Publications of Misha Kudryashev

Journal Article (52)

1.
Journal Article
Sogues, A.; Leigh, K. E.; Halingstad, E. V.; Van der Verren, S. E.; Cecil, A. J.; Fioravanti, A.; Pak, A. J.; Kudryashev, M.; Remaut, H.: Architecture of the Sap S-layer of Bacillus anthracis revealed by integrative structural biology. Proceedings of the National Academy of Sciences of the United States of America 121 (51), e2415351121 (2024)
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2.
Journal Article
Introini, B.; Cui, W.; Chu, X.; Zhang, Y.; Alves, A. C.; Eckhardt-Strelau, L.; Golusik, S.; Tol, M.; Vogel, H.; Yuan, S. et al.; Kudryashev, M.: Structure of tetrameric forms of the serotonin-gated 5-HT3A receptor ion channel. The EMBO Journal 43 (20), pp. 4451 - 4471 (2024)
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3.
Journal Article
Balyschew, N.; Yushkevich, A.; Mikirtumov, V.; Sanchez, R. M.; Sprink, T.; Kudryashev, M.: Streamlined structure determination by cryo-electron tomography and subtomogram averaging using TomoBEAR. Nature Communications 14, 6543 (2023)
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4.
Journal Article
Chang, S.-Y. S.; Dijkman, P. M.; Wiessing, S. A.; Kudryashev, M.: Determining the structure of the bacterial voltage-gated sodium channel NaChBac embedded in liposomes by cryo electron tomography and subtomogram averaging. Scientific Reports 13, 11523 (2023)
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5.
Journal Article
Lo, W.-T.; Zhang, Y.; Vadas, O.; Roske, Y.; Gulluni, F.; De Santis, M. C.; Zagar, A. V.; Stephanowitz, H.; Hirsch, E.; Liu, F. et al.; Daumke, O.; Kudryashev, M.; Haucke, V.: Structural basis of phosphatidylinositol 3-kinase C2α function. Nature Structural and Molecular Biology 29 (3), pp. 218 - 228 (2022)
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6.
Journal Article
Sanchez, C. P.; Patra, P.; Chang, S.-Y. S.; Karathanasis, C.; Hanebutte, L.; Kilian, N.; Cyrklaff, M.; Heilemann, M.; Schwarz, U. S.; Kudryashev, M. et al.; Lanzer, M.: KAHRP dynamically relocalizes to remodeled actin junctions and associates with knob spirals in P. falciparum-infected erythrocytes. Molecular Microbiology 117 (2), pp. 274 - 292 (2022)
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7.
Journal Article
Dijkman, P. M.; Marzluf, T.; Zhang, Y.; Chang, S.-Y. S.; Helm, D.; Lanzer, M.; Bujard, H.; Kudryashev, M.: Structure of the merozoite surface protein 1 from Plasmodium falciparum. Science Advances 7 (23), eabg0465 (2021)
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8.
Journal Article
Berger, C.; Ravelli, R. B. G.; López-Iglesias, C.; Kudryashev, M.; Diepold, A.; Peters, P. J.: Structure of the Yersinia injectisome in intracellular host cell phagosomes revealed by cryo FIB electron tomography. Journal of Structural Biology 213 (1), 107701 (2021)
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9.
Journal Article
Zhang, Y.; Dijkman, P. M.; Zou, R.; Zandl-Lang, M.; Sanchez, R. M.; Eckhardt-Strelau, L.; Köfeler, H.; Vogel, H.; Yuan, S.; Kudryashev, M.: Asymmetric opening of the homopentameric 5-HT3A serotonin receptor in lipid bilayers. Nature Communications 12 (1), 1074 (2021)
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10.
Journal Article
Sanchez, R. M.; Zhang, Y.; Chen, W.; Dietrich, L.; Kudryashev, M.: Subnanometer-resolution structure determination in situ by hybrid subtomogram averaging - single particle cryo-EM. Nature Communications 11, 3709 (2020)
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11.
