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.
- Loizos N. Mapping protein-ligand interactions by hydroxyl-radical protein footprinting. Methods Mol Biol. 2004;261:199-210 pubmedHydroxyl-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...
- Yu S, Mei F, Lee J, Cheng X. Probing cAMP-dependent protein kinase holoenzyme complexes I alpha and II beta by FT-IR and chemical protein footprinting. Biochemistry. 2004;43:1908-20 pubmed..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 ..
- Guan J, Vorobiev S, Almo S, Chance M. Mapping the G-actin binding surface of cofilin using synchrotron protein footprinting. Biochemistry. 2002;41:5765-75 pubmed..Synchrotron protein footprinting is used to identify specific side chain residues on the cofilin surface that are buried in the formation of ..
- Smedley J, Sharp J, Kuhn J, Tomer K. Probing the pH-dependent prepore to pore transition of Bacillus anthracis protective antigen with differential oxidative protein footprinting. Biochemistry. 2008;47:10694-704 pubmed publisher..Oxidative protein footprinting (OPF) can provide dynamic structural information about a protein complex through analysis of amino acid ..
- Watson C, Janik I, Zhuang T, Charvátová O, Woods R, Sharp J. Pulsed electron beam water radiolysis for submicrosecond hydroxyl radical protein footprinting. Anal Chem. 2009;81:2496-505 pubmed publisher..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 ..
- Gau B, Garai K, Frieden C, Gross M. Mass spectrometry-based protein footprinting characterizes the structures of oligomeric apolipoprotein E2, E3, and E4. Biochemistry. 2011;50:8117-26 pubmed publisher..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...
- Xu G, Chance M. Radiolytic modification and reactivity of amino acid residues serving as structural probes for protein footprinting. Anal Chem. 2005;77:4549-55 pubmedHydroxyl 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...
- Guan J, Chance M. Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry. Trends Biochem Sci. 2005;30:583-92 pubmed..Hydroxyl-radical-mediated protein footprinting using mass spectrometry can define macromolecular structure, macromolecular assembly and conformational ..
- Takamoto K, Chance M. Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes. Annu Rev Biophys Biomol Struct. 2006;35:251-76 pubmed..Hydroxyl radical-mediated protein footprinting using mass spectrometry has recently been developed to define structure, assembly, and conformational ..
- Kvaratskhelia M, Miller J, Budihas S, Pannell L, Le Grice S. Identification of specific HIV-1 reverse transcriptase contacts to the viral RNA:tRNA complex by mass spectrometry and a primary amine selective reagent. Proc Natl Acad Sci U S A. 2002;99:15988-93 pubmedWe have devised a high-resolution protein footprinting methodology to dissect HIV-1 reverse transcriptase (RT) contacts to the viral RNA:tRNA complex...
- Goldsmith S, Guan J, Almo S, Chance M. Synchrotron protein footprinting: a technique to investigate protein-protein interactions. J Biomol Struct Dyn. 2001;19:405-18 pubmed..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. ..
- Fowler J, Brown J, Kvaratskhelia M, Suo Z. Probing conformational changes of human DNA polymerase lambda using mass spectrometry-based protein footprinting. J Mol Biol. 2009;390:368-79 pubmed publisher..gene 1 C-terminal domain and a proline-rich domain at its N-terminus, we used a mass spectrometry-based protein footprinting approach...
- Hampel K, Tinsley M. Evidence for preorganization of the glmS ribozyme ligand binding pocket. Biochemistry. 2006;45:7861-71 pubmed..This mode of action is different from that observed for other riboswitches characterized to date, which act by inducing secondary and tertiary structure changes. ..
- Hancock M, Shephard E. Detection of regulatory polymorphisms: high-throughput capillary DNase I footprinting. Methods Mol Biol. 2013;987:269-82 pubmed publisher..The method is applicable to the identification of base changes, e.g., single-nucleotide polymorphisms (SNPs), that eliminate protein binding to DNA. ..
- Damgaard C, Tange T, Kjems J. hnRNP A1 controls HIV-1 mRNA splicing through cooperative binding to intron and exon splicing silencers in the context of a conserved secondary structure. RNA. 2002;8:1401-15 pubmed
- Chaudhuri A, Seetharamalu P, Schwarz P, Hausheer F, Luduena R. The interaction of the B-ring of colchicine with alpha-tubulin: a novel footprinting approach. J Mol Biol. 2000;303:679-92 pubmed..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. ..
- Li X, Li Z, Xie B, Sharp J. Improved identification and relative quantification of sites of peptide and protein oxidation for hydroxyl radical footprinting. J Am Soc Mass Spectrom. 2013;24:1767-76 pubmed publisher..oxidative labeling is used to probe protein structure and protein-ligand interactions in hydroxyl radical protein footprinting (HRPF)...
- Stevenson C, Assaad A, Chandra G, Le T, Greive S, Bibb M, et al. Investigation of DNA sequence recognition by a streptomycete MarR family transcriptional regulator through surface plasmon resonance and X-ray crystallography. Nucleic Acids Res. 2013;41:7009-22 pubmed publisher..8 Å resolution, enabling molecular level rationalization of the SPR data. Taken together, our observations support a DNA recognition mechanism involving both direct and indirect sequence readout...
