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1-27 of 27
Keywords: DNA binding
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Articles
Aflatoxin biosynthesis regulators AflR and AflS: DNA binding affinity, stoichiometry, and kinetics
Available to Purchase
Journal:
Biochemical Journal
Biochem J (2024) 481 (12): 805–821.
Published: 17 June 2024
... biosynthetic enzymes and pathway-specific regulators, notably AflR and AflS. While AflR, a DNA-binding protein, activates gene transcription within the cluster, AflS enhances AF production through mechanisms that are not fully understood. In this study, we developed protocols to purify recombinant AflR...
Includes: Supplementary data
Articles
Polypharmacological repurposing approach identifies approved drugs as potential inhibitors of Mycobacterium tuberculosis
Available to PurchaseJasdeep Singh, Neha Quadir, Shubham Vashishtha, Ankan Chakraborty, Anwar Alam, Bishwajit Kundu, Uzair Ahmad, Durai Sundar, Nasreen Z. Ehtesham, Seyed E. Hasnain
Journal:
Biochemical Journal
Biochem J (2023) 480 (14): 1079–1096.
Published: 17 July 2023
... nm), Rg (∼1.4 nm) (Figure 4a). AAA proteins DNA binding drug discovery and design Mycobacterium tuberculosis Drug resistance in M. tb is developing very rapidly and various strains showing multi- or extremely drug resistance [MDR/XDR] have affected 10 million (range, 8.9–11.0...
Includes: Supplementary data
Articles
Soumyananda Chakraborti, Dhanasekaran Balakrishnan, Alexander J. Trotter, William H. Gittens, Ally W.H. Yang, Arttu Jolma, Joy R. Paterson, Sylwia Świątek, Jacek Plewka, Fiona A. Curtis, Laura Y. Bowers, Lars-Olof Pålsson, Timothy R. Hughes, Michał Taube, Maciej Kozak, Jonathan G. Heddle, Gary J. Sharples
Journal:
Biochemical Journal
Biochem J (2020) 477 (7): 1345–1362.
Published: 17 April 2020
... reinforced the proposed similarity to Fis and supported the identification of residues involved in DNA binding which were demonstrated experimentally. Overexpression of NinH proved toxic and this correlated with its capacity to associate with DNA. NinH is the first example of a phage-encoded Fis-like NAP...
Includes: Supplementary data
Articles
Helicobacter pylori helicase loader protein Hp0897 shows unique functions of N- and C-terminal regions
Available to Purchase
Journal:
Biochemical Journal
Biochem J (2019) 476 (21): 3261–3279.
Published: 11 November 2019
... the DNA binding activity of HpDnaB. Furthermore, overexpression of Hp0897 full-length protein in H. pylori leads to an elongated cell phenotype. While the overexpression of Hp0897CTD does not show a phenotype of cell elongation, overexpression of Hp0897NTD shows extensive cell elongation. These results...
Includes: Supplementary data
Articles
Venkatasubramanian Vidhyasagar, Yujiong He, Manhong Guo, Tanu Talwar, Ravi Shankar Singh, Manisha Yadav, George Katselis, Franco J. Vizeacoumar, Kiven E. Lukong, Yuliang Wu
Journal:
Biochemical Journal
Biochem J (2018) 475 (1): 45–60.
Published: 02 January 2018
... cellular processes like replication and transcription, where single-stranded DNA (ssDNA) is exposed, making it more vulnerable to damage and enzymatic degradation. Single-stranded DNA-binding proteins (SSBs) protect these structures from nuclease attack, and also recruit appropriate proteins like DNA...
Includes: Supplementary data
Articles
Mycobacterium smegmatis Ku binds DNA without free ends
Available to Purchase
Journal:
Biochemical Journal
Biochem J (2013) 456 (2): 275–282.
Published: 08 November 2013
... extensions that modulate DNA-binding properties. We report in the present paper that the lysine-rich C-terminal extension of M. smegmatis Ku contacts the core protein domain as evidenced by an increase in DNA-binding affinity and a decrease in thermal stability and intrinsic tryptophan fluorescence upon its...
Includes: Supplementary data
Articles
DNA-binding regulates site-specific ubiquitination of IRF-1
Available to Purchase
Journal:
Biochemical Journal
Biochem J (2013) 449 (3): 707–717.
