Genomes and Genes
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.
Publications142 found, 100 shown here
- Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteinsInna Shcherbakova
Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
Nucleic Acids Res 34:e48. 2006....
- Mass spectrometry-based protein footprinting characterizes the structures of oligomeric apolipoprotein E2, E3, and E4Brian 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...
- A detailed interpretation of OH radical footprints in a TBP-DNA complex reveals the role of dynamics in the mechanism of sequence-specific bindingN 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...
- Mapping the G-actin binding surface of cofilin using synchrotron protein footprintingJing-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 ..
- Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometryJing-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 ..
- DNA and protein footprinting analysis of the modulation of DNA binding by the N-terminal domain of the Saccharomyces cerevisiae TATA binding proteinSayan Gupta
Center for Synchrotron Biosciences, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, New York 11973, USA
Biochemistry 46:9886-98. 2007..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...
- Secondary reactions and strategies to improve quantitative protein footprintingGuozhong 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...
- Mapping protein-ligand interactions by hydroxyl-radical protein footprintingNick Loizos
Department of Protein Chemistry, ImClone Systems Inc, New York, NY, USA
Methods Mol Biol 261:199-210. 2004Hydroxyl-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...
- Pulsed electron beam water radiolysis for submicrosecond hydroxyl radical protein footprintingCaroline 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 ..
- Radiolytic modification and reactivity of amino acid residues serving as structural probes for protein footprintingGuozhong 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. 2005Hydroxyl 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...
- Aliphatic peptidyl hydroperoxides as a source of secondary oxidation in hydroxyl radical protein footprintingJessica Saladino
Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30605, USA
J Am Soc Mass Spectrom 20:1123-6. 2009....
- Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexesKeiji 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 ..
- Identification of specific HIV-1 reverse transcriptase contacts to the viral RNA:tRNA complex by mass spectrometry and a primary amine selective reagentMamuka Kvaratskhelia
HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA
Proc Natl Acad Sci U S A 99:15988-93. 2002We have devised a high-resolution protein footprinting methodology to dissect HIV-1 reverse transcriptase (RT) contacts to the viral RNA:tRNA complex...
- Monitoring regulated protein-protein interactions using split TEVMichael C Wehr
Max Planck Institute of Experimental Medicine, Hermann Rein Str. 3, , Germany
Nat Methods 3:985-93. 2006..In a first biological application, we monitored neuregulin-induced ErbB2/ErbB4 receptor tyrosine kinase heterodimerization...
- Probing conformational changes of human DNA polymerase lambda using mass spectrometry-based protein footprintingJason 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...
- Footprinting protein-DNA complexes using the hydroxyl radicalSwapan 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...
- The Beamline X28C of the Center for Synchrotron Biosciences: a national resource for biomolecular structure and dynamics experiments using synchrotron footprintingSayan 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...
- Footprint of the retrotransposon R2Bm protein on its target site before and after cleavageShawn 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...
- Three-dimensional structure of cofilin bound to monomeric actin derived by structural mass spectrometry dataJ 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 ..
- Position of eukaryotic initiation factor eIF1 on the 40S ribosomal subunit determined by directed hydroxyl radical probingIvan B Lomakin
Department of Microbiology and Immunology, SUNY Downstate Medical Center Brooklyn, New York 11203, USA
Genes Dev 17:2786-97. 2003....
- Expanding the repertoire of an ERK2 recruitment site: cysteine footprinting identifies the D-recruitment site as a mediator of Ets-1 bindingOlga 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...
- Structural reorganization of proteins revealed by radiolysis and mass spectrometry: G-actin solution structure is divalent cation dependentJing-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...
- Synchrotron protein footprinting supports substrate translocation by ClpA via ATP-induced movements of the D2 loopJen Bohon
Center for Proteomics and Center for Synchrotron Biosciences, Case Western Reserve University, Cleveland, OH 44106, USA
Structure 16:1157-65. 2008Synchrotron X-ray protein footprinting is used to study structural changes upon formation of the ClpA hexamer...
