protein footprinting

Summary

Summary: A method for determining points of contact between interacting proteins or binding sites of proteins to nucleic acids. Protein footprinting utilizes a protein cutting reagent or protease. Protein cleavage is inhibited where the proteins, or nucleic acids and protein, contact each other. After completion of the cutting reaction, the remaining peptide fragments are analyzed by electrophoresis.

Top Publications

  1. pmc Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins
    Inna Shcherbakova
    Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Nucleic Acids Res 34:e48. 2006
  2. ncbi Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes
    Keiji Takamoto
    Case Center for Proteomics, Case Western Reserve University, Cleveland, Ohio 44106, USA
    Annu Rev Biophys Biomol Struct 35:251-76. 2006
  3. ncbi A detailed interpretation of OH radical footprints in a TBP-DNA complex reveals the role of dynamics in the mechanism of sequence-specific binding
    N Pastor
    Facultad de Ciencias, UAEM, Av Universidad 1001, Col Chamilpa, Cuernavaca, Morelos, 62210, Mexico
    J Mol Biol 304:55-68. 2000
  4. ncbi Probing cAMP-dependent protein kinase holoenzyme complexes I alpha and II beta by FT-IR and chemical protein footprinting
    Shaoning Yu
    Department of Human Biological Chemistry and Genetics, School of Medicine, The University of Texas Medical Branch, Galveston, Texas 77555 1031, USA
    Biochemistry 43:1908-20. 2004
  5. pmc Correlating protein footprinting with mutational analysis in the bacterial transcription factor sigma54 (sigmaN)
    Siva R Wigneshweraraj
    Department of Biological Sciences, Imperial College of Science, Technology and Medicine, Sir Alexander Fleming Building, Imperial College Road, London SW7 2AZ, UK
    Nucleic Acids Res 30:1016-28. 2002
  6. ncbi Radiolytic modification of sulfur-containing amino acid residues in model peptides: fundamental studies for protein footprinting
    Guozhong Xu
    Center for Synchrotron Biosciences, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, USA
    Anal Chem 77:2437-49. 2005
  7. ncbi Synchrotron protein footprinting: a technique to investigate protein-protein interactions
    S C Goldsmith
    Center for Synchrotron Biosciences, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    J Biomol Struct Dyn 19:405-18. 2001
  8. pmc Protein footprinting in a complex milieu: identifying the interaction surfaces of the chemotaxis adaptor protein CheW
    Eric S Underbakke
    Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706, USA
    J Mol Biol 409:483-95. 2011
  9. pmc Mass spectrometry-based protein footprinting characterizes the structures of oligomeric apolipoprotein E2, E3, and E4
    Brian Gau
    Department of Chemistry, Washington University, One Brookings Drive, St Louis, Missouri 63130, USA
    Biochemistry 50:8117-26. 2011
  10. ncbi Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry
    Jing Qu Guan
    Case Center for Proteomics and Mass Spectrometry, 930 BRB, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
    Trends Biochem Sci 30:583-92. 2005

Research Grants

  1. MECHANISMS OF COOPERATIVE PROTEIN-DNA INTERACTIONS
    Michael Brenowitz; Fiscal Year: 2006
  2. Mechanisms of RNA binding and remodeling proteins
    KEVIN RANEY; Fiscal Year: 2009
  3. Mechanisms of RNA binding and remodeling proteins
    KEVIN D contact RANEY; Fiscal Year: 2010
  4. MOLECULAR AND CELLULAR INTERACTIONS OF FACTOR XI
    Peter Walsh; Fiscal Year: 1993
  5. REGULATION OF NITROGEN METABOLISM IN BACILLUS SUBTILIS
    Susan Fisher; Fiscal Year: 2006
  6. Cellular Footprinting of Transferrin-Receptor Complex
    MARK CHANCE; Fiscal Year: 2005
  7. MECHANISMS OF COOPERATIVE PROTEIN-DNA INTERACTIONS
    Michael Brenowitz; Fiscal Year: 2003
  8. Erythropoietin receptor /Janus Kinase 2 complex
    Lily Huang; Fiscal Year: 2006
  9. Mulitvalent Ligands as Effectors
    LAURA KIESSLING; Fiscal Year: 2007
  10. Mulitvalent Ligands as Effectors
    LAURA KIESSLING; Fiscal Year: 2009

Scientific Experts

Detail Information

Publications146 found, 100 shown here

  1. pmc Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins
    Inna Shcherbakova
    Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Nucleic Acids Res 34:e48. 2006
    ....
  2. ncbi Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes
    Keiji Takamoto
    Case Center for Proteomics, Case Western Reserve University, Cleveland, Ohio 44106, USA
    Annu Rev Biophys Biomol Struct 35:251-76. 2006
    ..Hydroxyl radical-mediated protein footprinting using mass spectrometry has recently been developed to define structure, assembly, and conformational ..
  3. ncbi A detailed interpretation of OH radical footprints in a TBP-DNA complex reveals the role of dynamics in the mechanism of sequence-specific binding
    N Pastor
    Facultad de Ciencias, UAEM, Av Universidad 1001, Col Chamilpa, Cuernavaca, Morelos, 62210, Mexico
    J Mol Biol 304:55-68. 2000
    ..This mechanism results in an enthalpic advantage to complex formation at a low entropic cost...
  4. ncbi Probing cAMP-dependent protein kinase holoenzyme complexes I alpha and II beta by FT-IR and chemical protein footprinting
    Shaoning Yu
    Department of Human Biological Chemistry and Genetics, School of Medicine, The University of Texas Medical Branch, Galveston, Texas 77555 1031, USA
    Biochemistry 43:1908-20. 2004
    ..amide hydrogen-deuterium exchange coupled with Fourier transform infrared spectroscopy (FT-IR) and chemical protein footprinting. Binding of cAMP to PKA holoenzymes Ialpha and IIbeta leads to a downshift in the wavenumber for both the ..
  5. pmc Correlating protein footprinting with mutational analysis in the bacterial transcription factor sigma54 (sigmaN)
    Siva R Wigneshweraraj
    Department of Biological Sciences, Imperial College of Science, Technology and Medicine, Sir Alexander Fleming Building, Imperial College Road, London SW7 2AZ, UK
    Nucleic Acids Res 30:1016-28. 2002
    ..Their properties support the view that the interface between sigma54 and core RNAP is functionally specialised...
