Daniel Clare

Dan has always been interested in the relationship between the three-dimensional structure of proteins and their function. In his research career he initially used electron crystallography to study the structure of integral membrane proteins. However, over time Dan has become more interested in larger biomolecular complexes, and so he turned to single particle electron microscopy (EM) as a method to investigate these larger structures. 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 their data collection methods they 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 them to describe in detail the changes ATP induces on the conformation of GroEL.

During the last few years Dan has become more interested in even larger biological systems and has focused on the preparation methods and data acquisition for electron tomography. To facilitate this he has taken part in the NIBSC cryo preparation course (2009) and the IMOD image processing course (2011). Using these techniques, in collaboration with cell biologists, they have identified that the obligate intracellular pathogen Chlamydia assembles a pathogen synapse in order to hijack the host endoplasmic reticulum during its infection cycle. They have also used electron tomography to understand the organization of the cytoskeleton at the cortex of multiciliated cells in the trachea of wild type and Galectin-3 knock out mice. Dan has also been involved with electron tomography projects looking at both prions and Plasmodium falciparum.

Dan has also kept up his 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 a pseudo atomic model. This was the first time that BSMV was reconstructed with that level of detail. In 2014 he was involved with the testing and setting up of two of the new direct electron detectors at Birkbeck. One of the test samples Dan used was TMV, a helical plant virus of known structure, that he was able to get to reconstruct at a resolution where side chains could be easily identified, and an atomic structure determined (not published). They also showed with this sample that you could achieve this with both integrating and counting direct electron detectors.

Microscopes
Dan has extensive experience with FEI microscopes including, T10, T12, F20, Polara and Krios. Dan also has experience with various data collection software such as EPU, TOMO and SerialEM.

Sample preparation
Dan has experience with various plunge freezing devices, including the Vitrobot and Leica GP, used for preparing cryo single particle grids. Dan also has 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
Dan has experience with a number of EM software packages including Imagic, Spider, Imod, PEET, parts of EMAN and Relion.  Dan also has experience with various motion correction software associated with direct detector data. Dan was also a demonstrator/lecturer on the EMBO image processing for cryo-electron microscopy course that has been running at Birkbeck every 2 years since 2003.

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.