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Staff at EMBL

Dr. Vladimir Rybin

Senior Officer - Biophysical Support
Protein Expression and Purification Core Facility

EMBL Heidelberg, Meyerhofstra├če 1, 69117 Heidelberg, Germany

E-mail: send a mail

Biophysical Support


Publications

Structural and functional characterization of a phosphatase domain within yeast general transcription factor IIIC. Taylor, N.M., Glatt, S., Hennrich, M.L., von Scheven, G., Grotsch, H., Fernandez-Tornero, C., Rybin, V., Gavin, A.C., Kolb, P. & Muller, C.W. J Biol Chem. 2013 May 24;288(21):15110-20. doi: 10.1074/jbc.M112.427856. Epub2013 Apr 8. Europe PMC

A family of macrodomain proteins reverses cellular mono-ADP-ribosylation. Jankevicius, G., Hassler, M., Golia, B., Rybin, V., Zacharias, M., Timinszky, G. & Ladurner, A.G. Nat Struct Mol Biol. 2013 Apr;20(4):508-14. doi: 10.1038/nsmb.2523. Epub 2013 Mar10. Europe PMC

Structural basis of histone H2A-H2B recognition by the essential chaperone FACT. Hondele, M., Stuwe, T., Hassler, M., Halbach, F., Bowman, A., Zhang, E.T., Nijmeijer, B., Kotthoff, C., Rybin, V., Amlacher, S., Hurt, E. & Ladurner, A.G. Nature. 2013 Jul 4;499(7456):111-4. doi: 10.1038/nature12242. Epub 2013 May 22. Europe PMC

Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. van Noort, V., Seebacher, J., Bader, S., Mohammed, S., Vonkova, I., Betts, M.J., Kuhner, S., Kumar, R., Maier, T., O'Flaherty, M., Rybin, V., Schmeisky, A., Yus, E., Stulke, J., Serrano, L., Russell, R.B., Heck, A.J., Bork, P. & Gavin, A.C. Mol Syst Biol. 2012 Feb 28;8:571. doi: 10.1038/msb.2012.4. Europe PMC

The Xist RNA A-repeat comprises a novel AUCG tetraloop fold and a platform for multimerization. Duszczyk, M.M., Wutz, A., Rybin, V. & Sattler, M. RNA. 2011 Nov;17(11):1973-82. Epub 2011 Sep 26. Europe PMC

Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF. Mackereth, C.D., Madl, T., Bonnal, S., Simon, B., Zanier, K., Gasch, A., Rybin, V., Valcarcel, J. & Sattler, M. Nature. 2011 Jul 13;475(7356):408-11. doi: 10.1038/nature10171. Europe PMC

Chromatin-modifying Complex Component Nurf55/p55 Associates with Histones H3 and H4 and Polycomb Repressive Complex 2 Subunit Su(z)12 through Partially Overlapping Binding Sites. Nowak, A.J., Alfieri, C., Stirnimann, C.U., Rybin, V., Baudin, F., Ly-Hartig, N., Lindner, D. & Muller, C.W. J Biol Chem. 2011 Jul 1;286(26):23388-96. Epub 2011 May 5. Europe PMC

Insights into the function of the CRM1 cofactor RanBP3 from the structure of its Ran-binding domain. Langer, K., Dian, C., Rybin, V., Muller, C.W. & Petosa, C. PLoS One. 2011 Feb 25;6(2):e17011. Europe PMC

A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae. Gallego, O., Betts, M.J., Gvozdenovic-Jeremic, J., Maeda, K., Matetzki, C., Aguilar-Gurrieri, C., Beltran-Alvarez, P., Bonn, S., Fernandez-Tornero, C., Jensen, L.J., Kuhn, M., Trott, J., Rybin, V., Muller, C.W., Bork, P., Kaksonen, M., Russell, R.B. & Gavin, A.C. Mol Syst Biol. 2010 Nov 30;6:430. doi: 10.1038/msb.2010.87. Europe PMC

Structural insights into the pH-controlled targeting of plant cell-wall invertase by a specific inhibitor protein. Hothorn, M., Van den Ende, W., Lammens, W., Rybin, V. & Scheffzek, K. Proc Natl Acad Sci U S A. 2010 Oct 5;107(40):17427-32. Epub 2010 Sep 21. Europe PMC

CHIP participates in protein triage decisions by preferentially ubiquitinating Hsp70-bound substrates. Stankiewicz, M., Nikolay, R., Rybin, V. & Mayer, M.P. FEBS J. 2010 Aug;277(16):3353-67. Epub 2010 Jul 8. Europe PMC

Analysis of the specific interactions between the lectin domain of malectin and diglucosides. Schallus, T., Feher, K., Sternberg, U., Rybin, V. & Muhle-Goll, C. Glycobiology. 2010 Aug;20(8):1010-20. Epub 2010 Apr 26. Europe PMC

