Davies | Biomedical and Molecular Sciences | School of Medicine

Peter L. Davies

Position(s)

Professor

Canada Research Chair in Protein Engineering

Contact Info

daviesp@queensu.ca

613-533-2983

Botterell Hall, Room 643

Lab: https://www.peterldavies.com/

Faculty Bio

B.Sc. (Hons) in Biochemistry and Soil Science. The University of Wales, UK

Ph.D. in Biochemistry. The University of British Columbia.

Postdoctoral fellowship. Biochemistry. University of Lund, Sweden.

Postdoctoral fellowship. Medical Biochemistry. University of Calgary.

Visiting Professor. National University of Singapore. 2009, 2012.

Visiting Professor. HUJI, Rehovot, Israel. 2013.

Visiting Professor. University of Otago, New Zealand. 2015

Visiting Professor. Technical University of Eindhoven, The Netherlands. 2018.

Research Interests:

We are studying the relationship between structure and function in three different types of proteins: antifreeze proteins (AFPs), which help organisms to resist or tolerate freezing; bacterial adhesins, which play a role in biofilm formation and infection; and calpains, enzymes that selectively cut proteins within the cell in response to calcium signals. (Funded by CIHR and NSERC)

Antifreeze proteins are found in some fishes, insects, plants and microorganisms. They bind to ice crystals and prevent them from growing to a size where they would damage the host. Our research involves the isolation and characterization of antifreeze proteins from different sources, the study of their evolution, and the cloning and expression of their genes to produce recombinant proteins for 3-D structural analysis by NMR and/or X-ray crystallography. AFPs are proving to have remarkably diverse structures. We are trying to identify their ice-binding sites/residues using site-directed mutagenesis in order to learn more about their mechanism(s) of action and what structural features are required for binding to ice. We are also engineering superior AFPs based on this information, and are applying them to the sub-zero storage of organs, tissues and cells.

Bacterial adhesins are long, thin proteins attached to the outer membrane of bacteria, which anchor their hosts to various surfaces where the bacteria can form biofilms. Structural characterization and functional analysis of all the adhesins are revealing methods for blocking biofilm formation that will be useful in preventing infections.

Calpains are complex, multi-domain calcium-dependent proteases involved in calcium signaling. We are studying their mechanism of activation and inhibition, and are using peptide and combinatorial compound libraries to develop calpain-specific inhibitors and substrates. The latter will be used to better define the physiological roles of calpain, and as leads for developing drugs to help prevent the calpain-mediated damage associated with heart attacks, stroke, neurodegeneration, and muscular dystrophy.

Representative Publications

2021

Guo. S., Vance, T.D.R., Zahiri, H., Eves, R., Stevens, C., Hehemann, J.H., Vidal-Melgosa, S., Davies, P.L. (2021). Structural basis of ligand selectivity by a bacterial adhesin lectin involved in multispecies biofilm formation. mBio. 2021 April 6; 12(2): e00130-21. doi: 10.1128/mBio.00130-21. PubMed: 33824212
Graham, L.A., Davies, P.L. (2021). Horizontal gene transfer in vertebrates: A fishy tale. Trends in Genetics. 2021 March 10; 37(6): 501-503. doi: 10.1016/j.tig.2021.02.006. PubMed: 33714557
Gruneberg, A.K., Graham, L.A., Eves, R., Agrawal, P., Oleschuk, R.D., Davies, P.L. (2021). Ice recrystallization inhibition activity varies with ice-binding protein type and does not correlate with thermal hysteresis. Cryobiology. 2021 Jan 30; 99: 28-39. doi: 10.1016/j.cryobiol.2021.01.017. PubMed: 33529683
Scholl, C.L., Tsuda, S., Graham, L.A., Davies, P.L. (2021). Crystal waters on the nine polyproline type II helical bundle springtail antifreeze protein from Granisotoma rainieri match the ice lattice. FEBS J. 2021 Jan 18; Online ahead of print. doi: 10.1111/febs.15717. PubMed: 33460499

