Publications - Scientific Papers

  • 2012

  • Becker T, Franckenberg S, Wickles S, Shoemaker CJ, Anger AM, Armache JP, Sieber H, Ungewickell C, Berninghausen O, Daberkow I, Karcher A, Thomm M, Hopfner KP, Green R, Beckmann R.
    Structural basis of highly conserved ribosome recycling in eukaryotes and archaea.
    Nature. 2012 Feb 22;482(7386):501-6. doi: 10.1038/nature10829.

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  • Strasser D, Neumann K, Bergmann H, Marakalala MJ, Guler R, Rojowska A, Hopfner
    KP, Brombacher F, Urlaub H, Baier G, Brown GD, Leitges M, Ruland J.
    Syk Kinase-Coupled C-type Lectin Receptors Engage Protein Kinase C-δ to Elicit
    Card9 Adaptor-Mediated Innate Immunity.
    Immunity. 2012 Jan 18. [Epub ahead of print]

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  • 2011

  • Fenn S, Gerhold CB, Hopfner KP.
    Nuclear actin-related proteins take shape.
    Bioarchitecture. 2011 Jul;1(4):192-195. Epub 2011 Jul 1.

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  • Civril F, Bennett M, Moldt M, Deimling T, Witte G, Schiesser S, Carell T, Hopfner KP
    The RIG-I ATPase domain structure reveals insights into ATP-dependent antiviral signalling
    EMBO reports (2011) 12, 1127 - 1134;doi:10.1038/embor.2011.190

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  • Blattner C, Jennebach S, Herzog F, Mayer A, Cheung ACM, Witte G, Lorenzen K, Hopfner KP, Heck AJR, Aebersold R and Cramer P
    Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth
    Genes Dev. 2011 Sep 22. [Epub ahead of print]

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  • Möckel C, Lammens K, Schele A, Hopfner KP
    ATP driven structural changes of the bacterial Mre11:Rad50 catalytic head complex
    Nucl. Acids Res. (2011) September 21, 2011 doi:10.1093/nar/gkr749

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  • Wollmann P, Cui S, Viswanathan R, Berninghausen O, Wells MN, Moldt M, Witte G, Butryn A, Wendler P, Beckmann R, Auble DT, Hopfner KP.
    Structure and mechanism of the Swi2/Snf2 remodeller Mot1 in complex with its substrate TBP.
    Nature. 2011 Jul 6;475(7356):403-7. doi: 10.1038/nature10215.
    News and Views article in NSMB "A bottle opener for TBP." by Sabbi Lall (Nat Struct Mol Biol. 2011 Aug 3;18(8):865. doi: 10.1038/nsmb0811-865.)

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  • Metz S, Haas AK, Daub K, Croasdale R, Stracke J, Lau W, Georges G, Josel HP, Dziadek S, Hopfner KP, Lammens A, Scheuer W, Hoffmann E, Mundigl O, Brinkmann U.
    Bispecific digoxigenin-binding antibodies for targeted payload delivery.
    Proc Natl Acad Sci U S A. 2011 May 17;108(20):8194-9. Epub 2011 May 2.

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  • Fenn S, Breitsprecher D, Gerhold CB, Witte G, Faix J, Hopfner KP.
    Structural biochemistry of nuclear actin-related proteins 4 and 8 reveals their interaction with actin.
    EMBO J. 2011 Apr 15.
    Commentary in EMBO J 2011 Jun 1;30(11):2097-8.