Published: 09 January 2013
... cognate) 70-interacting protein] and MDM2 (murine double minute 2), which dock to the Mf2 domain, was specific for lysine residues found predominantly in loop structures that extend from the DNA-binding domain, whereas no modification was detected in the more conformationally flexible C-terminal half...
Includes: Supplementary data
Articles
The crystal structure of the Sox4 HMG domain–DNA complex suggests a mechanism for positional interdependence in DNA recognition
Available to Purchase
Journal:
Biochemical Journal
Biochem J (2012) 443 (1): 39–47.
Published: 14 March 2012
...Ralf Jauch; Calista K. L. Ng; Kamesh Narasimhan; Prasanna R. Kolatkar It has recently been proposed that the sequence preferences of DNA-binding TFs (transcription factors) can be well described by models that include the positional interdependence of the nucleotides of the target sites...
Articles
Solution structure of the Pdp1 PWWP domain reveals its unique binding sites for methylated H4K20 and DNA
Available to PurchaseYu Qiu, Wen Zhang, Chen Zhao, Yan Wang, Weiwei Wang, Jiahai Zhang, Zhiyong Zhang, Guohong Li, Yunyu Shi, Xiaoming Tu, Jihui Wu
Journal:
Biochemical Journal
Biochem J (2012) 442 (3): 527–538.
Published: 24 February 2012
... role of the PWWP domain in chromatin regulation or modification. Several structures of the PWWP domain have been solved in recent years. Some of them were reported as DNA-binding folds, such as PWWP domains in Dnmt3b (DNA methyltransferase 3b) [ 22 ] and HDGF [ 23 ], whereas others were identified...
Includes: Supplementary data
Articles
Mutants of the tumour suppressor p53 L1 loop as second-site suppressors for restoring DNA binding to oncogenic p53 mutations: structural and biochemical insights
Available to PurchaseAssia Merabet, Hellen Houlleberghs, Kate Maclagan, Ester Akanho, Tam T. T. Bui, Bruno Pagano, Alex F. Drake, Franca Fraternali, Penka V. Nikolova
Journal:
Biochemical Journal
Biochem J (2010) 427 (2): 225–236.
Published: 29 March 2010
... ‘hot spot’ mutations has been investigated using the double-mutant approach. The effects of these two mutants on the p53 hot spots in terms of thermal stability and DNA binding were evaluated. The results show that: (i) the p53 mutants H115N and S116M are thermally more stable than wild-type p53; (ii...
Includes: Multimedia, Supplementary data
Articles
Characterization of the DNA-binding motif of the arsenic-responsive transcription factor Yap8p
Available to PurchaseYulia Ilina, Ewa Sloma, Ewa Maciaszczyk-Dziubinska, Marian Novotny, Michael Thorsen, Robert Wysocki, Markus J. Tamás
Journal:
Biochemical Journal
Biochem J (2008) 415 (3): 467–475.
Published: 15 October 2008
... expression of ACR2 and ACR3 . We conclude that Yap8p and other yeast AP-1 proteins require distinct DNA-binding motifs to induce gene expression and propose that this fact contributed towards a separation of function between AP-1 proteins during evolution. 1 These authors contributed equally...
Includes: Supplementary data
Articles
DNA topology influences p53 sequence-specific DNA binding through structural transitions within the target sites
Available to Purchase
Journal:
Biochemical Journal
Biochem J (2008) 412 (1): 57–63.
Published: 25 April 2008
... phosphoprotein and its biochemical function is closely associated with its ability to bind DNA in a sequence-specific manner and operate as a transcription factor. Using a competition assay, we investigated the effect of DNA topology on the DNA binding of human wild-type p53 protein. We prepared sets...
Articles
The U3 small nucleolar ribonucleoprotein component Imp4p is a telomeric DNA-binding protein
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Journal:
Biochemical Journal
Biochem J (2007) 408 (3): 387–393.
Published: 28 November 2007
... is a novel telomeric DNA-binding protein that, in addition to its role in rRNA processing, might participate in telomere function. To purify His 6 -tagged Imp4p or hImp4, a 2 litre culture of Escherichia coli BL21 (DE3) pLysS cells harbouring the expression plasmids was grown at 37 °C to an attenuance...
Articles
YB-1 represses AP1-dependent gene transactivation and interacts with an AP-1 DNA sequence
Available to Purchase
Journal:
Biochemical Journal
Biochem J (2005) 388 (3): 921–928.