  6. ncbi Radiolytic modification of sulfur-containing amino acid residues in model peptides: fundamental studies for protein footprinting
    Guozhong Xu
    Center for Synchrotron Biosciences, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, USA
    Anal Chem 77:2437-49. 2005
    b>Protein footprinting based on hydroxyl radical-mediated modification and quantitative mass spectroscopic analysis is a proven technique for examining protein structure, protein-ligand interactions, and structural allostery upon protein ..
  7. ncbi Synchrotron protein footprinting: a technique to investigate protein-protein interactions
    S C Goldsmith
    Center for Synchrotron Biosciences, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    J Biomol Struct Dyn 19:405-18. 2001
    ..The results presented here establish synchrotron footprinting as a broadly applicable method to probe structural features of macromolecular complexes that are not amenable to conventional approaches...
  8. pmc Protein footprinting in a complex milieu: identifying the interaction surfaces of the chemotaxis adaptor protein CheW
    Eric S Underbakke
    Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706, USA
    J Mol Biol 409:483-95. 2011
    ..To study protein-protein interactions in a biologically relevant complex milieu, we employed a protein footprinting strategy based on isotope-coded affinity tag (ICAT) reagents...
  9. pmc Mass spectrometry-based protein footprinting characterizes the structures of oligomeric apolipoprotein E2, E3, and E4
    Brian Gau
    Department of Chemistry, Washington University, One Brookings Drive, St Louis, Missouri 63130, USA
    Biochemistry 50:8117-26. 2011
    ..In this study, we report two comparative studies of the ApoE family by using the mass spectrometry-based protein footprinting methods of FPOP and glycine ethyl ester (GEE) labeling...
  10. ncbi Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry
    Jing Qu Guan
    Case Center for Proteomics and Mass Spectrometry, 930 BRB, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
    Trends Biochem Sci 30:583-92. 2005
    ..Hydroxyl-radical-mediated protein footprinting using mass spectrometry can define macromolecular structure, macromolecular assembly and conformational ..
  11. ncbi Radiolytic modification and reactivity of amino acid residues serving as structural probes for protein footprinting
    Guozhong Xu
    Department of Physiology and Biophysics, Center for Synchrotron Biosciences, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461 1602, USA
    Anal Chem 77:4549-55. 2005
    Hydroxyl radical-mediated protein footprinting is a convenient and sensitive technique for mapping solvent-accessible surfaces of proteins and examining the structure and dynamics of biological assemblies...
  12. ncbi Secondary reactions and strategies to improve quantitative protein footprinting
    Guozhong Xu
    Center for Synchrotron Biosciences, Department of Physiology and Biophysics, and Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
    Anal Chem 77:3029-37. 2005
    ..The disulfides can be reduced before mass spectrometric analysis by reducing agents such as TCEP, while methionine sulfoxide is refractory to reduction by this reagent under typical reducing conditions...
  13. ncbi Mapping protein-ligand interactions by hydroxyl-radical protein footprinting
    Nick Loizos
    Department of Protein Chemistry, ImClone Systems Inc, New York, NY, USA
    Methods Mol Biol 261:199-210. 2004
    Hydroxyl-radical protein footprinting is a direct method to map protein sites involved in macromolecular interactions. The first step is to radioactively end-label the protein...
  14. ncbi Mapping the G-actin binding surface of cofilin using synchrotron protein footprinting
    Jing Qu Guan
    Center for Synchrotron Biosciences, Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
    Biochemistry 41:5765-75. 2002
    ..Synchrotron protein footprinting is used to identify specific side chain residues on the cofilin surface that are buried in the formation of ..
  15. pmc Identification of specific HIV-1 reverse transcriptase contacts to the viral RNA:tRNA complex by mass spectrometry and a primary amine selective reagent
    Mamuka Kvaratskhelia
    HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA
    Proc Natl Acad Sci U S A 99:15988-93. 2002
    We have devised a high-resolution protein footprinting methodology to dissect HIV-1 reverse transcriptase (RT) contacts to the viral RNA:tRNA complex...
  16. pmc Aliphatic peptidyl hydroperoxides as a source of secondary oxidation in hydroxyl radical protein footprinting
    Jessica Saladino
    Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30605, USA
    J Am Soc Mass Spectrom 20:1123-6. 2009
    ....
  17. pmc Pulsed electron beam water radiolysis for submicrosecond hydroxyl radical protein footprinting
    Caroline Watson
    Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
    Anal Chem 81:2496-505. 2009
    ..We have developed a novel method for submicrosecond hydroxyl radical protein footprinting using a pulsed electron beam from a 2 MeV Van de Graaff electron accelerator to generate a high ..
  18. ncbi DNA and protein footprinting analysis of the modulation of DNA binding by the N-terminal domain of the Saccharomyces cerevisiae TATA binding protein
    Sayan Gupta
    Center for Synchrotron Biosciences, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, New York 11973, USA
    Biochemistry 46:9886-98. 2007
    ..of the N-terminal domain on DNA binding by TBP were explored in comparative studies of TBPc and TBP by "protein footprinting" with hydroxyl radical (*OH) side chain oxidation...
  19. ncbi Monitoring regulated protein-protein interactions using split TEV
    Michael C Wehr
    Max Planck Institute of Experimental Medicine, Hermann Rein Str 3, D 37075 Gottingen, Germany
    Nat Methods 3:985-93. 2006
    ..In a first biological application, we monitored neuregulin-induced ErbB2/ErbB4 receptor tyrosine kinase heterodimerization...
  20. pmc Probing conformational changes of human DNA polymerase lambda using mass spectrometry-based protein footprinting
    Jason D Fowler
    Department of Biochemistry, The Ohio State University, Columbus, 43210, USA
    J Mol Biol 390:368-79. 2009
    ..gene 1 C-terminal domain and a proline-rich domain at its N-terminus, we used a mass spectrometry-based protein footprinting approach...
  21. ncbi Assessment of solvent residues accessibility using three Sulfo-NHS-biotin reagents in parallel: application to footprint changes of a methyltransferase upon binding its substrate
    Guillaume Gabant
    CEA VALRHO, DSV, IBEB, SBTN, LBSP, Institut de Biologie Environnementale et Biotechnologie, Service de Biochimie et Toxicologie Nucléaire, Laboratoire de Biochimie des Systèmes Perturbés, F 30207 Bagnols sur Ceze, France
    J Mass Spectrom 43:360-70. 2008
    ..This method was used to identify two lysine residues of the TrmG10 methyltransferase from Pyrococcus abyssi that were differentially reactive, modified in the protein but not in the tRNA-protein complex...