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  • Schmidt A, Rothenfusser S, Hopfner KP.
    Sensing of viral nucleic acids by RIG-I: From translocation to translation.
    Eur J Cell Biol. 2011 Apr 13. [Epub ahead of print]

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  • Lammens K, Bemeleit DJ, Möckel C, Clausing E, Schele A, Hartung S, Schiller C.B., Lucas M, Angermüller C, Söding J, Sträßer K, Hopfner KP
    The Mre11:Rad50 Structure Shows an ATP-Dependent Molecular Clamp in DNA Double-Strand Break Repair

    Cell. 2011 Apr 1; Vol 145, Issue 1, p.54-66 [Epub ahead of print]

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  • Niederfellner G, Lammens A, Mundigl O, Georges GJ, Schaefer W, Schwaiger M, Franke A, Wiechmann K, Jenewein S, Slootstra JW, Timmerman P, Brännström A, Lindstrom F, Mössner E, Umana P, Hopfner KP, Klein C.
    Epitope characterization and crystal structure of GA101 provide insights into the molecular basis for type I/II distinction of CD20 antibodies.
    Blood. 2011 Mar 28. [Epub ahead of print]

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  • Cario H, Smith DE, Blom H, Blau N, Bode H, Holzmann K, Pannicke U, Hopfner KP, Rump EM, Ayric Z, Kohne E, Debatin KM, Smulders Y, Schwarz K.
    Dihydrofolate reductase deficiency due to a homozygous DHFR mutation causes megaloblastic anemia and cerebral folate deficiency leading to severe neurologic disease.
    Am J Hum Genet. 2011 Feb 11;88(2):226-31.

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  • Niederberger T, Hartung S, Hopfner KP, Tresch A.
    Processive RNA decay by the exosome: Merits of a quantitative Bayesian sampling approach.
    RNA Biol. 2011 Jan 1;8(1). [Epub ahead of print]

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  • Griese JJ, Hopfner KP.
    Structure and DNA-binding activity of the Pyrococcus furiosus SMC protein hinge domain.
    Proteins. 2011 Feb;79(2):558-68.

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  • 2010

  • Lee G, Hartung S, Hopfner KP, Ha T.
    Reversible and Controllable Nanolocomotion of an RNA-Processing Machinery.
    Nano Lett. 2010 Nov 17. [Epub ahead of print]

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  • Schorr S, Schneider S, Lammens K, Hopfner KP, Carell T.
    Mechanism of replication blocking and bypass of Y-family polymerase eta by bulky acetylaminofluorene DNA adducts.
    Proc Natl Acad Sci USA. 2010 Nov 12. [Epub ahead of print]

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  • Lammens A, Hopfner KP
    Structural Basis for Adenylate Kinase Activity in ABC ATPases.
    J Mol Biol. 2010 Jun 19. [Epub ahead of print]

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  • Hartung S, Niederberger T, Hartung M, Tresch A, Hopfner KP
    Quantitative analysis of processive RNA degradation by the archaeal RNA exosome.
    Nucleic Acids Res. 2010 Apr 14. [Epub ahead of print]

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  • Griese JJ, Witte G, Hopfner KP
    Structure and DNA binding activity of the mouse condensin hinge domain highlight common and diverse features of SMC proteins.
    Nucleic Acids Res. 2010 Feb 5.

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  • 2009

  • Kirchhofer A, Helma J, Schmidthals K, Frauer C, Cui S, Karcher A, Pellis M, Muyldermans S, Casas-Delucchi CS, Cardoso MC, Leonhardt H, Hopfner KP, Rothbauer U.
    Modulation of protein properties in living cells using nanobodies.
    Nat Struct Mol Biol. 2010 Jan;17(1):133-8. Epub 2009 Dec 13.
    Research Highlight in Nature Methods (Nat. Methods, February 2010 Vol. 7, No.2, p102)

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  • Hopfner, KP
    DNA double-strand breaks come into focus.
    Cell. 2009 Oct 2;139(1):25-7

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  • Schmidt A, Schwerd T, Hamm W, Hellmuth JC, Cui S, Wenzel M, Hoffmann FS, Michallet MC, Besch R, Hopfner KP, Endres S, Rothenfusser S.
    5'-triphosphate RNA requires base-paired structures to activate antiviral signaling via RIG-I.
    Proc Natl Acad Sci USA. 2009 Jul 21;106(29):12067-72. Epub 2009 Jul 2.

