Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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 Community
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INTRODUCTION
1
5
[ "b1", "b11", "b1", "b2", "b3", "b4", "b8", "b5", "b5", "b9", "b6", "b10", "b11" ]
16,914,444
pmid-4818131|pmid-11875038|pmid-4818131|pmid-7517036|pmid-10404975|pmid-12813031|pmid-9657874|pmid-9083691|pmid-9083691|pmid-9772751|pmid-9465029|pmid-9990031|pmid-11875038|pmid-11875038|pmid-8948639|pmid-11168395|pmid-8948639|pmid-3196313
FCCS utilizes separate channels to detect two distinct fluorophores, as well as the cross-correlated signals, in real time (5).
[ "1", "11", "1", "2", "3", "4", "8", "5", "5", "9", "6", "10", "11" ]
127
8,600
1
false
FCCS utilizes separate channels to detect two distinct fluorophores, as well as the cross-correlated signals, in real time.
[ "5" ]
FCCS utilizes separate channels to detect two distinct fluorophores, as well as the cross-correlated signals, in real time.
true
true
true
true
true
1,382
0
INTRODUCTION
1
1
[ "b1", "b11", "b1", "b2", "b3", "b4", "b8", "b5", "b5", "b9", "b6", "b10", "b11" ]
16,914,444
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With FCCS, bound molecules can be detected even if the differences of diffusion are not great.
[ "1", "11", "1", "2", "3", "4", "8", "5", "5", "9", "6", "10", "11" ]
94
8,601
0
false
With FCCS, bound molecules can be detected even if the differences of diffusion are not great.
[]
With FCCS, bound molecules can be detected even if the differences of diffusion are not great.
true
true
true
true
true
1,382
0
INTRODUCTION
1
11
[ "b1", "b11", "b1", "b2", "b3", "b4", "b8", "b5", "b5", "b9", "b6", "b10", "b11" ]
16,914,444
pmid-4818131|pmid-11875038|pmid-4818131|pmid-7517036|pmid-10404975|pmid-12813031|pmid-9657874|pmid-9083691|pmid-9083691|pmid-9772751|pmid-9465029|pmid-9990031|pmid-11875038|pmid-11875038|pmid-8948639|pmid-11168395|pmid-8948639|pmid-3196313
So far, FCCS has been applied to the studies of DNA hybridization (5), PCR (9), enzymatic cleavage of a DNA substrate by EcoRI endonuclease (6,10) and protein–DNA interactions (11).
[ "1", "11", "1", "2", "3", "4", "8", "5", "5", "9", "6", "10", "11" ]
181
8,602
1
false
So far, FCCS has been applied to the studies of DNA hybridization, PCR, enzymatic cleavage of a DNA substrate by EcoRI endonuclease and protein–DNA interactions.
[ "5", "9", "6,10", "11" ]
So far, FCCS has been applied to the studies of DNA hybridization, PCR, enzymatic cleavage of a DNA substrate by EcoRI endonuclease and protein–DNA interactions.
true
true
true
true
true
1,382
1
INTRODUCTION
1
12
[ "b12", "b13", "b14", "b17", "b18", "b19", "b11", "b11", "b11" ]
16,914,444
pmid-8041795|pmid-9653115|pmid-9811841|pmid-16648840|pmid-10580088|pmid-12888530|pmid-11875038|pmid-11875038|pmid-11875038|pmid-2503872|pmid-9252412|pmid-10545100
Fluorescence labeling of proteins is a key step for the FCS and FCCS analysis of protein interactions.
[ "12", "13", "14", "17", "18", "19", "11", "11", "11" ]
102
8,603
0
false
Fluorescence labeling of proteins is a key step for the FCS and FCCS analysis of protein interactions.
[]
Fluorescence labeling of proteins is a key step for the FCS and FCCS analysis of protein interactions.
true
true
true
true
true
1,383
1
INTRODUCTION
1
12
[ "b12", "b13", "b14", "b17", "b18", "b19", "b11", "b11", "b11" ]
16,914,444
pmid-8041795|pmid-9653115|pmid-9811841|pmid-16648840|pmid-10580088|pmid-12888530|pmid-11875038|pmid-11875038|pmid-11875038|pmid-2503872|pmid-9252412|pmid-10545100
So far, chemical modifications (12,13) and recombinant fusion tagging with fluorescent proteins (14–17) have been used for fluorescence labeling of proteins.
[ "12", "13", "14", "17", "18", "19", "11", "11", "11" ]
157
8,604
0
false
So far, chemical modifications and recombinant fusion tagging with fluorescent proteins have been used for fluorescence labeling of proteins.
[ "12,13", "14–17" ]
So far, chemical modifications and recombinant fusion tagging with fluorescent proteins have been used for fluorescence labeling of proteins.
true
true
true
true
true
1,383
1
INTRODUCTION
1
12
[ "b12", "b13", "b14", "b17", "b18", "b19", "b11", "b11", "b11" ]
16,914,444
pmid-8041795|pmid-9653115|pmid-9811841|pmid-16648840|pmid-10580088|pmid-12888530|pmid-11875038|pmid-11875038|pmid-11875038|pmid-2503872|pmid-9252412|pmid-10545100
These methods are often useful, but the modifications of internal amino acid residues or the addition of relatively large fluorescent proteins may affect the functions of labeled proteins.
[ "12", "13", "14", "17", "18", "19", "11", "11", "11" ]
188
8,605
0
false
These methods are often useful, but the modifications of internal amino acid residues or the addition of relatively large fluorescent proteins may affect the functions of labeled proteins.
[]
These methods are often useful, but the modifications of internal amino acid residues or the addition of relatively large fluorescent proteins may affect the functions of labeled proteins.
true
true
true
true
true
1,383
1
INTRODUCTION
1
12
[ "b12", "b13", "b14", "b17", "b18", "b19", "b11", "b11", "b11" ]
16,914,444
pmid-8041795|pmid-9653115|pmid-9811841|pmid-16648840|pmid-10580088|pmid-12888530|pmid-11875038|pmid-11875038|pmid-11875038|pmid-2503872|pmid-9252412|pmid-10545100
As an alternative approach, we have previously developed a puromycin-based method for fluorescence labeling of proteins (18,19).
[ "12", "13", "14", "17", "18", "19", "11", "11", "11" ]
128
8,606
0
false
As an alternative approach, we have previously developed a puromycin-based method for fluorescence labeling of proteins.
[ "18,19" ]
As an alternative approach, we have previously developed a puromycin-based method for fluorescence labeling of proteins.
true
true
true
true
true
1,383
1
INTRODUCTION
1
11
[ "b12", "b13", "b14", "b17", "b18", "b19", "b11", "b11", "b11" ]
16,914,444
pmid-8041795|pmid-9653115|pmid-9811841|pmid-16648840|pmid-10580088|pmid-12888530|pmid-11875038|pmid-11875038|pmid-11875038|pmid-2503872|pmid-9252412|pmid-10545100
By using this method, various fluorophores can be incorporated into full-length proteins in the presence of a low concentration of fluorophore-conjugated puromycin in a cell-free translation system (11).
[ "12", "13", "14", "17", "18", "19", "11", "11", "11" ]
203
8,607
1
false
By using this method, various fluorophores can be incorporated into full-length proteins in the presence of a low concentration of fluorophore-conjugated puromycin in a cell-free translation system.
[ "11" ]
By using this method, various fluorophores can be incorporated into full-length proteins in the presence of a low concentration of fluorophore-conjugated puromycin in a cell-free translation system.
true
true
true
true
true
1,383
1
INTRODUCTION
1
12
[ "b12", "b13", "b14", "b17", "b18", "b19", "b11", "b11", "b11" ]
16,914,444
pmid-8041795|pmid-9653115|pmid-9811841|pmid-16648840|pmid-10580088|pmid-12888530|pmid-11875038|pmid-11875038|pmid-11875038|pmid-2503872|pmid-9252412|pmid-10545100
Small fluorescent probes are expected to be less likely to interfere with the structure or biological function of proteins and cell-free protein synthesis is suitable for a high-throughput format owing to its simplicity.
[ "12", "13", "14", "17", "18", "19", "11", "11", "11" ]
220
8,608
0
false
Small fluorescent probes are expected to be less likely to interfere with the structure or biological function of proteins and cell-free protein synthesis is suitable for a high-throughput format owing to its simplicity.
[]
Small fluorescent probes are expected to be less likely to interfere with the structure or biological function of proteins and cell-free protein synthesis is suitable for a high-throughput format owing to its simplicity.
true
true
true
true
true
1,383
1
INTRODUCTION
1
11
[ "b12", "b13", "b14", "b17", "b18", "b19", "b11", "b11", "b11" ]
16,914,444
pmid-8041795|pmid-9653115|pmid-9811841|pmid-16648840|pmid-10580088|pmid-12888530|pmid-11875038|pmid-11875038|pmid-11875038|pmid-2503872|pmid-9252412|pmid-10545100
We have previously reported the FCCS analysis of protein–DNA interactions between RhG (rhodamine green)-labeled proteins and Cy5-labeled DNA (11).
[ "12", "13", "14", "17", "18", "19", "11", "11", "11" ]
146
8,609
1
false
We have previously reported the FCCS analysis of protein–DNA interactions between RhG (rhodamine green)-labeled proteins and Cy5-labeled DNA.
[ "11" ]
We have previously reported the FCCS analysis of protein–DNA interactions between RhG (rhodamine green)-labeled proteins and Cy5-labeled DNA.
true
true
true
true
true
1,383
1
INTRODUCTION
1
11
[ "b12", "b13", "b14", "b17", "b18", "b19", "b11", "b11", "b11" ]
16,914,444
pmid-8041795|pmid-9653115|pmid-9811841|pmid-16648840|pmid-10580088|pmid-12888530|pmid-11875038|pmid-11875038|pmid-11875038|pmid-2503872|pmid-9252412|pmid-10545100
Although high-throughput analysis of protein–protein interactions in solution using FCCS is of great interest, detection of cross-correlations between differently labeled proteins has been difficult, because the labeling efficiency of our method ranges from only 10 to 30% (11), and the remaining unlabeled proteins in s...
