Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
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1
DISCUSSION
1
72
[ "B72", "B14", "B44", "B44", "B20", "B28" ]
17,567,608
pmid-8066464|pmid-10357855|pmid-6329717|pmid-8910403|pmid-11030336|pmid-11030336|pmid-12192033|pmid-17302439
Both mutant proteins bound DNA in a nucleotide-dependent manner (Figure 2; data not shown).
[ "72", "14", "44", "44", "20", "28" ]
91
300
0
false
Both mutant proteins bound DNA in a nucleotide-dependent manner (Figure 2; data not shown).
[]
Both mutant proteins bound DNA in a nucleotide-dependent manner.
true
true
true
true
true
49
1
DISCUSSION
1
72
[ "B72", "B14", "B44", "B44", "B20", "B28" ]
17,567,608
pmid-8066464|pmid-10357855|pmid-6329717|pmid-8910403|pmid-11030336|pmid-11030336|pmid-12192033|pmid-17302439
However, only the Rad51-K191R protein formed filaments that displayed DNA strand invasion activity and normal stimulation of Rad54 ATPase activity [Table 3 and data not shown; (14,44)].
[ "72", "14", "44", "44", "20", "28" ]
185
301
0
false
However, only the Rad51-K191R protein formed filaments that displayed DNA strand invasion activity and normal stimulation of Rad54 ATPase activity.
[ "Table 3 and data not shown; (14,44)" ]
However, only the Rad51-K191R protein formed filaments that displayed DNA strand invasion activity and normal stimulation of Rad54 ATPase activity.
true
true
true
true
true
49
1
DISCUSSION
1
72
[ "B72", "B14", "B44", "B44", "B20", "B28" ]
17,567,608
pmid-8066464|pmid-10357855|pmid-6329717|pmid-8910403|pmid-11030336|pmid-11030336|pmid-12192033|pmid-17302439
Whereas, the Rad51-K191A-DNA complexes were non-functional and defective in stimulating Rad54 ATPase activity or promoting strand invasion [data not shown; (44)].
[ "72", "14", "44", "44", "20", "28" ]
162
302
0
false
Whereas, the Rad51-K191A-DNA complexes were non-functional and defective in stimulating Rad54 ATPase activity or promoting strand invasion.
[ "data not shown; (44)" ]
Whereas, the Rad51-K191A-DNA complexes were non-functional and defective in stimulating Rad54 ATPase activity or promoting strand invasion.
true
true
true
true
true
49
1
DISCUSSION
1
20
[ "B72", "B14", "B44", "B44", "B20", "B28" ]
17,567,608
pmid-8066464|pmid-10357855|pmid-6329717|pmid-8910403|pmid-11030336|pmid-11030336|pmid-12192033|pmid-17302439
These biochemical data are consistent with in vivo observations that determined that the budding yeast rad51-K191A is phenotypically null (20).
[ "72", "14", "44", "44", "20", "28" ]
143
303
1
false
These biochemical data are consistent with in vivo observations that determined that the budding yeast rad51-K191A is phenotypically null.
[ "20" ]
These biochemical data are consistent with in vivo observations that determined that the budding yeast rad51-K191A is phenotypically null.
true
true
true
true
true
49
1
DISCUSSION
1
28
[ "B72", "B14", "B44", "B44", "B20", "B28" ]
17,567,608
pmid-8066464|pmid-10357855|pmid-6329717|pmid-8910403|pmid-11030336|pmid-11030336|pmid-12192033|pmid-17302439
Also the human Rad51-K133A protein was found to bind ATP (also with lower affinity) (28), confirming our observation that this amino acid change in the Walker A box does not always eliminate ATP binding.
[ "72", "14", "44", "44", "20", "28" ]
203
304
1
false
Also the human Rad51-K133A protein was found to bind ATP (also with lower affinity), confirming our observation that this amino acid change in the Walker A box does not always eliminate ATP binding.
[ "28" ]
Also the human Rad51-K133A protein was found to bind ATP (also with lower affinity), confirming our observation that this amino acid change in the Walker A box does not always eliminate ATP binding.
true
true
true
true
true
49
2
DISCUSSION
1
73
[ "B73", "B61", "B74", "B15", "B16" ]
17,567,608
pmid-15568977|pmid-12192033|pmid-8910403|pmid-12192033|pmid-8133517|pmid-8371266|pmid-9973562|pmid-9973561|pmid-8910403|pmid-12192033|pmid-16388992|NA|pmid-2147722|pmid-17030607|pmid-12359723|pmid-16979659|pmid-16388992|NA
Unexpectedly, Rad51-K191R displayed a DNA binding defect that is revealed by a requirement for higher protein concentrations to form DNA complexes (Figure 2A) and by lower STMs in the formation of protein DNA complexes (73).
[ "73", "61", "74", "15", "16" ]
224
305
1
false
Unexpectedly, Rad51-K191R displayed a DNA binding defect that is revealed by a requirement for higher protein concentrations to form DNA complexes (Figure 2A) and by lower STMs in the formation of protein DNA complexes.
[ "73" ]
Unexpectedly, Rad51-K191R displayed a DNA binding defect that is revealed by a requirement for higher protein concentrations to form DNA complexes (Figure 2A) and by lower STMs in the formation of protein DNA complexes.
true
true
true
true
true
50
2
DISCUSSION
1
73
[ "B73", "B61", "B74", "B15", "B16" ]
17,567,608
pmid-15568977|pmid-12192033|pmid-8910403|pmid-12192033|pmid-8133517|pmid-8371266|pmid-9973562|pmid-9973561|pmid-8910403|pmid-12192033|pmid-16388992|NA|pmid-2147722|pmid-17030607|pmid-12359723|pmid-16979659|pmid-16388992|NA
The nucleoprotein gel analysis showed that Rad51-K191R protein formed fewer complexes with intermediate electrophoretic mobility, which could be a reflection of a nucleation defect or of increased cooperativity.
[ "73", "61", "74", "15", "16" ]
211
306
0
false
The nucleoprotein gel analysis showed that Rad51-K191R protein formed fewer complexes with intermediate electrophoretic mobility, which could be a reflection of a nucleation defect or of increased cooperativity.
[]
The nucleoprotein gel analysis showed that Rad51-K191R protein formed fewer complexes with intermediate electrophoretic mobility, which could be a reflection of a nucleation defect or of increased cooperativity.
true
true
true
true
true
50
2
DISCUSSION
1
61
[ "B73", "B61", "B74", "B15", "B16" ]
17,567,608
pmid-15568977|pmid-12192033|pmid-8910403|pmid-12192033|pmid-8133517|pmid-8371266|pmid-9973562|pmid-9973561|pmid-8910403|pmid-12192033|pmid-16388992|NA|pmid-2147722|pmid-17030607|pmid-12359723|pmid-16979659|pmid-16388992|NA
Rad51 is known to display significantly lower cooperativity than RecA protein (61).
[ "73", "61", "74", "15", "16" ]
83
307
1
false
Rad51 is known to display significantly lower cooperativity than RecA protein.