  22. ncbi Distinct footprints of TCR engagement with highly homologous ligands
    Fabio R Santori
    Michael Heidelberger Division of Immunology, Department of Pathology and New York University Cancer Center, New York University School of Medicine, New York, NY 10016, USA
    J Immunol 172:7466-75. 2004
    ..These findings explain differences in functional versatility of TCR ligands, as well as anomalies in the relationship between affinity/avidity of the TCR for the peptide/MHC and cellular responses of T cells...
  23. ncbi DNA binding provides a molecular strap activating the adenovirus proteinase
    Sayan Gupta
    Center for Synchrotron Biosciences, Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Mol Cell Proteomics 3:950-9. 2004
    ..Synchrotron protein footprinting was used to map the solvent accessible cofactor binding sites and to identify conformational changes ..
  24. pmc RNA secondary structure of the feline immunodeficiency virus 5'UTR and Gag coding region
    Laurie James
    CNRS UPR2167 Centre de Génétique Moléculaire, Avenue de la Terrasse, 91190 Gif sur Yvette, France
    Nucleic Acids Res 36:4653-66. 2008
    ..In addition, we observed footprints of Gag protein on each side of the initiation codon, this sheds light on the role of the sequences required for encapsidation...
  25. pmc Synchrotron protein footprinting supports substrate translocation by ClpA via ATP-induced movements of the D2 loop
    Jen Bohon
    Center for Proteomics and Center for Synchrotron Biosciences, Case Western Reserve University, Cleveland, OH 44106, USA
    Structure 16:1157-65. 2008
    Synchrotron X-ray protein footprinting is used to study structural changes upon formation of the ClpA hexamer...
  26. ncbi Footprint of the retrotransposon R2Bm protein on its target site before and after cleavage
    Shawn Christensen
    Department of Biology, University of Rochester, Hutchinson Hall 334, Rochester, NY 14627 0211, USA
    J Mol Biol 336:1035-45. 2004
    ..We suggest that this increased protection after cleavage is the RT domain that is positioned over the free DNA end to begin reverse transcription on the nicked DNA substrate...
  27. ncbi Footprinting protein-DNA complexes using the hydroxyl radical
    Swapan S Jain
    Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
    Nat Protoc 3:1092-1100. 2008
    ..This protocol can be completed in 2 d...
  28. ncbi Structural reorganization of proteins revealed by radiolysis and mass spectrometry: G-actin solution structure is divalent cation dependent
    Jing Qu Guan
    Center for Synchrotron Biosciences, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
    Biochemistry 42:11992-2000. 2003
    ..These conformational variations for isolated Mg(2+)-G-actin provide a structural basis for its greater tendency to polymerize into filaments as compared to Ca(2+)-G-actin...
  29. ncbi The HIV-1 Nef protein enhances the affinity of reverse transcriptase for RNA in vitro
    Cecile Fournier
    Laboratoire de Virologie and Pathogénèse Virale, CNRS UMR 5537, Faculté de médecine RTH Laennec, 7, Rue Guillaume Paradin 69008, Lyon, France
    Virus Genes 25:255-69. 2002
    ....
  30. pmc Ribosomal protein S15 represses its own translation via adaptation of an rRNA-like fold within its mRNA
    Alexander Serganov
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    EMBO J 22:1898-908. 2003
    ..Our results highlight an astonishing plasticity of mRNA in its ability to adapt to evolutionary constraints, that contrasts with the extreme conservation of the rRNA-binding site...
  31. ncbi Solution structure and interdomain interactions of the Saccharomyces cerevisiae "TATA binding protein" (TBP) probed by radiolytic protein footprinting
    Hassan Rashidzadeh
    Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
    Biochemistry 42:3655-65. 2003
    ..The functional implications of these results are discussed...
  32. ncbi Smad affinity can direct distinct readouts of the embryonic extracellular Dpp gradient in Drosophila
    Stephen J Wharton
    School of Biological Sciences, University of Manchester, Manchester, M13 9PT, United Kingdom
    Curr Biol 14:1550-8. 2004
    ..An activity gradient of Dpp specifies distinct cell fates in the dorsal ectoderm of the embryo through the activation of different transcriptional threshold responses...
  33. ncbi Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster
    Casey M Bergman
    Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
    Bioinformatics 21:1747-9. 2005
    ....
  34. ncbi [Binding of human ribosomal protein S5 with the 18S rRNA fragment 1203-1236/1521-1698]
    D D Ian'shina
    Mol Biol (Mosk) 40:460-7. 2006
    ..Besides, we also found nucleotides in the transcript regions corresponding to 16S rRNA regions that do not contact S7 in the 30S subunit...
  35. ncbi Evidence for preorganization of the glmS ribozyme ligand binding pocket
    Ken J Hampel
    Department of Microbiology and Molecular Genetics, University of Vermont, 95 Carrigan Drive, 222 Stafford Hall, Burlington, Vermont 05405, USA
    Biochemistry 45:7861-71. 2006
    ..This mode of action is different from that observed for other riboswitches characterized to date, which act by inducing secondary and tertiary structure changes...
  36. pmc Interactions between HIV-1 Gag molecules in solution: an inositol phosphate-mediated switch
    Siddhartha A K Datta
    HIV Drug Resistance Program, National Cancer Institute Frederick, Frederick, MD 21702, USA
    J Mol Biol 365:799-811. 2007
    ..As Gag is an extended rod in immature virions, this apparent proximity of the ends in solution implies that it undergoes a major conformational change during particle assembly...
  37. ncbi Biochemical implications of a three-dimensional model of monomeric actin bound to magnesium-chelated ATP
    Keiji Takamoto
    Case Center for Proteomics, Case Western Reserve University, 10090 Euclid Avenue, Cleveland, OH 44106, USA
    Structure 15:39-51. 2007
    ..The key conclusion of this study is that the structure of the nucleotide binding cleft defined by subdomains 2 and 4 is essentially closed, with specific contacts between two subdomains predicted by the data...