[ "12", "13", "14", "17", "18", "19", "11", "11", "11" ]
407
8,610
1
false
Although high-throughput analysis of protein–protein interactions in solution using FCCS is of great interest, detection of cross-correlations between differently labeled proteins has been difficult, because the labeling efficiency of our method ranges from only 10 to 30%, and the remaining unlabeled proteins in soluti...
[ "11" ]
Although high-throughput analysis of protein–protein interactions in solution using FCCS is of great interest, detection of cross-correlations between differently labeled proteins has been difficult, because the labeling efficiency of our method ranges from only 10 to 30%, and the remaining unlabeled proteins in soluti...
true
true
true
true
true
1,383
1
INTRODUCTION
1
12
[ "b12", "b13", "b14", "b17", "b18", "b19", "b11", "b11", "b11" ]
16,914,444
pmid-8041795|pmid-9653115|pmid-9811841|pmid-16648840|pmid-10580088|pmid-12888530|pmid-11875038|pmid-11875038|pmid-11875038|pmid-2503872|pmid-9252412|pmid-10545100
In this study, we have improved the purification process of fluorescence-labeled proteins by using novel iminobiotin-conjugated fluorescent puromycin derivatives to aid the removal of unlabeled proteins, thereby making protein–protein interaction assay using FCCS practically feasible.
[ "12", "13", "14", "17", "18", "19", "11", "11", "11" ]
285
8,611
0
false
In this study, we have improved the purification process of fluorescence-labeled proteins by using novel iminobiotin-conjugated fluorescent puromycin derivatives to aid the removal of unlabeled proteins, thereby making protein–protein interaction assay using FCCS practically feasible.
[]
In this study, we have improved the purification process of fluorescence-labeled proteins by using novel iminobiotin-conjugated fluorescent puromycin derivatives to aid the removal of unlabeled proteins, thereby making protein–protein interaction assay using FCCS practically feasible.
true
true
true
true
true
1,383
1
INTRODUCTION
1
12
[ "b12", "b13", "b14", "b17", "b18", "b19", "b11", "b11", "b11" ]
16,914,444
pmid-8041795|pmid-9653115|pmid-9811841|pmid-16648840|pmid-10580088|pmid-12888530|pmid-11875038|pmid-11875038|pmid-11875038|pmid-2503872|pmid-9252412|pmid-10545100
We used three model systems, proto-oncogenes c-Fos and c-Jun, archetypes of the family of Ca2+-modulated calmodulin (CaM) and CaM-related binding proteins, and the polycomb group (PcG) complex proteins to confirm the usefulness of our method.
[ "12", "13", "14", "17", "18", "19", "11", "11", "11" ]
242
8,612
0
false
We used three model systems, proto-oncogenes c-Fos and c-Jun, archetypes of the family of Ca2+-modulated calmodulin (CaM) and CaM-related binding proteins, and the polycomb group (PcG) complex proteins to confirm the usefulness of our method.
[]
We used three model systems, proto-oncogenes c-Fos and c-Jun, archetypes of the family of Ca2+-modulated calmodulin (CaM) and CaM-related binding proteins, and the polycomb group (PcG) complex proteins to confirm the usefulness of our method.
true
true
true
true
true
1,383
0
DISCUSSION
1
11
[ "b11", "b25", "b26", "b25", "b27" ]
16,914,444
pmid-4818131|pmid-11875038|pmid-4818131|pmid-7517036|pmid-10404975|pmid-12813031|pmid-9657874|pmid-9083691|pmid-9083691|pmid-9772751|pmid-9465029|pmid-9990031|pmid-11875038|pmid-11875038|pmid-8948639|pmid-11168395|pmid-8948639|pmid-3196313
Purification of fluorescently labeled proteins by using a secondary affinity tag, iminobiotin, introduced on to fluorescent puromycin as described here, improved the sensitivity for FCCS analysis of interactions between two distinct fluorescence-labeled proteins.
[ "11", "25", "26", "25", "27" ]
263
8,613
0
false
Purification of fluorescently labeled proteins by using a secondary affinity tag, iminobiotin, introduced on to fluorescent puromycin as described here, improved the sensitivity for FCCS analysis of interactions between two distinct fluorescence-labeled proteins.
[]
Purification of fluorescently labeled proteins by using a secondary affinity tag, iminobiotin, introduced on to fluorescent puromycin as described here, improved the sensitivity for FCCS analysis of interactions between two distinct fluorescence-labeled proteins.
true
true
true
true
true
1,384
0
DISCUSSION
1
11
[ "b11", "b25", "b26", "b25", "b27" ]
16,914,444
pmid-4818131|pmid-11875038|pmid-4818131|pmid-7517036|pmid-10404975|pmid-12813031|pmid-9657874|pmid-9083691|pmid-9083691|pmid-9772751|pmid-9465029|pmid-9990031|pmid-11875038|pmid-11875038|pmid-8948639|pmid-11168395|pmid-8948639|pmid-3196313
Indeed, the c-JunRhG/c-JunCy5 interactions both with and without non-labeled AP-1 oligonucleotide could be detected in this study, whereas the interaction among c-JunRhG/Cy5-labeled AP-1/non-labeled Jun was not detected in the previous study (11).
[ "11", "25", "26", "25", "27" ]
247
8,614
1
false
Indeed, the c-JunRhG/c-JunCy5 interactions both with and without non-labeled AP-1 oligonucleotide could be detected in this study, whereas the interaction among c-JunRhG/Cy5-labeled AP-1/non-labeled Jun was not detected in the previous study.
[ "11" ]
Indeed, the c-JunRhG/c-JunCy5 interactions both with and without non-labeled AP-1 oligonucleotide could be detected in this study, whereas the interaction among c-JunRhG/Cy5-labeled AP-1/non-labeled Jun was not detected in the previous study.
true
true
true
true
true
1,384
0
DISCUSSION
1
11
[ "b11", "b25", "b26", "b25", "b27" ]
16,914,444
pmid-4818131|pmid-11875038|pmid-4818131|pmid-7517036|pmid-10404975|pmid-12813031|pmid-9657874|pmid-9083691|pmid-9083691|pmid-9772751|pmid-9465029|pmid-9990031|pmid-11875038|pmid-11875038|pmid-8948639|pmid-11168395|pmid-8948639|pmid-3196313
The apparent Kd of c-Fos/c-Jun/AP-1 found in this study was in good agreement with reported values (25,26).
[ "11", "25", "26", "25", "27" ]
107
8,615
0
false
The apparent Kd of c-Fos/c-Jun/AP-1 found in this study was in good agreement with reported values.
[ "25,26" ]
The apparent Kd of c-Fos/c-Jun/AP-1 found in this study was in good agreement with reported values.
true
true
true
true
true
1,384
0
DISCUSSION
1
25
[ "b11", "b25", "b26", "b25", "b27" ]
16,914,444
pmid-4818131|pmid-11875038|pmid-4818131|pmid-7517036|pmid-10404975|pmid-12813031|pmid-9657874|pmid-9083691|pmid-9083691|pmid-9772751|pmid-9465029|pmid-9990031|pmid-11875038|pmid-11875038|pmid-8948639|pmid-11168395|pmid-8948639|pmid-3196313
The Kd of c-Jun homodimer and AP-1 sequence also coincided with the value of 140 nM determined previously (25).
[ "11", "25", "26", "25", "27" ]
111
8,616
1
false
The Kd of c-Jun homodimer and AP-1 sequence also coincided with the value of 140 nM determined previously.
[ "25" ]
The Kd of c-Jun homodimer and AP-1 sequence also coincided with the value of 140 nM determined previously.
true
true
true
true
true
1,384
0
DISCUSSION
1
27
[ "b11", "b25", "b26", "b25", "b27" ]
16,914,444
pmid-4818131|pmid-11875038|pmid-4818131|pmid-7517036|pmid-10404975|pmid-12813031|pmid-9657874|pmid-9083691|pmid-9083691|pmid-9772751|pmid-9465029|pmid-9990031|pmid-11875038|pmid-11875038|pmid-8948639|pmid-11168395|pmid-8948639|pmid-3196313
Further, the Kd of CaM and caldesmon was in agreement with the reported value of 550 nM (27).
[ "11", "25", "26", "25", "27" ]
93
8,617
1
false
Further, the Kd of CaM and caldesmon was in agreement with the reported value of 550 nM.
[ "27" ]
Further, the Kd of CaM and caldesmon was in agreement with the reported value of 550 nM.
true
true
true
true
true
1,384
0
DISCUSSION
1
11
[ "b11", "b25", "b26", "b25", "b27" ]
16,914,444
pmid-4818131|pmid-11875038|pmid-4818131|pmid-7517036|pmid-10404975|pmid-12813031|pmid-9657874|pmid-9083691|pmid-9083691|pmid-9772751|pmid-9465029|pmid-9990031|pmid-11875038|pmid-11875038|pmid-8948639|pmid-11168395|pmid-8948639|pmid-3196313
The apparent Kd was independent of the concentrations of fluorescence-labeled proteins (data not shown).
[ "11", "25", "26", "25", "27" ]
104
8,618
0
false
The apparent Kd was independent of the concentrations of fluorescence-labeled proteins (data not shown).
[]
The apparent Kd was independent of the concentrations of fluorescence-labeled proteins (data not shown).
true
true
true
true
true
1,384
0
DISCUSSION
1
11
[ "b11", "b25", "b26", "b25", "b27" ]
16,914,444
pmid-4818131|pmid-11875038|pmid-4818131|pmid-7517036|pmid-10404975|pmid-12813031|pmid-9657874|pmid-9083691|pmid-9083691|pmid-9772751|pmid-9465029|pmid-9990031|pmid-11875038|pmid-11875038|pmid-8948639|pmid-11168395|pmid-8948639|pmid-3196313
These results indicate that FCCS analysis with puromycin-based labeling of proteins is effective and convenient for protein–protein interaction assay, and that the puromycin derivatives and affinity tags did not interfere substantially with the protein interactions.
[ "11", "25", "26", "25", "27" ]
266
8,619
0
false
These results indicate that FCCS analysis with puromycin-based labeling of proteins is effective and convenient for protein–protein interaction assay, and that the puromycin derivatives and affinity tags did not interfere substantially with the protein interactions.
