Site-Specific Protein-DNA Photo-Cross-Linking: Analysis of Structural Organization of Protein-DNA and Multiprotein-DNA Complexes

2006 ◽  
Vol 2006 (6) ◽  
pp. pdb.prot4588-pdb.prot4588
Author(s):  
N. Naryshkin ◽  
A. Revyakin ◽  
R. H. Ebright
Keyword(s):  
Structural Organization ◽  
Specific Protein ◽  
Cross Linking ◽  
Dna Complexes ◽  
Site Specific

scholarly journals Mapping Precursor-binding Site on TatC Subunit of Twin Arginine-specific Protein Translocase by Site-specific Photo Cross-linking

2012 ◽  
Vol 287 (16) ◽  
pp. 13430-13441 ◽  
Author(s):  
Stefan Zoufaly ◽  
Julia Fröbel ◽  
Patrick Rose ◽  
Tobias Flecken ◽  
Carlo Maurer ◽  
...  
Keyword(s):  
Binding Site ◽  
Specific Protein ◽  
Cross Linking ◽  
Site Specific

scholarly journals Site-specific Protein Cross-Linking with Genetically Incorporated 3,4-Dihydroxy-L-Phenylalanine

ChemBioChem ◽  
2009 ◽  
Vol 10 (8) ◽  
pp. 1302-1304 ◽  
Author(s):  
Aiko Umeda ◽  
Gabrielle Nina Thibodeaux ◽  
Jie Zhu ◽  
YungAh Lee ◽  
Zhiwen Jonathan Zhang
Keyword(s):  
Specific Protein ◽  
Cross Linking ◽  
Site Specific ◽  
Protein Cross Linking

Role of the hydrophobic effect in stability of site-specific protein-DNA complexes

1989 ◽  
Vol 209 (4) ◽  
pp. 801-816 ◽  
Author(s):  
Jeung-Hoi Ha ◽  
Ruth S. Spolar ◽  
M.Thomas Record
Keyword(s):  
Hydrophobic Effect ◽  
Specific Protein ◽  
Dna Complexes ◽  
Site Specific

scholarly journals TFIIIB subunit locations on U6 gene promoter DNA mapped by site-specific protein-DNA photo-cross-linking

FEBS Letters ◽  
2016 ◽  
Vol 590 (10) ◽  
pp. 1488-1497 ◽  
Author(s):  
Jin Joo Kang ◽  
Yoon Soon Kang ◽  
William E. Stumph
Keyword(s):  
Gene Promoter ◽  
Specific Protein ◽  
Cross Linking ◽  
Site Specific ◽  
Promoter Dna ◽  
U6 Gene

scholarly journals The PCNA unloader Elg1 promotes recombination at collapsed replication forks in fission yeast

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Sanjeeta Tamang ◽  
Anastasiya Kishkevich ◽  
Carl A Morrow ◽  
Fekret Osman ◽  
Manisha Jalan ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Replication Fork ◽  
Specific Protein ◽  
Replication Forks ◽  
Dna Complexes ◽  
Site Specific ◽  
Dna Helicases ◽  
Sliding Clamp ◽  
Recombination Proteins ◽  
Stalled Fork

Protein-DNA complexes can impede DNA replication and cause replication fork collapse. Whilst it is known that homologous recombination is deployed in such instances to restart replication, it is unclear how a stalled fork transitions into a collapsed fork at which recombination proteins can load. Previously we established assays in Schizosaccharomyces pombe for studying recombination induced by replication fork collapse at the site-specific protein-DNA barrier RTS1 (Nguyen et al., 2015). Here, we provide evidence that efficient recruitment/retention of two key recombination proteins (Rad51 and Rad52) to RTS1 depends on unloading of the polymerase sliding clamp PCNA from DNA by Elg1. We also show that, in the absence of Elg1, reduced recombination is partially suppressed by deleting fbh1 or, to a lesser extent, srs2, which encode known anti-recombinogenic DNA helicases. These findings suggest that PCNA unloading by Elg1 is necessary to limit Fbh1 and Srs2 activity, and thereby enable recombination to proceed.