Journal Article
Chen, W.; Kudryashev, M.: Structure of RyR1 in native membranes. EMBO Reports 21 (5), e49891 (2020)
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12.
Journal Article
Faelber, K.; Dietrich, L.; Noel, J. K.; Wollweber, F.; Pfitzner, A.-K.; Mühleip, A.; Sánchez, R.; Kudryashev, M.; Chiaruttini, N.; Lilie, H. et al.; Schlegel, J.; Rosenbaum, E.; Hessenberger, M.; Matthaeus, C.; Kunz, S.; von der Malsburg, A.; Noè, F.; Roux, A.; van der Laan, M.; Kühlbrandt, W.; Daumke, O.: Structure and assembly of the mitochondrial membrane remodelling GTPase Mgm1. Nature 571 (7765), pp. 429 - 433 (2019)
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13.
Journal Article
Bhaskara, R.; Grumati, P.; Garcia-Pardo, J.; Kalayil, S.; Covarrubias-Pinto, A.; Chen, W.; Kudryashev, M.; Đikić, I.; Hummer, G.: Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy. Nature Communications 10, 2370 (2019)
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14.
Journal Article
Kehrer, J.; Kuss, C.; Andres-Pons, A.; Reustle, A.; Dahan, N.; Devos, D.; Kudryashev, M.; Beck, M.; Mair, G. R.; Frischknecht, F.: Nuclear Pore Complex Components in the Malaria Parasite Plasmodium Berghei. Scientific Reports 8, 11249 (2018)
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15.
Journal Article
Cyrklaff, M.; Frischknecht, F.; Kudryashev, M.: Functional insights into pathogen biology from 3D electron microscopy. FEMS Microbiology Reviews 41 (6), pp. 828 - 853 (2017)
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16.
Journal Article
Wang, J.; Brackmann, M.; Castaño-Díez, D.; Kudryashev, M.; Goldie, K. N.; Maier, T.; Stahlberg, H.; Basler, M.: Cryo-EM structure of the extended type VI secretion system sheath–tube complex. Nature Microbiology 2, pp. 1507 - 1512 (2017)
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17.
Journal Article
Devos, S.; Van Putte, W.; Vitse, J.; Van Driessche, G.; Stremersch, S.; Van den Broek, W.; Raemdonck, K.; Braeckmans, K.; Stahlberg, H.; Kudryashev, M. et al.; Savvides, S. N.; Devreese, B.: Membrane vesicle secretion and prophage induction in multidrug-resistant Stenotrophomonas maltophilia in response to ciprofloxacin stress. Environmental Microbiology 19 (10), pp. 3930 - 3937 (2017)
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18.
Journal Article
Castaño-Díez, D.; Kudryashev, M.; Stahlberg, H.: Dynamo Catalogue: Geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms. Journal of Structural Biology 197 (2), pp. 135 - 144 (2017)
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19.
Journal Article
Kudryashev, M.; Castaño-Díez, D.; Deluz, C.; Hassaine, G.; Grasso, L.; Graf-Meyer, A.; Vogel, H.; Stahlberg, H.: The Structure of the Mouse Serotonin 5-HT3 Receptor in Lipid Vesicles. Structure 24 (1), pp. 165 - 170 (2016)
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20.
Journal Article
Kudryashev, M.; Castaño-Díez, D.; Deluz, C.; Hassaine, G.; Grasso, L.; Graf-Meyer, A.; Vogel, H.; Stahlberg, H.: The Structure of the Mouse Serotonin 5-HT3 Receptor in Lipid Vesicles. Structure 24 (1), pp. 165 - 170 (2016)
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21.
Journal Article
Gold, V.; Kudryashev, M.: Recent progress in structure and dynamics of dual-membrane-spanning bacterial nanomachines. Current Opinion in Structural Biology 39, pp. 1 - 7 (2016)
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22.
Journal Article
Nans, A.; Kudryashev, M.; Saibil, H. R.; Hayward, R. D.: Structure of a bacterial type III secretion system in contact with a host membrane in situ. Nature Communications 6, 10114 (2015)
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23.