[]
These results indicate that FCCS analysis with puromycin-based labeling of proteins is effective and convenient for protein–protein interaction assay, and that the puromycin derivatives and affinity tags did not interfere substantially with the protein interactions.
true
true
true
true
true
1,384
0
DISCUSSION
1
11
[ "b11", "b25", "b26", "b25", "b27" ]
16,914,444
pmid-4818131|pmid-11875038|pmid-4818131|pmid-7517036|pmid-10404975|pmid-12813031|pmid-9657874|pmid-9083691|pmid-9083691|pmid-9772751|pmid-9465029|pmid-9990031|pmid-11875038|pmid-11875038|pmid-8948639|pmid-11168395|pmid-8948639|pmid-3196313
It should be noted that the Kd values obtained from FCCS are minimum estimates because small amounts of unlabeled proteins may remain.
[ "11", "25", "26", "25", "27" ]
134
8,620
0
false
It should be noted that the Kd values obtained from FCCS are minimum estimates because small amounts of unlabeled proteins may remain.
[]
It should be noted that the Kd values obtained from FCCS are minimum estimates because small amounts of unlabeled proteins may remain.
true
true
true
true
true
1,384
1
DISCUSSION
1
28
[ "b28", "b29", "b30" ]
16,914,444
pmid-8041795|pmid-9653115|pmid-9811841|pmid-16648840|pmid-10580088|pmid-12888530|pmid-11875038|pmid-11875038|pmid-11875038|pmid-2503872|pmid-9252412|pmid-10545100
The interaction of c-Fos homodimer and CaM/Rab3A mediated by Ca2+ could not be identified in this study.
[ "28", "29", "30" ]
104
8,621
0
false
The interaction of c-Fos homodimer and CaM/Rab3A mediated by Ca2+ could not be identified in this study.
[]
The interaction of c-Fos homodimer and CaM/Rab3A mediated by Ca2+ could not be identified in this study.
true
true
true
true
true
1,385
1
DISCUSSION
1
28
[ "b28", "b29", "b30" ]
16,914,444
pmid-8041795|pmid-9653115|pmid-9811841|pmid-16648840|pmid-10580088|pmid-12888530|pmid-11875038|pmid-11875038|pmid-11875038|pmid-2503872|pmid-9252412|pmid-10545100
The Kd of c-Fos homodimer and AP-1 sequence was previously reported to be ∼6 μM (28).
[ "28", "29", "30" ]
85
8,622
1
false
The Kd of c-Fos homodimer and AP-1 sequence was previously reported to be ∼6 μM.
[ "28" ]
The Kd of c-Fos homodimer and AP-1 sequence was previously reported to be ∼6 μM.
true
true
true
true
true
1,385
1
DISCUSSION
1
28
[ "b28", "b29", "b30" ]
16,914,444
pmid-8041795|pmid-9653115|pmid-9811841|pmid-16648840|pmid-10580088|pmid-12888530|pmid-11875038|pmid-11875038|pmid-11875038|pmid-2503872|pmid-9252412|pmid-10545100
The Kd of CaM/Rab3A was also reported to be 20−50 μM (29,30).
[ "28", "29", "30" ]
61
8,623
0
false
The Kd of CaM/Rab3A was also reported to be 20−50 μM.
[ "29,30" ]
The Kd of CaM/Rab3A was also reported to be 20−50 μM.
true
true
true
true
true
1,385
1
DISCUSSION
1
28
[ "b28", "b29", "b30" ]
16,914,444
pmid-8041795|pmid-9653115|pmid-9811841|pmid-16648840|pmid-10580088|pmid-12888530|pmid-11875038|pmid-11875038|pmid-11875038|pmid-2503872|pmid-9252412|pmid-10545100
The interaction of c-Fos homodimer (and c-Jun homodimer) in this study might include interactions between single-colored proteins, but the molecular brightness was not greater than that of other probed proteins (data not shown).
[ "28", "29", "30" ]
228
8,624
0
false
The interaction of c-Fos homodimer (and c-Jun homodimer) in this study might include interactions between single-colored proteins, but the molecular brightness was not greater than that of other probed proteins (data not shown).
[]
The interaction of c-Fos homodimer (and c-Jun homodimer) in this study might include interactions between single-colored proteins, but the molecular brightness was not greater than that of other probed proteins (data not shown).
true
true
true
true
true
1,385
1
DISCUSSION
1
28
[ "b28", "b29", "b30" ]
16,914,444
pmid-8041795|pmid-9653115|pmid-9811841|pmid-16648840|pmid-10580088|pmid-12888530|pmid-11875038|pmid-11875038|pmid-11875038|pmid-2503872|pmid-9252412|pmid-10545100
Such weak interactions might be detected if the concentrations of fluorescently labeled proteins were increased.
[ "28", "29", "30" ]
112
8,625
0
false
Such weak interactions might be detected if the concentrations of fluorescently labeled proteins were increased.
[]
Such weak interactions might be detected if the concentrations of fluorescently labeled proteins were increased.
true
true
true
true
true
1,385
2
DISCUSSION
1
31
[ "b31", "b32", "b33" ]
16,914,444
pmid-12939158|pmid-7925982|pmid-8703910
A surface plasmon resonance (SPR) biosensor allows real-time analysis of specific interactions on a solid phase, whereas FCS and FCCS detect interactions in solution.
[ "31", "32", "33" ]
166
8,626
0
false
A surface plasmon resonance (SPR) biosensor allows real-time analysis of specific interactions on a solid phase, whereas FCS and FCCS detect interactions in solution.
[]
A surface plasmon resonance (SPR) biosensor allows real-time analysis of specific interactions on a solid phase, whereas FCS and FCCS detect interactions in solution.
true
true
true
true
true
1,386
2
DISCUSSION
1
31
[ "b31", "b32", "b33" ]
16,914,444
pmid-12939158|pmid-7925982|pmid-8703910
Schubert et al.
[ "31", "32", "33" ]
15
8,627
0
false
Schubert et al.
[]
Schubert et al.
true
true
true
true
true
1,386
2
DISCUSSION
1
31
[ "b31", "b32", "b33" ]
16,914,444
pmid-12939158|pmid-7925982|pmid-8703910
(31) compared the entropic contribution to the free energy between SPR and FCS and concluded that the reaction entropy determined from an SPR experiment was lower than that from an FCS experiment.
[ "31", "32", "33" ]
196
8,628
1
false
compared the entropic contribution to the free energy between SPR and FCS and concluded that the reaction entropy determined from an SPR experiment was lower than that from an FCS experiment.
[ "31" ]
compared the entropic contribution to the free energy between SPR and FCS and concluded that the reaction entropy determined from an SPR experiment was lower than that from an FCS experiment.
false
true
true
true
false
1,386
2
DISCUSSION
1
32
[ "b31", "b32", "b33" ]
16,914,444
pmid-12939158|pmid-7925982|pmid-8703910
Indeed, the Kd between CaM and calcineurin was determined as 1.7 × 10−8 M by means of an SPR biosensor (32), and this is 10 times lower than our value using FCCS.
[ "31", "32", "33" ]
162
8,629
1
false
Indeed, the Kd between CaM and calcineurin was determined as 1.7 × 10−8 M by means of an SPR biosensor, and this is 10 times lower than our value using FCCS.
[ "32" ]
Indeed, the Kd between CaM and calcineurin was determined as 1.7 × 10−8 M by means of an SPR biosensor, and this is 10 times lower than our value using FCCS.
true
true
true
true
true
1,386
2
DISCUSSION
1
33
[ "b31", "b32", "b33" ]
16,914,444
pmid-12939158|pmid-7925982|pmid-8703910
Similarly, interaction assay of c-Fos/c-Jun heterodimer immobilized on a polystyrene tray gave a Kd of 1 nM (33), whereas our FCCS analysis gave 70 nM.
[ "31", "32", "33" ]
151
8,630
1
false
Similarly, interaction assay of c-Fos/c-Jun heterodimer immobilized on a polystyrene tray gave a Kd of 1 nM, whereas our FCCS analysis gave 70 nM.
[ "33" ]
Similarly, interaction assay of c-Fos/c-Jun heterodimer immobilized on a polystyrene tray gave a Kd of 1 nM, whereas our FCCS analysis gave 70 nM.
true
true
true
true
true
1,386
2
DISCUSSION
1
31
[ "b31", "b32", "b33" ]
16,914,444
pmid-12939158|pmid-7925982|pmid-8703910
Although the immobilizing method may be advantageous for the detection of protein interactions with low affinity, we believe that Kd values in living cells are likely to be more similar to those determined using FCCS in solution than to those determined on a solid phase.
[ "31", "32", "33" ]
271
8,631
0
false
Although the immobilizing method may be advantageous for the detection of protein interactions with low affinity, we believe that Kd values in living cells are likely to be more similar to those determined using FCCS in solution than to those determined on a solid phase.
[]
Although the immobilizing method may be advantageous for the detection of protein interactions with low affinity, we believe that Kd values in living cells are likely to be more similar to those determined using FCCS in solution than to those determined on a solid phase.
true
true
true
true
true
1,386
3
DISCUSSION
1
34
[ "b34", "b35", "b36", "b37", "b38", "b39" ]
16,914,444
pmid-15337121|pmid-9571155|pmid-9009205|pmid-12167701|pmid-10369680|pmid-14585976
The PcG proteins form multimeric complexes that bind to specific genomic sites of polycomb repressive elements (34).
[ "34", "35", "36", "37", "38", "39" ]
116
8,632
1
false
The PcG proteins form multimeric complexes that bind to specific genomic sites of polycomb repressive elements.
[ "34" ]
The PcG proteins form multimeric complexes that bind to specific genomic sites of polycomb repressive elements.
true
true
true
true
true
1,387
3
DISCUSSION
1
34
[ "b34", "b35", "b36", "b37", "b38", "b39" ]
16,914,444
pmid-15337121|pmid-9571155|pmid-9009205|pmid-12167701|pmid-10369680|pmid-14585976
We applied FCCS to analyze in detail the individual associations of some PcG proteins by interaction assay of the pairs under homogeneous conditions.