- Assessment of solvent residues accessibility using three Sulfo-NHS-biotin reagents in parallel: application to footprint changes of a methyltransferase upon binding its substrateGuillaume 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...
- Ribosomal protein S15 represses its own translation via adaptation of an rRNA-like fold within its mRNAAlexander 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...
- Solution structure and interdomain interactions of the Saccharomyces cerevisiae "TATA binding protein" (TBP) probed by radiolytic protein footprintingHassan 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...
- Recognition of DNA interstrand cross-link of antitumor cisplatin by HMGB1 proteinJana 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...
- Distinct footprints of TCR engagement with highly homologous ligandsFabio 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...
- DNA binding provides a molecular strap activating the adenovirus proteinaseSayan 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 ..
- RNA secondary structure of the feline immunodeficiency virus 5'UTR and Gag coding regionLaurie 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...
- Evidence for preorganization of the glmS ribozyme ligand binding pocketKen 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...
- [Binding of human ribosomal protein S5 with the 18S rRNA fragment 1203-1236/1521-1698]A A Malygin
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...
- Mapping of the hepatitis B virus pre-S1 domain involved in receptor recognitionAzeneth 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....
- The flexible N-terminal domain of ribosomal protein L11 from Escherichia coli is necessary for the activation of stringent factorRose 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...
- Interactions between HIV-1 Gag molecules in solution: an inositol phosphate-mediated switchSiddhartha 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...
- Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNANatalia Ivanova
Department of Cell and Molecular Biology, BMC, Uppsala University Box 596, S 75 124 Uppsala, Sweden
Nucleic Acids Res 33:3529-39. 2005....
- Biochemical implications of a three-dimensional model of monomeric actin bound to magnesium-chelated ATPKeiji 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...
- Ligand-mediated anticodon conformational changes occur during tRNA methylation by a TrmD methyltransferaseJoseph 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...
- Structure and dynamics of the actin filamentJing-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...
- Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogasterCasey M Bergman
Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
Bioinformatics 21:1747-9. 2005..AVAILABILITY: http://www.flyreg.org/ CONTACT: firstname.lastname@example.org...
- Smad affinity can direct distinct readouts of the embryonic extracellular Dpp gradient in DrosophilaStephen 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...
- The HIV-1 Nef protein enhances the affinity of reverse transcriptase for RNA in vitroCecile 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....
- hnRNP A1 controls HIV-1 mRNA splicing through cooperative binding to intron and exon splicing silencers in the context of a conserved secondary structureChristian Kroun Damgaard
Department of Molecular and Structural Biology, University of Aarhus, DK 8000 Aarhus C, Denmark
RNA 8:1401-15. 2002....
- 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 RF2Debbie 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...
- Solvent accessibility of the thrombin-thrombomodulin interfaceJ 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...
- Peptide bis-intercalator binds DNA via threading mode with sequence specific contacts in the major grooveV Guelev
Department of Chemistry and Biochemistry, The University of Texas at Austin, 78722, USA
Chem Biol 8:415-25. 2001....
- Synchrotron protein footprinting: a technique to investigate protein-protein interactionsS 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...
- 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...
- Trans-acting glmS catalytic riboswitch: locked and loadedRebecca 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...
- [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...
- Mutational changes of conserved residues in the Q-loop region of transcription factor Rho greatly reduce secondary site RNA-bindingR R Wei
Departments of Biology, Indiana University, Bloomington, 47405, USA
J Mol Biol 314:1007-15. 2001....
- A complex with chromatin modifiers that occupies E2F- and Myc-responsive genes in G0 cellsHidesato 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...
- Recognition of tRNALeu by Aquifex aeolicus leucyl-tRNA synthetase during the aminoacylation and editing stepsPeng 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....
- The interaction between sigmaS, the stationary phase sigma factor, and the core enzyme of Escherichia coli RNA polymeraseFrederic 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...