Published: 07 June 2005
... metalloproteinase-12 (metalloelastase). YB-1 transrepression of both the minimal and matrix metalloproteinase-12 promoter reporter constructs is dependent on the AP-1 sequence. To identify new nuclear proteins that bind specifically to the AP-1 DNA-binding site, we devised a DNA-affinity-chromatography-based assay...
Articles
Quantitative analysis of nucleotide modulation of DNA binding by DnaC protein of Escherichia coli
Available to Purchase
Journal:
Biochemical Journal
Biochem J (2004) 379 (3): 553–562.
Published: 01 May 2004
... at oriC , the origin of E. coli DNA replication. In eukaryotes, Cdc6 protein may play a similar role in the DNA helicase loading in the replication fork during replication initiation at the origin. We have analysed the DNA-binding properties of DnaC protein and a quantitative analysis of the nucleotide...
Articles
Redox regulation of DNA binding activity of DREF (DNA replication-related element binding factor) in Drosophila
Available to PurchaseTae-Yeong CHOI, S. Young PARK, Ho-Sung KANG, Jae-Hun CHEONG, Han-Do KIM, Bok Luel LEE, Fumiko HIROSE, Masamitsu YAMAGUCHI, Mi-Ae YOO
Journal:
Biochemical Journal
Biochem J (2004) 378 (3): 833–838.
Published: 15 March 2004
... genes. Both DNA binding and dimer formation activities are associated with residues 16–115 of the N-terminal region. However, the mechanisms by which DREF dimerization and DNA binding are regulated remain unknown. Here, we report that the DNA binding activity of DREF is regulated by a redox mechanism...
Articles
Activation of the DNA-binding ability of latent p53 protein by protein kinase C is abolished by protein kinase CK2
Available to PurchaseŠárka POSPÍŠILOVÁ, Václav BRÁZDA, Kateřina KUCHAŘÍKOVÁ, M. Gloria LUCIANI, Ted R. HUPP, Petr SKLÁDAL, Emil PALEČEK, Bořivoj VOJTĚŠEK
Journal:
Biochemical Journal
Biochem J (2004) 378 (3): 939–947.
Published: 15 March 2004
... in response to different cellular stress signals. The sequence-specific DNA-binding function of p53 protein can be activated by several different stimuli that modulate the C-terminal domain of this protein. The predominant mechanism of activation of p53 sequence-specific DNA binding is phosphorylation...
Articles
Biochemical analysis of the recombinant Fur (ferric uptake regulator) protein from Anabaena PCC 7119: factors affecting its oligomerization state
Available to Purchase
Journal:
Biochemical Journal
Biochem J (2002) 366 (1): 315–322.
Published: 15 August 2002
...José A. HERNÁNDEZ; M. Teresa BES; María F. FILLAT; José L. NEIRA; M. Luisa PELEATO Fur (ferric uptake regulator) protein is a DNA-binding protein which regulates iron-responsive genes. Recombinant Fur from the nitrogen-fixing cyanobacterium Anabaena PCC 7119 has been purified and characterized...
Articles
Structural and functional characterization of the human and mouse fibulin-1 gene promoters: role of Sp1 and Sp3
Available to Purchase
Journal:
Biochemical Journal
Biochem J (2002) 362 (1): 41–50.
Published: 08 February 2002
... membrane cardiovascular DNA binding extracellular matrix transcription Abbreviations used: AP-2, activator protein 2; EMSA, electrophoretic mobility-shift assay. Biochem. J. (2002) 362, 41 50 (Printed in Great Britain) 41 Structural and functional characterization of the human and mouse...
Articles
Nucleotides and heteroduplex DNA preserve the active conformation of Pseudomonas aeruginosa MutS by preventing protein oligomerization
Available to Purchase
Journal:
Biochemical Journal
Biochem J (2002) 361 (1): 87–95.
Published: 17 December 2001
... the protein in an active conformation by preventing protein oligomerization. 1 To whom correspondence should be addressed (e-mail [email protected] ). 30 7 2001 8 10 2001 23 10 2001 The Biochemical Society, London ©2002 2002 DNA binding electron microscopy MutS...