  38. pmc Trans-acting glmS catalytic riboswitch: locked and loaded
    Rebecca A Tinsley
    Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 1055, USA
    RNA 13:468-77. 2007
    ..These findings suggest that the glmS ribozyme is fully folded in solution prior to binding its activating ligand, supporting recent observations in the crystalline state...
  39. ncbi The Beamline X28C of the Center for Synchrotron Biosciences: a national resource for biomolecular structure and dynamics experiments using synchrotron footprinting
    Sayan Gupta
    Center for Proteomics and Mass Spectrometry, Case Western Reserve University, Cleveland, OH, USA
    J Synchrotron Radiat 14:233-43. 2007
    ..Lastly, several examples of published results provide illustrations of the kinds of experiments likely to be successful using these approaches...
  40. pmc Three-dimensional structure of cofilin bound to monomeric actin derived by structural mass spectrometry data
    J K Amisha Kamal
    Center for Proteomics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
    Proc Natl Acad Sci U S A 104:7910-5. 2007
    ..We used radiolytic protein footprinting with mass spectrometry and molecular modeling to provide an atomic model of how cofilin binds to monomeric ..
  41. pmc Expanding the repertoire of an ERK2 recruitment site: cysteine footprinting identifies the D-recruitment site as a mediator of Ets-1 binding
    Olga Abramczyk
    Division of Medicinal Chemistry, University of Texas at Austin, Texas 78712, USA
    Biochemistry 46:9174-86. 2007
    ..This suggests that Ets-1 may contain a novel or cryptic D-site. To investigate this possibility a protein footprinting strategy was developed to elucidate ERK2-ligand interactions...
  42. pmc Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA
    Natalia Ivanova
    Department of Cell and Molecular Biology, BMC, Uppsala University Box 596, S 75 124 Uppsala, Sweden
    Nucleic Acids Res 33:3529-39. 2005
    ....
  43. ncbi Ligand-mediated anticodon conformational changes occur during tRNA methylation by a TrmD methyltransferase
    Joseph M Watts
    Department of Biochemistry, Medical College of Virginia Campus of Virginia Commonwealth University, Institute for Structural Biology and Drug Discovery, 800 East Leigh Street, Suite 212, Richmond, Virginia 23219, USA
    Biochemistry 44:6629-39. 2005
    ..Taken together, these results suggest that the base to be methylated by the TrmD protein is mobilized into the active center after tRNA binding only when the AdoMet site is occupied...
  44. pmc Mapping of the hepatitis B virus pre-S1 domain involved in receptor recognition
    Azeneth Barrera
    Department of Virology and Immunology, Southwest National Primate Research Center, Southwest Foundation for Biomedical Research, TX 78227, USA
    J Virol 79:9786-98. 2005
    ....
  45. ncbi Structure and dynamics of the actin filament
    Jing Qu Guan
    Center for Synchrotron Biosciences, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, USA
    Biochemistry 44:3166-75. 2005
    ..K., and Schriemer, D.C. (2003) J. Mol. Biol. 334, 373-385], which also did not detect any burial of the H plug upon formation of filaments...
  46. ncbi The flexible N-terminal domain of ribosomal protein L11 from Escherichia coli is necessary for the activation of stringent factor
    Rose Marie Jenvert
    School of Life Sciences, Södertörns högskola, S 141 04 Huddinge, Sweden
    J Mol Biol 365:764-72. 2007
    ..This suggests that the N-terminal domain can activate stringent factor in trans. It is also shown that this activation is dependent on unacylated tRNA...
  47. ncbi Recognition of DNA interstrand cross-link of antitumor cisplatin by HMGB1 protein
    Jana Kasparkova
    Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, CZ 61265 Brno, Czech Republic
    Biochemistry 42:1234-44. 2003
    ..The model structure is consistent with the hypothesis that the enhancement of binding affinity afforded by the basic lysine-rich A/B linker is a consequence of its tight binding to the sugar-phosphate backbone of both DNA strands...
  48. ncbi Mutational changes of conserved residues in the Q-loop region of transcription factor Rho greatly reduce secondary site RNA-binding
    R R Wei
    Departments of Biology, Indiana University, Bloomington, 47405, USA
    J Mol Biol 314:1007-15. 2001
    ....
  49. ncbi Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail
    K S Hamilton
    Department of Biochemistry, The University of Alberta, Edmonton, Alberta T6G 2H7, Canada
    Structure 9:897-904. 2001
    ..The model supports in vivo and in vitro experiments of E2 derivatives carrying surface residue substitutions. Furthermore, the model provides insights into the arrangement of Ub, E2, and E3 within a ternary targeting complex...
  50. ncbi Solvent accessibility of the thrombin-thrombomodulin interface
    J G Mandell
    Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0359, USA
    J Mol Biol 306:575-89. 2001
    ..These partially inaccessible regions of thrombin form both surface and buried contacts into the active site of thrombin and contain residues implicated in allosteric changes in thrombin upon TM binding...
  51. pmc Position of eukaryotic initiation factor eIF1 on the 40S ribosomal subunit determined by directed hydroxyl radical probing
    Ivan B Lomakin
    Department of Microbiology and Immunology, SUNY Downstate Medical Center Brooklyn, New York 11203, USA
    Genes Dev 17:2786-97. 2003
    ....
  52. ncbi [Identification of a fragment of ceruloplasmin, interacting with copper-transporting Menkes ATPase]
    N V Tsymbalenko
    Research Institute of Experimental Medicine, Russian Academy of Medical Sciences, St Petersburg, Russia
    Bioorg Khim 26:579-86. 2000
    ..The protein footprinting showed that P16 binds to a fragment of the ceruloplasmin domain 6...
  53. ncbi Peptide bis-intercalator binds DNA via threading mode with sequence specific contacts in the major groove
    V Guelev
    Department of Chemistry and Biochemistry, The University of Texas at Austin, 78722, USA
    Chem Biol 8:415-25. 2001
    ....
  54. ncbi A complex with chromatin modifiers that occupies E2F- and Myc-responsive genes in G0 cells
    Hidesato Ogawa
    Dana Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA
    Science 296:1132-6. 2002
    ..The E2F-6 complex preferentially occupies target promoters in G0 cells rather than in G1 cells. These data suggest that these chromatin modifiers contribute to silencing of E2F- and Myc-responsive genes in quiescent cells...