Regulation of oscillatory contraction in insect flight muscle by troponin. Krzic, U., Rybin, V., Leonard, K.R., Linke, W.A. & Bullard, B. J Mol Biol. 2010 Mar 19;397(1):110-8. Epub 2010 Jan 25. Europe PMC

E6 proteins from diverse papillomaviruses self-associate both in vitro and in vivo. Zanier, K., Ruhlmann, C., Melin, F., Masson, M., Ould M'hamed Ould Sidi, A., Bernard, X., Fischer, B., Brino, L., Ristriani, T., Rybin, V., Baltzinger, M., Vande Pol, S., Hellwig, P., Schultz, P. & Trave, G. J Mol Biol. 2010 Feb 12;396(1):90-104. Epub 2009 Nov 13. Europe PMC

Identification of unusual E6 and E7 proteins within avian papillomaviruses: cellular localization, biophysical characterization, and phylogenetic analysis. Van Doorslaer, K., Sidi, A.O., Zanier, K., Rybin, V., Deryckere, F., Rector, A., Burk, R.D., Lienau, E.K., van Ranst, M. & Trave, G. J Virol. 2009 Sep;83(17):8759-70. doi: 10.1128/JVI.01777-08. Epub 2009 Jun 24. Europe PMC

Molecular recognition of histone lysine methylation by the Polycomb group repressor dSfmbt. Grimm, C., Matos, R., Ly-Hartig, N., Steuerwald, U., Lindner, D., Rybin, V., Muller, J. & Muller, C.W. EMBO J. 2009 Jul 8;28(13):1965-77. Epub 2009 Jun 4. Europe PMC

Catalytic core of a membrane-associated eukaryotic polyphosphate polymerase. Hothorn, M., Neumann, H., Lenherr, E.D., Wehner, M., Rybin, V., Hassa, P.O., Uttenweiler, A., Reinhardt, M., Schmidt, A., Seiler, J., Ladurner, A.G., Herrmann, C., Scheffzek, K. & Mayer, A. Science. 2009 Apr 24;324(5926):513-6. Europe PMC

Lipids regulate P2X7-receptor-dependent actin assembly by phagosomes via ADP translocation and ATP synthesis in the phagosome lumen. Kuehnel, M.P., Rybin, V., Anand, P.K., Anes, E. & Griffiths, G. J Cell Sci. 2009 Feb 15;122(Pt 4):499-504. Epub 2009 Jan 27. Europe PMC

Dimerization and protein binding specificity of the U2AF homology motif of the splicing factor Puf60. Corsini, L., Hothorn, M., Stier, G., Rybin, V., Scheffzek, K., Gibson, T.J. & Sattler, M. J Biol Chem. 2009 Jan 2;284(1):630-9. doi: 10.1074/jbc.M805395200. Epub 2008 Oct29. Europe PMC

Proteome organization in a genome-reduced bacterium. Kuhner, S., van Noort, V., Betts, M.J., Leo-Macias, A., Batisse, C., Rode, M., Yamada, T., Maier, T., Bader, S., Beltran-Alvarez, P., Castano-Diez, D., Chen, W.H., Devos, D., Guell, M., Norambuena, T., Racke, I., Rybin, V., Schmidt, A., Yus, E., Aebersold, R., Herrmann, R., Bottcher, B., Frangakis, A.S., Russell, R.B., Serrano, L., Bork, P. & Gavin, A.C. Science. 2009 Nov 27;326(5957):1235-40. doi: 10.1126/science.1176343.
Full text Europe PMC

The FACT Spt16 "peptidase" domain is a histone H3-H4 binding module. Stuwe, T., Hothorn, M., Lejeune, E., Rybin, V., Bortfeld, M., Scheffzek, K. & Ladurner, A.G. Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):8884-9. Epub 2008 Jun 25. Europe PMC

The redox switch of gamma-glutamylcysteine ligase via a reversible monomer-dimer transition is a mechanism unique to plants. Gromes, R., Hothorn, M., Lenherr, E.D., Rybin, V., Scheffzek, K. & Rausch, T. Plant J. 2008 May 8;. Europe PMC

Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex. Fiedler, M., Sanchez-Barrena, M.J., Nekrasov, M., Mieszczanek, J., Rybin, V., Muller, J., Evans, P. & Bienz, M. Mol Cell. 2008 May 23;30(4):507-18. Europe PMC

Muscle RING-finger protein-1 (MuRF1) as a connector of muscle energy metabolism and protein synthesis. Koyama, S., Hata, S., Witt, C.C., Ono, Y., Lerche, S., Ojima, K., Chiba, T., Doi, N., Kitamura, F., Tanaka, K., Abe, K., Witt, S.H., Rybin, V., Gasch, A., Franz, T., Labeit, S. & Sorimachi, H. J Mol Biol. 2008 Mar 7;376(5):1224-36. Epub 2007 Nov 22. Europe PMC