Articles
Targeting of the transcription factor Max during apoptosis: phosphorylation-regulated cleavage by caspase-5 at an unusual glutamic acid residue in position P1
Available to PurchaseAnja KRIPPNER-HEIDENREICH, Robert V. TALANIAN, Renate SEKUL, Regine KRAFT, Hubert THOLE, Holger OTTLEBEN, Bernhard LÜSCHER
Journal:
Biochemical Journal
Biochem J (2001) 358 (3): 705–715.
Published: 10 September 2001
... only with full-length, DNA-binding competent Max protein but not with corresponding peptides, suggesting that structural determinants might be important for this activity. Furthermore, cleavage by caspase-5 is inhibited by the protein kinase CK2-mediated phosphorylation of Max at Ser-11, a previously...
Articles
Activity of hepatocyte nuclear factor 1α and hepatocyte nuclear factor 1β isoforms is differently affected by the inhibition of protein phosphatases 1/2A
Available to Purchase
Journal:
Biochemical Journal
Biochem J (2001) 354 (2): 301–308.
Published: 22 February 2001
... is inhibited in the enterocytic Caco-2 clone TC7 by okadaic acid at a concentration that is known to inhibit protein phosphatases 1/2A and that does not affect cell viability. At the same concentration, phosphorylation of the HNF1α and HNF1β isoforms is greatly enhanced and their DNA-binding capacity...
Articles
Heteroduplex DNA and ATP induced conformational changes of a MutS mismatch repair protein from Thermus aquaticus
Available to Purchase
Journal:
Biochemical Journal
Biochem J (2000) 347 (3): 881–886.
Published: 25 April 2000
... aquaticus ( Taq ) MutS protein in solution. Analytical gel filtration and cross-linking of MutS protein with disuccinimidyl suburate suggest that Taq MutS is a dimer in the presence of ATP. ATP binding and hydrolysis by Taq MutS reduces the heteroduplex-DNA binding by the protein. Using limited proteolysis...
Articles
Cytoplasmic STAT proteins associate prior to activation
Available to PurchaseSerge HAAN, Marcin KORTYLEWSKI, Iris BEHRMANN, Werner MÜLLER-ESTERL, Peter C. HEINRICH, Fred SCHAPER
Journal:
Biochemical Journal
Biochem J (2000) 345 (3): 417–421.
Published: 25 January 2000
... 7 12 1999 The Biochemical Society, London © 2000 2000 DNA binding HepG2 hepatoma cells interleukin-6 A375 melanoma cells nuclear translocation Biochem. J. (2000) 345, 417 421 (Printed in Great Britain) 417 RESEARCH COMMUNICATION Cytoplasmic STAT proteins associate prior...
Articles
Polycitone A, a novel and potent general inhibitor of retroviral reverse transcriptases and cellular DNA polymerases
Available to Purchase
Journal:
Biochemical Journal
Biochem J (1999) 344 (1): 85–92.
Published: 08 November 1999
... as a model for a universal inhibitor of the superfamily of DNA polymerases. 1 To whom correspondence should be addressed (e-mail: [email protected]). 28 5 1999 3 8 1999 31 8 1999 The Biochemical Society, London © 1999 1999 DNA binding polycitrin A reverse...
Articles
Structural defects of a Pax8 mutant that give rise to congenital hypothyroidism
Available to PurchaseGianluca TELL, Lucia PELLIZZARI, Gennaro ESPOSITO, Carlo PUCILLO, Paolo Emidio MACCHIA, Roberto DI LAURO, Giuseppe DAMANTE
Journal:
Biochemical Journal
Biochem J (1999) 341 (1): 89–93.
Published: 24 June 1999
... 2 1999 12 3 1999 20 4 1999 The Biochemical Society, London © 1999 1999 DNA binding human mutation induced fit Pax genes protein structure Biochem. J. (1999) 341, 89 93 (Printed in Great Britain) 89 Structural defects of a Pax8 mutant that give rise to congenital...
Articles
Co-operation between the PAI and RED subdomains of Pax-8 in the interaction with the thyroglobulin promoter
Available to Purchase
Journal:
Biochemical Journal
Biochem J (1999) 337 (2): 253–262.
Published: 08 January 1999
... accounting for a sort of chronology of events during DNA binding. Since the RED subdomain is much more variable than the PAI subdomain among Pax proteins, these results could explain how distinct Pax proteins may select different target genes. The Biochemical Society, London © 1999 1999 Biochem. J...