2020

Vance, T.D.R., Ye, Q., Conroy, B., Davies, P.L. (2020). Essential role of calcium in extending RTX adhesins to their target. J Struct Biol X. 2020 Sep 8; 4: 100036. doi: 10.1016/j.yjsbx.2020.100036. PubMed: 32984811
Ye, Q., Eves, R., Campbell, R.L., Davies, P.L. (2020). Crystal structure of an insect antifreeze protein reveals ordered waters on the ice-binding surface. Biochem J. 2020 Sep 18; 477 (17): 3271-3286. doi: 10.1042/BCJ20200539. PubMed: 32794579
Graham, L.A., Boddington, M., Holmstrup, M., Davies, P.L. (2020) Antifreeze protein complements cryoprotective dehydration in the freeze-avoiding springtail Megaphorura arctica. Sci. Rep. 2020 Feb 20; 10(1): 3047. doi: 10.1038/s41598-020-60060-z. PubMed: 32080305
Kinrade, B., Davies, P.L., Vance, T.D.R. (2020) Bacterial sugar-binding protein as a one-step affinity purification tag on dextran-containing resins. Protein Expr Purif. 2019 Dec 26:105564. doi: 10.1016/j.pep.2019.105564. Epub 2019 Dec 26. PubMed: 31883939

2019

Vance, T.D.R., Guo S., Assaie-Ardakany S., Conroy B., Davies, P.L. (2019). Structure and functional analysis of a bacterial adhesin sugar-binding domain. PLoS One. 2019 Aug 8;14(8):e0221101. doi: 10.1371/journal.pone.0221101.
Tomalty, H.E, Graham, L.A., Eves, R., Gruneberg, A.K., Davies, P.L. (2019) Laboratory-scale isolation of insect antifreeze protein for cryobiology. Biomolecules (in press)
Vance, T.D.R., Bayer-Giraldi, M., Davies, P.L., Mangiagalli, M. (2019). Ice-binding proteins and the 'domain of unknown function' 3494 family. FEBS J 286, 855-873.
Guo, S., Vance, T.D.R., Stevens, C.A., Voets, I., Davies, P.L. (2019). RTX adhesins are key bacterial surface megaproteins in the formation of biofilms. Trends in Microbiology. Jan 15. pii: S0966-842X(18)30279-8. doi: 10.1016/j.tim.2018.12.003. PubMed: 30658900

2018

Guo, S., Langelaan, D.N., Phippen, S.W., Smith, S.P., Voets, I.K., Davies, P.L. (2018) Conserved structural features anchor biofilm-associated RTX-adhesins to the outer membrane of bacteria. FEBS J. 2018 Mar 25. doi: 10.1111/febs.14441 [Epub ahead of print] PubMed: 29575515.
Rismani Yazdi, S., Nosrati, R., Stevens, C.A., Vogel, D., Davies, P.L., Escobedo, C. (2018) Magnetotaxis Enables Magnetotactic Bacteria to Navigate in Flow. Small. 2018 Feb;14(5). doi: 10.1002/smll.201702982. Epub 2017 Dec 4. https://doi.org/10.1002/smll.201702982 PubMed: 29205792.
Vance, T.D.R., Graham, L.A., Davies, P.L. (2018) An ice-binding and tandem beta-sandwich domain-containing protein in Shewanella frigidimarina is a potential new type of ice adhesin. FEBS J. 2018 Mar 2. doi: 10.1111/febs.14424 [Epub ahead of print] PubMed: 29498209.
Ye, Q., Campbell, R.L., Davies, P.L. (2018) Structures of human calpain-3 protease core with and without bound inhibitor reveal mechanisms of calpain activation. J Biol Chem. 2018 Jan 30. pii: jbc.RA117.001097. doi: 10.1074/jbc.RA117.001097 [Epub ahead of print] PubMed: 29382717.

2017

Guo, S., Stevens, C.A. Vance, T. D.R., Olijve, L.L.C., Graham, L.A., Campbell, R.L., Yazdi, S.R., Escobedo, C., Bar-Dolev, M. Yashunsky, V., Braslavsky, I., Langelaan, D.N., Smith, S.P., Allingham, J.S., Voets, I. K., Davies P.L. (2017) Structure of a 1.5-MDa adhesin that binds its Antarctic bacterium to diatoms and ice. Sci Adv. 2017 Aug 9;3(8):e1701440. doi: 10.1126/sciadv.1701440. eCollection 2017 Aug PubMed: 28808685.
Stevens, C.A., Semrau, J., Chiriac, D., Litschko, M., Campbell, R.L., Langelaan, D.N., Smith, S.P., Davies, P.L., Allingham, J.S. (2017) Peptide backbone circularization enhances antifreeze protein thermostability. Protein Sci. 2017 Jul 10. doi: 10.1002/pro.3228. [Epub ahead of print] PubMed: 28691252
Oude Vrielink, A.S., Vance, T.D.R., de Jong A.M., Davies, P.L., Voets, I.K. (2017) Unusually high mechanical stability of bacterial adhesin extender domains having calcium clamps. PLoS ONE 2017 Apr 4;12(4):e0174682. doi: 10.1371/journal.pone.0174682. eCollection 2017 PubMed: 28376122.