scholarly journals Site-specific Protein Cross-Linking with Genetically Incorporated 3,4-Dihydroxy-L-Phenylalanine

ChemBioChem ◽  
2009 ◽  
Vol 10 (9) ◽  
pp. 1426-1426
Author(s):  
Aiko Umeda ◽  
Gabrielle Nina Thibodeaux ◽  
Jie Zhu ◽  
YungAh Lee ◽  
Zhiwen Jonathan Zhang
Keyword(s):  
Specific Protein ◽  
Cross Linking ◽  
Site Specific ◽  
Protein Cross Linking

Large-cluster and combined fluorescent and gold immunoprobes

1996 ◽  
Vol 54 ◽  
pp. 892-893
Author(s):  
Richard D. Powell ◽  
James F. Hainfeld ◽  
Carol M. R. Halsey ◽  
David L. Spector ◽  
Shelley Kaurin ◽  
...  
Keyword(s):  
Metal Cluster ◽  
Sulfonyl Chloride ◽  
Gel Filtration ◽  
Cross Linking ◽  
Site Specific ◽  
Fab Fragments ◽  
Cluster Label ◽  
Covalently Linked ◽  
Texas Red ◽  
Fold Excess

Two new types of covalently linked, site-specific immunoprobes have been prepared using metal cluster labels, and used to stain components of cells. Combined fluorescein and 1.4 nm “Nanogold” labels were prepared by using the fluorescein-conjugated tris (aryl) phosphine ligand and the amino-substituted ligand in the synthesis of the Nanogold cluster. This cluster label was activated by reaction with a 60-fold excess of (sulfo-Succinimidyl-4-N-maleiniido-cyclohexane-l-carboxylate (sulfo-SMCC) at pH 7.5, separated from excess cross-linking reagent by gel filtration, and mixed in ten-fold excess with Goat Fab’ fragments against mouse IgG (obtained by reduction of F(ab’)2 fragments with 50 mM mercaptoethylamine hydrochloride). Labeled Fab’ fragments were isolated by gel filtration HPLC (Superose-12, Pharmacia). A combined Nanogold and Texas Red label was also prepared, using a Nanogold cluster derivatized with both and its protected analog: the cluster was reacted with an eight-fold excess of Texas Red sulfonyl chloride at pH 9.0, separated from excess Texas Red by gel filtration, then deprotected with HC1 in methanol to yield the amino-substituted label.

Biochemical Chgaracterization of Recombinant Baculovirus 373 K/E p53 Protein

2018 ◽  
Vol 9 (03) ◽  
pp. 20204-20223
Author(s):  
Maghsoudi, Hossein ◽  
U Pati
Keyword(s):  
Dna Binding ◽  
P53 Protein ◽  
Expression System ◽  
Gel Filtration ◽  
Recombinant Baculovirus ◽  
Baculovirus Expression System ◽  
Cross Linking ◽  
Mobility Shift ◽  
Dna Complexes ◽  
P53 Antibodies

In this study, we expressed and purified the recombinant baculovirus 373 K/E p53 protein in a baculovirus expression system to characterize this mutant and compare it with wild type p53. Gel- filtration chromatography and chemical cross-linking experiments indicated that purified recombinant baculovirus 373 K/E p53 protein assembles into multimeric forms ranging from tetramers to polymers. Gel-mobility shift assays and protein-DNA cross-linking studies demonstrated that the recombinant protein binds, to a consensus DNA target as a dimer but that additional p53 mutant molecules may then associate with the preformed p53-dimer-DNA complexes to form a larger p53_DNA complexes. These observations suggest that the p53 mutant tetramers and polymers that forms the minimal p53 mutant complex in solution dissociated upon DNA binding to form p53 mutant dimmer DNA complexes. The DNA binding activity of this mutant was then investigated using electrophoretic mobility shift assays as well as supershift assay with anti-p53 antibodies. Binding of the anti-p53 antibody PAb421to the oligomerization promoting domain on p53 stimulated the sequential formation of both the p53_dimer DNA and larger p53-DNA complexes

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