[ "34", "35", "36", "37", "38", "39" ]
149
8,633
0
false
We applied FCCS to analyze in detail the individual associations of some PcG proteins by interaction assay of the pairs under homogeneous conditions.
[]
We applied FCCS to analyze in detail the individual associations of some PcG proteins by interaction assay of the pairs under homogeneous conditions.
true
true
true
true
true
1,387
3
DISCUSSION
1
34
[ "b34", "b35", "b36", "b37", "b38", "b39" ]
16,914,444
pmid-15337121|pmid-9571155|pmid-9009205|pmid-12167701|pmid-10369680|pmid-14585976
As shown in Table 1, significant interactions were found among M33/Bmi1, M33/Ring1A, M33/RYBP and Ring1A/RYBP, respectively, as previously confirmed by the yeast two-hybrid method and protein pulldown assay (35,36).
[ "34", "35", "36", "37", "38", "39" ]
215
8,634
0
false
As shown in Table 1, significant interactions were found among M33/Bmi1, M33/Ring1A, M33/RYBP and Ring1A/RYBP, respectively, as previously confirmed by the yeast two-hybrid method and protein pulldown assay.
[ "35,36" ]
As shown in Table 1, significant interactions were found among M33/Bmi1, M33/Ring1A, M33/RYBP and Ring1A/RYBP, respectively, as previously confirmed by the yeast two-hybrid method and protein pulldown assay.
true
true
true
true
true
1,387
3
DISCUSSION
1
34
[ "b34", "b35", "b36", "b37", "b38", "b39" ]
16,914,444
pmid-15337121|pmid-9571155|pmid-9009205|pmid-12167701|pmid-10369680|pmid-14585976
It appears that M33 is a mediator in the association of these proteins (Figure 6), but only the association of Bmi1/M33/Ring1A was confirmed (Figure 5F).
[ "34", "35", "36", "37", "38", "39" ]
153
8,635
0
false
It appears that M33 is a mediator in the association of these proteins (Figure 6), but only the association of Bmi1/M33/Ring1A was confirmed (Figure 5F).
[]
It appears that M33 is a mediator in the association of these proteins (Figure 6), but only the association of Bmi1/M33/Ring1A was confirmed (Figure 5F).
true
true
true
true
true
1,387
3
DISCUSSION
1
34
[ "b34", "b35", "b36", "b37", "b38", "b39" ]
16,914,444
pmid-15337121|pmid-9571155|pmid-9009205|pmid-12167701|pmid-10369680|pmid-14585976
The association of Bmi1/M33/Ring1A was also supported by applying a three-component model to fit the autocorrelation function of Bmi1 after the addition of non-labeled M33 (data not shown).
[ "34", "35", "36", "37", "38", "39" ]
189
8,636
0
false
The association of Bmi1/M33/Ring1A was also supported by applying a three-component model to fit the autocorrelation function of Bmi1 after the addition of non-labeled M33 (data not shown).
[]
The association of Bmi1/M33/Ring1A was also supported by applying a three-component model to fit the autocorrelation function of Bmi1 after the addition of non-labeled M33 (data not shown).
true
true
true
true
true
1,387
3
DISCUSSION
1
37
[ "b34", "b35", "b36", "b37", "b38", "b39" ]
16,914,444
pmid-15337121|pmid-9571155|pmid-9009205|pmid-12167701|pmid-10369680|pmid-14585976
Bmi1, M33 and Ring1A are components of a stable core PcG repressive complex, according to a biochemical study (37).
[ "34", "35", "36", "37", "38", "39" ]
115
8,637
1
false
Bmi1, M33 and Ring1A are components of a stable core PcG repressive complex, according to a biochemical study.
[ "37" ]
Bmi1, M33 and Ring1A are components of a stable core PcG repressive complex, according to a biochemical study.
true
true
true
true
true
1,387
3
DISCUSSION
1
34
[ "b34", "b35", "b36", "b37", "b38", "b39" ]
16,914,444
pmid-15337121|pmid-9571155|pmid-9009205|pmid-12167701|pmid-10369680|pmid-14585976
Interestingly, our results suggest that RYBP may interact with M33 or Ring1A in the free form without the formation of a core complex.
[ "34", "35", "36", "37", "38", "39" ]
134
8,638
0
false
Interestingly, our results suggest that RYBP may interact with M33 or Ring1A in the free form without the formation of a core complex.
[]
Interestingly, our results suggest that RYBP may interact with M33 or Ring1A in the free form without the formation of a core complex.
true
true
true
true
true
1,387
3
DISCUSSION
1
38
[ "b34", "b35", "b36", "b37", "b38", "b39" ]
16,914,444
pmid-15337121|pmid-9571155|pmid-9009205|pmid-12167701|pmid-10369680|pmid-14585976
This is consistent with the idea that RYBP plays a role in recruiting PcG components (38).
[ "34", "35", "36", "37", "38", "39" ]
90
8,639
1
false
This is consistent with the idea that RYBP plays a role in recruiting PcG components.
[ "38" ]
This is consistent with the idea that RYBP plays a role in recruiting PcG components.
true
true
true
true
true
1,387
3
DISCUSSION
1
34
[ "b34", "b35", "b36", "b37", "b38", "b39" ]
16,914,444
pmid-15337121|pmid-9571155|pmid-9009205|pmid-12167701|pmid-10369680|pmid-14585976
The FCCS analysis of the components of PcG complex proteins presented here should be a good model for detailed analysis of other protein complexes.
[ "34", "35", "36", "37", "38", "39" ]
147
8,640
0
false
The FCCS analysis of the components of PcG complex proteins presented here should be a good model for detailed analysis of other protein complexes.
[]
The FCCS analysis of the components of PcG complex proteins presented here should be a good model for detailed analysis of other protein complexes.
true
true
true
true
true
1,387
3
DISCUSSION
1
39
[ "b34", "b35", "b36", "b37", "b38", "b39" ]
16,914,444
pmid-15337121|pmid-9571155|pmid-9009205|pmid-12167701|pmid-10369680|pmid-14585976
For example, use of puromycin-based fluorescently labeled proteins would allow FCCS analysis, as well as FCS analysis, of the dynamics of complex formation of retinoblastoma tumor suppressor complex (39).
[ "34", "35", "36", "37", "38", "39" ]
204
8,641
1
false
For example, use of puromycin-based fluorescently labeled proteins would allow FCCS analysis, as well as FCS analysis, of the dynamics of complex formation of retinoblastoma tumor suppressor complex.
[ "39" ]
For example, use of puromycin-based fluorescently labeled proteins would allow FCCS analysis, as well as FCS analysis, of the dynamics of complex formation of retinoblastoma tumor suppressor complex.
true
true
true
true
true
1,387
3
DISCUSSION
1
34
[ "b34", "b35", "b36", "b37", "b38", "b39" ]
16,914,444
pmid-15337121|pmid-9571155|pmid-9009205|pmid-12167701|pmid-10369680|pmid-14585976
The range of detectable interactions should be improved by using FCCS.
[ "34", "35", "36", "37", "38", "39" ]
70
8,642
0
false
The range of detectable interactions should be improved by using FCCS.
[]
The range of detectable interactions should be improved by using FCCS.
true
true
true
true
true
1,387
4
DISCUSSION
1
40
[ "b40", "b41" ]
16,914,444
pmid-3507693|pmid-10929711
The tandem affinity purification method using a polyhistidine tag and an iminobiotin tag was further applied to over 30 proteins and all but three were sufficiently purified for FCCS analysis.
[ "40", "41" ]
192
8,643
0
false
The tandem affinity purification method using a polyhistidine tag and an iminobiotin tag was further applied to over 30 proteins and all but three were sufficiently purified for FCCS analysis.
[]
The tandem affinity purification method using a polyhistidine tag and an iminobiotin tag was further applied to over 30 proteins and all but three were sufficiently purified for FCCS analysis.
true
true
true
true
true
1,388
4
DISCUSSION
1
40
[ "b40", "b41" ]
16,914,444
pmid-3507693|pmid-10929711
We also observed the interactions between IgG and its binding domain ZZ region (40), and between Smac (second mitochondria-derived activator of caspase or DIABLO) and XIAP (X-linked inhibitor of apoptosis protein, data not shown) (41).
[ "40", "41" ]
235
8,644
1
false
We also observed the interactions between IgG and its binding domain ZZ region, and between Smac (second mitochondria-derived activator of caspase or DIABLO) and XIAP (X-linked inhibitor of apoptosis protein, data not shown).
[ "40", "41" ]
We also observed the interactions between IgG and its binding domain ZZ region, and between Smac (second mitochondria-derived activator of caspase or DIABLO) and XIAP (X-linked inhibitor of apoptosis protein, data not shown).
true
true
true
true
true
1,388
4
DISCUSSION
1
40
[ "b40", "b41" ]
16,914,444
pmid-3507693|pmid-10929711
Combinations of two affinity tags are expected to help high-throughput purification of the fluorescently labeled proteins, because nickel-chelate beads and streptavidin beads for high-throughput robotic systems are already available from several vendors.
[ "40", "41" ]
254
8,645
0
false
Combinations of two affinity tags are expected to help high-throughput purification of the fluorescently labeled proteins, because nickel-chelate beads and streptavidin beads for high-throughput robotic systems are already available from several vendors.
[]
Combinations of two affinity tags are expected to help high-throughput purification of the fluorescently labeled proteins, because nickel-chelate beads and streptavidin beads for high-throughput robotic systems are already available from several vendors.
true
true
true
true
true
1,388
4
DISCUSSION
1
40
[ "b40", "b41" ]
16,914,444
pmid-3507693|pmid-10929711
Thus, the method presented in this paper should be applicable to a large-scale analysis of protein–protein interactions and should also contribute to the elucidation of protein functions in the post-genomic era.
[ "40", "41" ]
211
8,646
0
false
Thus, the method presented in this paper should be applicable to a large-scale analysis of protein–protein interactions and should also contribute to the elucidation of protein functions in the post-genomic era.
[]
Thus, the method presented in this paper should be applicable to a large-scale analysis of protein–protein interactions and should also contribute to the elucidation of protein functions in the post-genomic era.
true
true
true
true
true
1,388
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,329,375
NA|pmid-11839499|pmid-16469698
Helicase proteins are essential components of most of the cellular systems that rely on the manipulation of DNA or RNA, including replication, repair, recombination and transcription.