[ "61" ]
Rad51 is known to display significantly lower cooperativity than RecA protein.
true
true
true
true
true
50
2
DISCUSSION
1
73
[ "B73", "B61", "B74", "B15", "B16" ]
17,567,608
pmid-15568977|pmid-12192033|pmid-8910403|pmid-12192033|pmid-8133517|pmid-8371266|pmid-9973562|pmid-9973561|pmid-8910403|pmid-12192033|pmid-16388992|NA|pmid-2147722|pmid-17030607|pmid-12359723|pmid-16979659|pmid-16388992|NA
These results demonstrate a reduced affinity for DNA (Figure 2, Table 2), consistent with data from single-molecule experiments using the human Rad51-K133R protein and phage λ dsDNA
[ "73", "61", "74", "15", "16" ]
181
308
0
false
These results demonstrate a reduced affinity for DNA (Figure 2, Table 2), consistent with data from single-molecule experiments using the human Rad51-K133R protein and phage λ dsDNA
[]
These results demonstrate a reduced affinity for DNA (Figure 2, Table 2), consistent with data from single-molecule experiments using the human Rad51-K133R protein and phage λ dsDNA
true
true
false
true
false
50
2
DISCUSSION
1
73
[ "B73", "B61", "B74", "B15", "B16" ]
17,567,608
pmid-15568977|pmid-12192033|pmid-8910403|pmid-12192033|pmid-8133517|pmid-8371266|pmid-9973562|pmid-9973561|pmid-8910403|pmid-12192033|pmid-16388992|NA|pmid-2147722|pmid-17030607|pmid-12359723|pmid-16979659|pmid-16388992|NA
Importantly, ATP hydrolysis appears to be critical for the dynamic turnover of the Rad51-ssDNA and dsDNA filaments, since the filaments formed by the Rad51-K191R protein were significantly more stable than filaments formed by wild-type Rad51 protein.
[ "73", "61", "74", "15", "16" ]
250
309
0
false
Importantly, ATP hydrolysis appears to be critical for the dynamic turnover of the Rad51-ssDNA and dsDNA filaments, since the filaments formed by the Rad51-K191R protein were significantly more stable than filaments formed by wild-type Rad51 protein.
[]
Importantly, ATP hydrolysis appears to be critical for the dynamic turnover of the Rad51-ssDNA and dsDNA filaments, since the filaments formed by the Rad51-K191R protein were significantly more stable than filaments formed by wild-type Rad51 protein.
true
true
true
true
true
50
2
DISCUSSION
1
73
[ "B73", "B61", "B74", "B15", "B16" ]
17,567,608
pmid-15568977|pmid-12192033|pmid-8910403|pmid-12192033|pmid-8133517|pmid-8371266|pmid-9973562|pmid-9973561|pmid-8910403|pmid-12192033|pmid-16388992|NA|pmid-2147722|pmid-17030607|pmid-12359723|pmid-16979659|pmid-16388992|NA
These results are consistent with previous observations made with the human Rad51 protein (15,16).
[ "73", "61", "74", "15", "16" ]
98
310
0
false
These results are consistent with previous observations made with the human Rad51 protein.
[ "15,16" ]
These results are consistent with previous observations made with the human Rad51 protein.
true
true
true
true
true
50
2
DISCUSSION
1
73
[ "B73", "B61", "B74", "B15", "B16" ]
17,567,608
pmid-15568977|pmid-12192033|pmid-8910403|pmid-12192033|pmid-8133517|pmid-8371266|pmid-9973562|pmid-9973561|pmid-8910403|pmid-12192033|pmid-16388992|NA|pmid-2147722|pmid-17030607|pmid-12359723|pmid-16979659|pmid-16388992|NA
Furthermore, our results show that the stability of the Rad51-K191R-dsDNA complexes is significantly more pronounced than that of the ssDNA complexes.
[ "73", "61", "74", "15", "16" ]
150
311
0
false
Furthermore, our results show that the stability of the Rad51-K191R-dsDNA complexes is significantly more pronounced than that of the ssDNA complexes.
[]
Furthermore, our results show that the stability of the Rad51-K191R-dsDNA complexes is significantly more pronounced than that of the ssDNA complexes.
true
true
true
true
true
50
3
DISCUSSION
1
20
[ "B20", "B73", "B20", "B73", "B75", "B76", "B20", "B77" ]
17,567,608
pmid-12826279|pmid-16935872|pmid-16818238|pmid-15568977|pmid-12560498|pmid-12826279|pmid-16935872|pmid-11459988|pmid-16862129|pmid-8631697|pmid-12087154|pmid-12192033|pmid-17030607|pmid-12192033|pmid-17030607|pmid-12748644|pmid-12748645|pmid-12192033|pmid-16980587
Together, these results suggest that the rad51-K191R mutant in vivo may lead to defects in presynapsis, in Rad51-ssDNA filament formation, and in postsynapsis, in Rad51-dsDNA filament dissociation.
[ "20", "73", "20", "73", "75", "76", "20", "77" ]
197
312
0
false
Together, these results suggest that the rad51-K191R mutant in vivo may lead to defects in presynapsis, in Rad51-ssDNA filament formation, and in postsynapsis, in Rad51-dsDNA filament dissociation.
[]
Together, these results suggest that the rad51-K191R mutant in vivo may lead to defects in presynapsis, in Rad51-ssDNA filament formation, and in postsynapsis, in Rad51-dsDNA filament dissociation.
true
true
true
true
true
51
3
DISCUSSION
1
20
[ "B20", "B73", "B20", "B73", "B75", "B76", "B20", "B77" ]
17,567,608
pmid-12826279|pmid-16935872|pmid-16818238|pmid-15568977|pmid-12560498|pmid-12826279|pmid-16935872|pmid-11459988|pmid-16862129|pmid-8631697|pmid-12087154|pmid-12192033|pmid-17030607|pmid-12192033|pmid-17030607|pmid-12748644|pmid-12748645|pmid-12192033|pmid-16980587
This interpretation of the biochemical data is supported by genetic analysis (20,73).
[ "20", "73", "20", "73", "75", "76", "20", "77" ]
85
313
0
false
This interpretation of the biochemical data is supported by genetic analysis.
[ "20,73" ]
This interpretation of the biochemical data is supported by genetic analysis.
true
true
true
true
true
51
3
DISCUSSION
1
20
[ "B20", "B73", "B20", "B73", "B75", "B76", "B20", "B77" ]
17,567,608
pmid-12826279|pmid-16935872|pmid-16818238|pmid-15568977|pmid-12560498|pmid-12826279|pmid-16935872|pmid-11459988|pmid-16862129|pmid-8631697|pmid-12087154|pmid-12192033|pmid-17030607|pmid-12192033|pmid-17030607|pmid-12748644|pmid-12748645|pmid-12192033|pmid-16980587
Overexpression of Rad51-K191R and deletion of the SRS2 gene were found to suppress the rad51-K191R defect (20,73).
[ "20", "73", "20", "73", "75", "76", "20", "77" ]
114
314
0
false
Overexpression of Rad51-K191R and deletion of the SRS2 gene were found to suppress the rad51-K191R defect.
[ "20,73" ]
Overexpression of Rad51-K191R and deletion of the SRS2 gene were found to suppress the rad51-K191R defect.
true
true
true
true
true
51
3
DISCUSSION
1
20
[ "B20", "B73", "B20", "B73", "B75", "B76", "B20", "B77" ]
17,567,608
pmid-12826279|pmid-16935872|pmid-16818238|pmid-15568977|pmid-12560498|pmid-12826279|pmid-16935872|pmid-11459988|pmid-16862129|pmid-8631697|pmid-12087154|pmid-12192033|pmid-17030607|pmid-12192033|pmid-17030607|pmid-12748644|pmid-12748645|pmid-12192033|pmid-16980587
Since Srs2 is only able to dissociate Rad51 from ssDNA (75,76), these findings support a defect of Rad51-K191R during presynapsis.
[ "20", "73", "20", "73", "75", "76", "20", "77" ]
130
315
0
false
Since Srs2 is only able to dissociate Rad51 from ssDNA, these findings support a defect of Rad51-K191R during presynapsis.