  55. pmc Recognition of tRNALeu by Aquifex aeolicus leucyl-tRNA synthetase during the aminoacylation and editing steps
    Peng Yao
    State Key Laboratory of Molecular Biology Graduate School of the Chinese Academy of Sciences, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, Shanghai, People s Republic of China
    Nucleic Acids Res 36:2728-38. 2008
    ....
  56. ncbi Inhibition of the U1A-RNA complex by an aminoacridine derivative
    Alicia Y Gayle
    Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA
    Bioorg Med Chem Lett 12:2839-42. 2002
    ..Either direct binding to the RNA or indirect alteration of the structure or dynamics of the loop would be likely to inhibit binding of the U1A protein to this RNA...
  57. pmc hnRNP A1 controls HIV-1 mRNA splicing through cooperative binding to intron and exon splicing silencers in the context of a conserved secondary structure
    Christian Kroun Damgaard
    Department of Molecular and Structural Biology, University of Aarhus, DK 8000 Aarhus C, Denmark
    RNA 8:1401-15. 2002
    ....
  58. ncbi Mapping functionally important motifs SPF and GGQ of the decoding release factor RF2 to the Escherichia coli ribosome by hydroxyl radical footprinting. Implications for macromolecular mimicry and structural changes in RF2
    Debbie Jane G Scarlett
    Department of Biochemistry and Centre for Gene Research, University of Otago, P O Box 56, Dunedin, New Zealand
    J Biol Chem 278:15095-104. 2003
    ..Our data suggest that RF2 may undergo gross conformational changes upon ribosome binding, the implications of which are discussed in terms of the mechanism of RF-mediated termination...
  59. ncbi The interaction between sigmaS, the stationary phase sigma factor, and the core enzyme of Escherichia coli RNA polymerase
    Frederic Colland
    Institut Pasteur, Laboratoire des Regulations Transcriptionnelles FRE 2364 CNRS, 75724 Paris Cedex 15, France
    Genes Cells 7:233-47. 2002
    ..Using labelled sigmaS and sigma70, we compared the affinities of both sigma factors for core binding and investigated the structural changes in the different subunits involved in the formation of the holoenzymes...
  60. ncbi Antibody modulation of antigen presentation: positive and negative effects on presentation of the tetanus toxin antigen via the murine B cell isoform of FcgammaRII
    Antony N Antoniou
    Division of Cell Biology and Immunology, Wellcome Trust Biocentre, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, GB
    Eur J Immunol 32:530-40. 2002
    ..These results show that the B cell isoform of FcgammaRII (FcgammaRIIB1) can mediate capture and presentation of some antigen/antibody complexes and might play a role in BCR-independent antigen presentation in vivo...
  61. pmc Checkpoint kinase ATR promotes nucleotide excision repair of UV-induced DNA damage via physical interaction with xeroderma pigmentosum group A
    Steven M Shell
    Department of Biochemistry and Molecular Biology, James H Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614, USA
    J Biol Chem 284:24213-22. 2009
    ..Using a mass spectrometry-based protein footprinting method, we found that ATR interacts with a helix-turn-helix motif in the minimal DNA-binding domain of XPA ..
  62. doi Probing conformational changes in Ape1 during the progression of base excision repair
    Eizadora Yu
    Biosystems Research Department, Sandia National Laboratories, Livermore, California 94551 0969, USA
    Biochemistry 49:3786-96. 2010
    ..In this study, we employed fluorescence spectroscopy and in vitro mass spectrometric protein footprinting to investigate Ape1 conformational changes during various nucleoprotein interactions along its reaction ..
  63. ncbi DNA vaccination with glutamic acid decarboxylase (GAD) generates a strong humoral immune response in BALB/c, C57BL/6, and in diabetes-prone NOD mice
    U Wiest-Ladenburger
    Department of Internal Medicine I, University of Ulm, Germany
    Horm Metab Res 30:605-9. 1998
    ..Epitope recognition of GAD was studied by protein footprinting, a technique which makes use of a limited proteolysis of antibody-bound antigen...
  64. ncbi Regions of the Escherichia coli primary sigma factor sigma70 that are involved in interaction with RNA polymerase core enzyme
    H Nagai
    Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka, Japan
    Genes Cells 2:725-34. 1997
    ..In this report, we employed the protein footprinting method to investigate the alteration of the structure and function of Escherichia coli sigma70 by binding ..
  65. pmc Core-sigma interaction: probing the interaction of the bacteriophage T4 gene 55 promoter recognition protein with E.coli RNA polymerase core
    J P Leonetti
    Department of Biology and Center for Molecular Genetics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0634, USA
    EMBO J 17:1467-75. 1998
    ..b>Protein footprinting was used to identify segments of gp55 that become buried upon binding to RNA polymerase core, and are ..
  66. pmc Future directions of structural mass spectrometry using hydroxyl radical footprinting
    Janna G Kiselar
    Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
    J Mass Spectrom 45:1373-82. 2010
    Hydroxyl radical protein footprinting coupled to mass spectrometry has been developed over the last decade and has matured to a powerful method for analyzing protein structure and dynamics...
  67. ncbi A zinc finger homeodomain transcription factor binds specific thyroid hormone response elements
    D S Darling
    Department of Biological and Biophysical Sciences, University of Louisville, School of Dentistry, Kentucky 40292, USA
    Mol Cell Endocrinol 139:25-35. 1998
    ..Interactions of non-receptor transcription factors (such as Zfhep) with certain TREs are important to modify gene-specific regulation by thyroid hormones...
  68. pmc Cold chemical oxidation of proteins
    David M Hambly
    Department of Chemistry, Washington University in St Louis, Missouri 63130, USA
    Anal Chem 81:7235-42. 2009
    Various methods of protein footprinting use hydrogen peroxide as an oxidant. Its removal by various solid-phase desalting methods, catalase treatment, or freeze drying after the footprinting is critical to ensure no uncontrolled oxidation...
  69. pmc Methylene as a possible universal footprinting reagent that will include hydrophobic surface areas: overview and feasibility: properties of diazirine as a precursor
    F M Richards
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
    Protein Sci 9:2506-17. 2000
    ..a very low specificity, which makes it essentially useless for synthesis, but suggests a possible role in protein footprinting with special importance in labeling solvent accessible nonpolar areas, identifying ligand binding sites, ..