Journal Article
Ray Yu-Ruei, R. Y.-R.; Kudryashev, M.; Li, X.; Egelman, E. H.; Basler, M.; Cheng, Y.; Baker, D.; DiMaio, F.: De novo protein structure determination from near-atomic-resolution cryo-EM maps. Nature Methods 12, pp. 335 - 338 (2015)
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24.
Journal Article
Kudryashev, M.; Diepold, A.; Amstutz, M.; Armitage, J. P.; Stahlberg, H.; Cornelis, G. R.: Yersinia enterocolitica type III secretion injectisomes form regularly spaced clusters, which incorporate new machines upon activation. Molecular Microbiology 95 (5), pp. 875 - 884 (2015)
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25.
Journal Article
Kudryashev, M.; Wang, R. Y.-R.; Brackmann, M.; Scherer, S.; Maier, T.; Baker, D.; DiMaio, F.; Stahlberg, H.; Egelman, E. H.; Basler, M.: Structure of the type VI secretion system contractile sheath. Cell 160 (5), pp. 952 - 962 (2015)
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26.
Journal Article
Diepold, A.; Kudryashev, M.; Delalez, N. J.; Berry, R. M.; Armitage, J. P.: Composition, formation, and regulation of the cytosolic c-ring, a dynamic component of the type III secretion injectisome. PLoS Biology 13 (1), e1002039 (2015)
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27.
Journal Article
Kudryashev, M.; Aktoudianaki, A.; Dedoglou, D.; Stahlberg, H.; Tsiotis, G.: The ultrastructure of Chlorobaculum tepidum revealed by cryo-electron tomography. Biochimica et Biophysica Acta, Bioenergetics 1837 (10), pp. 1635 - 1642 (2014)
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28.
Journal Article
Schwan, C.; Kruppke, A. S.; Nölke, A.; Schumacher, L.; Koch-Nolte, F.; Kudryashev, M.; Stahlberg, H.; Aktories, K.: Clostridium difficile toxin CDT hijacks microtubule organization and reroutes vesicle traffic to increase pathogen adherence. Proceedings of the National Academy of Sciences of the United States of America 111 (6), pp. 2313 - 2318 (2014)
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29.
Journal Article
Kowal, J.; Chami, M.; Müller, S. A.; Kudryashev, M.; Castaño-Díez, D.; Amstutz, M.; Cornelis, G. R.; Stahlberg, H.; Engel, A.: Structure of the dodecameric Yersinia enterocolitica secretin YscC and its trypsin-resistant core. Structure 21 (12), pp. 2152 - 2161 (2013)
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30.
Journal Article
Degiacomi, M. T.; Iacovache, I.; Pernot, L.; Chami, M.; Kudryashev, M.; Stahlberg, H.; van der Goot, F. G.; Dal Peraro, M.: Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism. Nature Chemical Biology 9 (10), pp. 623 - 629 (2013)
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31.
Journal Article
Hanssen, E.; Dekiwadia, C.; Riglar, D.; Rug, M.; Lemgruber, L.; Cowman, A. F.; Cyrklaff, M.; Kudryashev, M.; Frischknecht, F.; Baum, J. et al.; Ralph, S. A.: Electron tomography of Plasmodium falciparum merozoites reveals core cellular events that underpin erythrocyte invasion. Cellular Microbiology 15 (9), pp. 1457 - 1472 (2013)
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32.
Journal Article
Kudryashev, M.; Stenta, M.; Schmelz, S.; Amstutz, M.; Wiesand, U.; Castaño-Díez, D.; Degiacomi, M. T.; Münich, S.; Bleck, C. K.E.; Kowal, J. et al.; Diepold, A.; Heinz, D. W.; Dal Peraro, M.; Cornelis, G. R.; Stahlberg, H.: In situ structural analysis of the Yersinia enterocolitica injectisome. eLife 2, e00792 (2013)
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33.