[ "75,76" ]
Since Srs2 is only able to dissociate Rad51 from ssDNA, these findings support a defect of Rad51-K191R during presynapsis.
true
true
true
true
true
51
3
DISCUSSION
1
20
[ "B20", "B73", "B20", "B73", "B75", "B76", "B20", "B77" ]
17,567,608
pmid-12826279|pmid-16935872|pmid-16818238|pmid-15568977|pmid-12560498|pmid-12826279|pmid-16935872|pmid-11459988|pmid-16862129|pmid-8631697|pmid-12087154|pmid-12192033|pmid-17030607|pmid-12192033|pmid-17030607|pmid-12748644|pmid-12748645|pmid-12192033|pmid-16980587
It is not possible to distinguish whether this is due to decreased ATP binding, which may be the root cause for the DNA binding defect, or to the greatly reduced dynamics of the filament due to the higher stability of the Rad51-K191R-ssDNA filaments.
[ "20", "73", "20", "73", "75", "76", "20", "77" ]
250
316
0
false
It is not possible to distinguish whether this is due to decreased ATP binding, which may be the root cause for the DNA binding defect, or to the greatly reduced dynamics of the filament due to the higher stability of the Rad51-K191R-ssDNA filaments.
[]
It is not possible to distinguish whether this is due to decreased ATP binding, which may be the root cause for the DNA binding defect, or to the greatly reduced dynamics of the filament due to the higher stability of the Rad51-K191R-ssDNA filaments.
true
true
true
true
true
51
3
DISCUSSION
1
20
[ "B20", "B73", "B20", "B73", "B75", "B76", "B20", "B77" ]
17,567,608
pmid-12826279|pmid-16935872|pmid-16818238|pmid-15568977|pmid-12560498|pmid-12826279|pmid-16935872|pmid-11459988|pmid-16862129|pmid-8631697|pmid-12087154|pmid-12192033|pmid-17030607|pmid-12192033|pmid-17030607|pmid-12748644|pmid-12748645|pmid-12192033|pmid-16980587
On the other hand, overexpression of Rad54 also suppressed the rad51-K191R defect (20).
[ "20", "73", "20", "73", "75", "76", "20", "77" ]
87
317
1
false
On the other hand, overexpression of Rad54 also suppressed the rad51-K191R defect.
[ "20" ]
On the other hand, overexpression of Rad54 also suppressed the rad51-K191R defect.
true
true
true
true
true
51
3
DISCUSSION
1
20
[ "B20", "B73", "B20", "B73", "B75", "B76", "B20", "B77" ]
17,567,608
pmid-12826279|pmid-16935872|pmid-16818238|pmid-15568977|pmid-12560498|pmid-12826279|pmid-16935872|pmid-11459988|pmid-16862129|pmid-8631697|pmid-12087154|pmid-12192033|pmid-17030607|pmid-12192033|pmid-17030607|pmid-12748644|pmid-12748645|pmid-12192033|pmid-16980587
Since Rad54 can only dissociate Rad51 from dsDNA, these data suggest that the Rad51 ATPase activity is also required in vivo for turnover from dsDNA.
[ "20", "73", "20", "73", "75", "76", "20", "77" ]
149
318
0
false
Since Rad54 can only dissociate Rad51 from dsDNA, these data suggest that the Rad51 ATPase activity is also required in vivo for turnover from dsDNA.
[]
Since Rad54 can only dissociate Rad51 from dsDNA, these data suggest that the Rad51 ATPase activity is also required in vivo for turnover from dsDNA.
true
true
true
true
true
51
3
DISCUSSION
1
20
[ "B20", "B73", "B20", "B73", "B75", "B76", "B20", "B77" ]
17,567,608
pmid-12826279|pmid-16935872|pmid-16818238|pmid-15568977|pmid-12560498|pmid-12826279|pmid-16935872|pmid-11459988|pmid-16862129|pmid-8631697|pmid-12087154|pmid-12192033|pmid-17030607|pmid-12192033|pmid-17030607|pmid-12748644|pmid-12748645|pmid-12192033|pmid-16980587
Overexpression of Rad54 may also suppress a potential presynaptic defect by possibly enhancing the non-DNA bound Rad51 pool.
[ "20", "73", "20", "73", "75", "76", "20", "77" ]
124
319
0
false
Overexpression of Rad54 may also suppress a potential presynaptic defect by possibly enhancing the non-DNA bound Rad51 pool.
[]
Overexpression of Rad54 may also suppress a potential presynaptic defect by possibly enhancing the non-DNA bound Rad51 pool.
true
true
true
true
true
51
3
DISCUSSION
1
77
[ "B20", "B73", "B20", "B73", "B75", "B76", "B20", "B77" ]
17,567,608
pmid-12826279|pmid-16935872|pmid-16818238|pmid-15568977|pmid-12560498|pmid-12826279|pmid-16935872|pmid-11459988|pmid-16862129|pmid-8631697|pmid-12087154|pmid-12192033|pmid-17030607|pmid-12192033|pmid-17030607|pmid-12748644|pmid-12748645|pmid-12192033|pmid-16980587
Dissociation of dead-end complexes of Dmc1 and dsDNA appears to be a critical function for the Rdh54/Tid1 protein, which is closely related to Rad54 (77).
[ "20", "73", "20", "73", "75", "76", "20", "77" ]
154
320
1
false
Dissociation of dead-end complexes of Dmc1 and dsDNA appears to be a critical function for the Rdh54/Tid1 protein, which is closely related to Rad54.
[ "77" ]
Dissociation of dead-end complexes of Dmc1 and dsDNA appears to be a critical function for the Rdh54/Tid1 protein, which is closely related to Rad54.
true
true
true
true
true
51
4
DISCUSSION
1
61
[ "B61", "B31", "B78", "B62" ]
17,567,608
pmid-12887907|pmid-12887906|pmid-12359723|pmid-12453424|pmid-16785421|pmid-12359723|pmid-16818238|pmid-16916635|pmid-16785421
The Rad54 ATPase activity exhibits a basic mode of protein-free dsDNA, a filament mode with reduced ATPase activity on fully saturated Rad51-dsDNA filaments, and an enhanced mode on sub-saturated Rad51-dsDNA filaments (61).
[ "61", "31", "78", "62" ]
223
321
1
false
The Rad54 ATPase activity exhibits a basic mode of protein-free dsDNA, a filament mode with reduced ATPase activity on fully saturated Rad51-dsDNA filaments, and an enhanced mode on sub-saturated Rad51-dsDNA filaments.
[ "61" ]
The Rad54 ATPase activity exhibits a basic mode of protein-free dsDNA, a filament mode with reduced ATPase activity on fully saturated Rad51-dsDNA filaments, and an enhanced mode on sub-saturated Rad51-dsDNA filaments.
true
true
true
true
true
52
4
DISCUSSION
1
61
[ "B61", "B31", "B78", "B62" ]
17,567,608
pmid-12887907|pmid-12887906|pmid-12359723|pmid-12453424|pmid-16785421|pmid-12359723|pmid-16818238|pmid-16916635|pmid-16785421
Here, we provide kinetic data to distinguish these three modes.
[ "61", "31", "78", "62" ]
63
322
0
false
Here, we provide kinetic data to distinguish these three modes.
[]
Here, we provide kinetic data to distinguish these three modes.
true
true
true
true
true
52
4
DISCUSSION
1
61
[ "B61", "B31", "B78", "B62" ]
17,567,608
pmid-12887907|pmid-12887906|pmid-12359723|pmid-12453424|pmid-16785421|pmid-12359723|pmid-16818238|pmid-16916635|pmid-16785421
Stimulation of Rad54 ATPase activity on partial Rad51-dsDNA filaments compared with protein-free DNA is specifically due to an increase in the VMAX for ATP enhancing the catalytic efficiency about 6-fold with no significant change in the KM for ATP (Table 3).