2016

Bar-Dolev, M., Bernheim, R., Guo, S., Davies, P.L., Braslavsky, I. (2016) Putting life on ice: Bacteria that bind to frozen water. RSC Interface. 2016 Aug;13(121). pii: 20160210. doi: 10.1098/rsif.2016.0210. PubMed: 27534698
Bar-Dolev, M., Braslavsky, I., Davies, P.L. (2016) Antifreeze protein function. Ann. Rev. Biochem. 85, 515-542. PubMed: 27145844
Basu, K., Campbell, R.L., Guo, S., Sun, T., Davies, P.L. (2016) Modeling repetitive, non-globular proteins. Protein Sci. 25 (5), 946-58 Feb 23. doi: 10.1002/pro.2907. [Epub ahead of print] Review. PubMed:26914323
Basu, K., Wasserman, S.S., Jeronimo, P.S., Graham, L.A., Davies, P.L. (2016) Intermediate activity of midge antifreeze protein is due to a tyrosine-rich ice-binding site and atypical ice plane affinity. FEBS J. 283 (8) 2016 Feb 20. doi: 10.1111/febs.13687. [Epub ahead of print] PubMed:26896764

2015

Sun, T., Davies, P.L., Walker, V.K. (2015) Structural basis for the inhibition of gas hydrates by alpha-helical antifreeze proteins. Biophys. J. 109, 1698-1705. PubMed: 26488661
Stevens, C., Drori, R., Zalis, S., Braslavsky, I., Davies, P.L. (2015) Dendrimer-linked antifreeze proteins have superior activity and thermal recovery. Bioconjugate Chemistry. PubMed: 26267368
Basu, K., Graham, L.A., Campbell, R.L., Davies, P.L. (2015) Flies expand the repertoire of protein structures that bind ice. PNAS 112(3), 737-742. PubMed: 25561557

2014

Sun,T., Feng-Hsu Lin, F-H., Campbell, R.L., Allingham, J.S., and Davies, P.L. (2014) An antifreeze protein folds with an interior network of over 400 semi-clathrate waters. Science, 343(6172), 795-8 PubMed: 24531972
Vance, T.D.R., Olijve, L.L.C., Campbell, R.L., Voets, I.K., Davies, P.L., Guo, S. (2014) Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice. Bioscience Reports 34(4). PubMed: 24892750
Davies, P.L. (2014) Ice-binding proteins: a remarkable diversity of structures for stopping and starting ice growth. Trends in Biochemical Sciences 39(11), 548-555. PubMed: 25440715

2013

Graham L.A, Hobbs R.S, Fletcher G.L, Davies P.L. (2013) Helical antifreeze proteins have independently evolved in fishes on four occasions. PLoS ONE 8(12), e81285 PubMed: 24324684
Guo, S., Garnham, C.P., Partha, S.K., 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 adhesion. FEBS Journal Ref. no.: FJ-13-0467.R1.PubMed: 24024640
Celik Y., Drori R., Pertaya-Braun N., Altan A., Barton T., Bar-Dolev M., Groisman A., Davies P.L., Braslavsky I. (2013) Microfluidic experiments reveal that antifreeze proteins bound to ice crystals suffice to prevent their growth. Proc Natl Acad Sci U S A. 110,1309-14 PubMed: 23300286