Journal Article
Lemgruber, L.; Kudryashev, M.; Dekiwadia, C.; Riglar, D. T.; Baum, J.; Stahlberg, H.; Ralph, S. A.; Frischknecht, F.: Cryo-electron tomography reveals four-membrane architecture of the Plasmodium apicoplast. Malaria Journal 12, 25 (2013)
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34.
Journal Article
Kudryashev, M.; Münter, S.; Lemgruber, L.; Montagna, G. N.; Stahlberg, H.; Matuschewski, K.; Meissner, M.; Cyrklaff, M.; Frischknecht, F.: Structural basis for chirality and directional motility of Plasmodium sporozoites. Cellular Microbiology 14 (11), pp. 1757 - 1768 (2012)
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35.
Journal Article
Maiorca, M.; Hanssen, E.; Kazmierczak, E.; Maco, B.; Kudryashev, M.; Hall, R.; Quiney, H.; Tilley, L.: Improving the quality of electron tomography image volumes using pre-reconstruction filtering. Journal of Structural Biology 180 (1), pp. 132 - 142 (2012)
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36.
Journal Article
Kudryashev, M.; Castaño-Díez, D.; Stahlberg, H.: Limiting factors in single particle cryo electron tomography. Computational and Structural Biotechnology Journal 1 (2), e201207002 (2012)
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37.
Journal Article
Castaño-Díez, D.; Kudryashev, M.; Arheit, M.; Stahlberg, H.: Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments. Journal of Structural Biology 178 (2), pp. 139 - 151 (2012)
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38.
Journal Article
Kudryashev, M.; Stahlberg, H.; Castaño-Díez, D.: Assessing the benefits of focal pair cryo-electron tomography. Journal of Structural Biology 178 (2), pp. 88 - 97 (2012)
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39.
Journal Article
Dudkina, N. V.; Kudryashev, M.; Stahlberg, H.; Boekema, E. J.: Interaction of complexes I, III, and IV within the bovine respirasome by single particle cryoelectron tomography. Proceedings of the National Academy of Sciences of the United States of America 108 (37), pp. 15196 - 15200 (2011)
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40.
Journal Article
Hellmann, J. K.; Münter, S.; Kudryashev, M.; Schulz, S.; Heiss, K.; Müller, A.-K.; Matuschewski, K.; Spatz, J. P.; Schwarz, U. S.; Frischknecht, F.: Environmental constraints guide migration of malaria parasites during transmission. PLoS Pathogens 7 (6), e1002080 (2011)
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41.
Journal Article
Kudryashev, M.; Cyrklaff, M.; Alex, B.; Lemgruber, L.; Baumeister, W.; Wallich, R.; Frischknecht, F.: Evidence of direct cell-cell fusion in Borrelia by cryogenic electron tomography. Cellular Microbiology 13 (5), pp. 731 - 741 (2011)
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42.
Journal Article
Hegge, S.; Kudryashev, M.; Barniol, L.; Frischknecht, F.: Key factors regulating Plasmodium berghei sporozoite survival and transformation revealed by an automated visual assay. The FASEB Journal 24 (12), pp. 5003 - 5012 (2010)
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43.
Journal Article
Kudryashev, M.; Lepper, S.; Baumeister, W.; Cyrklaff, M.; Frischknecht, F.: Geometric constrains for detecting short actin filaments by cryogenic electron tomography. PMC Biophysics 3, 6 (2010)
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44.
Journal Article
Kudryashev, M.; Lepper, S.; Stanway, R.; Bohn, S.; Baumeister, W.; Cyrklaff, M.; Frischknecht, F.: Positioning of large organelles by a membrane- associated cytoskeleton in Plasmodium sporozoites. Cellular Microbiology 12 (3), pp. 362 - 371 (2010)
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45.
Journal Article
Kudryashev, M.; Cyrklaff, M.; Wallich, R.; Baumeister, W.; Frischknecht, F.: Distinct in situ structures of the Borrelia flagellar motor. Journal of Structural Biology 169 (1), pp. 54 - 61 (2010)
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46.