- Inhibition of the U1A-RNA complex by an aminoacridine derivativeAlicia 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...
- Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tailK 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...
- Antibody modulation of antigen presentation: positive and negative effects on presentation of the tetanus toxin antigen via the murine B cell isoform of FcgammaRIIAntony 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...
- Checkpoint kinase ATR promotes nucleotide excision repair of UV-induced DNA damage via physical interaction with xeroderma pigmentosum group ASteven 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 ..
- Probing conformational changes in Ape1 during the progression of base excision repairEizadora 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 ..
- DNA vaccination with glutamic acid decarboxylase (GAD) generates a strong humoral immune response in BALB/c, C57BL/6, and in diabetes-prone NOD miceU 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...
- Regions of the Escherichia coli primary sigma factor sigma70 that are involved in interaction with RNA polymerase core enzymeH 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 ..
- Core-sigma interaction: probing the interaction of the bacteriophage T4 gene 55 promoter recognition protein with E.coli RNA polymerase coreJ 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 ..
- Future directions of structural mass spectrometry using hydroxyl radical footprintingJanna G Kiselar
Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
J Mass Spectrom 45:1373-82. 2010Hydroxyl 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...
- A zinc finger homeodomain transcription factor binds specific thyroid hormone response elementsD 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...
- Cold chemical oxidation of proteinsDavid M Hambly
Department of Chemistry, Washington University in St Louis, Missouri 63130, USA
Anal Chem 81:7235-42. 2009Various 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...
- I(kappa)B(gamma) inhibits DNA binding of NF-kappaB p50 homodimers by interacting with residues that contact DNAS 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...
- Visualizing the Ca2+-dependent activation of gelsolin by using synchrotron footprintingJanna 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. 2003Radiolytic protein footprinting with a synchrotron source is used to reveal detailed structural changes that occur in the Ca(2+)-dependent activation of gelsolin...
- Subunit-specific protein footprinting reveals significant structural rearrangements and a role for N-terminal Lys-14 of HIV-1 Integrase during viral DNA bindingZhuojun 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...
- Methylene as a possible universal footprinting reagent that will include hydrophobic surface areas: overview and feasibility: properties of diazirine as a precursorF 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, ..
- RNA-protein interactions of an archaeal homotetrameric splicing endoribonuclease with an exceptional evolutionary historyJ 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 ..
- Molecular mechanism for establishment of signal-dependent regulation in the PhoP/PhoQ systemWei 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...
- Strong nucleic acid binding to the Escherichia coli RNase HI mutant with two arginine residues at the active siteY 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...
- Physical and genetic interactions of yeast Cwc21p, an ortholog of human SRm300/SRRM2, suggest a role at the catalytic center of the spliceosomeRichard 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...
- Analysis of RNA structure and RNA-protein interactions in mammalian cells by use of terminal transferase-dependent PCRHsiu Hua Chen
Beckman Research Institute of the City of Hope, Duarte, California, USA
Methods Mol Biol 488:319-41. 2008....
- Modeling of protein binary complexes using structural mass spectrometry dataJ 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 ..
- Millisecond radiolytic modification of peptides by synchrotron X-rays identified by mass spectrometryS 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 ..
- Targeted protein footprinting: where different transcription factors bind to RNA polymeraseS 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...
- Fast photochemical oxidation of protein footprints faster than protein unfoldingBrian 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...
- Structural changes in the SL5 and SL6 leader sequences of HIV-1 RNA following interactions with the viral mGag proteinAriel 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 ..
- Sulfate radical anion as a new reagent for fast photochemical oxidation of proteinsBrian 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" ..
- Time-resolved footprinting for the study of the structural dynamics of DNA-protein interactionsBianca 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.
- In vitro interaction between human immunodeficiency virus type 1 Rev protein and splicing factor ASF/SF2-associated protein, p32T 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...
- Interaction of the alpha-subunit of Escherichia coli RNA polymerase with DNA: rigid body nature of the protein-DNA contactE 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 ..