[ "61", "31", "78", "62" ]
259
323
0
false
Stimulation of Rad54 ATPase activity on partial Rad51-dsDNA filaments compared with protein-free DNA is specifically due to an increase in the VMAX for ATP enhancing the catalytic efficiency about 6-fold with no significant change in the KM for ATP (Table 3).
[]
Stimulation of Rad54 ATPase activity on partial Rad51-dsDNA filaments compared with protein-free DNA is specifically due to an increase in the VMAX for ATP enhancing the catalytic efficiency about 6-fold with no significant change in the KM for ATP (Table 3).
true
true
true
true
true
52
4
DISCUSSION
1
61
[ "B61", "B31", "B78", "B62" ]
17,567,608
pmid-12887907|pmid-12887906|pmid-12359723|pmid-12453424|pmid-16785421|pmid-12359723|pmid-16818238|pmid-16916635|pmid-16785421
In contrast, with saturated Rad51-dsDNA filament, the VMAX for ATP is reduced to about 70% coupled with a significant increase in affinity for ATP indicated by a 15-fold lower KM for ATP (Table 3) when compared with protein-free DNA.
[ "61", "31", "78", "62" ]
233
324
0
false
In contrast, with saturated Rad51-dsDNA filament, the VMAX for ATP is reduced to about 70% coupled with a significant increase in affinity for ATP indicated by a 15-fold lower KM for ATP (Table 3) when compared with protein-free DNA.
[]
In contrast, with saturated Rad51-dsDNA filament, the VMAX for ATP is reduced to about 70% coupled with a significant increase in affinity for ATP indicated by a 15-fold lower KM for ATP (Table 3) when compared with protein-free DNA.
true
true
true
true
true
52
4
DISCUSSION
1
61
[ "B61", "B31", "B78", "B62" ]
17,567,608
pmid-12887907|pmid-12887906|pmid-12359723|pmid-12453424|pmid-16785421|pmid-12359723|pmid-16818238|pmid-16916635|pmid-16785421
These data suggest that Rad54 undergoes a conformational change from a high KM form that can translocate on DNA (protein-free DNA, partial Rad51-dsDNA filament) to a low KM form when associated with fully saturated Rad51-DNA filaments.
[ "61", "31", "78", "62" ]
235
325
0
false
These data suggest that Rad54 undergoes a conformational change from a high KM form that can translocate on DNA (protein-free DNA, partial Rad51-dsDNA filament) to a low KM form when associated with fully saturated Rad51-DNA filaments.
[]
These data suggest that Rad54 undergoes a conformational change from a high KM form that can translocate on DNA to a low KM form when associated with fully saturated Rad51-DNA filaments.
true
true
true
true
true
52
4
DISCUSSION
1
31
[ "B61", "B31", "B78", "B62" ]
17,567,608
pmid-12887907|pmid-12887906|pmid-12359723|pmid-12453424|pmid-16785421|pmid-12359723|pmid-16818238|pmid-16916635|pmid-16785421
Rad54 is a bi-directional, processive motor protein on dsDNA (31).
[ "61", "31", "78", "62" ]
66
326
1
false
Rad54 is a bi-directional, processive motor protein on dsDNA.
[ "31" ]
Rad54 is a bi-directional, processive motor protein on dsDNA.
true
true
true
true
true
52
4
DISCUSSION
1
78
[ "B61", "B31", "B78", "B62" ]
17,567,608
pmid-12887907|pmid-12887906|pmid-12359723|pmid-12453424|pmid-16785421|pmid-12359723|pmid-16818238|pmid-16916635|pmid-16785421
This property is reminiscent of the FtsK motor protein, which forms a double-hexameric ring on dsDNA for translocation (78).
[ "61", "31", "78", "62" ]
124
327
1
false
This property is reminiscent of the FtsK motor protein, which forms a double-hexameric ring on dsDNA for translocation.
[ "78" ]
This property is reminiscent of the FtsK motor protein, which forms a double-hexameric ring on dsDNA for translocation.
true
true
true
true
true
52
4
DISCUSSION
1
62
[ "B61", "B31", "B78", "B62" ]
17,567,608
pmid-12887907|pmid-12887906|pmid-12359723|pmid-12453424|pmid-16785421|pmid-12359723|pmid-16818238|pmid-16916635|pmid-16785421
While the precise assembly of the translocating and non-translocating Rad54 protein remains to be determined, electron microscopic analysis of negatively stained specimens identified a Rad54 oligomeric assembly on protein-free dsDNA and dsDNA partially saturated by Rad51 protein (62), which is consistent with this hypothesis.
[ "61", "31", "78", "62" ]
327
328
1
false
While the precise assembly of the translocating and non-translocating Rad54 protein remains to be determined, electron microscopic analysis of negatively stained specimens identified a Rad54 oligomeric assembly on protein-free dsDNA and dsDNA partially saturated by Rad51 protein, which is consistent with this hypothesis.
[ "62" ]
While the precise assembly of the translocating and non-translocating Rad54 protein remains to be determined, electron microscopic analysis of negatively stained specimens identified a Rad54 oligomeric assembly on protein-free dsDNA and dsDNA partially saturated by Rad51 protein, which is consistent with this hypothesis.
true
true
true
true
true
52
5
DISCUSSION
1
31
[ "B31", "B31", "B31", "B31" ]
17,567,608
pmid-17302439|pmid-16818238|pmid-16818238|pmid-16818238|pmid-16818238
The KM (ATP) of Rad54 on protein-free dsDNA that we determined in our experiments is about 6–7-fold higher than that measured by Amitani et al.
[ "31", "31", "31", "31" ]
143
329
0
false
The KM (ATP) of Rad54 on protein-free dsDNA that we determined in our experiments is about 6–7-fold higher than that measured by Amitani et al.
[]
The KM (ATP) of Rad54 on protein-free dsDNA that we determined in our experiments is about 6–7-fold higher than that measured by Amitani et al.
true
true
true
true
true
53
5
DISCUSSION
1
31
[ "B31", "B31", "B31", "B31" ]
17,567,608
pmid-17302439|pmid-16818238|pmid-16818238|pmid-16818238|pmid-16818238
(31) in single-molecule experiments.
[ "31", "31", "31", "31" ]
36
330
1
false
in single-molecule experiments.
[ "31" ]
in single-molecule experiments.
false
true
true
true
false
53
5
DISCUSSION
1
31
[ "B31", "B31", "B31", "B31" ]
17,567,608
pmid-17302439|pmid-16818238|pmid-16818238|pmid-16818238|pmid-16818238
We ascertained our high KM in experiments using a different concentration of Rad54 (9 nM instead of 3.3 nM; data not shown).
[ "31", "31", "31", "31" ]
124
331
0
false
We ascertained our high KM in experiments using a different concentration of Rad54 (9 nM instead of 3.3 nM; data not shown).
[]
We ascertained our high KM in experiments using a different concentration of Rad54.
true
true
true
true
true
53
5
DISCUSSION
1
31
[ "B31", "B31", "B31", "B31" ]
17,567,608
pmid-17302439|pmid-16818238|pmid-16818238|pmid-16818238|pmid-16818238
We observe that Rad54 ATPase activities (Figure 3A) with protein-free and partial Rad51-dsDNA filaments very gradually approached the saturation point with only minor increases in ATPase activity above 1 mM, whereas the ATPase activity with fully saturated filaments (Figure 3B) approach saturation more rapidly with no increase above 1 mM.