Journal Article
Münter, S.; Sabass, B.; Selhuber-Unkel, C.; Kudryashev, M.; Hegge, S.; Engel, U.; Spatz, J. P.; Matuschewski, K.; Schwarz, U. S.; Frischknecht, F.: Plasmodium sporozoite motility is modulated by the turnover of discrete adhesion sites. Cell Host & Microbe 6 (6), pp. 551 - 562 (2009)
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47.
Journal Article
Hegge, S.; Kudryashev, M.; Smith, A.; Frischknecht, F.: Automated classification of Plasmodium sporozoite movement patterns reveals a shift towards productive motility during salivary gland infection. Biotechnology Journal 4 (6), pp. 903 - 913 (2009)
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48.
Journal Article
Kudryashev, M.; Cyrklaff, M.; Baumeister, W.; Simon, M. M.; Wallich, R.; Frischknecht, F.: Comparative cryo-electron tomography of pathogenic Lyme disease spirochetes. Molecular Microbiology 71 (6), pp. 1415 - 1434 (2009)
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49.
Journal Article
Rabinovich , M. L.; Burghardt, N.; Gorzka, G.; Kudryashev, M.; Leonov, A.; Konov, A.: Special: biotech in Russia. Biotechnology Journal 2 (7), pp. 775 - 789 (2007)
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50.
Journal Article
Cyrclaff, M.; Kudryashev, M.; Leis, A.; Leonard, K.; Baumeister, W.; Menard, R.; Meissner, M.; Frischknecht, F.: Cryoelectron tomography reveals periodic material at the inner side of subpellicular microtubules in apicomplexan parasites. Journal of Experimental Medicine 204 (6), pp. 1281 - 1287 (2007)
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51.
Journal Article
Kudryashev, M.; Münter, S.: Meeting report: Breaking barriers in microscopy. Biotechnology Journal 2 (1), pp. 30 - 32 (2007)
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52.
Journal Article
Garvalov, B. K.; Zuber, B.; Bouchet-Marquis, C.; Kudryashev, M.; Gruska, M.; Beck, M.; Leis, A.; Frischknecht, F.; Bradke, F.; Baumeister, W. et al.; Dubochet, J.; Cyrklaff, M.: Luminal particles within cellular microtubules. The Journal of Cell Biology 174 (6), pp. 759 - 765 (2006)
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Book Chapter (3)

53.
Book Chapter
Leigh, K. E.; Navarro, P. P.; Scaramuzza, S.; Chen, W.; Zhang, Y.; Castaño-Díez, D.; Kudryashev, M.: Subtomogram averaging from cryo-electron tomograms. In: Methods in Cell Biology, Vol. 152, 1 Ed., pp. 217 - 259 (Ed. Müller-Reichert, T.). Academic Press (2019)
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54.
Book Chapter
Sánchez, R.; Mester, R.; Kudryashev, M.: Fast Cross Correlation for Limited Angle Tomographic Data. In: Lecture Notes in Computer Science (LNCS), Vol. 11482, pp. 415 - 426 (Eds. Felsberg, M.; Forssén, P.-E.; Sintorn, I.-M.; Unger, J.). Springer (2019)
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55.
Book Chapter
Kudryashev, M.: Resolution in Electron Tomography. In: Biological and Medical Physics, Biomedical Engineering (BIOMEDICAL), pp. 261 - 282 (Ed. Hanson, E.). Springer International Publishing AG 2018, 6330 Cham Switzerland (2018)
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Conference Paper (1)

56.
Conference Paper
Sanchez, R. M.; Mester, R.; Kudryashev, M.: Fast Alignment of Limited Angle Tomograms by projected Cross Correlation. In: 27th European Signal Processing Conference (EUSIPCO). 27th European Signal Processing Conference (EUSIPCO), Coruna, Spain, September 02, 2019 - September 06, 2019. (2019)
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