Mutation analysis in Costello syndrome: functional and structural characterization of the HRAS p.Lys117Arg mutation. Denayer, E., Parret, A., Chmara, M., Schubbert, S., Vogels, A., Devriendt, K., Frijns, J.P., Rybin, V., de Ravel, T.J., Shannon, K., Cools, J., Scheffzek, K. & Legius, E. Hum Mutat. 2008 Feb;29(2):232-9. Europe PMC

Structural and functional analyses of methyl-lysine binding by the malignant brain tumour repeat protein Sex comb on midleg. Grimm, C., de Ayala Alonso, A.G., Rybin, V., Steuerwald, U., Ly-Hartig, N., Fischle, W., Muller, J. & Muller, C.W. EMBO Rep. 2007 Nov;8(11):1031-7. Epub 2007 Oct 12. Europe PMC

Crystal structure of human filamin C domain 23 and small angle scattering model for filamin C 23-24 dimer. Sjekloca, L., Pudas, R., Sjoblom, B., Konarev, P., Carugo, O., Rybin, V., Kiema, T.R., Svergun, D., Ylanne, J. & Carugo, K.D. J Mol Biol. 2007 May 11;368(4):1011-23. Epub 2007 Feb 20. Europe PMC

Structural and biochemical characterization of the yeast exosome component Rrp40. Oddone, A., Lorentzen, E., Basquin, J., Gasch, A., Rybin, V., Conti, E. & Sattler, M. EMBO Rep. 2007 Jan;8(1):63-9. Epub 2006 Dec 8. Europe PMC

cAMP synthesis and degradation by phagosomes regulate actin assembly and fusion events: consequences for mycobacteria. Kalamidas, S.A., Kuehnel, M.P., Peyron, P., Rybin, V., Rauch, S., Kotoulas, O.B., Houslay, M., Hemmings, B.A., Gutierrez, M.G., Anes, E. & Griffiths, G. J Cell Sci. 2006 Sep 1;119(Pt 17):3686-94. Europe PMC

HDAC6-p97/VCP controlled polyubiquitin chain turnover. Boyault, C., Gilquin, B., Zhang, Y., Rybin, V., Garman, E., Meyer-Klaucke, W., Matthias, P., Muller, C.W. & Khochbin, S. EMBO J. 2006 Jul 26;25(14):3357-66. Epub 2006 Jun 29. Europe PMC

YfhJ, a molecular adaptor in iron-sulfur cluster formation or a frataxin-like protein? Pastore, C., Adinolfi, S., Huynen, M.A., Rybin, V., Martin, S., Mayer, M., Bukau, B. & Pastore, A. Structure. 2006 May;14(5):857-67. Europe PMC

Mouse profilin 2 regulates endocytosis and competes with SH3 ligand binding to dynamin 1. Gareus, R., Di Nardo, A., Rybin, V. & Witke, W. J Biol Chem. 2006 Feb 3;281(5):2803-11. Epub 2005 Nov 29. Europe PMC

Substrate access to the active sites in aminopeptidase T, a representative of a new metallopeptidase clan. Odintsov, S.G., Sabala, I., Bourenkov, G., Rybin, V. & Bochtler, M. J Mol Biol 2005 Nov 25;354(2):403-12. Epub 2005 Sep 30. Europe PMC

Staphylococcus aureus aminopeptidase S is a founding member of a new peptidase clan. Odintsov, S.G., Sabala, I., Bourenkov, G., Rybin, V. & Bochtler, M. J Biol Chem 2005 Jul 29;280(30):27792-9. Epub 2005 Jun 2. Europe PMC

Computer-aided design of a PDZ domain to recognize new target sequences. Reina, J., Lacroix, E., Hobson, S.D., Fernandez-Ballester, G., Rybin, V., Schwab, M.S., Serrano, L. & Gonzalez, C. Nat Struct Biol 2002 Aug;9(8):621-7. Europe PMC

90S pre-ribosomes include the 35S pre-rRNA, the U3 snoRNP, and 40S subunit processing factors but predominantly lack 60S synthesis factors. Grandi, P., Rybin, V., Bassler, J., Petfalski, E., Strauss, D., Marzioch, M., Schafer, T., Kuster, B., Tschochner, H., Tollervey, D., Gavin, A.C. & Hurt, E. Mol Cell 2002 Jul;10(1):105-15. Europe PMC

Phosphoinositides regulate membrane-dependent actin assembly by latex bead phagosomes. Defacque, H., Bos, E., Garvalov, B., Barret, C., Roy, C., Mangeat, P., Shin, H.W., Rybin, V. & Griffiths, G. Mol Biol Cell 2002 Apr;13(4):1190-202. Europe PMC