  70. pmc I(kappa)B(gamma) inhibits DNA binding of NF-kappaB p50 homodimers by interacting with residues that contact DNA
    S Bell
    School of Biological and Medical Sciences, University of St Andrews, Fife, Scotland
    Mol Cell Biol 16:6477-85. 1996
    ..The interaction between NF-(kappa)B p50 and DNA was investigated by protein footprinting using chemical modification and partial proteolysis...
  71. pmc Subunit-specific protein footprinting reveals significant structural rearrangements and a role for N-terminal Lys-14 of HIV-1 Integrase during viral DNA binding
    Zhuojun Zhao
    Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA
    J Biol Chem 283:5632-41. 2008
    ..The experimental approach described here has general application to mapping interactions within functional nucleoprotein complexes...
  72. pmc Visualizing the Ca2+-dependent activation of gelsolin by using synchrotron footprinting
    Janna G Kiselar
    Department of Physiology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 1602, USA
    Proc Natl Acad Sci U S A 100:3942-7. 2003
    Radiolytic protein footprinting with a synchrotron source is used to reveal detailed structural changes that occur in the Ca(2+)-dependent activation of gelsolin...
  73. pmc RNA-protein interactions of an archaeal homotetrameric splicing endoribonuclease with an exceptional evolutionary history
    J Lykke-Andersen
    RNA Regulation Centre, Institute of Molecular Biology, Copenhagen University, Solvgade 83H, DK 1307 Copenhagen K, Denmark
    EMBO J 16:6290-300. 1997
    ..The complex was subjected to protein footprinting and the results implicated an RNP1-like sequence and a sequence region immediately N-terminal to a putative ..
  74. pmc Molecular mechanism for establishment of signal-dependent regulation in the PhoP/PhoQ system
    Wei Kong
    Center for Infectious Diseases and Vaccinology at the Biodesign Institute and The School of Life Sciences, Arizona State University, Tempe, Arizona 85287 4501, USA
    J Biol Chem 283:16612-21. 2008
    ..Therefore, H-NS should pair with SlyA and PhoP to establish a forward regulatory loop to regulate expression of pagC, and perhaps other PhoP- and SlyA-dependent genes...
  75. ncbi Strong nucleic acid binding to the Escherichia coli RNase HI mutant with two arginine residues at the active site
    Y Tsunaka
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, 565 0871, Osaka, Japan
    Biochim Biophys Acta 1547:135-42. 2001
    ..Instead, it showed high-nucleic-acid-binding affinity. Protein footprinting analyses suggest that DNA/RNA hybrid binds to or around the presumed substrate-binding site of the protein...
  76. pmc Physical and genetic interactions of yeast Cwc21p, an ortholog of human SRm300/SRRM2, suggest a role at the catalytic center of the spliceosome
    Richard J Grainger
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, United Kingdom
    RNA 15:2161-73. 2009
    ..Thus, the function of Cwc21p is likely conserved from yeast to humans...
  77. doi Analysis of RNA structure and RNA-protein interactions in mammalian cells by use of terminal transferase-dependent PCR
    Hsiu Hua Chen
    Beckman Research Institute of the City of Hope, Duarte, California, USA
    Methods Mol Biol 488:319-41. 2008
    ....
  78. ncbi Targeted protein footprinting: where different transcription factors bind to RNA polymerase
    S L Traviglia
    Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, USA
    Biochemistry 38:15774-8. 1999
    ..We have devised a new strategy that relies on targeted protein footprinting to make an extensive survey of proximity to the protein surface...
  79. pmc Modeling of protein binary complexes using structural mass spectrometry data
    J K Amisha Kamal
    Center for Proteomics and Mass Spectrometry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
    Protein Sci 17:79-94. 2008
    ..In the first step, hydroxyl radical mediated oxidative protein footprinting is used to identify residues that experience conformational reorganization due to binding or participate in ..
  80. doi Structural changes in the SL5 and SL6 leader sequences of HIV-1 RNA following interactions with the viral mGag protein
    Ariel Roldan
    McGill University AIDS Center, Lady Davis Institute for Medical Research, Sir Mortimer B Davis Jewish General Hospital, 3755 Chemin Cote Ste Catherine, Montreal, QC H3T 1E2, Canada
    Virus Res 155:98-105. 2011
    ..Now, we provide protein footprinting results on the +350 to +500 nucleotide region of viral RNA, based on use of different single-stranded and ..
  81. pmc Fast photochemical oxidation of protein footprints faster than protein unfolding
    Brian C Gau
    Department of Chemistry, Washington University in St Louis, St Louis, Missouri 63130, USA
    Anal Chem 81:6563-71. 2009
    ..This model breaks down when a scavenger is not used and/or hydrogen peroxide is not removed following photolysis. The outcome verifies that FPOP occurs on a time scale faster than conformational changes in these proteins...
  82. doi Time-resolved footprinting for the study of the structural dynamics of DNA-protein interactions
    Bianca Sclavi
    Laboratoire de Biotechnologies et Pharmacologie génétique Appliquée, UMR 8113 du CNRS, Ecole Normale Superieure de Cachan, Cachan, France
    Biochem Soc Trans 36:745-8. 2008
    ..Recent developments in protein footprinting allow for the direct characterization of conformational changes of the proteins in the complex.
  83. pmc Sulfate radical anion as a new reagent for fast photochemical oxidation of proteins
    Brian C Gau
    Department of Chemistry, Washington University in St Louis, St Louis, Missouri 63130, USA
    Anal Chem 82:7821-7. 2010
    ..SO(4)(-•), generated by 248 nm homolysis of low millimolar levels of persulfate, as a radical reactant in protein footprinting. FPOP is a chemical approach to footprinting proteins and protein complexes by "snapshot" reaction with ..
  84. ncbi Millisecond radiolytic modification of peptides by synchrotron X-rays identified by mass spectrometry
    S D Maleknia
    Albert Einstein Center for Synchrotron BioSciences, Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA
    Anal Chem 71:3965-73. 1999
    ..X-ray beams induces stable, covalent modifications of amino acid residues that are useful for synchrotron protein footprinting. A series of 5-14 amino acid residue peptides of varied sequences were selected to study their synchrotron ..
  85. pmc The iron-responsive regulator fur is transcriptionally autoregulated and not essential in Neisseria meningitidis
    Isabel Delany
    Biochemistry and Molecular Biology Unit, IRIS, Chiron s r l, 53100 Siena, Italy
    J Bacteriol 185:6032-41. 2003
    ..The presence of two independently regulated fur promoters may allow meningococcus to fine-tune expression of this regulator controlling iron homeostasis, possibly during infection...