[ "1", "2" ]
183
8,647
0
false
Helicase proteins are essential components of most of the cellular systems that rely on the manipulation of DNA or RNA, including replication, repair, recombination and transcription.
[]
Helicase proteins are essential components of most of the cellular systems that rely on the manipulation of DNA or RNA, including replication, repair, recombination and transcription.
true
true
true
true
true
1,389
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,329,375
NA|pmid-11839499|pmid-16469698
Classically helicases were identified as enzymes that couple the free energy of hydrolysis of ATP to the unwinding of double-stranded nucleic acids by translocating along a single strand in either 5′ to 3′ or 3′ to 5′ direction.
[ "1", "2" ]
228
8,648
0
false
Classically helicases were identified as enzymes that couple the free energy of hydrolysis of ATP to the unwinding of double-stranded nucleic acids by translocating along a single strand in either 5′ to 3′ or 3′ to 5′ direction.
[]
Classically helicases were identified as enzymes that couple the free energy of hydrolysis of ATP to the unwinding of double-stranded nucleic acids by translocating along a single strand in either 5′ to 3′ or 3′ to 5′ direction.
true
true
true
true
true
1,389
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,329,375
NA|pmid-11839499|pmid-16469698
Such proteins are characterized by a number of conserved amino acid motifs, and three ‘superfamilies’ and two families of helicase proteins have been defined on the basis of sequence and structural homologies (1).
[ "1", "2" ]
213
8,649
1
false
Such proteins are characterized by a number of conserved amino acid motifs, and three ‘superfamilies’ and two families of helicase proteins have been defined on the basis of sequence and structural homologies.
[ "1" ]
Such proteins are characterized by a number of conserved amino acid motifs, and three ‘superfamilies’ and two families of helicase proteins have been defined on the basis of sequence and structural homologies.
true
true
true
true
true
1,389
0
INTRODUCTION
1
2
[ "B1", "B2" ]
17,329,375
NA|pmid-11839499|pmid-16469698
The term ‘helicase’ has broadened in meaning, as many of the helicases identified on the basis of sequence homology turned out to be incapable of separating double-stranded nucleic acids, but instead couple ATP hydrolysis to some other mechanical motion such as movement along double-stranded DNA without strand separati...
[ "1", "2" ]
377
8,650
1
false
The term ‘helicase’ has broadened in meaning, as many of the helicases identified on the basis of sequence homology turned out to be incapable of separating double-stranded nucleic acids, but instead couple ATP hydrolysis to some other mechanical motion such as movement along double-stranded DNA without strand separati...
[ "2" ]
The term ‘helicase’ has broadened in meaning, as many of the helicases identified on the basis of sequence homology turned out to be incapable of separating double-stranded nucleic acids, but instead couple ATP hydrolysis to some other mechanical motion such as movement along double-stranded DNA without strand separati...
true
true
true
true
true
1,389
1
INTRODUCTION
1
3
[ "B3", "B4 B5 B6", "B3", "B7", "B8", "B9", "B10", "B11" ]
17,329,375
pmid-8465200|pmid-10214918|pmid-15474416|pmid-16464015|pmid-8465200|pmid-2250027|pmid-2554145|pmid-3664636|pmid-9535092|pmid-12787667|pmid-16469698
The Mfd protein is a helicase superfamily 2 member that functions as a transcription elongation factor in bacteria.
[ "3", "4–6", "3", "7", "8", "9", "10", "11" ]
115
8,651
0
false
The Mfd protein is a helicase superfamily 2 member that functions as a transcription elongation factor in bacteria.
[]
The Mfd protein is a helicase superfamily 2 member that functions as a transcription elongation factor in bacteria.
true
true
true
true
true
1,390
1
INTRODUCTION
1
3
[ "B3", "B4 B5 B6", "B3", "B7", "B8", "B9", "B10", "B11" ]
17,329,375
pmid-8465200|pmid-10214918|pmid-15474416|pmid-16464015|pmid-8465200|pmid-2250027|pmid-2554145|pmid-3664636|pmid-9535092|pmid-12787667|pmid-16469698
It was first characterized on the basis of its role in transcription-coupled DNA repair (3).
[ "3", "4–6", "3", "7", "8", "9", "10", "11" ]
92
8,652
1
false
It was first characterized on the basis of its role in transcription-coupled DNA repair.
[ "3" ]
It was first characterized on the basis of its role in transcription-coupled DNA repair.
true
true
true
true
true
1,390
1
INTRODUCTION
1
4–6
[ "B3", "B4 B5 B6", "B3", "B7", "B8", "B9", "B10", "B11" ]
17,329,375
pmid-8465200|pmid-10214918|pmid-15474416|pmid-16464015|pmid-8465200|pmid-2250027|pmid-2554145|pmid-3664636|pmid-9535092|pmid-12787667|pmid-16469698
Bulky DNA lesions such as the photoproducts induced by UV irradiation cannot be transcribed by prokaryotic RNA polymerase (RNAP), and so cause transcription elongation complexes to stall (4–6).
[ "3", "4–6", "3", "7", "8", "9", "10", "11" ]
193
8,653
1
false
Bulky DNA lesions such as the photoproducts induced by UV irradiation cannot be transcribed by prokaryotic RNA polymerase (RNAP), and so cause transcription elongation complexes to stall.
[ "4–6" ]
Bulky DNA lesions such as the photoproducts induced by UV irradiation cannot be transcribed by prokaryotic RNA polymerase (RNAP), and so cause transcription elongation complexes to stall.
true
true
true
true
true
1,390
1
INTRODUCTION
1
3
[ "B3", "B4 B5 B6", "B3", "B7", "B8", "B9", "B10", "B11" ]
17,329,375
pmid-8465200|pmid-10214918|pmid-15474416|pmid-16464015|pmid-8465200|pmid-2250027|pmid-2554145|pmid-3664636|pmid-9535092|pmid-12787667|pmid-16469698
The stalled transcription complex shields the lesion from detection by DNA repair complexes, but Mfd (the transcription-repair coupling factor, also referred to as TRCF) removes RNAP from the DNA and recruits nucleotide excision repair proteins to the site of damage (3,7).
[ "3", "4–6", "3", "7", "8", "9", "10", "11" ]
273
8,654
0
false
The stalled transcription complex shields the lesion from detection by DNA repair complexes, but Mfd (the transcription-repair coupling factor, also referred to as TRCF) removes RNAP from the DNA and recruits nucleotide excision repair proteins to the site of damage.
[ "3,7" ]
The stalled transcription complex shields the lesion from detection by DNA repair complexes, but Mfd (the transcription-repair coupling factor, also referred to as TRCF) removes RNAP from the DNA and recruits nucleotide excision repair proteins to the site of damage.
true
true
true
true
true
1,390
1
INTRODUCTION
1
3
[ "B3", "B4 B5 B6", "B3", "B7", "B8", "B9", "B10", "B11" ]
17,329,375
pmid-8465200|pmid-10214918|pmid-15474416|pmid-16464015|pmid-8465200|pmid-2250027|pmid-2554145|pmid-3664636|pmid-9535092|pmid-12787667|pmid-16469698
As a result of this transcription-coupled DNA repair pathway, bulky or non-coding lesions in the transcribed strand of an active gene are repaired ∼10-fold more rapidly than similar lesions in the non-transcribed strand or in untranscribed regions of the genome (8,9).
[ "3", "4–6", "3", "7", "8", "9", "10", "11" ]
268
8,655
0
false
As a result of this transcription-coupled DNA repair pathway, bulky or non-coding lesions in the transcribed strand of an active gene are repaired ∼10-fold more rapidly than similar lesions in the non-transcribed strand or in untranscribed regions of the genome.
[ "8,9" ]
As a result of this transcription-coupled DNA repair pathway, bulky or non-coding lesions in the transcribed strand of an active gene are repaired ∼10-fold more rapidly than similar lesions in the non-transcribed strand or in untranscribed regions of the genome.
true
true
true
true
true
1,390
1
INTRODUCTION
1
10
[ "B3", "B4 B5 B6", "B3", "B7", "B8", "B9", "B10", "B11" ]
17,329,375
pmid-8465200|pmid-10214918|pmid-15474416|pmid-16464015|pmid-8465200|pmid-2250027|pmid-2554145|pmid-3664636|pmid-9535092|pmid-12787667|pmid-16469698
In addition to its role in DNA repair, Mfd also participates in processes that regulate transcription, including catabolite repression in Bacillus subtilis (10) and transcription termination by the bacteriophage HK022 Nun protein (11).
[ "3", "4–6", "3", "7", "8", "9", "10", "11" ]
235
8,656
1
false
In addition to its role in DNA repair, Mfd also participates in processes that regulate transcription, including catabolite repression in Bacillus subtilis and transcription termination by the bacteriophage HK022 Nun protein.
[ "10", "11" ]
In addition to its role in DNA repair, Mfd also participates in processes that regulate transcription, including catabolite repression in Bacillus subtilis and transcription termination by the bacteriophage HK022 Nun protein.
true
true
true
true
true
1,390
1
INTRODUCTION
1
3
[ "B3", "B4 B5 B6", "B3", "B7", "B8", "B9", "B10", "B11" ]
17,329,375
pmid-8465200|pmid-10214918|pmid-15474416|pmid-16464015|pmid-8465200|pmid-2250027|pmid-2554145|pmid-3664636|pmid-9535092|pmid-12787667|pmid-16469698
In these systems, Mfd displaces transcription complexes that have been stalled by regulatory proteins bound to the DNA template (in the case of catabolite repression) or the nascent RNA (in the case of Nun-mediated termination).
[ "3", "4–6", "3", "7", "8", "9", "10", "11" ]
228
8,657
0
false
In these systems, Mfd displaces transcription complexes that have been stalled by regulatory proteins bound to the DNA template (in the case of catabolite repression) or the nascent RNA (in the case of Nun-mediated termination).