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  • Schwarz K, Iolascon A, Verissimo F, Trede NS, Horsley W, Chen W, Paw BH, Hopfner KP, Holzmann K, Russo R, Esposito MR, Spano D, De Falco L, Heinrich K, Joggerst B, Rojewski MT, Perrotta S, Denecke J, Pannicke U, Delaunay J, Pepperkok R, Heimpel H.
    Mutations affecting the secretory COPII coat component SEC23B cause congenital dyserythropoietic anemia type II Nat Genet. 2009 Aug;41(8):936-40. Epub 2009 Jun 28

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  • Pippig DA, Hellmuth JC, Cui S, Kirchhofer A, Lammens K, Lammens A, Schmidt A, Rothenfusser S, Hopfner KP
    The regulatory domain of the RIG-I family ATPase LGP2 senses double-stranded RNA
    Nucleic Acids Research 2009; doi: 10.1093/nar/gkp059

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  • Hartung S, Hopfner KP
    Lessons from structural and biochemical studies on the archaeal exosome.
    Biochem Soc Trans. 2009 Feb;37(Pt 1):83-7

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  • Myong S, Cui S, Cornish PV, Kirchhofer A, Gack MU, Jung JU, Hopfner KP, Ha T.
    Cytosolic Viral Sensor RIG-I Is a 5'-Triphosphate-Dependent Translocase on Double-Stranded RNA.
    Science. 2009 Jan 1. [Epub ahead of print]

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  • 2008

  • Gack MU, Kirchhofer A, Shin YC, Inn KS, Liang C, Cui S, Myong S, Ha T, Hopfner KP, Jung JU
    Roles of RIG-I N-terminal tandem CARD and splice variant in TRIM25-mediated antiviral signal transduction.
    Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16743-8. Epub 2008 Oct 23

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  • Witte G, Hartung S, Büttner K, Hopfner KP
    Structural Biochemistry of a Bacterial Checkpoint Protein Reveals Diadenylate Cyclase Activity Regulated by DNA Recombination Intermediates
    Mol Cell. 2008 Apr 25;30(2):167-178
    Editor's choice in Science Signaling (Sci. Signal., 29 April 2008 Vol. 1, Issue 17, p. ec151)
    Perspective in Science Signaling by Ute Römling (Sci. Signal., 19 August 2008 Vol. 1, Issue 33, p. pe39)
    Chosen as ESRF Scientific Highlight 2008 (ESRF Highlights 2008, p56)

    Link

  • Lewis R, Dürr H, Hopfner KP, Michaelis J
    Conformational changes of a Swi2/Snf2 ATPase during its mechano-chemical cycle
    Nucleic Acids Res., 2008 Apr;36(6):1881-90. Epub 2008 Feb 11.

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  • Cui S, Eisenächer K, Kirchhofer A, Brzózka K, Lammens A, Lammens K, Fujita T, Conzelmann KK, Krug A, Hopfner KP
    The C-Terminal Regulatory Domain Is the RNA 5'-Triphosphate Sensor of RIG-I.
    Mol Cell. 2008 Feb 1;29(2):169-179

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  • 2007

  • Karcher A, Schele A, Hopfner KP
    X-ray structure of the complete ABC enzyme ABCE1 from Pyrococcus abyssi.
    J Biol Chem. 2007 Dec 26; [Epub ahead of print]

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  • Carell T, Cramer P, Hopfner KP.
    The chemistry of transcription through damaged DNA and of translesion synthesis at atomic resolution.
    Nucleic Acids Symp Ser (Oxf). 2007;(51):103.

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  • Alt A, Lammens K, Chiocchini C, Lammens A, Pieck JC, Kuch D, Hopfner KP, Carell T
    Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta.
    Science. 2007 Nov 9;318(5852):967-70.