- Kamal J, Benchaar S, Takamoto K, Reisler E, Chance M. Three-dimensional structure of cofilin bound to monomeric actin derived by structural mass spectrometry data. Proc Natl Acad Sci U S A. 2007;104:7910-5 pubmed..We used radiolytic protein footprinting with mass spectrometry and molecular modeling to provide an atomic model of how cofilin binds to monomeric ..
- Gayle A, Baranger A. Inhibition of the U1A-RNA complex by an aminoacridine derivative. Bioorg Med Chem Lett. 2002;12:2839-42 pubmed..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. ..
- Santori F, Holmberg K, Ostrov D, Gascoigne N, Vukmanovic S. Distinct footprints of TCR engagement with highly homologous ligands. J Immunol. 2004;172:7466-75 pubmed..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. ..
- Gabant G, Augier J, Armengaud J. Assessment of solvent residues accessibility using three Sulfo-NHS-biotin reagents in parallel: application to footprint changes of a methyltransferase upon binding its substrate. J Mass Spectrom. 2008;43:360-70 pubmed..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. ..
- Ruh M, Chrivia J, Cox L, Ruh T. The interaction of the estrogen receptor with mononucleosomes. Mol Cell Endocrinol. 2004;214:71-9 pubmed..These studies will allow us to address the interactions of ER with core histones containing a multiplicity of variants and modifications in nucleosomal structure. ..
- Christensen S, Eickbush T. Footprint of the retrotransposon R2Bm protein on its target site before and after cleavage. J Mol Biol. 2004;336:1035-45 pubmed..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. ..
- Molina M, Cain C, Bargonetti J. In vivo footprinting and DNA affinity chromatography for analysis of p53 DNA binding ability. Methods Mol Biol. 2003;234:151-70 pubmed..The p53 research community needs to expand this analysis to complete the picture of how p53 differentially regulates transcription of target genes in nuclear chromatin. ..
- Viola I, Uberti Manassero N, Ripoll R, Gonzalez D. The Arabidopsis class I TCP transcription factor AtTCP11 is a developmental regulator with distinct DNA-binding properties due to the presence of a threonine residue at position 15 of the TCP domain. Biochem J. 2011;435:143-55 pubmed publisher..The results suggest that changes in DNA-binding preferences may be one of the mechanisms through which class I TCP proteins achieve functional specificity. ..
- Orban T, Gupta S, Palczewski K, Chance M. Visualizing water molecules in transmembrane proteins using radiolytic labeling methods. Biochemistry. 2010;49:827-34 pubmed publisher..In addition, methods of radiolysis, coupled to structural mass spectrometry (protein footprinting), reveal dynamic changes in water structure that mediate transmembrane signaling...
- Zhang W, Zhang T, Wu Y, Jiang J. Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis. Plant Cell. 2012;24:2719-31 pubmed publisher..Thus, genome-wide DH site mapping will be an important tool for systematic identification of all cis-regulatory DNA elements in plants. ..
- Sevilimedu A, Shi H, Lis J. TFIIB aptamers inhibit transcription by perturbing PIC formation at distinct stages. Nucleic Acids Res. 2008;36:3118-27 pubmed publisher..We demonstrate the high affinity and specificity of these reagents, their effect on transcription and preinitiation complex formation and discuss their potential use to address mechanistic questions in vitro as well as in vivo. ..
- Baran R, Bowen B, Price M, Arkin A, Deutschbauer A, Northen T. Metabolic footprinting of mutant libraries to map metabolite utilization to genotype. ACS Chem Biol. 2013;8:189-99 pubmed publisher..This generally applicable, high-throughput workflow has the potential both to discover novel metabolic capabilities of microorganisms and to identify the corresponding genes. ..
- Ian shina D, Malygin A, Karpova G. [Binding of human ribosomal protein S5 with the 18S rRNA fragment 1203-1236/1521-1698]. Mol Biol (Mosk). 2006;40:460-7 pubmed..Besides, we also found nucleotides in the transcript regions corresponding to 16S rRNA regions that do not contact S7 in the 30S subunit. ..
- Akinsiku O, Yu E, Fabris D. Mass spectrometric investigation of protein alkylation by the RNA footprinting probe kethoxal. J Mass Spectrom. 2005;40:1372-81 pubmed
- Ogawa H, Ishiguro K, Gaubatz S, Livingston D, Nakatani Y. A complex with chromatin modifiers that occupies E2F- and Myc-responsive genes in G0 cells. Science. 2002;296:1132-6 pubmed..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. ..
- Belcheva A, Verma V, Korenevsky A, Fridman M, Kumar K, Golemi Kotra D. Roles of DNA sequence and sigma A factor in transcription of the vraSR operon. J Bacteriol. 2012;194:61-71 pubmed publisher..Our study shows that sigma A factor does not bind to the vraSR operon control region in the absence of VraR, suggesting that VraR may interact directly with this factor. ..
