Daniel Clare

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Dan is a Senior EM Scientist for the electron Bio-Imaging Centre (eBIC).

Email: daniel.clare@diamond.ac.uk
Tel: +44 (0) 1235 77 7501

Key Research Area

Cryo-EM

Cryo-tomography

Structural Biology

Cell Biology

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  1. Research
  2. Technical
  3. Publications
Research -

I have always been interested in the relationship between the three-dimensional structure of proteins and their function. In my research career I initially used electron crystallography to study the structure of integral membrane proteins. However, over time I have become more interested in larger biomolecular complexes, and so I turned to single particle electron microscopy (EM) as a method to investigate these larger structures. Our initial EM studies on the GroEL-GroES complex determined its conformation in different nucleotide states and how it interacts with its substrate proteins. To improve the efficiency of our data collection methods we travelled to the SCRIPPS research institute, on a number of occasions, to collect data using Leginon automated data collection system. Automated data collection in combination with statistical methods allowed us to describe in detail the changes ATP induces on the conformation of GroEL.

During the last few years I have become more interested in even larger biological systems and have focused on the preparation methods and data acquisition for electron tomography. To facilitate this I have taken part in the NIBSC cryo preparation course (2009) and the IMOD image processing course (2011). Using these techniques, in collaboration with cell biologists, we have identified that the obligate intracellular pathogen Chlamydia assembles a pathogen synapse in order to hijack the host endoplasmic reticulum during its infection cycle. We have also used electron tomography to understand the organization of the cytoskeleton at the cortex of multicilated cells in the trachea of wild type and Galectin-3 knock out mice. I have also been invoved with electron tomography projects looking at both prions and Plasmodium falciparum.
 
I have also kept up my interest in protein structure and virus structures and was able to reconstruct a plant virus, BSMV, to a resolution that could be used to generate an pseudo atomic model. This was the first time that BSMV was reconstructed with that level of detail. In 2014 I was involved with the testing and setting up of two of the new direct electron detectors at Birkbeck. One of the test samples I used was TMV, a helical plant virus of known structure, that I was able to get to reconstruct at a resolution where side chains could be easily identified and an atomic structure determined (not published). We also showed with this sample that you could achieve this with both integrating and counting direct electron detectors.
 
 
Technical - +

Microscopes

I have extensive experience with FEI microscopes including, T10, T12, F20, Polara and Krios. I also have experience with various data collection softwares such as EPU, TOMO and SerialEM.

Sample preparation

I have experience with various plunge freezing devices, including the Vitrobot and Leica GP, used for preparing cryo single particle grids. I also have experience with the associated preparation equipment for electron tomography. This includes the Leica high pressure freezer, freeze substitution machine, microtomes (cryo- and room temperature) and a Zeiss fluorescence microscope fitted with a Linkam cryo-fluorescence stage.
 
Image processing
 
I have eexperience with a number of EM software packages including Imagic, Spider, Imod, PEET, parts of EMAN and Relion.  I also have experience with various motion correction software’s associated with direct detector data. I was also a demonstrator/lecture on the EMBO image processing for cryo-electron microscopy course that has been running at Birkbeck every 2 years since 2003.

 

