.A., Allingham, J.S., Loewen, M.C. (2020) Ste2 receptor-mediated chemotropism of Fusarium graminearum contributes to its pathogenicity against wheat. Scientific Reports. Jul 1;10(1):10770.

Hunter, B. and Allingham, J.S. (2020) These motors were made for walking. Protein Science. Aug;29(8):1707-1723.

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

Shoukat, I., Frazer, C., Allingham, J.S. (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, M.L., Stokman, M.F., 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, C.Y., Shan, X., Filges, I., Allingham, J.S., Kwok, B.H., Saunier, S., Giles, R.H., 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.

Team

Faculty