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  • Büttner K, Nehring S, Hopfner KP
    Structural basis for DNA duplex separation by a superfamily-2 helicase.
    Nat Struct Mol Biol. 2007 Jul;14(7):647-52. Epub 2007 Jun 10.

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  • Hartung S, Hopfner KP
    The exosome, plugged
    EMBO Rep. 2007 May; 8(5):456-7.

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  • Hopfner KP, Michaelis J
    Mechanisms of nucleic acid translocases: lessons from structural biology and single-molecule biophysics.
    Curr Opin Struct Biol. 2007 Feb;17(1):87-95.

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  • 2006

  • Lengronne A, McIntyre J, Katou Y, Kanoh Y, Hopfner KP, Shirahige K, Uhlmann F.
    Establishment of sister chromatid cohesion and the S. cerevisiae replication fork.
    Mol. Cell 2006;23:1-13.

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  • Büttner K, Wenig K, Hopfner KP.
    The exosome: a macromolecular cage for controlled RNA degradation.
    Mol. Microbiology 2006;61:1372-1379.

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  • Büttner K, Hopfner KP.
    Das Exosom.
    Bioforum 2006; 29:19-21.

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  • Durr H, Flaus A, Owen-Hughes TA, Hopfner KP.
    Snf2 family ATPases and DExx box helicases: differences and unifying concepts from high-resolution crystal structures.
    Nucleic Acids Research. 2006;409:375-88.

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  • Durr H, Hopfner KP.
    Structure-function analysis of SWI2/SNF2 enzymes.
    Methods Enzymol. 2006;409:375-88.

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  • Uhlmann F, Hopfner KP.
    Chromosome biology: the crux of the ring.
    Curr Biol. 2006 Feb 7;16(3):R102-5.

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  • Reindl C, Bagrintseva K, Vempati S, Schnittger S, Ellwart JW, Wenig K, Hopfner KP, Hiddemann W, Spiekermann K.
    Point mutations found in the juxtamembrane domain of FLT3 define a new class of activating mutations in AML.
    Blood. 2006 Jan 12; [Epub ahead of print]

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  • Hopfner KP
    Structure and Function of Rad50/SMC Protein Complexes in Chromosome Biology.
    In Genome Integrity: Facets and Perspectives, Editor D. Lankenau, Springer, Heidelberg

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  • Hopfner KP
    The Mre11/Rad50/Nbs1 Complex.
    In DNA Damage Recognition, Editor W Siede, P Doetsch, YW Kow, Taylor & Francis, New York

  • Assenmacher N, Wenig K, Lammens A, Hopfner KP
    Structural Basis for Transcription Coupled Repair: the N Terminus of Mfd Resembles UvrB with Degenerate ATPase Motifs
    J Mol Biol. 2006 Jan 27;355(4):675-83. Epub 2005 Nov 8.

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  • 2005

  • Büttner K, Wenig K, Hopfner KP
    Structural Framework for the Mechanism of Archaeal Exosomes in RNA Processing.
    Mol Cell. 2005 Nov 11;20(3):461-71.

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  • Simeoni F, Arvai A, Bello P, Gondeau C, Hopfner KP, Neyroz P, Heitz F, Tainer J, Divita G
    Biochemical Characterization and Crystal Structure of a Dim1 Family Associated Protein: Dim2.
    Biochemistry. 2005 Sep 13;44(36):11997-12008.

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  • Dürr H, Körner C, Müller M, Hickmann V, Hopfner KP
    X-Ray Structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase Core and Its Complex with DNA.
    Cell. 2005 May 6;121(3):363-73.

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  • Karcher A, Buettner K, Märtens B, Jansen RP, Hopfner KP.
    X-Ray Structure of RLI, an Essential Twin Cassette ABC ATPase Involved in Ribosome Biogenesis and HIV Capsid Assembly .
    Structure (Camb). 2005 Apr;13(4):649-659.