- Ranjan A, Sharma S, Banerjee R, Sen U, Sen R. Structural and mechanistic basis of anti-termination of Rho-dependent transcription termination by bacteriophage P4 capsid protein Psu. Nucleic Acids Res. 2013;41:6839-56 pubmed publisher..We show that this configuration of Psu makes the central channel of Rho inaccessible, and it causes a mechanical impediment to its translocase activity. ..
- Sundd P, Gutierrez E, Pospieszalska M, Zhang H, Groisman A, Ley K. Quantitative dynamic footprinting microscopy reveals mechanisms of neutrophil rolling. Nat Methods. 2010;7:821-4 pubmed publisher..Each rolling neutrophil formed three to four long tethers that extended up to 16 ?m behind the rolling cell. ..
- Kiselar J, Janmey P, Almo S, Chance M. Structural analysis of gelsolin using synchrotron protein footprinting. Mol Cell Proteomics. 2003;2:1120-32 pubmedb>Protein footprinting provides detailed structural information on protein structure in solution by directly identifying accessible and hydroxyl radical-reactive side chain residues...
- Chen X, Hoffman M, Bilmes J, Hesselberth J, Noble W. A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data. Bioinformatics. 2010;26:i334-42 pubmed publisher..Supplementary material is available at Bioinformatics online. ..
- Zhu Y, Guo T, Park J, Li X, Meng W, Datta A, et al. Elucidating in vivo structural dynamics in integral membrane protein by hydroxyl radical footprinting. Mol Cell Proteomics. 2009;8:1999-2010 pubmed publisher..Thus, this novel method can be a potentially efficient method to study the structural dynamics of the membrane proteins of a living cell. ..
- Fitzgerald M, West G. Painting proteins with covalent labels: what's in the picture?. J Am Soc Mass Spectrom. 2009;20:1193-206 pubmed publisher..Also discussed are the relative strengths and weaknesses of the different methods for probing the wide range of conformational states that proteins and protein-ligand complexes can adopt when they are in solution. ..
- Abramczyk O, Rainey M, Barnes R, Martin L, Dalby K. Expanding the repertoire of an ERK2 recruitment site: cysteine footprinting identifies the D-recruitment site as a mediator of Ets-1 binding. Biochemistry. 2007;46:9174-86 pubmed..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...
- Jaeger S, Martin F, Rudinger Thirion J, Giege R, Eriani G. Binding of human SLBP on the 3'-UTR of histone precursor H4-12 mRNA induces structural rearrangements that enable U7 snRNA anchoring. Nucleic Acids Res. 2006;34:4987-95 pubmed..These results suggest that initial binding of the SLBP functions in making the HDE more accessible for U7 snRNA anchoring. ..
- Mercenne G, Bernacchi S, Richer D, Bec G, Henriet S, Paillart J, et al. HIV-1 Vif binds to APOBEC3G mRNA and inhibits its translation. Nucleic Acids Res. 2010;38:633-46 pubmed publisher..Results using a Vif protein mutated in the multimerization domain suggested that the molecular mechanism of translational control is more complicated than a simple physical blockage of scanning ribosomes. ..
- Mandell J, BAERGA ORTIZ A, Akashi S, Takio K, Komives E. Solvent accessibility of the thrombin-thrombomodulin interface. J Mol Biol. 2001;306:575-89 pubmed..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. ..
- Charvátová O, Foley B, Bern M, Sharp J, Orlando R, Woods R. Quantifying protein interface footprinting by hydroxyl radical oxidation and molecular dynamics simulation: application to galectin-1. J Am Soc Mass Spectrom. 2008;19:1692-705 pubmed publisher..The precision of this relationship was enhanced through the use of average solvent accessibilities computed from 10 ns molecular dynamics simulations of the protein. ..
- Wei R, Richardson J. Mutational changes of conserved residues in the Q-loop region of transcription factor Rho greatly reduce secondary site RNA-binding. J Mol Biol. 2001;314:1007-15 pubmed
- Cai Y, Huang H. Advances in the study of protein-DNA interaction. Amino Acids. 2012;43:1141-6 pubmed publisher..The classical methods and the novel technologies advanced have been developed for the interaction of protein-DNA. Recent developments of these methods and research achievements have been reviewed in this paper. ..
- Scholle M, Gerdes S. Whole-genome detection of conditionally essential and dispensable genes in Escherichia coli via genetic footprinting. Methods Mol Biol. 2008;416:83-102 pubmed publisher..Gene essentiality conclusions were drawn based on a semiautomatic analysis of the number and relative positions of inserts retained within each gene after selective outgrowth. ..
- Tijerina P, Mohr S, Russell R. DMS footprinting of structured RNAs and RNA-protein complexes. Nat Protoc. 2007;2:2608-23 pubmed..This protocol takes 1.5-3 d to complete, depending on the type of analysis used. ..
- Datta S, Zhao Z, Clark P, Tarasov S, Alexandratos J, Campbell S, et al. Interactions between HIV-1 Gag molecules in solution: an inositol phosphate-mediated switch. J Mol Biol. 2007;365:799-811 pubmed..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. ..