2012

Guo, S., Garnham, C.P., Whitney J.C., Graham, L.A. and Davies, P.L. (2012) Re-evaluation of a bacterial antifreeze protein as an adhesin with ice-binding activity. PLoS ONE 7, e48805 PubMed: 23144980
Garnham C.P., Nishimiya Y., Tsuda S., Davies P.L. (2012) Engineering a naturally inactive isoform of type III antifreeze protein into one that can stop the growth of ice. FEBS Lett. 586(21), 3876-81. PubMed: 23017208
Campbell R.L., Davies P.L. (2012) Structure-function relationships in calpains. Biochem J. 447, 335-51 PubMed: 23035980
Middleton, A.J., Marshall, C.B., Faucher, F., Bar-Dolev, M., Braslavsky, I., Campbell, R.L., Walker, V.K. and Davies, P.L. (2012) Antifreeze protein from freeze-tolerant grass has a beta-roll fold with an irregularly structured ice-binding site. J. Mol. Biol. 416, 713-724 PubMed: 22306740

2011

Garnham, C.P., Campbell, R.L., Walker, V.K and Davies, P.L. (2011) Novel dimeric β-helical model of an ice nucleation protein with bridged active sites. BMC Structural Biology 11, 36 PubMed: 21951648 Free PDF at BioMed Central
Lin, F.H.,Davies, P.L. and Graham, L.A. (2011) The Thr- and Ala-rich hyperactive antifreeze protein from inch worm folds as a flat silk-like β-helix. Biochemistry 50, 4467-4478. PubMed: 21486083
Garnham, C.P., Campbell, R.L. and Davies, P.L. (2011) Anchored clathrate waters bind antifreeze proteins to ice. PNAS 108, 7363-7367. PubMed: 21482800 PubMed Central: PMC3088597

2010

Garnham, C.P,. Natarajan, A,. Middleton, A.J., Kuiper, M.J., Braslavsky, I., Davies, P.L. (2010) Compound ice-binding site of an antifreeze protein revealed by mutagenesis and fluorescent tagging. Biochemistry 49, 9063-9071. PubMed: 20853841
Mok, Y.F., Lin, F.H., Graham, L.A., Celik, Y. Braslavsky, I., Davies, P.L. (2010) Structural basis for the superior activity of the large isoform of snow flea antifreeze protein. Biochemistry 49, 2593-2603. PubMed: 20158269
Celik Y., Graham, L.A., Mok, Y.F., Bar, M., Davies, P.L., Braslavsky I. (2010) Superheating of ice crystals in antifreeze protein solutions. Proc Natl Acad Sci U S A. 107, 5423-5428. PubMed: 20215465

2009

Garnham, C.P., Hanna, R.A., Chou, J.S., Low, K.E., Gourlay, K., Campbell, R.L., Beckmann, J.S. and Davies, P.L. (2009) Limb-girdle muscular dystrophy type 2A can result from accelerated autoproteolytic inactivation of calpain 3. Biochemistry 48, 3457-3467. PubMed: 19226146
Middleton, A.J., Brown, A.M., Davies, P.L. and Walker, V.K. (2009) Identification of the ice-binding face of a plant antifreeze protein. FEBS Lett. 583, 815-819. PubMed: 19185572
Ravulapalli, R., Campbell, R.L., Gauthier, S.Y., Dhe-Paganon, S. and Davies, PL. (2009) Distinguishing between calpain heterodimerization and homodimerization. FEBS J. 276, 973-982. PubMed: 19215300

2008

Hanna, R.A., Campbell, R.L. and Davies, P.L. (2008) Calcium-bound structure of calpain and its mechanism of inhibition by calpastatin. Nature 456, 409-412. PubMed: 19020623
Graham, L.A., Ewart, K.V., Lougheed, S.C. and Davies, P.L. (2008) Lateral transfer of a lectin-like antifreeze protein gene in fishes. PLoS ONE 3, e2616. PubMed: 18612417
Garnham, C.P., Gilbert, J.A., Hartman, C.P., Campbell, R.L., Laybourn-Parry, J. and Davies, P.L. (2008) A Ca2+-dependent bacterial antifreeze protein domain has a novel β-helical ice-binding fold. Biochem J. 411, 171-180. PubMed: 8095937
Graham, L.A., Marshall, C.B., Lin, F.H., Campbell, R.L. and Davies, PL. (2008) Hyperactive antifreeze protein from fish contains multiple ice-binding sites. Biochemistry 47, 2051-2063. PubMed: 18225917

Team

Lab: https://www.peterldavies.com/

Faculty Bio

Research Interests:

Representative Publications

Faculty