Karen Davies

Dr Karen Davies uses an array of electron cryo-microscopy techniques (cryo-EM) to investigate how proteins interact with and modulate biological membranes. Karen’s interest in electron microscopy (EM) developed during her BA (Hons) degree in biological sciences at St John’s College, Oxford University, UK where she used thin-sectioning EM to determine how the dragline silk of the golden orb weaving spider obtained its strength. For her Ph.D., Karen stayed at St John’s College, Oxford University but switched to molecular biophysics where she learnt how to clone and purify proteins to determine the structure of the response regulator protein (HupR)
by 2D electron and 3D X-ray crystallography.

In 2007, Karen moved to the Max Planck Institute of Biophysics (MPIBP), Frankfurt-am-Main, Germany where she combined her love of protein structure with cellular ultrastructure through the technique of electron cryo-tomography (cryo-ET) and subtomogram averaging. During her stay at MPIBP, Karen contributed some fundamental research to the bioenergetics field including:
1) providing the first definitive structure of the a-subunit in F-type ATP synthases (PMID: 25707805), 2) proving the existence of respiratory chain supercomplexes in situ (PMID 29519876), and
3) showing how the structure and organisation of ATP synthases in mitochondria contribute to cristae morphology (PMID: 30760595, 29643173, 28096380, 27402755, 22864911, 21836051).

In 2016, Karen started her own lab at Lawrence Berkeley National Lab (LBNL) in California, USA where she focused her attention on photosynthesis and the interplay between linear and cyclic electron flow. One of her chief achievements was determining the structure of the cyanobacterial NAD(P)H-dehydrogenase-like complex of photosynthesis, a large membrane protein responsible for transferring electrons from photosystems I to the plastoquinone pool during cyclic electron flow (PMID: 30742075). During her stay at LBNL, Karen was introduced to bacterial warfare and switched her primary research direction to focus on understanding how bacteriophage and bacteriophage-like particles recognise and kill bacteria with the aim of providing fundamental structural knowledge necessary to design new targeted narrow-range antimicrobial agents.

In 2021, Karen returned to the UK as principal EM scientist at eBIC, Diamond Light source, where she helps run the UK’s national cryoEM user facility in addition to her independent research group at the Research Complex, Harwell (RCaH).

Microscopes
Dr Karen Davies has extensive experience in using and maintaining the following transmission electron microscopes: CM120, Tecani12, Polara, Krios, Jeol1200, Jeol1400Flash and Jeol3200.

For data collection Karen has used SerialEM, Latitude, Tomo and more recently EPU. Karen has collected data on Gatan oneview, K2 and K3, and used both an in column and post column energy filter.

Sample preparation
Karen has extensive experience with both manual and automatic plunge freezing devices (primarily Vitrobot). Karen also has some experience of high pressure freezing, freeze substitution and room temperature microtomy.

Image processing
Karen has extensive experience with Imod and Peet and some experience with Spider, parts of EMAN and Relion.

Davide Zabeo, Karen M. Davies. (2022) Studying membrane modulation mechanisms by electron cryo-tomography.
Current Opinion in Structural Biology Volume 77, 102464. doi.org/10.1016/j.sbi.2022.102464.

Volland JM, Gonzalez-Rizzo S, Gros O, Tyml T, Ivanova N, Schulz F, Goudeau D, Elisabeth NH, Nath N, Udwary D, Malmstrom RR, Guidi-Rontani C, Bolte-Kluge S, Davies KM, Jean MR, Mansot JL, Mouncey NJ, Angert ER, Woyke T, Date SV. (2022) A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles. 
Science 2022, 376:1453-1458. doi: 10.1126/science.abb3634. 

Zhao Y, Wang H, Wiesehoefer C, Shah NB, Reetz E, Hwang JY, Huang X, Wang TE, Lishko PV, Davies KM, Wennemuth G, Nicastro D, Chung JJ. (2022) 3D structure and in situ arrangements of CatSper channel in the sperm flagellum. 
Nat Commun. 13:3439. doi: 10.1038/s41467-022-31050-8. 

Zik JJ, Yoon SH, Guan Z, Stankeviciute Skidmore G, Gudoor RR, Davies KM, Deutschbauer AM, Goodlett DR, Klein EA, Ryan KR. (2022) Caulobacter lipid A is conditionally dispensable in the absence of fur and in the presence of anionic sphingolipids. Cell Rep. 39(9):110888. doi: 10.1016/j.celrep.2022.110888.

Serwas D, Akamatsu M, Moayed A, Vegesna K, Vasan R, Hill JM, Schöneberg J, Davies KM, Rangamani P, Drubin DG (2022). Mechanistic insights into actin force generation during vesicle formation from cryo-electron tomography. Dev Cell. 57(9):1132-1145.e5. doi: 10.1016/j.devcel.2022.04.012.

Serwas D.S., & Davies K.M. (2021) Getting started with in situ cryo-electron tomography. Methods in Molecular Biology 2215:3-23. doi: 10.1007/978-1-0716-0966-8_1.

Laughlin T.G., Savage D.F., Davies K.M. (2020) Recent advances on the structure and function of NDH-1: the complex I of oxygenic photosynthesis. BBA 2020 Nov 1;1861(11):148254. doi: 10.1016/j.bbabio.2020.148254. Epub 2020 Jul 6.

Blum T.B., Hahn A., Meier T., Davies K.M. Kühlbrandt W. (2019) Dimers of mitochondrial ATP synthase induce membrane curvature and self-assemble into rows. PNAS 116: 4250-4255.

Laughlin T.G., Bayne A.N., Trempe J.F., Savage D.F., Davies K.M. (2019) Structure of the complex I-like molecule NDH of oxygenic photosynthesis. Nature 566: 411-414.