[]
In these systems, Mfd displaces transcription complexes that have been stalled by regulatory proteins bound to the DNA template (in the case of catabolite repression) or the nascent RNA (in the case of Nun-mediated termination).
true
true
true
true
true
1,390
2
INTRODUCTION
1
3
[ "B3", "B12", "B12", "B13", "B14", "B12", "B15", "B16", "B17", "B12", "B12" ]
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
Escherichia coli Mfd is a 130-kDa monomeric protein comprised of eight domains (Figure 1) (3,12).
[ "3", "12", "12", "13", "14", "12", "15", "16", "17", "12", "12" ]
97
8,658
0
false
Escherichia coli Mfd is a 130-kDa monomeric protein comprised of eight domains (Figure 1).
[ "3,12" ]
Escherichia coli Mfd is a 130-kDa monomeric protein comprised of eight domains (Figure 1).
true
true
true
true
true
1,391
2
INTRODUCTION
1
3
[ "B3", "B12", "B12", "B13", "B14", "B12", "B15", "B16", "B17", "B12", "B12" ]
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
The three most N-terminal domains of the protein (1a, 2 and 1b) show a high degree of structural homology with the UvrB protein, which is a central component of the prokaryotic nucleotide excision repair apparatus (12,13).
[ "3", "12", "12", "13", "14", "12", "15", "16", "17", "12", "12" ]
222
8,659
0
false
The three most N-terminal domains of the protein (1a, 2 and 1b) show a high degree of structural homology with the UvrB protein, which is a central component of the prokaryotic nucleotide excision repair apparatus.
[ "12,13" ]
The three most N-terminal domains of the protein (1a, 2 and 1b) show a high degree of structural homology with the UvrB protein, which is a central component of the prokaryotic nucleotide excision repair apparatus.
true
true
true
true
true
1,391
2
INTRODUCTION
1
14
[ "B3", "B12", "B12", "B13", "B14", "B12", "B15", "B16", "B17", "B12", "B12" ]
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
This region of Mfd interacts with UvrA, the ‘molecular matchmaker’ that is responsible for recruiting UvrB to DNA damage during nucleotide excision repair, and this Mfd–UvrA interaction is thought to be responsible for the enhanced rate of repair that is observed during transcription-coupled repair (14).
[ "3", "12", "12", "13", "14", "12", "15", "16", "17", "12", "12" ]
305
8,660
1
false
This region of Mfd interacts with UvrA, the ‘molecular matchmaker’ that is responsible for recruiting UvrB to DNA damage during nucleotide excision repair, and this Mfd–UvrA interaction is thought to be responsible for the enhanced rate of repair that is observed during transcription-coupled repair.
[ "14" ]
This region of Mfd interacts with UvrA, the ‘molecular matchmaker’ that is responsible for recruiting UvrB to DNA damage during nucleotide excision repair, and this Mfd–UvrA interaction is thought to be responsible for the enhanced rate of repair that is observed during transcription-coupled repair.
true
true
true
true
true
1,391
2
INTRODUCTION
1
3
[ "B3", "B12", "B12", "B13", "B14", "B12", "B15", "B16", "B17", "B12", "B12" ]
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
Domain 4 (the RNAP-interaction domain: RID) interacts with the β subunit of RNAP (12,15).
[ "3", "12", "12", "13", "14", "12", "15", "16", "17", "12", "12" ]
89
8,661
0
false
Domain 4 (the RNAP-interaction domain: RID) interacts with the β subunit of RNAP.
[ "12,15" ]
Domain 4 (the RNAP-interaction domain: RID) interacts with the β subunit of RNAP.
true
true
true
true
true
1,391
2
INTRODUCTION
1
3
[ "B3", "B12", "B12", "B13", "B14", "B12", "B15", "B16", "B17", "B12", "B12" ]
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
Domains 5 and 6 contain the seven conserved superfamily 2 helicase motifs responsible for the ATPase activity of the protein.
[ "3", "12", "12", "13", "14", "12", "15", "16", "17", "12", "12" ]
125
8,662
0
false
Domains 5 and 6 contain the seven conserved superfamily 2 helicase motifs responsible for the ATPase activity of the protein.
[]
Domains 5 and 6 contain the seven conserved superfamily 2 helicase motifs responsible for the ATPase activity of the protein.
true
true
true
true
true
1,391
2
INTRODUCTION
1
3
[ "B3", "B12", "B12", "B13", "B14", "B12", "B15", "B16", "B17", "B12", "B12" ]
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
These domains are homologous in both sequence and structure to the DNA translocase domains of RecG, a bacterial motor protein involved in the interplay between DNA replication, recombination and repair.
[ "3", "12", "12", "13", "14", "12", "15", "16", "17", "12", "12" ]
202
8,663
0
false
These domains are homologous in both sequence and structure to the DNA translocase domains of RecG, a bacterial motor protein involved in the interplay between DNA replication, recombination and repair.
[]
These domains are homologous in both sequence and structure to the DNA translocase domains of RecG, a bacterial motor protein involved in the interplay between DNA replication, recombination and repair.
true
true
true
true
true
1,391
2
INTRODUCTION
1
3
[ "B3", "B12", "B12", "B13", "B14", "B12", "B15", "B16", "B17", "B12", "B12" ]
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
In addition to the helicase motifs this region of homology also contains a DNA translocation motif that is unique to RecG and Mfd, termed the TRG motif (for translocation in Rec G) (16,17).
[ "3", "12", "12", "13", "14", "12", "15", "16", "17", "12", "12" ]
189
8,664
0
false
In addition to the helicase motifs this region of homology also contains a DNA translocation motif that is unique to RecG and Mfd, termed the TRG motif (for translocation in Rec G).
[ "16,17" ]
In addition to the helicase motifs this region of homology also contains a DNA translocation motif that is unique to RecG and Mfd, termed the TRG motif (for translocation in Rec G).
true
true
true
true
true
1,391
2
INTRODUCTION
1
3
[ "B3", "B12", "B12", "B13", "B14", "B12", "B15", "B16", "B17", "B12", "B12" ]
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
Mfd domains 3 and 7 are novel folds with no well-established function.
[ "3", "12", "12", "13", "14", "12", "15", "16", "17", "12", "12" ]
70
8,665
0
false
Mfd domains 3 and 7 are novel folds with no well-established function.
[]
Mfd domains 3 and 7 are novel folds with no well-established function.
true
true
true
true
true
1,391
2
INTRODUCTION
1
12
[ "B3", "B12", "B12", "B13", "B14", "B12", "B15", "B16", "B17", "B12", "B12" ]
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
However, it has been proposed that domain 7 may regulate Mfd–UvrA interactions, as in the crystal structure of Mfd it occludes the surface of domain 2 that is thought to interact with UvrA (12).
[ "3", "12", "12", "13", "14", "12", "15", "16", "17", "12", "12" ]
194
8,666
1
false
However, it has been proposed that domain 7 may regulate Mfd–UvrA interactions, as in the crystal structure of Mfd it occludes the surface of domain 2 that is thought to interact with UvrA.
[ "12" ]
However, it has been proposed that domain 7 may regulate Mfd–UvrA interactions, as in the crystal structure of Mfd it occludes the surface of domain 2 that is thought to interact with UvrA.
true
true
true
true
true
1,391
2
INTRODUCTION
1
3
[ "B3", "B12", "B12", "B13", "B14", "B12", "B15", "B16", "B17", "B12", "B12" ]
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
Figure 1.Structure of E. coli Mfd.
[ "3", "12", "12", "13", "14", "12", "15", "16", "17", "12", "12" ]
34
8,667
0
false
Figure 1.Structure of E. coli Mfd.
[]
Figure 1.Structure of E. coli Mfd.
true
true
true
true
true
1,391
2
INTRODUCTION
1
3
[ "B3", "B12", "B12", "B13", "B14", "B12", "B15", "B16", "B17", "B12", "B12" ]
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
The three most N-terminal domains (domains 1A, 2 and 1B: blue) show a high degree of structural homology with UvrB.
[ "3", "12", "12", "13", "14", "12", "15", "16", "17", "12", "12" ]
115
8,668
0
false
The three most N-terminal domains (domains 1A, 2 and 1B: blue) show a high degree of structural homology with UvrB.
[]
The three most N-terminal domains (domains 1A, 2 and 1B: blue) show a high degree of structural homology with UvrB.
true
true
true
true
true
1,391
2
INTRODUCTION
1
3
[ "B3", "B12", "B12", "B13", "B14", "B12", "B15", "B16", "B17", "B12", "B12" ]
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
Domain 4 (magenta) is the RNA polymerase interaction domain (RID), which interacts with a region of the β subunit of RNAP.
[ "3", "12", "12", "13", "14", "12", "15", "16", "17", "12", "12" ]
122
8,669
0
false
Domain 4 (magenta) is the RNA polymerase interaction domain (RID), which interacts with a region of the β subunit of RNAP.
[]
Domain 4 (magenta) is the RNA polymerase interaction domain (RID), which interacts with a region of the β subunit of RNAP.
true
true
true
true
true
1,391
2
INTRODUCTION
1
3
[ "B3", "B12", "B12", "B13", "B14", "B12", "B15", "B16", "B17", "B12", "B12" ]
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
Domains 5 and 6 (yellow and green) contain the seven conserved superfamily 2 helicase motifs (shown in space-fill representation), and are structurally homologous to the DNA translocation domains of RecG.
[ "3", "12", "12", "13", "14", "12", "15", "16", "17", "12", "12" ]
204
8,670
0
false
Domains 5 and 6 (yellow and green) contain the seven conserved superfamily 2 helicase motifs (shown in space-fill representation), and are structurally homologous to the DNA translocation domains of RecG.
[]
Domains 5 and 6 (yellow and green) contain the seven conserved superfamily 2 helicase motifs (shown in space-fill representation), and are structurally homologous to the DNA translocation domains of RecG.
true
true
true
true
true
1,391
2
INTRODUCTION
1
3
[ "B3", "B12", "B12", "B13", "B14", "B12", "B15", "B16", "B17", "B12", "B12" ]
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
Domains 3 (orange) and 7 (red) are novel folds with as yet no clearly defined function.
[ "3", "12", "12", "13", "14", "12", "15", "16", "17", "12", "12" ]
87
8,671
0
false
Domains 3 (orange) and 7 (red) are novel folds with as yet no clearly defined function.