  86. ncbi Mapping interactions of Escherichia coli GreB with RNA polymerase and ternary elongation complexes
    N Loizos
    The Rockefeller University, New York, New York 10021, USA
    J Biol Chem 274:23378-86. 1999
    ..Hydroxyl radical protein footprinting and alanine-scanning mutagenesis were used to investigate the interactions of GreB with RNA polymerase ..
  87. doi Ability of N-acetylcarnosine to protect lens crystallins from oxidation and oxidative damage by radical probe mass spectrometry (RP-MS)
    Ji Won Ha
    School of Molecular Bioscience, University of Sydney, Sydney, Australia
    Rapid Commun Mass Spectrom 24:2900-8. 2010
    The application of Radical Probe Mass Spectrometry based on protein footprinting studies is described to investigate the effectiveness of the antioxidant N-acetylcarnosine (NAC) in preventing oxidative damage to lens crystallins present ..
  88. ncbi In vitro interaction between human immunodeficiency virus type 1 Rev protein and splicing factor ASF/SF2-associated protein, p32
    T O Tange
    Department of Molecular Biology, University of Aarhus, C F Møllers Alle, Building 130, DK 8000 Aarhus C, Denmark
    J Biol Chem 271:10066-72. 1996
    ..b>Protein footprinting data suggest that Rev interacts specifically with amino acids within the 196-208 region of p32...
  89. ncbi Unfolding of apomyoglobin examined by synchrotron footprinting
    M R Chance
    Center for Synchrotron Biosciences, Department of Physiology, Albert Einstein College of Medicine, Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, USA
    Biochem Biophys Res Commun 287:614-21. 2001
    ..Unlike previous cleavage based footprinting methods, synchrotron X-ray protein footprinting is based on a quantitative determination of the extent and the site of radiolytic modification of amino ..
  90. pmc Dynamic modulation of HIV-1 integrase structure and function by cellular lens epithelium-derived growth factor (LEDGF) protein
    Christopher J McKee
    Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA
    J Biol Chem 283:31802-12. 2008
    ..LEDGF strongly stabilized these interactions and promoted IN tetramerization. Mass spectrometric protein footprinting and molecular modeling experiments uncovered novel intra- and inter-protein-protein contacts in the full-..
  91. ncbi Binding site of Escherichia coli RNA polymerase to an RNA promoter
    Martin Pelchat
    Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ont, Canada K1H 8M5
    Biochem Biophys Res Commun 319:636-42. 2004
    ..mechanism of RNA promoter recognition by this RNAP, we have used nucleic acid intercalators and RNA:protein footprinting experiments to study the interaction between the polymerase and an RNA promoter at the initiation site...
  92. ncbi Interaction of the alpha-subunit of Escherichia coli RNA polymerase with DNA: rigid body nature of the protein-DNA contact
    E Heyduk
    Edward A Doisy Department of Biochemistry and Molecular Biology, St Louis University Medical School, St Louis, Missouri 63104, USA
    J Biol Chem 276:44598-603. 2001
    ..b>Protein footprinting with hydroxyradicals showed that the protein did not change its conformation upon protein-DNA contact ..
  93. pmc Structural characterization of HIV gp41 with the membrane-proximal external region
    Wuxian Shi
    Center for Synchrotron Biosciences, Case Western Reserve University, Cleveland, OH 44106, USA
    J Biol Chem 285:24290-8. 2010
    ..Hydroxyl radical-mediated protein footprinting of the antigen in solution reveals specifically protected and accessible regions consistent with the ..
  94. doi A C-terminal hydrophobic, solvent-protected core and a flexible N-terminus are potentially required for human papillomavirus 18 E7 protein functionality
    Shuqing Liu
    Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China
    Biochimie 92:901-8. 2010
    ..Hydroxyl radical mediated protein footprinting coupled to mass spectrometry and other biochemical and biophysical data indicate that near the C-terminus, ..
  95. ncbi Structure of the guanine nucleotide exchange factor Sec7 domain of human arno and analysis of the interaction with ARF GTPase
    E Mossessova
    Memorial Sloan Kettering Cancer Center, Sloan Kettering Division, Graduate School of Medical Sciences, Cornell University, New York, New York 10021, USA
    Cell 92:415-23. 1998
    ..The sites of Sec7 domain interaction on ARF1 have subsequently been mapped, by protein footprinting experiments, to the switch 1 and switch 2 GTPase regions, leading to a model for the interaction between ..
  96. pmc Mapping protein-protein interactions by localized oxidation: consequences of the reach of hydroxyl radical
    Sarah M Cheal
    Department of Chemistry, University of California, Davis, California 95616, USA
    Biochemistry 48:4577-86. 2009
    ..The results provide fundamental information for interpreting protein footprinting experiments in other systems.
  97. ncbi An mRNA loop/bulge in the ferritin iron-responsive element forms in vivo and Was detected by radical probing with Cu-1,10-phenantholine and iron regulatory protein footprinting
    Yaohuang Ke
    Children s Hospital Oakland Research Institute, Oakland, California 94609 1673, USA
    J Biol Chem 277:2373-6. 2002
    ....
  98. pmc Chromatin structure of the EGFR gene suggests a role for intron 1 sequences in its regulation in breast cancer cells
    S A Chrysogelos
    Lombardi Cancer Research Center, Georgetown University, Washington, DC 20007
    Nucleic Acids Res 21:5736-41. 1993
    ....
  99. pmc Higher-order interactions bridge the nitric oxide receptor and catalytic domains of soluble guanylate cyclase
    Eric S Underbakke
    Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 110:6777-82. 2013
    ..We used protein footprinting to map interdomain interaction surfaces of the sGC signaling domains...
  100. doi Protein-RNA footprinting: an evolving tool
    Dominique Fourmy
    Centre de Génétique Moléculaire UPR 3404, CNRS, Universite Paris Sud, Gif sur Yvette, France
    Wiley Interdiscip Rev RNA 3:557-66. 2012
    ..In this article, after a brief historical overview, we summarize recent advances in RNA-protein footprinting methodologies that now integrate tools for massive parallel analysis.