Functional organization of the yeast proteome by systematic analysis of protein complexes. Gavin, A.C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., Michon, A.M., Cruciat, C.M., Remor, M., Hofert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M.A., Copley, R.R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G. & Superti-Furga, G. Nature 2002 Jan 10;415(6868):141-7. Europe PMC

Functional synergy between Rab5 effector Rabaptin-5 and exchange factor Rabex-5 when physically associated in a complex. Lippe, R., Miaczynska, M., Rybin, V., Runge, A. & Zerial, M. Mol Biol Cell. 2001 Jul;12(7):2219-28. Europe PMC

Vps9, Rabex-5 and DSS4: proteins with weak but distinct nucleotide-exchange activities for Rab proteins. Esters, H., Alexandrov, K., Iakovenko, A., Ivanova, T., Thoma, N., Rybin, V., Zerial, M., Scheidig, A.J. & Goody, R.S. J Mol Biol. 2001 Jun 29;310(1):141-56. Europe PMC

Mice with a homozygous gene trap vector insertion in mgcRacGAP die during pre-implantation development. Van de Putte, T., Zwijsen, A., Lonnoy, O., Rybin, V., Cozijnsen, M., Francis, A., Baekelandt, V., Kozak, C.A., Zerial, M. & Huylebroeck, D. Mech Dev. 2001 Apr;102(1-2):33-44. Europe PMC

ATP-dependent membrane assembly of F-actin facilitates membrane fusion. Jahraus, A., Egeberg, M., Hinner, B., Habermann, A., Sackman, E., Pralle, A., Faulstich, H., Rybin, V., Defacque, H. & Griffiths, G. Mol Biol Cell 2001 Jan;12(1):155-70. Europe PMC

The Eps8 protein coordinates EGF receptor signalling through Rac and trafficking through Rab5. Lanzetti, L., Rybin, V., Malabarba, M.G., Christoforidis, S., Scita, G., Zerial, M. & Di Fiore, P.P. Nature. 2000 Nov 16;408(6810):374-7. Europe PMC

Crystal structure of the protein disulfide bond isomerase, DsbC, from Escherichia coli. McCarthy, A.A., Haebel, P.W., Torronen, A., Rybin, V., Baker, E.N. & Metcalf, P. Nat Struct Biol. 2000 Mar;7(3):196-9. Europe PMC

Oligomeric complexes link Rab5 effectors with NSF and drive membrane fusion via interactions between EEA1 and syntaxin 13. McBride, H.M., Rybin, V., Murphy, C., Giner, A., Teasdale, R. & Zerial, M. Cell 1999 Aug 6;98(3):377-86 Europe PMC

Distinct Rab-binding domains mediate the interaction of Rabaptin-5 with GTP-bound Rab4 and Rab5. Vitale, G., Rybin, V., Christoforidis, S., Thornqvist, P., McCaffrey, M., Stenmark, H. & Zerial, M. EMBO J 1998 Apr 1 17(7) 1941-1951 Europe PMC

Two distinct effectors of the small GTPase Rab5 cooperate in endocytic membrane fusion. Gournier, H., Stenmark, H., Rybin, V., Lippe, R. & Zerial, M. EMBO J 1998 Apr 1 17(7) 1930-1940 Europe PMC

A novel Rab5 GDP/GTP exchange factor complexed to Rabaptin-5 links nucleotide exchange to effector recruitment and function. Horiuchi, H., Lippe, R., McBride, H.M., Rubino, M., Woodman, P., Stenmark, H., Rybin, V., Wilm, M., Ashman, K., Mann, M. & Zerial, M. Cell. 1997 Sep 19;90(6):1149-59. Europe PMC

Endosome dynamics regulated by a Rho protein. Murphy, C., Saffrich, R., Grummt, M., Gournier, H., Rybin, V., Rubino, M., Auvinen, P., Lutcke, A., Parton, R.G. & Zerial, M. Nature. 1996 Dec 5;384(6608):427-32. Europe PMC

Crystallization of DsbC, the disulfide bond isomerase of Escherichia coli. Rybin, V., Zapun, A., Torronen, A., Raina, S., Missiakas, D., Creighton, T.E. & Metcalf, P. Acta Crystallogr D Biol Crystallogr. 1996 Nov 1;52(Pt 6):1219-21. Europe PMC

GTPase activity of Rab5 acts as a timer for endocytic membrane fusion. Rybin, V., Ullrich, O., Rubino, M., Alexandrov, K., Simon, I., Seabra, M.C., Goody, R. & Zerial, M. Nature. 1996 Sep 19;383(6597):266-9. Europe PMC