[]
Domains 3 (orange) and 7 (red) are novel folds with as yet no clearly defined function.
true
true
true
true
true
1,391
2
INTRODUCTION
1
3
[ "B3", "B12", "B12", "B13", "B14", "B12", "B15", "B16", "B17", "B12", "B12" ]
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
The location of R953 within the TRG motif is indicated by a black circle, and the point of truncation in MfdΔD7 is indicated by an arrow.
[ "3", "12", "12", "13", "14", "12", "15", "16", "17", "12", "12" ]
137
8,672
0
false
The location of R953 within the TRG motif is indicated by a black circle, and the point of truncation in MfdΔD7 is indicated by an arrow.
[]
The location of R953 within the TRG motif is indicated by a black circle, and the point of truncation in MfdΔD7 is indicated by an arrow.
true
true
true
true
true
1,391
2
INTRODUCTION
1
12
[ "B3", "B12", "B12", "B13", "B14", "B12", "B15", "B16", "B17", "B12", "B12" ]
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
The figure was produced using Pymol software (Delano Scientific) and is based on pdb file 2EYQ (12).
[ "3", "12", "12", "13", "14", "12", "15", "16", "17", "12", "12" ]
100
8,673
1
false
The figure was produced using Pymol software (Delano Scientific) and is based on pdb file 2EYQ.
[ "12" ]
The figure was produced using Pymol software (Delano Scientific) and is based on pdb file 2EYQ.
true
true
true
true
true
1,391
3
INTRODUCTION
1
12
[ "B12" ]
17,329,375
pmid-16469698|pmid-16469698|pmid-12554672|pmid-16469698|pmid-12554672|pmid-16469698
Structure of E. coli Mfd.
[ "12" ]
25
8,674
0
false
Structure of E. coli Mfd.
[]
Structure of E. coli Mfd.
true
true
true
true
true
1,392
3
INTRODUCTION
1
12
[ "B12" ]
17,329,375
pmid-16469698|pmid-16469698|pmid-12554672|pmid-16469698|pmid-12554672|pmid-16469698
The three most N-terminal domains (domains 1A, 2 and 1B: blue) show a high degree of structural homology with UvrB.
[ "12" ]
115
8,675
0
false
The three most N-terminal domains (domains 1A, 2 and 1B: blue) show a high degree of structural homology with UvrB.
[]
The three most N-terminal domains show a high degree of structural homology with UvrB.
true
true
true
true
true
1,392
3
INTRODUCTION
1
12
[ "B12" ]
17,329,375
pmid-16469698|pmid-16469698|pmid-12554672|pmid-16469698|pmid-12554672|pmid-16469698
Domain 4 (magenta) is the RNA polymerase interaction domain (RID), which interacts with a region of the β subunit of RNAP.
[ "12" ]
122
8,676
0
false
Domain 4 (magenta) is the RNA polymerase interaction domain (RID), which interacts with a region of the β subunit of RNAP.
[]
Domain 4 (magenta) is the RNA polymerase interaction domain (RID), which interacts with a region of the β subunit of RNAP.
true
true
true
true
true
1,392
3
INTRODUCTION
1
12
[ "B12" ]
17,329,375
pmid-16469698|pmid-16469698|pmid-12554672|pmid-16469698|pmid-12554672|pmid-16469698
Domains 5 and 6 (yellow and green) contain the seven conserved superfamily 2 helicase motifs (shown in space-fill representation), and are structurally homologous to the DNA translocation domains of RecG.
[ "12" ]
204
8,677
0
false
Domains 5 and 6 (yellow and green) contain the seven conserved superfamily 2 helicase motifs (shown in space-fill representation), and are structurally homologous to the DNA translocation domains of RecG.
[]
Domains 5 and 6 (yellow and green) contain the seven conserved superfamily 2 helicase motifs (shown in space-fill representation), and are structurally homologous to the DNA translocation domains of RecG.
true
true
true
true
true
1,392
3
INTRODUCTION
1
12
[ "B12" ]
17,329,375
pmid-16469698|pmid-16469698|pmid-12554672|pmid-16469698|pmid-12554672|pmid-16469698
Domains 3 (orange) and 7 (red) are novel folds with as yet no clearly defined function.
[ "12" ]
87
8,678
0
false
Domains 3 (orange) and 7 (red) are novel folds with as yet no clearly defined function.
[]
Domains 3 (orange) and 7 (red) are novel folds with as yet no clearly defined function.
true
true
true
true
true
1,392
3
INTRODUCTION
1
12
[ "B12" ]
17,329,375
pmid-16469698|pmid-16469698|pmid-12554672|pmid-16469698|pmid-12554672|pmid-16469698
The location of R953 within the TRG motif is indicated by a black circle, and the point of truncation in MfdΔD7 is indicated by an arrow.
[ "12" ]
137
8,679
0
false
The location of R953 within the TRG motif is indicated by a black circle, and the point of truncation in MfdΔD7 is indicated by an arrow.
[]
The location of R953 within the TRG motif is indicated by a black circle, and the point of truncation in MfdΔD7 is indicated by an arrow.
true
true
true
true
true
1,392
3
INTRODUCTION
1
12
[ "B12" ]
17,329,375
pmid-16469698|pmid-16469698|pmid-12554672|pmid-16469698|pmid-12554672|pmid-16469698
The figure was produced using Pymol software (Delano Scientific) and is based on pdb file 2EYQ (12).
[ "12" ]
100
8,680
1
false
The figure was produced using Pymol software (Delano Scientific) and is based on pdb file 2EYQ.
[ "12" ]
The figure was produced using Pymol software (Delano Scientific) and is based on pdb file 2EYQ.
true
true
true
true
true
1,392
4
INTRODUCTION
1
15
[ "B15", "B18", "B18", "B15", "B19", "B20", "B20", "B15", "B21" ]
17,329,375
pmid-12086674|pmid-16551743|pmid-16551743|pmid-12086674|pmid-15695524|pmid-11595187|pmid-11595187|pmid-12086674|pmid-15687384|pmid-7876261
Mfd dissociates stalled transcription complexes by pushing RNAP forward along the DNA in an ATP-dependent fashion (15,18).
[ "15", "18", "18", "15", "19", "20", "20", "15", "21" ]
122
8,681
0
false
Mfd dissociates stalled transcription complexes by pushing RNAP forward along the DNA in an ATP-dependent fashion.
[ "15,18" ]
Mfd dissociates stalled transcription complexes by pushing RNAP forward along the DNA in an ATP-dependent fashion.
true
true
true
true
true
1,393
4
INTRODUCTION
1
18
[ "B15", "B18", "B18", "B15", "B19", "B20", "B20", "B15", "B21" ]
17,329,375
pmid-12086674|pmid-16551743|pmid-16551743|pmid-12086674|pmid-15695524|pmid-11595187|pmid-11595187|pmid-12086674|pmid-15687384|pmid-7876261
This is thought to destabilize the transcription complex by unwinding the DNA–RNA hybrid and rewinding the single-stranded transcription bubble (18).
[ "15", "18", "18", "15", "19", "20", "20", "15", "21" ]
149
8,682
1
false
This is thought to destabilize the transcription complex by unwinding the DNA–RNA hybrid and rewinding the single-stranded transcription bubble.
[ "18" ]
This is thought to destabilize the transcription complex by unwinding the DNA–RNA hybrid and rewinding the single-stranded transcription bubble.
true
true
true
true
true
1,393
4
INTRODUCTION
1
15
[ "B15", "B18", "B18", "B15", "B19", "B20", "B20", "B15", "B21" ]
17,329,375
pmid-12086674|pmid-16551743|pmid-16551743|pmid-12086674|pmid-15695524|pmid-11595187|pmid-11595187|pmid-12086674|pmid-15687384|pmid-7876261
RNAP displacement requires the interaction of Mfd with the DNA immediately upstream of the stalled RNAP (15), and, by analogy to RecG, Mfd is thought to act as an ATP-dependent double-stranded DNA translocase.
[ "15", "18", "18", "15", "19", "20", "20", "15", "21" ]
209
8,683
1
false
RNAP displacement requires the interaction of Mfd with the DNA immediately upstream of the stalled RNAP, and, by analogy to RecG, Mfd is thought to act as an ATP-dependent double-stranded DNA translocase.
[ "15" ]
RNAP displacement requires the interaction of Mfd with the DNA immediately upstream of the stalled RNAP, and, by analogy to RecG, Mfd is thought to act as an ATP-dependent double-stranded DNA translocase.
true
true
true
true
true
1,393
4
INTRODUCTION
1
15
[ "B15", "B18", "B18", "B15", "B19", "B20", "B20", "B15", "B21" ]
17,329,375
pmid-12086674|pmid-16551743|pmid-16551743|pmid-12086674|pmid-15695524|pmid-11595187|pmid-11595187|pmid-12086674|pmid-15687384|pmid-7876261
RecG consists of two translocase domains attached to a ‘wedge’ domain that binds specifically to branched DNA structures (19,20).
[ "15", "18", "18", "15", "19", "20", "20", "15", "21" ]
129
8,684
0
false
RecG consists of two translocase domains attached to a ‘wedge’ domain that binds specifically to branched DNA structures.
[ "19,20" ]
RecG consists of two translocase domains attached to a ‘wedge’ domain that binds specifically to branched DNA structures.
true
true
true
true
true
1,393
4
INTRODUCTION
1
20
[ "B15", "B18", "B18", "B15", "B19", "B20", "B20", "B15", "B21" ]
17,329,375
pmid-12086674|pmid-16551743|pmid-16551743|pmid-12086674|pmid-15695524|pmid-11595187|pmid-11595187|pmid-12086674|pmid-15687384|pmid-7876261
As the translocase domains hydrolyse ATP they move along double-stranded DNA and pull the DNA across the attached wedge domain, which strips the strands apart (20).
[ "15", "18", "18", "15", "19", "20", "20", "15", "21" ]
164
8,685
1
false
As the translocase domains hydrolyse ATP they move along double-stranded DNA and pull the DNA across the attached wedge domain, which strips the strands apart.