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  • 2004

  • Lammens A, Schele A, Hopfner KP.
    Structural Biochemistry of ATP-Driven Dimerization and DNA-Stimulated Activation of SMC ATPases.
    Curr Biol. 2004 Oct 5;14(19):1778-82. 

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  • Assenmacher N, Hopfner KP.
    MRE11/RAD50/NBS1: complex activities.
    Chromosoma. 2004 Oct;113(4):157-66. Epub 2004 Aug 10.

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  • de Jager M, Trujillo KM, Sung P, Hopfner KP, Carney JP, Tainer JA, Connelly JC, Leach DR, Kanaar R, Wyman C.
    Differential arrangements of conserved building blocks among homologs of the Rad50/Mre11 DNA repair protein complex.
    J Mol Biol. 2004 Jun 11;339(4):937-49.

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  • Manzan A, Pfeiffer G, Hefferin ML, Cara EL, Carney JP, Hopfner KP (2004).
    MlaA, a hexameric ATPase linked to the Mre11 complex in archaeal genomes.
    EMBO Reports 5. 54-9.

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  • Pannicke U, Ma Y, Hopfner KP, Niewolik D, Lieber MR, Schwarz K (2004).
    Functional and biochemical dissection of the structure-specific nuclease ARTEMIS.
    EMBO J. 2004

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  • Arthur LM, Gustausson K, Hopfner KP, Carson CT, Stracker TH, Karcher A, Felton D, Weitzman MD, Tainer J, Carney JP
    Structural and functional analysis of Mre11-3.
    Nucleic Acids Res. 32. 1886-93.

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  • Moncalian G, Lengsfeld B, Bhaskara V, Hopfner KP, Karcher A, Alden E, Tainer JA, Paull TT
    The Rad50 signature motif: essential to ATP binding and biological function.
    J Mol Biol 335. 937-51.

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  • 2003 and before

  • Hopfner KP
    Chromosme cohesion: closing time.
    Current Biology. 13. R866-8.

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  • Hopfner KP, Tainer JA
    Rad50/SMC proteins and ABC transporters: unifying concepts from high-resolution structures
    Curr Op Struct Biol 13. 249-55.

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  • Sichler K, Kopetzki E, Huber R, Bode W, Hopfner KP, Brandstetter H
    Physiological fIXa activation involves a cooperative conformational rearrangement of the 99-loop.
    J Biol Chem 278. 4121-6

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  • Hopfner KP, Craig L, Moncalian G, Zinkel, RA, Usui T, Owen BA, Karcher A, Henderson B, Bodmer JL, McMurray CT, Carney JP, Petrini JH , Tainer JA
    The Rad50 zinc-hook is a structure joining Mre11 complexes in DNA recombination and repair.
    Nature 418. 562-566.

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  • Hopfner KP, Putnam , Tainer JA
    DNA double-strand break repair from head to tail.
    Curr. Op. Struct. Biol. 12.  115-122. Review.

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  • Sichler K, Banner DW, D'Arcy A, Hopfner KP, Huber R, Bode W, Kresse GB, Kopetzki E, Brandstetter H
    Crystal structure of uninhibited factor VIIa link its cofactor and substrate assisted activation to specific interactions.
    J. Mol. Biol. 322. 591-603.

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  • Sichler K, Hopfner KP, Kopetzki E, Huber R, Bode W, Brandstetter H
    The influence of residue 190 in the S1 site of trypsin-like serine proteases on substrate selectivity is universally conserved.
    FEBS Lett. 530. 220.

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  • Karcher A, Hopfner KP
    Die molekularen Wächter des Genoms.
    Bioforum 25. 384-6.

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  • Hopfner KP, Karcher A, Craig L, Woo TT, Carney JP, Tainer JA (2001).
    Structural biochemistry and interaction architecture of the DNA double-strand break repair Mre11 nuclease and Rad50 ATPase.
    Cell 105. 473-485.