  101. pmc Integrated algorithms for high-throughput examination of covalently labeled biomolecules by structural mass spectrometry
    Parminder Kaur
    Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, Ohio 44106, USA
    Anal Chem 81:8141-9. 2009
    ..The structures of both monomeric and hexameric forms of insulin were investigated by oxidative protein footprinting followed by high-resolution mass spectrometry...

Research Grants70

  1. MECHANISMS OF COOPERATIVE PROTEIN-DNA INTERACTIONS
    Michael Brenowitz; Fiscal Year: 2006
    ..Radiolytic (hydroxyl radical) "protein footprinting" and intrinsic protein fluorescence will be used to map in solution the structures of the nonconserved N-..
  2. Mechanisms of RNA binding and remodeling proteins
    KEVIN RANEY; Fiscal Year: 2009
    ..We will identify the specific sites of protein-protein interactions by using protein footprinting coupled with mass spectrometry...
  3. Mechanisms of RNA binding and remodeling proteins
    KEVIN D contact RANEY; Fiscal Year: 2010
    ..We will identify the specific sites of protein-protein interactions by using protein footprinting coupled with mass spectrometry...
  4. MOLECULAR AND CELLULAR INTERACTIONS OF FACTOR XI
    Peter Walsh; Fiscal Year: 1993
    ..4. To employ protein footprinting techniques to identify and characterize domains within the FXI/XIa molecule that interact with inhibitory ..
  5. REGULATION OF NITROGEN METABOLISM IN BACILLUS SUBTILIS
    Susan Fisher; Fiscal Year: 2006
    ..The TnrA binding site will be defined by protein footprinting. All the available genetic evidence indicates that the feedback-inhibited form of GS also regulates the ..
  6. Cellular Footprinting of Transferrin-Receptor Complex
    MARK CHANCE; Fiscal Year: 2005
    ..In this R21 proposal under PA-02-008, we will establish the feasibility of a cellular protein footprinting assay to provide molecular details of the conformational changes of transferrin when it binds its membrane ..
  7. MECHANISMS OF COOPERATIVE PROTEIN-DNA INTERACTIONS
    Michael Brenowitz; Fiscal Year: 2003
    ..Radiolytic (hydroxyl radical) "protein footprinting" and intrinsic protein fluorescence will be used to map in solution the structures of the nonconserved N-..
  8. Erythropoietin receptor /Janus Kinase 2 complex
    Lily Huang; Fiscal Year: 2006
    ..b>Protein footprinting experiments will identify global interaction surfaces and potential conformational changes in the EpoR/JAK2 ..
  9. Mulitvalent Ligands as Effectors
    LAURA KIESSLING; Fiscal Year: 2007
    ..These include the synthesis and testing of monovalent and multivalent chemoeffectors, protein footprinting experiments, and x-ray crystallography...
  10. Mulitvalent Ligands as Effectors
    LAURA KIESSLING; Fiscal Year: 2009
    ..These include the synthesis and testing of monovalent and multivalent chemoeffectors, protein footprinting experiments, and x-ray crystallography...
  11. Erythropoietin receptor signaling in erythropoiesis
    LILY JUNSHEN HUANG; Fiscal Year: 2010
    ..We will also use a novel "protein footprinting" method based on protease sensitivity to map the global interacting surface between the EpoR and the JAK2 N-..
  12. Erythropoietin receptor signaling in erythropoiesis
    Lily Huang; Fiscal Year: 2009
    ..We will also use a novel "protein footprinting" method based on protease sensitivity to map the global interacting surface between the EpoR and the JAK2 N-..
  13. DYNAMICS OF MACROMOLECULAR INTERACTIONS
    MARK CHANCE; Fiscal Year: 2003
    ..Time-resolved protein footprinting, when perfected, will be applicable to studying macromolecular interactions critical to replication, ..
  14. MECHANISM OF UREASE METALLOCENTER BIOSYNTHESIS
    Robert P Hausinger; Fiscal Year: 2010
    ..D) Identify the specific sites of protein:protein interaction by developing an innovative "protein footprinting" technology that should be widely applicable to other systems...
  15. MECHANISM OF UREASE METALLOCENTER BIOSYNTHESIS
    ROBERT HAUSINGER; Fiscal Year: 2007
    ..D) Identify the specific sites of protein:protein interaction by developing an innovative "protein footprinting" technology that should be widely applicable to other systems...
  16. NUCLEOPROTEIN STRUCTURES AND GENOME DUPLICATION
    Marcin Filutowicz; Fiscal Year: 2002
    ..DNA and protein footprinting, photo-crosslinking and genetic fusion techniques will be employed in these investigations...
  17. QUANTITATIVE STUDIES OF THE BIOTIN REGULATORY SYSTEM
    Dorothy Beckett; Fiscal Year: 2000
    ..in the transcriptional repression complex will be probed using Chemical DNA Footprinting and Chemical Protein Footprinting techniques...
  18. A Protein Footprinting Toolbox
    PEHR HARBURY; Fiscal Year: 2007
    Our goal is to develop a protein footprinting toolbox for measuring at single amino-acid resolution the structures, energetics and conformational changes of large proteins in complex mixtures...
  19. Copper-Induced Amyloidosis Studied by Mass Spectrometry
    RICHARD VACHET; Fiscal Year: 2007
    ..3). Radical-based protein footprinting will be used to study changes in B2m structure during unfolding and oligomerization...
  20. Epac/cAMP-GEF, A Novel Intracellular cAMP Receptor
    Xiaodong Cheng; Fiscal Year: 2007
    ..by cAMP and Epac- Rap1 and Epac-tubulin interactions that are important to Epac functions using chemical protein footprinting and a sensitive MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mapping technique...
  21. Radiolytic Footprinting Methods for Structural Mass Spectrometry
    Mark R Chance; Fiscal Year: 2010
    ..In this proposal we will: increase the sensitivity of protein footprinting methods ~1000 fold;integrate docking approaches with protein footprinting data to probe the structure of ..
  22. MECHANISMS OF COOPERATIVE PROTEIN/DNA INTERACTIONS
    Michael Brenowitz; Fiscal Year: 2001
    ..The protein-protein association reactions linked to the cooperative formation of ternary complexes will be quantitatively analyzed by a new method of protein footprinting.
  23. Characterization of HIV-1 Gag-LysRS Interactions
    Robert Kennedy; Fiscal Year: 2004
    ..be accomplished by employing isothermal titration calorimetry (ITC), fluorescence polarization (FP), and protein footprinting techniques...