[ "31", "31", "31", "31" ]
340
332
0
false
We observe that Rad54 ATPase activities (Figure 3A) with protein-free and partial Rad51-dsDNA filaments very gradually approached the saturation point with only minor increases in ATPase activity above 1 mM, whereas the ATPase activity with fully saturated filaments (Figure 3B) approach saturation more rapidly with no increase above 1 mM.
[]
We observe that Rad54 ATPase activities with protein-free and partial Rad51-dsDNA filaments very gradually approached the saturation point with only minor increases in ATPase activity above 1 mM, whereas the ATPase activity with fully saturated filaments approach saturation more rapidly with no increase above 1 mM.
true
true
true
true
true
53
5
DISCUSSION
1
31
[ "B31", "B31", "B31", "B31" ]
17,567,608
pmid-17302439|pmid-16818238|pmid-16818238|pmid-16818238|pmid-16818238
Our KM determination is based on ATPase activity as an output, whereas Amitani et al.
[ "31", "31", "31", "31" ]
85
333
0
false
Our KM determination is based on ATPase activity as an output, whereas Amitani et al.
[]
Our KM determination is based on ATPase activity as an output, whereas Amitani et al.
true
true
true
true
true
53
5
DISCUSSION
1
31
[ "B31", "B31", "B31", "B31" ]
17,567,608
pmid-17302439|pmid-16818238|pmid-16818238|pmid-16818238|pmid-16818238
(31) measured translocation velocity, detecting no increase in velocity above 0.5 mM (31).
[ "31", "31", "31", "31" ]
90
334
2
true
measured translocation velocity, detecting no increase in velocity above 0.5 mM.
[ "31", "31" ]
measured translocation velocity, detecting no increase in velocity above 0.5 mM.
false
true
true
true
false
53
5
DISCUSSION
1
31
[ "B31", "B31", "B31", "B31" ]
17,567,608
pmid-17302439|pmid-16818238|pmid-16818238|pmid-16818238|pmid-16818238
It is possible that the low KM determined in the translocation experiments reflects the ATP-binding of the DNA-bound subunit of an oligomeric assembly.
[ "31", "31", "31", "31" ]
151
335
0
false
It is possible that the low KM determined in the translocation experiments reflects the ATP-binding of the DNA-bound subunit of an oligomeric assembly.
[]
It is possible that the low KM determined in the translocation experiments reflects the ATP-binding of the DNA-bound subunit of an oligomeric assembly.
true
true
true
true
true
53
5
DISCUSSION
1
31
[ "B31", "B31", "B31", "B31" ]
17,567,608
pmid-17302439|pmid-16818238|pmid-16818238|pmid-16818238|pmid-16818238
In our ATPase experiments, the minor increase in ATPase activity at high ATP concentrations may reflect ATP binding of the non-DNA bound subunits.
[ "31", "31", "31", "31" ]
146
336
0
false
In our ATPase experiments, the minor increase in ATPase activity at high ATP concentrations may reflect ATP binding of the non-DNA bound subunits.
[]
In our ATPase experiments, the minor increase in ATPase activity at high ATP concentrations may reflect ATP binding of the non-DNA bound subunits.
true
true
true
true
true
53
5
DISCUSSION
1
31
[ "B31", "B31", "B31", "B31" ]
17,567,608
pmid-17302439|pmid-16818238|pmid-16818238|pmid-16818238|pmid-16818238
Consistent with this interpretation, our Rad54 KM data measuring ATPase activity with fully saturated Rad51-dsDNA filaments (Table 3), where Rad54 is likely in a non-translocating oligomeric state, are essentially identical with the KM determined by velocity in the translocation experiments on protein-free DNA (31).
[ "31", "31", "31", "31" ]
317
337
1
false
Consistent with this interpretation, our Rad54 KM data measuring ATPase activity with fully saturated Rad51-dsDNA filaments (Table 3), where Rad54 is likely in a non-translocating oligomeric state, are essentially identical with the KM determined by velocity in the translocation experiments on protein-free DNA.
[ "31" ]
Consistent with this interpretation, our Rad54 KM data measuring ATPase activity with fully saturated Rad51-dsDNA filaments, where Rad54 is likely in a non-translocating oligomeric state, are essentially identical with the KM determined by velocity in the translocation experiments on protein-free DNA.
true
true
true
true
true
53
6
DISCUSSION
1
79
[ "B79", "B70", "B10", "B70", "B15", "B16", "B41", "B61" ]
17,567,608
pmid-1831022|pmid-9915828|pmid-8066464|pmid-9915828|pmid-16388992|NA|pmid-12453424|pmid-12359723
Despite their evolutionary conservation, significant differences exist between RecA, yeast Rad51 and human Rad51 with respect to their ATPase activity and DNA binding properties.
[ "79", "70", "10", "70", "15", "16", "41", "61" ]
178
338
0
false
Despite their evolutionary conservation, significant differences exist between RecA, yeast Rad51 and human Rad51 with respect to their ATPase activity and DNA binding properties.
[]
Despite their evolutionary conservation, significant differences exist between RecA, yeast Rad51 and human Rad51 with respect to their ATPase activity and DNA binding properties.
true
true
true
true
true
54
6
DISCUSSION
1
79
[ "B79", "B70", "B10", "B70", "B15", "B16", "B41", "B61" ]
17,567,608
pmid-1831022|pmid-9915828|pmid-8066464|pmid-9915828|pmid-16388992|NA|pmid-12453424|pmid-12359723
RecA autonomously toggles between a high affinity (ATP) and low affinity binding state (ADP) by nucleotide cofactor binding and cooperative hydrolysis, resulting in dynamic assembly and turnover of RecA filaments (79).
[ "79", "70", "10", "70", "15", "16", "41", "61" ]
218
339
1
false
RecA autonomously toggles between a high affinity (ATP) and low affinity binding state (ADP) by nucleotide cofactor binding and cooperative hydrolysis, resulting in dynamic assembly and turnover of RecA filaments.
[ "79" ]
RecA autonomously toggles between a high affinity (ATP) and low affinity binding state (ADP) by nucleotide cofactor binding and cooperative hydrolysis, resulting in dynamic assembly and turnover of RecA filaments.
true
true
true
true
true
54
6
DISCUSSION
1
70
[ "B79", "B70", "B10", "B70", "B15", "B16", "B41", "B61" ]
17,567,608
pmid-1831022|pmid-9915828|pmid-8066464|pmid-9915828|pmid-16388992|NA|pmid-12453424|pmid-12359723
Unlike RecA (and human Rad51), yeast Rad51 binding to DNA depends on the presence of nucleotide cofactor at neutral pH (70).
[ "79", "70", "10", "70", "15", "16", "41", "61" ]
124
340
1
false
Unlike RecA (and human Rad51), yeast Rad51 binding to DNA depends on the presence of nucleotide cofactor at neutral pH.
[ "70" ]
Unlike RecA (and human Rad51), yeast Rad51 binding to DNA depends on the presence of nucleotide cofactor at neutral pH.
true
true
true
true
true
54
6
DISCUSSION
1
10
[ "B79", "B70", "B10", "B70", "B15", "B16", "B41", "B61" ]
17,567,608
pmid-1831022|pmid-9915828|pmid-8066464|pmid-9915828|pmid-16388992|NA|pmid-12453424|pmid-12359723
The significantly lower (∼200-fold) and non-cooperative ATPase activity of Rad51 (10) results in a far less dynamic filament.
[ "79", "70", "10", "70", "15", "16", "41", "61" ]
125
341
1
false
The significantly lower (∼200-fold) and non-cooperative ATPase activity of Rad51 results in a far less dynamic filament.
