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Comparative footprinting of DNA-binding proteins

B. Contreras-Moreira, J. Collado-Vides
2006 Bioinformatics  
This work is the first to systematically analyze whether comparative models of protein-DNA complexes could be built and be useful for predicting DNA binding sites.  ...  Results: First, we describe the structural and evolutionary conservation of protein-DNA interfaces, and the limits they impose on modelling accuracy.  ...  ABBREVIATIONS PDF, Protein Data Bank; RMSD, root-median-square deviation; SCOP, structural classification of proteins; ID, sequence identity; IID, interface sequence identity; PSSM; position-specific scoring  ... 
doi:10.1093/bioinformatics/btl215 pmid:16873524 fatcat:gobhrkvkbnbmblks2q4rbu37ne

Page 956 of EMBO (European Molecular Biology Organization) Journal Vol. 22, Issue 4 [page]

2003 EMBO (European Molecular Biology Organization) Journal  
We determined whether the El DBD behaves like the full- length El protein by comparing footprints of El and the El DBD in the presence of competitor DNA (Figure 1B).  ...  Interestingly, El] and E2 proteins binding together gave rise to a combined small footprint corresponding to the sum of the individual protections observed with the El DBD and E2 (compare lanes 9 and 10  ... 

E1 initiator DNA binding specificity is unmasked by selective inhibition of non-specific DNA binding

A. Stenlund
2003 EMBO Journal  
Initiator proteins are critical components of the DNA replication machinery and mark the site of initiation.  ...  We propose that this arrangement, where one DNA-binding activity tethers the initiator to ori while another alters DNA structure, is a characteristic of other viral and cellular initiator proteins.  ...  Acknowledgements We thank W.Herr and K.Fien for critical reading of the manuscript. This work was supported by Public Health Service grant CA 13106 from the National Cancer Institute.  ... 
doi:10.1093/emboj/cdg091 pmid:12574131 pmcid:PMC145451 fatcat:hqx4rjl5mvcunkl62tpxhvzk3q

High Resolution Footprinting of a Type I Methyltransferase Reveals a Large Structural Distortion within the DNA Recognition Site

D. R. Mernagh, G. G. Kneale
1996 Nucleic Acids Research  
The DNase I footprint is unusually large: the protein protects the DNA on both strands for at least two complete turns of the helix, indicating that the enzyme completely encloses the DNA in the complex  ...  The hydroxyl radical footprint is unaffected by the presence of the cofactor S-adenosyl methionine, showing that the distorted DNA structure induced by M.EcoR124I is formed during the initial DNA binding  ...  ACKNOWLEDGEMENTS We thank our colleagues Drs Ian Taylor, Iain Manfield and Michelle Webb for their generous advice on aspects of this work, and to Damian Watts for assistance with protein preparation.  ... 
doi:10.1093/nar/24.24.4853 pmid:9016653 pmcid:PMC146333 fatcat:j455eqfb4bhfblclrmnuw2sx6i

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data

Jason Piper, Markus C. Elze, Pierre Cauchy, Peter N. Cockerill, Constanze Bonifer, Sascha Ott
2014 Nucleic Acids Research  
In this study, we describe an imbalance in the DNA strandspecific alignment information of DNase-seq data surrounding protein-DNA interactions that allows accurate prediction of occupied TF binding sites  ...  The expression of eukaryotic genes is regulated by cis-regulatory elements such as promoters and enhancers, which bind sequence-specific DNAbinding proteins.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gku727 pmcid:PMC4176159 fatcat:xri2pkz4qjcqnofgpbyatzokty

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data

Jason Piper, Markus C. Elze, Pierre Cauchy, Peter N. Cockerill, Constanze Bonifer, Sascha Ott
2013 Nucleic Acids Research  
In this study, we describe an imbalance in the DNA strandspecific alignment information of DNase-seq data surrounding protein-DNA interactions that allows accurate prediction of occupied TF binding sites  ...  The expression of eukaryotic genes is regulated by cis-regulatory elements such as promoters and enhancers, which bind sequence-specific DNAbinding proteins.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkt850 pmid:24071585 pmcid:PMC3834841 fatcat:3n5uoz6z5rfgtnhqyr6ha2szku