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  • Hopfner KP, Karcher A, Shin DS, Craig L, Arthur LM, Carney JP, Tainer JA
    Structural biology of Rad50 ATPase: ATP-driven conformational control in DNA double-strand break repair and the ABC-ATPase superfamily.
    Cell 23. 789-800.

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  • Hopfner KP, Parikh SS, Tainer JA
    Envisioning the fourth dimension of the genetic code: the structural biology of macromolecular recognition and conformational switching in DNA repair.
    Cold Spring Harbor Symp. Quant. Biol. Vol. 65.

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  • Hopfner KP, Tainer JA (2000).
    DNA mismatch repair: the hands of a genome guardian.
    Structure 8. R237-41. Review.

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  • Hopfner KP, Karcher A, Shin D, Fairley C, Tainer JA, Carney JP
    Mre11 and Rad50 from Pyrococcus furiosus: cloning and biochemical characterization reveal an evolutionarily conserved multiprotein machine.
    J. Bacteriol. 182. 6036-41.

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  • Bode W, Brandstetter H, Hopfner KP, Stubbs M
    Three-dimensional structures of coagulation factors: pieces of a complex puzzle.
    In New Frontiers In Vascular Biology. Thrombosis and Hemostasis. 75-92. Eibun Press Ltd.

  • Hopfner KP, Lang A, Karcher A, Sichler K, Kopetzki E, Brandstetter H, Huber R, Bode W, Engh RA
    Coagulation factor IXa: the relaxed conformation of Tyr99 blocks substrate binding.
    Structure 1999, 15. 989-96.

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  • Hopfner KP, Eichinger A, Engh RA, Laue F, Ankenbauer W, Huber R, Angerer B
    Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius.
    Proc. Natl. Acad. Sci. USA 1999, 96. 3600-5.

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  • Parry MA, Fernandez-Catalan C, Bergner A, Huber R, Hopfner KP, Schlott B, Guhrs KH, Bode W
    The ternary microplasmin-staphylokinase-microplasmin complex is a proteinase-cofactor-substrate complex in action.
    Nat. Struct. Biol. 1998, 5. 917-23.

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  • Hopfner KP, Kopetzki E, Kresse GB, Bode W, Huber R, Engh RA
    New enzyme lineages by subdomain shuffling.
    Proc. Natl. Acad. Sci. USA 1998, 95. 9813-8.

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  • Hopfner KP, Brandstetter H, Karcher A, Kopetzki E, Huber R, Engh RA, Bode W
    Converting blood coagulation factor IXa into factor Xa: dramatic increase in amidolytic activity identifies important active site determinants.
    EMBO J. 1997, 16. 6626-35.

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  • Sturzebecher J, Kopetzki E, Bode W, Hopfner KP
    Dramatic enhancement of the catalytic activity of coagulation factor IXa by alcohols.
    FEBS Lett. 1997, 412. 295-300.

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  • Di Cera E, Hopfner KP, Dang QD (1996).
    Theory of allosteric effects in serine proteases.
    Biophys J. 1996, 70. 174-81.

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  • Lord ST, Rooney MM, Hopfner KP, Di Cera E (1995).
    Binding of fibrinogen A alpha 1-50-beta-galactosidase fusion protein to thrombin stabilizes the slow form.
    J. Biol. Chem. 1995, 270. 24790-3.

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  • Hopfner KP, Ayala Y, Szewczuk Z, Konishi Y, Di Cera E
    Chemical compensation in macromolecular bridge-binding to thrombin.
    Biochemistry 1993, 32. 2947-53.

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  • Hopfner KP, Di Cera E
    Energetics of thrombin-fibrinogen interaction.
    Biochemistry 1992, 31. 11567-71.

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  • Di Cera E, Hopfner KP, Wyman J
    Symmetry conditions for binding processes.
    Proc. Natl. Acad. Sci. USA 1992, 89. 2727-31.

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