Clara L Kielkopf

Summary

Affiliation: Johns Hopkins Bloomberg School of Public Health
Country: USA

Publications

  1. pmc U2AF homology motifs: protein recognition in the RRM world
    Clara L Kielkopf
    Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
    Genes Dev 18:1513-26. 2004
  2. pmc Structural basis for polypyrimidine tract recognition by the essential pre-mRNA splicing factor U2AF65
    E Allen Sickmier
    Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
    Mol Cell 23:49-59. 2006
  3. pmc Alternative conformations at the RNA-binding surface of the N-terminal U2AF(65) RNA recognition motif
    Karen R Thickman
    Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
    J Mol Biol 366:703-10. 2007
  4. pmc Multiple U2AF65 binding sites within SF3b155: thermodynamic and spectroscopic characterization of protein-protein interactions among pre-mRNA splicing factors
    Karen R Thickman
    Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
    J Mol Biol 356:664-83. 2006
  5. pmc Crystallization and preliminary X-ray analysis of a U2AF65 variant in complex with a polypyrimidine-tract analogue by use of protein engineering
    E Allen Sickmier
    Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:457-9. 2006
  6. pmc X-ray structures of U2 snRNA-branchpoint duplexes containing conserved pseudouridines
    Yuan Lin
    Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
    Biochemistry 47:5503-14. 2008
  7. pmc Structure of a DNA repair substrate containing an alkyl interstrand cross-link at 1.65 A resolution
    Matthew C Swenson
    Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
    Biochemistry 46:4545-53. 2007
  8. ncbi request reprint X-ray structure of a Rex-family repressor/NADH complex insights into the mechanism of redox sensing
    E Allen Sickmier
    Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
    Structure 13:43-54. 2005
  9. pmc Major phosphorylation of SF1 on adjacent Ser-Pro motifs enhances interaction with U2AF65
    Valérie Manceau
    INSERM, U706, UPMC, Institut du Fer a Moulin, Paris, France
    FEBS J 273:577-87. 2006
  10. pmc Structure of the central RNA recognition motif of human TIA-1 at 1.95A resolution
    Amit O Kumar
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    Biochem Biophys Res Commun 367:813-9. 2008

Collaborators

  • Katherine E Frato
  • Stephen K Burley
  • Haihong Shen
  • M S Paget
  • E Allen Sickmier
  • Matthew C Swenson
  • Valérie Manceau
  • Karen R Thickman
  • Amit O Kumar
  • Yuan Lin
  • Andre Sobel
  • Alexandre Maucuer
  • Shanthi R Paranawithana
  • Matthew M Benning
  • Paul S Miller
  • Matthew Swenson
  • Joseph M Kabogo
  • Zygmunt Gryczynski
  • Jean Pierre Le Caer
  • Michael R Green
  • Shanthi Paranawithana
  • Jeffrey B Bonanno
  • Dimitris Brekasis

Detail Information

Publications12

  1. pmc U2AF homology motifs: protein recognition in the RRM world
    Clara L Kielkopf
    Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
    Genes Dev 18:1513-26. 2004
    ..The resulting implications for the functional and evolutionary relationships among candidate UHM family members are discussed...
  2. pmc Structural basis for polypyrimidine tract recognition by the essential pre-mRNA splicing factor U2AF65
    E Allen Sickmier
    Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
    Mol Cell 23:49-59. 2006
    ..The energetic importance of conserved residues for Py tract binding is established by analysis of site-directed mutant U2AF(65) proteins using surface plasmon resonance...
  3. pmc Alternative conformations at the RNA-binding surface of the N-terminal U2AF(65) RNA recognition motif
    Karen R Thickman
    Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
    J Mol Biol 366:703-10. 2007
    ..This rare, high-resolution view of an important member of the RRM class of RNA-binding domains highlights the role of alternative side-chain conformations in RNA recognition...
  4. pmc Multiple U2AF65 binding sites within SF3b155: thermodynamic and spectroscopic characterization of protein-protein interactions among pre-mRNA splicing factors
    Karen R Thickman
    Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
    J Mol Biol 356:664-83. 2006
    ..Comparison of the SF3b155 sites defines an (R/K)nXRW(DE) consensus sequence for predicting U2AF65-UHM ligands from genomic sequences, where parentheses denote residues that contribute to, but are not required for binding...
  5. pmc Crystallization and preliminary X-ray analysis of a U2AF65 variant in complex with a polypyrimidine-tract analogue by use of protein engineering
    E Allen Sickmier
    Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:457-9. 2006
    ..Cocrystals of a U2AF65 variant with a deoxyuridine dodecamer diffract X-rays to 2.9 angstroms resolution and contain one complex per asymmetric unit...
  6. pmc X-ray structures of U2 snRNA-branchpoint duplexes containing conserved pseudouridines
    Yuan Lin
    Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
    Biochemistry 47:5503-14. 2008
    ....
  7. pmc Structure of a DNA repair substrate containing an alkyl interstrand cross-link at 1.65 A resolution
    Matthew C Swenson
    Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
    Biochemistry 46:4545-53. 2007
    ....
  8. ncbi request reprint X-ray structure of a Rex-family repressor/NADH complex insights into the mechanism of redox sensing
    E Allen Sickmier
    Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
    Structure 13:43-54. 2005
    ..We show that T-Rex binds to the Rex operator, and NADH but not NAD(+) inhibits T-Rex/DNA binding activity. A mechanism for redox sensing by Rex family members is proposed by analogy with domain closure of NAD(H)-dependent enzymes...
  9. pmc Major phosphorylation of SF1 on adjacent Ser-Pro motifs enhances interaction with U2AF65
    Valérie Manceau
    INSERM, U706, UPMC, Institut du Fer a Moulin, Paris, France
    FEBS J 273:577-87. 2006
    ..These results further suggest that this phosphorylation event has an important role for the function of SF1, and possibly for the structural rearrangements associated with spliceosome assembly and function...
  10. pmc Structure of the central RNA recognition motif of human TIA-1 at 1.95A resolution
    Amit O Kumar
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    Biochem Biophys Res Commun 367:813-9. 2008
    ..In contrast with previous assumptions, the mutated residues are buried within the hydrophobic interior of the domain, where they would be likely to destabilize the RRM fold rather than directly inhibit RNA binding...
  11. ncbi request reprint X-ray structures of threonine aldolase complexes: structural basis of substrate recognition
    Clara L Kielkopf
    Laboratories of Molecular Biophysics and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Biochemistry 41:11711-20. 2002
    ..Variation in the threonine binding pocket may explain preferences for L-allo-threonine versus L-threonine among TA family members...
  12. pmc Different requirements of the kinase and UHM domains of KIS for its nuclear localization and binding to splicing factors
    Valérie Manceau
    Institut National de la Sante et de la Recherche Medicale, UMR839, 17, rue du Fer à Moulin, F 75005 Paris, France
    J Mol Biol 381:748-62. 2008
    ....