Publications - +
 
  • Terry, C., Wenborn, A., Gros N, Sells, J., Joiner, S., Hosszu, L. L., Tattum, M. H., Panico, S., Clare, D. K., Collinge, J., Saibil, H. R., Wadsworth, J. D. (2016) Ex vivo mammalian prions are formed of paired double helical prion protein fibrils. Open Biol. 6 160035.
  • Joseph, A. P., Malhotra, S., Burnley, T., Wood, C., Clare, D. K., Winn, M., Topf, M. (2016) Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment. Methods, 100, 42-9.
  • Watermeyer, J. M., Hale, V. L., Hackett, F., Clare, D. K., Cutts, E. E., Vakonakis, I., Fleck, R. A., Blackman, M. J., Saibil, H. R. (2016) A spiral scaffold underlies cytoadherent knobs in Plasmodium falciparum-infected erythrocytes. Blood. 127, 343-51.
  • Clare, D. K., Pechnikova, E., Skurat, E., Makarov, V., Sokolova, O. S., Solovyev, A. G., OrlovaE. V. (2015) Novel inter-subunit contacts in Barley Stripe Mosaic Virus revealed by cryo-EM (2015) Structure, 10, 1815-26.
  • McMullan, G., Faruqi AR, Clare, D. & Henderson R. (2014) Comparison of optimal performance at 300keV of three direct electron detectors for use in low dose electron microscopy. Ultramicroscopy, 147,156-63.
  • Clare, D. K, Magescas, J., Piolot, T., Dumoux, M., Vesque, C., Pichard, E., Dang, T., Duvauchelle, B., Poirier, F., Delacour, D. (2014) Basal foot MTOC organizes pillar MTs required for coordination of beating cilia. Nat. Commun. 5, 4888.
  • Carroni, M., Kummer, E., Oguchi, Y., Wendler, P., Clare, D. K., Sinning, I., Kopp, J., Mogk, A., Bukau, B. & Saibil, H. R. (2014) Head-to-tail interactions of the coiled-coil domains regulate ClpB activity and cooperation with Hsp70 in protein disaggregation. Elife, 3, e02481.
  • Clare, D. K. & Saibil, H. R. (2013) ATP-driven molecular chaperone machines. Biopolymers, 99, 846-59.
  • Saibil, H. R, Fenton, W. A., Clare, D. K. & Horwich, A. L. (2013) Structure and allostery of the chaperonin GroEL. J. Mol. Biol. 425, 1476-87.
  • Fitzpatrick, A. W., Debelouchina, G. T., Bayro, M. J., Clare, D. K., Caporini, M. A., Bajaj, V. S., Jaroniec, C. P., Wang, L., Ladizhansky, V., Müller, S. A., MacPhee, C. E., Waudby, C. A., Mott, H. R., De Simone, A., Knowles, T. P., Saibil, H. R., Vendruscolo, M., Orlova, E. V., Griffin, R. G. & Dobson, C. M. (2013) Atomic structure and hierarchical assembly of a cross-β amyloid fibril. Proc. Natl. Acad. Sci. USA. 110, 5468-73.
  • Dumoux, M, Clare, D. K., Saibil, H. R., Hayward, R. D. (2012) Chlamydiae assemble a pathogen synapse to hijack the host endoplasmic reticulum. Traffic, 13, 1612-27.
  • Clare, D. K., Vasishtan, D., Stagg, S., Quispe, J., Farr, G. W., Topf, M., Horwich, A. L., & Saibil, H. R. (2012) ATP-triggered molecular mechanics of the chaperonin GroEL. Cell, 149, 113-23
  • Malet, H., Topf, M., Clare, D. K., Ebert, J., Bonneau, F., Basquin, J., Drazkowska, K., Tomecki, R., Dziembowski, A., Conti, E., Saibil, H. R. & Lorentzen, E. (2010) RNA channelling by the eukaryotic exosome. EMBO Rep. 11, 936-42.
  • Fourniol, F. J., Sindelar, C. V., Amigues, B., Clare, D. K., Thomas, G., Perderiset, M., Francis, F., Houdusse, A. & Moores, C. A. (2010) Template-free 13-protofilament microtubule-MAP assembly visualized at 8 A resolution. J. Cell Biol. 191, 463-70.
  • Clare, D. K. & Orlova, E. V. (2010) 4.6A Cryo-EM reconstruction of tobacco mosaic virus from images recorded at 300 keV on a 4k x 4k CCD camera. J. Struct. Biol. 171, 303-8.
  • Wendler, P., Shorter, J., Snead, D., Plisson, C., Clare, D. K., Lindquist, S. & Saibil, H. R. (2009) Motor mechanism for protein threading through Hsp104. Mol. Cell, 34, 81-92.
  • Clare, D. K., Bakkes, P. J., van Heerikhuizen, H., van der Vies, S.M. & Saibil H. R. (2009) Chaperonin complex with a newly folded protein encapsulated in the folding chamber. Nature, 457, 107-10.
  • Clare, D. K., Stagg, S., Quispe, J., Farr, G. W., Horwich, A. L. and Saibil, H. R. (2008) Multiple conformations of GroEL-ATP7 visualised by Cryo-EM. Structure, 16, 528-34.
  • Elad, N., Clare, D. K., Saibil, H.R. & Orlova, E.V. (2008) Detection and separation of heterogeneity in molecular complexes by statistical analysis of their two-dimensional projections. J. Struct. Biol. 162, 108-120.
  • Clare, D. K., Stagg, S., Quispe, J., Farr, G. W., Horwich, A. L. and Saibil, H. R. (2008) Multiple states of a nucleotide-bound group 2 chaperonin. Structure, 16, 528-534.
  • Elad, N., Farr, G. W., Clare, D. K., Orlova, E.V. Horwich, A. L. and Saibil, H. R (2007) Topologies of a substrate protein bound to the chaperonin GroEL. Mol. Cell, 26, 415-26.
  • Clare, D. K., Orlova, E. V., Finbow, M. A., Harrison, M. A., Findlay, J. B. and Saibil, H. R. (2006) An expanded and flexible form of the vacuolar ATPase membrane sector. Structure, 14,1149-56.
  • Clare, D. K., Bakkes, P. J., van Heerikhuizen, H., van der Vies, S. M. and Saibil, H. R. (2006) An expanded protein folding cage in the GroEL-gp31 complex. J. Mol. Biol. 358, 905-11.
  • Ranson, N.. A., Clare, D. K., Farr, G. W., Houldershaw, D., Horwich, A. L. and Saibil, H. R. (2006) Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes. Nat. Struct. Mol. Biol. 13, 147-52.
  • Farr, G. W., Fenton, W. A., Chaudhuri, T. K., Clare, D. K., Saibil, H. R. and Horwich, A. L. (2003) Folding with and without encapsulation by cis- and trans-only GroEL-GroES complexes. EMBO J. 22, 3220-30.