Sutter M, Laughlin T.G., Sloan N, Serwas D.S., Davies K.M., Kerfeld C. (2019) Structure of a synthetic beta-carboxysome shell. Plant Physiology, accepted doi:10.1104/pp19.00885.

Anselmi A, Davies K.M. Faraldo-Gomez, J.D. (2018) Mitochondrial ATP synthase dimers spontaneously associate due to a long-range membrane-induced force. Journal of General Physiology 150(5). DOI: 10.1085/jgp.201812033.

Davies K.M., Blum T.B., Kühlbrandt W. (2018) Conserved in situ arrangement of complex I and III₂ in mitochondrial respiratory chain supercomplexes of mammals, yeast, and plants. PNAS 115, 3024-3029.

Davies K.M., Kühlbrandt W. (2018) Structure of the catalytic F(1) head of the F(1)-F(o)ATP synthase from Trypanosoma brucei. PNAS 115, E2906-E2907.

Eydt. K., Davies K.M., Behrendt, C., Wittig, I., Reichert, A. (2017) Cristae architecture is determined by an interplay of the MICOS complex and the F1FO ATP synthase via Mic27 and Mic10. Microbial Cell. 4, 259-272.

Mühleip A.W., Dewar C.E., Schnaufer A., Kühlbrandt W., Davies K.M. (2017) In situ structure of trypanosomal ATP synthase dimer reveals a unique arrangement of catalytic subunits. PNAS 114, 992-997.

Mühleip, A.W., Joos, J., Wigge, C., Frangakis, A.S., Kühlbrandt W., & Davies, K.M. (2016) Helical arrays of U-shaped ATP synthase dimers form tubular cristae in ciliate mitochondria, PNAS 113, 8442-8447.

Kühlbrandt, W & Davies, K.M. (2016) Rotary ATPases: A new twist to an ancient machine. TIBS, 41, 106-116.

Kukat, C., Davies, K.M., Wurm, C.A., Spahr H., Bonekamp N.A., Kühl I., Joos, F., Loguercio Polosa P., Bae Park. C., Posse, V., Falkenberg, M., Jakobs S., Kühlbrandt W., Larsson, N-G. (2015) Cross-strand binding of TFAM to a single mtDNA molecule forms the mitochondrial nucleoid PNAS, 112, 11288-93.

Allegretti, M., Klusch, N., Mills, D.J., Vonck J., Kühlbrandt W.^# and Davies, K.M^#. (2015) Horizontal membrane-intrinsic α-helices in the stator a-subunit of an F-type ATP synthase Nature 521, 237-240, doi 10.1038/nature14185 ^#shared corresponding author.

Bohnert, M., Zerbes, R.M., Davies, K.M., Mühleip, A.W., Rampelt, H., Boenke, T., Kram, A., Perschil, I., Veenhuis, M., Kühlbrandt, W., van der Klei, I.J., Pfanner, N., and van der Laan, M. (2015) Central Role of Mic10 in the Mitochondrial Contact Site and Cristae Organizing System. Cell metabolism 21, 747-55.

Jiko, C^†., Davies, K.M^†#., Shinzawa-Itoh, K., Tani, K., Maeda, S., Mills, D.J., Tsukihara, T., Fujiyoshi, Y., Kühlbrandt, W., & Gerle, C^#. (2015) Bovine F1Fo ATP synthase monomers bend the lipid bilayer in 2D membrane crystals eLife (published online) doi 10.7554/eLife.06119 ^#shared corresponding author, ^† shared first author.

Davies, K.M., Daum, B., Gold, V.A.M., Mühleip, A.W., Brandt, T., Blum, T.B., Mills, D.J., and Kühlbrandt, W. (2014) Visualization of ATP synthase dimers in mitochondria by electron cryo-tomography. J. Vis. Exp. (91), e51228, doi:10.3791/51228 .

Herrmann, J., Berberich H., Hartmann, J., Beyer S., Davies K.M, and Kock J., (2014) Homo-oligomerization of the activating natural killer cell receptor NKp30 ectodomain increases its binding affinity for cellular ligands. J. Biol Chem. 289, 765-77.

Davies, K.M., and Daum, B. (2013) Role of cryo-ET in membrane bioenergetics research. Biochem Soc T 41, 1227-1234. (review).

Davies, K.M., Anselmi, C., Wittig, I., Faraldo-Gomez, J.D., and Kuhlbrandt, W. (2012) Structure of the yeast F1Fo-ATP synthase dimer and its role in shaping the mitochondrial cristae. Proc Natl Acad Sci U S A 109, 13602-13607.

Althoff, T., Davies, K.M., Schulze, S., Joos, F., and Kuhlbrandt, W. (2012) GRecon: a method for the lipid reconstitution of membrane proteins. Angew Chem Int Ed Engl 51, 8343-8347.

Davies, K.M^#., Strauss, M^#., Daum, B^#., Kief, J.H., Osiewacz, H.D., Rycovska, A., Zickermann, V., and Kuhlbrandt, W. (2011) Macromolecular organization of ATP synthase and complex I in whole mitochondria. Proc Natl Acad Sci U S A 108, 14121-14126. ^#shared first author.

Sinclair, J.C., Davies, K.M., Venien-Bryan, C., and Noble, M.E.M. (2011) Generation of protein lattices by fusing proteins with matching rotational symmetry. Nat Nanotechnol 6, 558-562.

Davies, K.M., Lowe, E.D., Venien-Bryan, C., and Johnson, L.N. (2009) The HupR Receiver Domain Crystal Structure in its Nonphospho and Inhibitory Phospho States. J Mol Biol 385, 51-64.

Davies, K.M., Skamnaki, V., Johnson, L.N., and Venien-Bryan, C. (2006) Structural and functional studies of the response regulator HupR. J Mol Biol 359, 276-288.