[ "10" ]
The significantly lower and non-cooperative ATPase activity of Rad51 results in a far less dynamic filament.
true
true
true
true
true
54
6
DISCUSSION
1
70
[ "B79", "B70", "B10", "B70", "B15", "B16", "B41", "B61" ]
17,567,608
pmid-1831022|pmid-9915828|pmid-8066464|pmid-9915828|pmid-16388992|NA|pmid-12453424|pmid-12359723
Also unlike RecA, which has a kinetic impediment to bind dsDNA, yeast and human Rad51 readily bind dsDNA (70).
[ "79", "70", "10", "70", "15", "16", "41", "61" ]
110
342
1
false
Also unlike RecA, which has a kinetic impediment to bind dsDNA, yeast and human Rad51 readily bind dsDNA.
[ "70" ]
Also unlike RecA, which has a kinetic impediment to bind dsDNA, yeast and human Rad51 readily bind dsDNA.
true
true
true
true
true
54
6
DISCUSSION
1
79
[ "B79", "B70", "B10", "B70", "B15", "B16", "B41", "B61" ]
17,567,608
pmid-1831022|pmid-9915828|pmid-8066464|pmid-9915828|pmid-16388992|NA|pmid-12453424|pmid-12359723
Human Rad51 resembles more RecA than yeast Rad51 in its ability to bind DNA independent of nucleotide co-factor, but shares the low and non-cooperative ATPase activity with its yeast counterpart (15,28,80,81).
[ "79", "70", "10", "70", "15", "16", "41", "61" ]
209
343
0
false
Human Rad51 resembles more RecA than yeast Rad51 in its ability to bind DNA independent of nucleotide co-factor, but shares the low and non-cooperative ATPase activity with its yeast counterpart.
[ "15,28,80,81" ]
Human Rad51 resembles more RecA than yeast Rad51 in its ability to bind DNA independent of nucleotide co-factor, but shares the low and non-cooperative ATPase activity with its yeast counterpart.
true
true
true
true
true
54
6
DISCUSSION
1
79
[ "B79", "B70", "B10", "B70", "B15", "B16", "B41", "B61" ]
17,567,608
pmid-1831022|pmid-9915828|pmid-8066464|pmid-9915828|pmid-16388992|NA|pmid-12453424|pmid-12359723
Likely as a consequence, Rad51-DNA complexes are much more stable and less dynamic than RecA filaments [(15,16) and this study].
[ "79", "70", "10", "70", "15", "16", "41", "61" ]
128
344
0
false
Likely as a consequence, Rad51-DNA complexes are much more stable and less dynamic than RecA filaments.
[ "(15,16) and this study" ]
Likely as a consequence, Rad51-DNA complexes are much more stable and less dynamic than RecA filaments.
true
true
true
true
true
54
6
DISCUSSION
1
79
[ "B79", "B70", "B10", "B70", "B15", "B16", "B41", "B61" ]
17,567,608
pmid-1831022|pmid-9915828|pmid-8066464|pmid-9915828|pmid-16388992|NA|pmid-12453424|pmid-12359723
Rad51 binding to dsDNA and the relative stability of these complexes will lead to dead-end complexes on undamaged DNA.
[ "79", "70", "10", "70", "15", "16", "41", "61" ]
118
345
0
false
Rad51 binding to dsDNA and the relative stability of these complexes will lead to dead-end complexes on undamaged DNA.
[]
Rad51 binding to dsDNA and the relative stability of these complexes will lead to dead-end complexes on undamaged DNA.
true
true
true
true
true
54
6
DISCUSSION
1
79
[ "B79", "B70", "B10", "B70", "B15", "B16", "B41", "B61" ]
17,567,608
pmid-1831022|pmid-9915828|pmid-8066464|pmid-9915828|pmid-16388992|NA|pmid-12453424|pmid-12359723
Moreover, Rad51 is stuck on the heteroduplex DNA product after DNA strand exchange.
[ "79", "70", "10", "70", "15", "16", "41", "61" ]
83
346
0
false
Moreover, Rad51 is stuck on the heteroduplex DNA product after DNA strand exchange.
[]
Moreover, Rad51 is stuck on the heteroduplex DNA product after DNA strand exchange.
true
true
true
true
true
54
6
DISCUSSION
1
79
[ "B79", "B70", "B10", "B70", "B15", "B16", "B41", "B61" ]
17,567,608
pmid-1831022|pmid-9915828|pmid-8066464|pmid-9915828|pmid-16388992|NA|pmid-12453424|pmid-12359723
We have previously proposed that a major role of Rad54 is to function as an extrinsic turnover factor for the Rad51-dsDNA filament, suggesting that the combination of Rad51 and Rad54 reflect the eukaryotic equivalent of RecA in recombination (41,61).
[ "79", "70", "10", "70", "15", "16", "41", "61" ]
250
347
0
false
We have previously proposed that a major role of Rad54 is to function as an extrinsic turnover factor for the Rad51-dsDNA filament, suggesting that the combination of Rad51 and Rad54 reflect the eukaryotic equivalent of RecA in recombination.
[ "41,61" ]
We have previously proposed that a major role of Rad54 is to function as an extrinsic turnover factor for the Rad51-dsDNA filament, suggesting that the combination of Rad51 and Rad54 reflect the eukaryotic equivalent of RecA in recombination.
true
true
true
true
true
54
7
DISCUSSION
1
41
[ "B41", "B61" ]
17,567,608
pmid-12453424|pmid-12359723
Previously we established that the Rad54 motor activity was required for Rad51 dissociation from dsDNA (41,61).
[ "41", "61" ]
111
348
0
false
Previously we established that the Rad54 motor activity was required for Rad51 dissociation from dsDNA.
[ "41,61" ]
Previously we established that the Rad54 motor activity was required for Rad51 dissociation from dsDNA.
true
true
true
true
true
55
7
DISCUSSION
1
41
[ "B41", "B61" ]
17,567,608
pmid-12453424|pmid-12359723
Here, we show that both the Rad51 and Rad54 ATPase activities are required for efficient turnover of the Rad51-dsDNA complex.
[ "41", "61" ]
125
349
0
false
Here, we show that both the Rad51 and Rad54 ATPase activities are required for efficient turnover of the Rad51-dsDNA complex.
[]
Here, we show that both the Rad51 and Rad54 ATPase activities are required for efficient turnover of the Rad51-dsDNA complex.
true
true
true
true
true
55
7
DISCUSSION
1
41
[ "B41", "B61" ]
17,567,608
pmid-12453424|pmid-12359723
The reduced dissociation efficiency of Rad51-K191R-dsDNA filaments by Rad54 appears to be a direct consequence of the ATP hydrolysis defect by Rad51-K191R protein.
[ "41", "61" ]
163
350
0
false
The reduced dissociation efficiency of Rad51-K191R-dsDNA filaments by Rad54 appears to be a direct consequence of the ATP hydrolysis defect by Rad51-K191R protein.
[]
The reduced dissociation efficiency of Rad51-K191R-dsDNA filaments by Rad54 appears to be a direct consequence of the ATP hydrolysis defect by Rad51-K191R protein.
true
true
true
true
true
55
7
DISCUSSION
1
41
[ "B41", "B61" ]
17,567,608
pmid-12453424|pmid-12359723
To rule out an unrelated defect of this protein, we assembled wild-type Rad51-dsDNA filaments in the presence of ATP-γ-S, a very slowly hydrolyzable ATP analog, and showed a similar turnover defect as with Rad51-K191R-dsDNA filaments.