- Unfolding of apomyoglobin examined by synchrotron footprintingM 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 ..
- A C-terminal hydrophobic, solvent-protected core and a flexible N-terminus are potentially required for human papillomavirus 18 E7 protein functionalityShuqing 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, ..
- Mapping interactions of Escherichia coli GreB with RNA polymerase and ternary elongation complexesN 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 ..
- Dynamic modulation of HIV-1 integrase structure and function by cellular lens epithelium-derived growth factor (LEDGF) proteinChristopher 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-..
- The iron-responsive regulator fur is transcriptionally autoregulated and not essential in Neisseria meningitidisIsabel 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...
- 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. 2010The 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 ..
- Structural characterization of HIV gp41 with the membrane-proximal external regionWuxian 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 ..
- Binding site of Escherichia coli RNA polymerase to an RNA promoterMartin 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...
- Structure of the guanine nucleotide exchange factor Sec7 domain of human arno and analysis of the interaction with ARF GTPaseE 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 ..
- Mapping protein-protein interactions by localized oxidation: consequences of the reach of hydroxyl radicalSarah 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.
- Protein-RNA footprinting: an evolving toolDominique 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.
- Vinylogous ureas as a novel class of inhibitors of reverse transcriptase-associated ribonuclease H activityMichaela Wendeler
HIV Drug Resistance Program, National Cancer Institute, Frederick, Maryland, USA
ACS Chem Biol 3:635-44. 2008..Mass spectrometric protein footprinting of the NSC727447 binding site indicated that residues Cys280 and Lys281 in helix I of the thumb subdomain ..
- Heat-shock proteins associated with base excision repair enzymes in HeLa cellsF Mendez
Departments of Radiation Oncology and Radiology, Montefiore Medical Center, Albert Einstein College of Medicine, 111 East 210th Street, Bronx, New York 10467, USA
Radiat Res 153:186-95. 2000..The association of HSPs with BER enzymes was confirmed by hydroxyl radical protein-protein footprinting and immunoaffinity tests. The association of HSPs and BER enzymes is a novel finding...
- Interaction of the eIF4G initiation factor with the aphthovirus IRES is essential for internal translation initiation in vivoS López de Quinto
Centro de Biologia Molecular Severo Ochoa, CSIC UAM, Madrid, Spain
RNA 6:1380-92. 2000..The strong correlation found between eIF4G-RNA interaction and IRES activity in transfected cells suggests that eIF4G acts as a linker to recruit the translational machinery in IRES-dependent initiation...
- Search for the autoantibody immunodominant region on thyroid peroxidase: epitopic footprinting with a human monoclonal autoantibody locates a facet on the native antigen containing a highly conformational epitopeJ Guo
Autoimmune Disease Unit, Cedars-Sinai Research Institute, and University of California School of Medicine, Los Angeles, CA 90048, USA
J Immunol 166:1327-33. 2001..This focal residue localizes the facet on the large, highly complex TPO molecule that contains the immunodominant region and provides the basis for rational guided mutagenesis studies to more fully characterize this region...
- Footprinting of protein interactions by tritium labelingGuillaume Mousseau
iBiTecS, CNRS CEA, F 91191 Gif sur Yvette, France
Biochemistry 49:4297-9. 2010..Application of this footprinting method to the complex formed by the histone H3 fragment H3(122-135) and the protein hAsf1A(1-156) afforded data in good agreement with NMR results...
- The interaction of the B-ring of colchicine with alpha-tubulin: a novel footprinting approachA R Chaudhuri
Department of Biochemistry, University of Texas Health Science Center at San Antonio, TX 78229, USA
J Mol Biol 303:679-92. 2000..Our results therefore, support a model whereby colchicine binds at the alpha/beta interface of tubulin with the B-ring on the alpha-subunit and the A and the C-rings on the beta-subunit...