[ "20" ]
As the translocase domains hydrolyse ATP they move along double-stranded DNA and pull the DNA across the attached wedge domain, which strips the strands apart.
true
true
true
true
true
1,393
4
INTRODUCTION
1
15
[ "B15", "B18", "B18", "B15", "B19", "B20", "B20", "B15", "B21" ]
17,329,375
pmid-12086674|pmid-16551743|pmid-16551743|pmid-12086674|pmid-15695524|pmid-11595187|pmid-11595187|pmid-12086674|pmid-15687384|pmid-7876261
Mfd lacks the wedge domain of RecG, but instead binds to the β subunit of RNAP (15,21): once recruited to the stalled transcription complex via the RID–RNAP interaction, it is thought that domains 5 and 6 engage with the upstream DNA and the DNA translocation activity of Mfd pushes RNAP forward.
[ "15", "18", "18", "15", "19", "20", "20", "15", "21" ]
296
8,686
0
false
Mfd lacks the wedge domain of RecG, but instead binds to the β subunit of RNAP : once recruited to the stalled transcription complex via the RID–RNAP interaction, it is thought that domains 5 and 6 engage with the upstream DNA and the DNA translocation activity of Mfd pushes RNAP forward.
[ "15,21" ]
Mfd lacks the wedge domain of RecG, but instead binds to the β subunit of RNAP : once recruited to the stalled transcription complex via the RID–RNAP interaction, it is thought that domains 5 and 6 engage with the upstream DNA and the DNA translocation activity of Mfd pushes RNAP forward.
true
true
true
true
true
1,393
5
INTRODUCTION
1
3
[ "B3" ]
17,329,375
pmid-8465200|pmid-12581657|pmid-15687384|pmid-16551743|pmid-9182561|pmid-9094712|pmid-15695524
Previous studies have shown that Mfd has no detectable strand-separating helicase activity on either double-stranded DNA or on DNA–RNA hybrids (3).
[ "3" ]
147
8,687
1
false
Previous studies have shown that Mfd has no detectable strand-separating helicase activity on either double-stranded DNA or on DNA–RNA hybrids.
[ "3" ]
Previous studies have shown that Mfd has no detectable strand-separating helicase activity on either double-stranded DNA or on DNA–RNA hybrids.
true
true
true
true
true
1,394
5
INTRODUCTION
1
3
[ "B3" ]
17,329,375
pmid-8465200|pmid-12581657|pmid-15687384|pmid-16551743|pmid-9182561|pmid-9094712|pmid-15695524
In this work, we have investigated the motor activity of Mfd using an oligonucleotide displacement assay that is able to detect DNA translocation in the absence of strand separation.
[ "3" ]
182
8,688
0
false
In this work, we have investigated the motor activity of Mfd using an oligonucleotide displacement assay that is able to detect DNA translocation in the absence of strand separation.
[]
In this work, we have investigated the motor activity of Mfd using an oligonucleotide displacement assay that is able to detect DNA translocation in the absence of strand separation.
true
true
true
true
true
1,394
5
INTRODUCTION
1
3
[ "B3" ]
17,329,375
pmid-8465200|pmid-12581657|pmid-15687384|pmid-16551743|pmid-9182561|pmid-9094712|pmid-15695524
We show that a derivative of Mfd that lacks domain 7 (MfdΔD7) is an efficient DNA-based motor that can remove a triplex-forming oligonucleotide (TFO) from double-stranded DNA.
[ "3" ]
175
8,689
0
false
We show that a derivative of Mfd that lacks domain 7 (MfdΔD7) is an efficient DNA-based motor that can remove a triplex-forming oligonucleotide (TFO) from double-stranded DNA.
[]
We show that a derivative of Mfd that lacks domain 7 (MfdΔD7) is an efficient DNA-based motor that can remove a triplex-forming oligonucleotide (TFO) from double-stranded DNA.
true
true
true
true
true
1,394
5
INTRODUCTION
1
3
[ "B3" ]
17,329,375
pmid-8465200|pmid-12581657|pmid-15687384|pmid-16551743|pmid-9182561|pmid-9094712|pmid-15695524
This activity is ATP dependent, and requires the TRG DNA translocation motif of the protein.
[ "3" ]
92
8,690
0
false
This activity is ATP dependent, and requires the TRG DNA translocation motif of the protein.
[]
This activity is ATP dependent, and requires the TRG DNA translocation motif of the protein.
true
true
true
true
true
1,394
5
INTRODUCTION
1
3
[ "B3" ]
17,329,375
pmid-8465200|pmid-12581657|pmid-15687384|pmid-16551743|pmid-9182561|pmid-9094712|pmid-15695524
Full-length Mfd shows little TFO displacement activity in isolation, but displaces a TFO efficiently when able to interact with a stalled transcription elongation complex positioned adjacent to the TFO-binding site.
[ "3" ]
215
8,691
0
false
Full-length Mfd shows little TFO displacement activity in isolation, but displaces a TFO efficiently when able to interact with a stalled transcription elongation complex positioned adjacent to the TFO-binding site.
[]
Full-length Mfd shows little TFO displacement activity in isolation, but displaces a TFO efficiently when able to interact with a stalled transcription elongation complex positioned adjacent to the TFO-binding site.
true
true
true
true
true
1,394
5
INTRODUCTION
1
3
[ "B3" ]
17,329,375
pmid-8465200|pmid-12581657|pmid-15687384|pmid-16551743|pmid-9182561|pmid-9094712|pmid-15695524
Our results indicate that domain 7 of Mfd is a cis-acting regulatory element that inhibits the motor activity of isolated wild-type Mfd, and suggest that interaction of Mfd with stalled transcription elongation complexes removes this inhibitory effect to unmask the motor activity necessary for RNAP displacement.
[ "3" ]
313
8,692
0
false
Our results indicate that domain 7 of Mfd is a cis-acting regulatory element that inhibits the motor activity of isolated wild-type Mfd, and suggest that interaction of Mfd with stalled transcription elongation complexes removes this inhibitory effect to unmask the motor activity necessary for RNAP displacement.
[]
Our results indicate that domain 7 of Mfd is a cis-acting regulatory element that inhibits the motor activity of isolated wild-type Mfd, and suggest that interaction of Mfd with stalled transcription elongation complexes removes this inhibitory effect to unmask the motor activity necessary for RNAP displacement.
true
true
true
true
true
1,394
0
DISCUSSION
1
12
[ "B12" ]
17,329,375
NA|pmid-11839499|pmid-16469698
Like many members of the helicase superfamilies Mfd does not function in isolation, but acts in concert with other proteins as part of a macromolecular complex.
[ "12" ]
160
8,693
0
false
Like many members of the helicase superfamilies Mfd does not function in isolation, but acts in concert with other proteins as part of a macromolecular complex.
[]
Like many members of the helicase superfamilies Mfd does not function in isolation, but acts in concert with other proteins as part of a macromolecular complex.
true
true
true
true
true
1,395
0
DISCUSSION
1
12
[ "B12" ]
17,329,375
NA|pmid-11839499|pmid-16469698
During transcription-coupled repair its DNA translocation activity forms just one link in a chain of events that leads to RNAP displacement and the recruitment of DNA repair enzymes.
[ "12" ]
182
8,694
0
false
During transcription-coupled repair its DNA translocation activity forms just one link in a chain of events that leads to RNAP displacement and the recruitment of DNA repair enzymes.
[]
During transcription-coupled repair its DNA translocation activity forms just one link in a chain of events that leads to RNAP displacement and the recruitment of DNA repair enzymes.
true
true
true
true
true
1,395
0
DISCUSSION
1
12
[ "B12" ]
17,329,375
NA|pmid-11839499|pmid-16469698
Successful completion of the pathway is likely to require coordinated control of the various steps.
[ "12" ]
99
8,695
0
false
Successful completion of the pathway is likely to require coordinated control of the various steps.
[]
Successful completion of the pathway is likely to require coordinated control of the various steps.
true
true
true
true
true
1,395
0
DISCUSSION
1
12
[ "B12" ]
17,329,375
NA|pmid-11839499|pmid-16469698
In this work, we have found that DNA translocation activity of Mfd is regulated by the action of an autoinhibitory domain.
[ "12" ]
122
8,696
0
false
In this work, we have found that DNA translocation activity of Mfd is regulated by the action of an autoinhibitory domain.
[]
In this work, we have found that DNA translocation activity of Mfd is regulated by the action of an autoinhibitory domain.
true
true
true
true
true
1,395
0
DISCUSSION
1
12
[ "B12" ]
17,329,375
NA|pmid-11839499|pmid-16469698
In the isolated protein domain D7 inhibits the translocation activity.
[ "12" ]
70
8,697
0
false
In the isolated protein domain D7 inhibits the translocation activity.
[]
In the isolated protein domain D7 inhibits the translocation activity.
true
true
true
true
true
1,395
0
DISCUSSION
1
12
[ "B12" ]
17,329,375
NA|pmid-11839499|pmid-16469698
This inhibitory effect is relieved when the Mfd protein interacts with a stalled RNAP to form the initial complex on the transcription-coupled DNA repair pathway, suggesting that the interaction with RNAP results in repositioning of the autoinhibitory domain (Figure 7).
[ "12" ]
270
8,698
0
false
This inhibitory effect is relieved when the Mfd protein interacts with a stalled RNAP to form the initial complex on the transcription-coupled DNA repair pathway, suggesting that the interaction with RNAP results in repositioning of the autoinhibitory domain (Figure 7).
[]
This inhibitory effect is relieved when the Mfd protein interacts with a stalled RNAP to form the initial complex on the transcription-coupled DNA repair pathway, suggesting that the interaction with RNAP results in repositioning of the autoinhibitory domain (Figure 7).
true
true
true
true
true
1,395
0
DISCUSSION
1
12
[ "B12" ]
17,329,375
NA|pmid-11839499|pmid-16469698
Figure 7.Model for the control of Mfd activity by autoinhibitory domain D7.
[ "12" ]
75
8,699
0
false
Figure 7.Model for the control of Mfd activity by autoinhibitory domain D7.
[]
Figure 7.Model for the control of Mfd activity by autoinhibitory domain D7.
true
true
true
true
true
1,395