[ "41", "61" ]
234
351
0
false
To rule out an unrelated defect of this protein, we assembled wild-type Rad51-dsDNA filaments in the presence of ATP-γ-S, a very slowly hydrolyzable ATP analog, and showed a similar turnover defect as with Rad51-K191R-dsDNA filaments.
[]
To rule out an unrelated defect of this protein, we assembled wild-type Rad51-dsDNA filaments in the presence of ATP-γ-S, a very slowly hydrolyzable ATP analog, and showed a similar turnover defect as with Rad51-K191R-dsDNA filaments.
true
true
true
true
true
55
7
DISCUSSION
1
41
[ "B41", "B61" ]
17,567,608
pmid-12453424|pmid-12359723
This demonstrates that the Rad51-dsDNA filament is not a passive remodeling substrate for the Rad54 motor, but that both ATPase activities modulate Rad51-dsDNA filament dynamics.
[ "41", "61" ]
178
352
0
false
This demonstrates that the Rad51-dsDNA filament is not a passive remodeling substrate for the Rad54 motor, but that both ATPase activities modulate Rad51-dsDNA filament dynamics.
[]
This demonstrates that the Rad51-dsDNA filament is not a passive remodeling substrate for the Rad54 motor, but that both ATPase activities modulate Rad51-dsDNA filament dynamics.
true
true
true
true
true
55
8
DISCUSSION
1
82
[ "B82", "B83", "B79", "B62", "B46" ]
17,567,608
pmid-12600310|pmid-11297925|pmid-1831022|pmid-16785421|pmid-11030338
Since ATP hydrolysis is closely associated with the disassembly of the Rad51-dsDNA complex, the nucleotide factors bound to Rad51 may act as a signal that determines the dynamic state of the nucleoprotein filament.
[ "82", "83", "79", "62", "46" ]
214
353
0
false
Since ATP hydrolysis is closely associated with the disassembly of the Rad51-dsDNA complex, the nucleotide factors bound to Rad51 may act as a signal that determines the dynamic state of the nucleoprotein filament.
[]
Since ATP hydrolysis is closely associated with the disassembly of the Rad51-dsDNA complex, the nucleotide factors bound to Rad51 may act as a signal that determines the dynamic state of the nucleoprotein filament.
true
true
true
true
true
56
8
DISCUSSION
1
82
[ "B82", "B83", "B79", "B62", "B46" ]
17,567,608
pmid-12600310|pmid-11297925|pmid-1831022|pmid-16785421|pmid-11030338
It is well known in actin filaments and microtubules that ATP-bound subunits associate at one end and ADP-bound subunits dissociate from the other end, leading to a treadmilling of subunits in the steady state (82,83).
[ "82", "83", "79", "62", "46" ]
218
354
0
false
It is well known in actin filaments and microtubules that ATP-bound subunits associate at one end and ADP-bound subunits dissociate from the other end, leading to a treadmilling of subunits in the steady state.
[ "82,83" ]
It is well known in actin filaments and microtubules that ATP-bound subunits associate at one end and ADP-bound subunits dissociate from the other end, leading to a treadmilling of subunits in the steady state.
true
true
true
true
true
56
8
DISCUSSION
1
79
[ "B82", "B83", "B79", "B62", "B46" ]
17,567,608
pmid-12600310|pmid-11297925|pmid-1831022|pmid-16785421|pmid-11030338
A similar model has been proposed for RecA filaments (79).
[ "82", "83", "79", "62", "46" ]
58
355
1
false
A similar model has been proposed for RecA filaments.
[ "79" ]
A similar model has been proposed for RecA filaments.
true
true
true
true
true
56
8
DISCUSSION
1
82
[ "B82", "B83", "B79", "B62", "B46" ]
17,567,608
pmid-12600310|pmid-11297925|pmid-1831022|pmid-16785421|pmid-11030338
When Rad51-dsDNA filaments were formed in the presence of ADP, spontaneous disassembly appeared unchanged.
[ "82", "83", "79", "62", "46" ]
106
356
0
false
When Rad51-dsDNA filaments were formed in the presence of ADP, spontaneous disassembly appeared unchanged.
[]
When Rad51-dsDNA filaments were formed in the presence of ADP, spontaneous disassembly appeared unchanged.
true
true
true
true
true
56
8
DISCUSSION
1
82
[ "B82", "B83", "B79", "B62", "B46" ]
17,567,608
pmid-12600310|pmid-11297925|pmid-1831022|pmid-16785421|pmid-11030338
However, in the presence of Rad54 the ADP-containing filaments were dissociated more efficiently in an ADP concentration-dependent manner (Figures 6A, B and C).
[ "82", "83", "79", "62", "46" ]
160
357
0
false
However, in the presence of Rad54 the ADP-containing filaments were dissociated more efficiently in an ADP concentration-dependent manner (Figures 6A, B and C).
[]
However, in the presence of Rad54 the ADP-containing filaments were dissociated more efficiently in an ADP concentration-dependent manner (Figures 6A, B and C).
true
true
true
true
true
56
8
DISCUSSION
1
82
[ "B82", "B83", "B79", "B62", "B46" ]
17,567,608
pmid-12600310|pmid-11297925|pmid-1831022|pmid-16785421|pmid-11030338
Hence, Rad51-ADP-dsDNA complexes are better substrates for Rad54, suggesting that the Rad54 motor may have a preference for binding to the ADP-bound end compared with the ATP-bound end.
[ "82", "83", "79", "62", "46" ]
185
358
0
false
Hence, Rad51-ADP-dsDNA complexes are better substrates for Rad54, suggesting that the Rad54 motor may have a preference for binding to the ADP-bound end compared with the ATP-bound end.
[]
Hence, Rad51-ADP-dsDNA complexes are better substrates for Rad54, suggesting that the Rad54 motor may have a preference for binding to the ADP-bound end compared with the ATP-bound end.
true
true
true
true
true
56
8
DISCUSSION
1
62
[ "B82", "B83", "B79", "B62", "B46" ]
17,567,608
pmid-12600310|pmid-11297925|pmid-1831022|pmid-16785421|pmid-11030338
This interpretation is consistent with electron microscopic observations, showing an overabundance of Rad54 particles associated with a single end of the Rad51-dsDNA filament (62).
[ "82", "83", "79", "62", "46" ]
180
359
1
false
This interpretation is consistent with electron microscopic observations, showing an overabundance of Rad54 particles associated with a single end of the Rad51-dsDNA filament.
[ "62" ]
This interpretation is consistent with electron microscopic observations, showing an overabundance of Rad54 particles associated with a single end of the Rad51-dsDNA filament.
true
true
true
true
true
56
8
DISCUSSION
1
82
[ "B82", "B83", "B79", "B62", "B46" ]
17,567,608
pmid-12600310|pmid-11297925|pmid-1831022|pmid-16785421|pmid-11030338
It is also possible that Rad54 dissociates an ATP-bound terminal subunit that leads to faster dissociation of ADP-containing Rad51 filaments.
[ "82", "83", "79", "62", "46" ]
141
360
0
false
It is also possible that Rad54 dissociates an ATP-bound terminal subunit that leads to faster dissociation of ADP-containing Rad51 filaments.
[]
It is also possible that Rad54 dissociates an ATP-bound terminal subunit that leads to faster dissociation of ADP-containing Rad51 filaments.
true
true
true
true
true
56
8
DISCUSSION
1
46
[ "B82", "B83", "B79", "B62", "B46" ]
17,567,608
pmid-12600310|pmid-11297925|pmid-1831022|pmid-16785421|pmid-11030338
During recombination, Rad54 is targeted to the pairing site by its interaction with the Rad51-ssDNA filament (46), possibly orienting the motor to the ADP-Rad51 end of the Rad51-dsDNA product complex to aid in Rad51 dissociation from dsDNA.