- Characterization of the mouse islet-specific glucose-6-phosphatase catalytic subunit-related protein gene promoter by in situ footprinting: correlation with fusion gene expression in the islet-derived betaTC-3 and hamster insulinoma tumor cell linesL J Bischof
Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, Tennessee 37232-0615, USA
Diabetes 50:502-14. 2001..In addition, binding sites for several trans-acting factors not previously associated with islet gene expression, as well as binding sites for potentially novel proteins, were identified...
- Mechanisms of RNA binding and remodeling proteinsKEVIN RANEY; Fiscal Year: 2009..We will identify the specific sites of protein-protein interactions by using protein footprinting coupled with mass spectrometry...
- Mechanisms of RNA binding and remodeling proteinsKEVIN D contact RANEY; Fiscal Year: 2010..We will identify the specific sites of protein-protein interactions by using protein footprinting coupled with mass spectrometry...
- MOLECULAR AND CELLULAR INTERACTIONS OF FACTOR XIPeter Walsh; Fiscal Year: 1993..4. To employ protein footprinting techniques to identify and characterize domains within the FXI/XIa molecule that interact with inhibitory ..
- REGULATION OF NITROGEN METABOLISM IN BACILLUS SUBTILISSusan 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 ..
- MECHANISMS OF COOPERATIVE PROTEIN-DNA INTERACTIONSMichael 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-..
- Cellular Footprinting of Transferrin-Receptor ComplexMARK 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 ..
- Erythropoietin receptor /Janus Kinase 2 complexLily Huang; Fiscal Year: 2006..b>Protein footprinting experiments will identify global interaction surfaces and potential conformational changes in the EpoR/JAK2 ..
- Mulitvalent Ligands as EffectorsLAURA KIESSLING; Fiscal Year: 2009..These include the synthesis and testing of monovalent and multivalent chemoeffectors, protein footprinting experiments, and x-ray crystallography...
- Mulitvalent Ligands as EffectorsLAURA KIESSLING; Fiscal Year: 2007..These include the synthesis and testing of monovalent and multivalent chemoeffectors, protein footprinting experiments, and x-ray crystallography...
- MECHANISMS OF COOPERATIVE PROTEIN-DNA INTERACTIONSMichael 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-..
- Erythropoietin receptor signaling in erythropoiesisLILY 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-..
- Erythropoietin receptor signaling in erythropoiesisLily 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-..
- DYNAMICS OF MACROMOLECULAR INTERACTIONSMARK CHANCE; Fiscal Year: 2003..Time-resolved protein footprinting, when perfected, will be applicable to studying macromolecular interactions critical to replication, ..
- MECHANISM OF UREASE METALLOCENTER BIOSYNTHESISROBERT 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...
- MECHANISM OF UREASE METALLOCENTER BIOSYNTHESISRobert 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...
- NUCLEOPROTEIN STRUCTURES AND GENOME DUPLICATIONMarcin Filutowicz; Fiscal Year: 2002..DNA and protein footprinting, photo-crosslinking and genetic fusion techniques will be employed in these investigations...
- QUANTITATIVE STUDIES OF THE BIOTIN REGULATORY SYSTEMDorothy Beckett; Fiscal Year: 2000..in the transcriptional repression complex will be probed using Chemical DNA Footprinting and Chemical Protein Footprinting techniques...
- A Protein Footprinting ToolboxPEHR HARBURY; Fiscal Year: 2007Our 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...
- Copper-Induced Amyloidosis Studied by Mass SpectrometryRICHARD VACHET; Fiscal Year: 2007..3). Radical-based protein footprinting will be used to study changes in B2m structure during unfolding and oligomerization...
- Epac/cAMP-GEF, A Novel Intracellular cAMP ReceptorXiaodong 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...
- MECHANISMS OF COOPERATIVE PROTEIN/DNA INTERACTIONSMichael 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.
- Characterization of HIV-1 Gag-LysRS InteractionsRobert Kennedy; Fiscal Year: 2004..be accomplished by employing isothermal titration calorimetry (ITC), fluorescence polarization (FP), and protein footprinting techniques...