Drunken-cell footprints: nuclease treatment of ethanol-permeabilized bacteria reveals an initiation-like nucleoprotein complex in stationary phase replication origins

M. Cassler
1999 Nucleic Acids Research  
During the cell cycle, high levels of the initiator DnaA and a bending protein, IHF, bind to oriC at the time of initiation of DNA replication, while binding of Fis, another bending protein, is reduced  ...  In order to probe the structure of nucleoprotein complexes at oriC in more detail, we have developed an in situ footprinting method, termed drunken-cell footprinting, that allows enzymatic DNA modifying  ...  ACKNOWLEDGEMENTS We are extremely indebted to Reid Johnson, Howard Nash and Elliott Crooke for their kind gifts of purified proteins.  ... 
doi:10.1093/nar/27.23.4570 pmid:10556312 pmcid:PMC148744 fatcat:ufwkqrg7irgxfnpimfzinhtz3m

Nucleoprotein complex formation by the enhancer binding protein nifA

X. Wang
1997 Nucleic Acids Research  
Footprints with UV light were made on 5-BrdU-substituted DNA and DNase I and laser UV footprints on conventional DNA templates.  ...  Binding of holoenzyme resulted in a specific increase in 5-BrdU reactivity at -9 within the holoenzyme binding site, likely reflecting DNA distortion.  ...  We thank Henri Buc and Malcolm Buckle for their interest and use of the laser and Ray Dixon for pDB737.  ... 
doi:10.1093/nar/25.17.3478 pmid:9254707 pmcid:PMC146925 fatcat:zyu6iwfsxzecfonsz7fmn5ywhu

Maternal-specific footprints at putative CTCF sites in the H19 imprinting control region give evidence for insulator function

Piroska E. Szabó, Shih-Huey E. Tang, Altan Rentsendorj, Gerd P. Pfeifer, Jeffrey R. Mann
2000 Current Biology  
Here, we report that prominent DNA footprints were found in vivo on the unmethylated maternal ICR at all four 21 bp repeats, demonstrating the presence of protein binding.  ...  Significantly, the maternal-specific footprints were localized to putative binding sites for CTCF, a highly conserved zinc-finger DNA-binding protein with multiple roles in gene regulation including that  ...  Acknowledgements We thank Art Riggs and Mike Reed for valuable discussions, Steven Lloyd for T4 endonuclease V and Tim O'Connor for providing AlkA protein.  ... 
doi:10.1016/s0960-9822(00)00489-9 pmid:10837224 fatcat:pjxhqamtrrhsvnkxl7tsyomgdy

Directional binding of HMG-I(Y) on four-way junction DNA and the molecular basis for competitive binding with HMG-1 and histone H1

D. A. Hill, M. L. Pedulla, R. Reeves
1999 Nucleic Acids Research  
Histone H1, HMG-1 and HMG-I(Y) are mammalian nuclear proteins possessing distinctive DNA-binding domain structures that share the common property of preferentially binding to four-way junction (4H) DNA  ...  Each of these proteins had a unique binding pattern on 4H DNA and yet shared certain common nucleotide contacts on the arms of the 4H DNA molecule near the branch point.  ...  ACKNOWLEDGEMENTS We thank Dr Jeffrey Hayes for his generous gift of the recombinant Xenopus GH1 (also known as NG-H1_) protein, Dr A.R. Srinivasan and Dr Wilma K.  ... 
doi:10.1093/nar/27.10.2135 pmid:10219086 pmcid:PMC148433 fatcat:yols7a5knrbhfgbhpcn72mf74i

3D-footprint: a database for the structural analysis of protein–DNA complexes

Bruno Contreras-Moreira
2009 Nucleic Acids Research  
3D-footprint is a living database, updated and curated on a weekly basis, which provides estimates of binding specificity for all protein-DNA complexes available at the Protein Data Bank.  ...  The web interface allows the user to: (i) browse DNA-binding proteins by keyword; (ii) find proteins that recognize a similar DNA motif and (iii) BLAST similar DNA-binding proteins, highlighting interface  ...  3D-footprint.  ... 
doi:10.1093/nar/gkp781 pmid:19767616 pmcid:PMC2808867 fatcat:5pwlfif6izdpdcojkmbf2c4pkm

Two domains within N ( 54) cooperate for DNA binding

W. V. Cannon, M. K. Chaney, X.- Y. Wang, M. Buck
1997 Proceedings of the National Academy of Sciences of the United States of America  
The -N ( N ) subunit of the bacterial RNA polymerase is a sequence specific DNA-binding protein.  ...  We now provide evidence to show that the DNA-binding activity of N involves two distinct domains: a C-terminal DNA-binding domain that directly contacts DNA and an adjacent domain that enhances DNA-binding  ...  Table 1 . 1 Combinations of peptides that gave increased DNA footprints compared to single peptide footprints Sigma peptides DNA-binding Enhancing 329-477 ϩ 70-324 329-477 ϩ 180-306 323-477  ... 
doi:10.1073/pnas.94.10.5006 pmid:9144180 pmcid:PMC24621 fatcat:zetpyvkrxzghjhczluvmczdk7e

Role of the Bombyx mori R2 element N-terminal domain in the target-primed reverse transcription (TPRT) reaction

S. M. Christensen
2005 Nucleic Acids Research  
Mutations in these DNA sites or of the N-terminal protein domain blocked binding and the activity of the downstream subunit.  ...  The role in the retrotransposition reaction of two conserved DNA-binding motifs, a C 2 H 2 zinc finger (ZF) and a Myb motif, located within the N-terminal domain of the protein are explored in this report  ...  This work was supported by the National Institutes of Health grant GM42790 to T.H.E.  ... 
doi:10.1093/nar/gki957 pmid:16284201 pmcid:PMC1283540 fatcat:ah3qyxc2l5hezegxziwlhdg2y4

Two forms of transcription factor TFIIIC in extracts from HeLa cells

Michael W. Van Dyke, Robert G. Roeder
1987 Nucleic Acids Research  
On the basis of mixing experiments, this difference could not be ascribed to either transcriptional or DNA-binding inhibitors.  ...  , although it was possible to detect sequence-specific binding to the VAI RNA gene promoter by DNase I footprinting only with TFIIIC (NE).  ...  I footprinting with fractions containing an excess of nonspecific DNA binding proteins.  ... 
doi:10.1093/nar/15.13.5031 pmid:3601665 pmcid:PMC305945 fatcat:l4becq5tqnf25fieyyc4v6i6b4

DNase Footprint Signatures Are Dictated by Factor Dynamics and DNA Sequence

Myong-Hee Sung, Michael J. Guertin, Songjoon Baek, Gordon L. Hager
2014 Molecular Cell  
Moreover, the nuclease cleavage profile within a footprint originates from the DNA sequence in the factor binding site, rather than from the protein occupying specific nucleotides.  ...  A basic premise of footprinting is that sequence-specific TF-DNA interactions are associated with localized resistance to nucleases, leaving observable signatures of cleavage within accessible chromatin  ...  Acknowledgments Extensive use was made of the NIH Biowulf cluster, a GNU/Linux parallel processing system for computational analysis; we acknowledge the NIH Helix Systems Staff for management of this system  ... 
doi:10.1016/j.molcel.2014.08.016 pmid:25242143 pmcid:PMC4272573 fatcat:z555jgoc6nhyxcfdzikvim5w6y
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