[ "82", "83", "79", "62", "46" ]
240
361
1
false
During recombination, Rad54 is targeted to the pairing site by its interaction with the Rad51-ssDNA filament, possibly orienting the motor to the ADP-Rad51 end of the Rad51-dsDNA product complex to aid in Rad51 dissociation from dsDNA.
[ "46" ]
During recombination, Rad54 is targeted to the pairing site by its interaction with the Rad51-ssDNA filament, possibly orienting the motor to the ADP-Rad51 end of the Rad51-dsDNA product complex to aid in Rad51 dissociation from dsDNA.
true
true
true
true
true
56
8
DISCUSSION
1
82
[ "B82", "B83", "B79", "B62", "B46" ]
17,567,608
pmid-12600310|pmid-11297925|pmid-1831022|pmid-16785421|pmid-11030338
Regulation of the dynamic state of the Rad51-dsDNA filament is likely of biological significance.
[ "82", "83", "79", "62", "46" ]
97
362
0
false
Regulation of the dynamic state of the Rad51-dsDNA filament is likely of biological significance.
[]
Regulation of the dynamic state of the Rad51-dsDNA filament is likely of biological significance.
true
true
true
true
true
56
8
DISCUSSION
1
82
[ "B82", "B83", "B79", "B62", "B46" ]
17,567,608
pmid-12600310|pmid-11297925|pmid-1831022|pmid-16785421|pmid-11030338
It not only allows recycling of Rad51, but also coordinates the transition to downstream events in the HR pathway, in particular the access of DNA polymerases to the invading 3′ end.
[ "82", "83", "79", "62", "46" ]
182
363
0
false
It not only allows recycling of Rad51, but also coordinates the transition to downstream events in the HR pathway, in particular the access of DNA polymerases to the invading 3′ end.
[]
It not only allows recycling of Rad51, but also coordinates the transition to downstream events in the HR pathway, in particular the access of DNA polymerases to the invading 3′ end.
true
true
true
true
true
56
0
INTRODUCTION
1
1
[ "b1", "b8", "b9" ]
16,914,440
pmid-16273103|pmid-16298991|pmid-12422209|pmid-15016374|pmid-15016373|pmid-15196470|pmid-10499798|pmid-8622917|pmid-12213654|pmid-14622598
Studies of bacterial transcription have traditionally involved Escherichia coli RNAP.
[ "1", "8", "9" ]
85
364
0
false
Studies of bacterial transcription have traditionally involved Escherichia coli RNAP.
[]
Studies of bacterial transcription have traditionally involved Escherichia coli RNAP.
true
true
true
true
true
57
0
INTRODUCTION
1
1
[ "b1", "b8", "b9" ]
16,914,440
pmid-16273103|pmid-16298991|pmid-12422209|pmid-15016374|pmid-15016373|pmid-15196470|pmid-10499798|pmid-8622917|pmid-12213654|pmid-14622598
While a large body of biochemical and genetic data are available for this enzyme, high-resolution structural data are still lacking.
[ "1", "8", "9" ]
132
365
0
false
While a large body of biochemical and genetic data are available for this enzyme, high-resolution structural data are still lacking.
[]
While a large body of biochemical and genetic data are available for this enzyme, high-resolution structural data are still lacking.
true
true
true
true
true
57
0
INTRODUCTION
1
1
[ "b1", "b8", "b9" ]
16,914,440
pmid-16273103|pmid-16298991|pmid-12422209|pmid-15016374|pmid-15016373|pmid-15196470|pmid-10499798|pmid-8622917|pmid-12213654|pmid-14622598
On the other hand, RNAPs from thermophilic bacteria, namely Thermus thermophilus and Thermus aquaticus, have emerged as excellent models for structural studies.
[ "1", "8", "9" ]
160
366
0
false
On the other hand, RNAPs from thermophilic bacteria, namely Thermus thermophilus and Thermus aquaticus, have emerged as excellent models for structural studies.
[]
On the other hand, RNAPs from thermophilic bacteria, namely Thermus thermophilus and Thermus aquaticus, have emerged as excellent models for structural studies.
true
true
true
true
true
57
0
INTRODUCTION
1
1
[ "b1", "b8", "b9" ]
16,914,440
pmid-16273103|pmid-16298991|pmid-12422209|pmid-15016374|pmid-15016373|pmid-15196470|pmid-10499798|pmid-8622917|pmid-12213654|pmid-14622598
In the past few years, structures of the holo enzyme (α2ββ′ωσ) of Thermus RNAPs in the presence or absence of various ligands and antibiotics have become available (1–8).
[ "1", "8", "9" ]
170
367
0
false
In the past few years, structures of the holo enzyme (α2ββ′ωσ) of Thermus RNAPs in the presence or absence of various ligands and antibiotics have become available.
[ "1–8" ]
In the past few years, structures of the holo enzyme (α2ββ′ωσ) of Thermus RNAPs in the presence or absence of various ligands and antibiotics have become available.
true
true
true
true
true
57
0
INTRODUCTION
1
1
[ "b1", "b8", "b9" ]
16,914,440
pmid-16273103|pmid-16298991|pmid-12422209|pmid-15016374|pmid-15016373|pmid-15196470|pmid-10499798|pmid-8622917|pmid-12213654|pmid-14622598
However, crystallographic characterization of transcription complexes in association with nucleic acids or transcription factors is still lagging.
[ "1", "8", "9" ]
146
368
0
false
However, crystallographic characterization of transcription complexes in association with nucleic acids or transcription factors is still lagging.
[]
However, crystallographic characterization of transcription complexes in association with nucleic acids or transcription factors is still lagging.
true
true
true
true
true
57
0
INTRODUCTION
1
9
[ "b1", "b8", "b9" ]
16,914,440
pmid-16273103|pmid-16298991|pmid-12422209|pmid-15016374|pmid-15016373|pmid-15196470|pmid-10499798|pmid-8622917|pmid-12213654|pmid-14622598
Previous efforts have shown that such studies require an extensive prior biochemical characterization to define the nature of the complexes and to provide conditions for successful crystallization (9).
[ "1", "8", "9" ]
201
369
1
false
Previous efforts have shown that such studies require an extensive prior biochemical characterization to define the nature of the complexes and to provide conditions for successful crystallization.
[ "9" ]
Previous efforts have shown that such studies require an extensive prior biochemical characterization to define the nature of the complexes and to provide conditions for successful crystallization.
true
true
true
true
true
57
0
INTRODUCTION
1
1
[ "b1", "b8", "b9" ]
16,914,440
pmid-16273103|pmid-16298991|pmid-12422209|pmid-15016374|pmid-15016373|pmid-15196470|pmid-10499798|pmid-8622917|pmid-12213654|pmid-14622598
This work represents a significant step in this direction.
[ "1", "8", "9" ]
58
370
0
false
This work represents a significant step in this direction.
[]
This work represents a significant step in this direction.
true
true
true
true
true
57
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13", "b14", "b16", "b17", "b11" ]
16,914,440
pmid-15016367|pmid-15016374|pmid-15610738|pmid-15016373|pmid-8995520|pmid-16284617|pmid-8085999|pmid-15016374|pmid-10860741|pmid-9094712|pmid-10915625
During elongation, RNAP alternates between different conformational states that are defined by the position of 3′ end of the transcript relative to the enzyme catalytic site (10,11).
[ "10", "11", "12", "13", "14", "16", "17", "11" ]
182
371
0
false
During elongation, RNAP alternates between different conformational states that are defined by the position of 3′ end of the transcript relative to the enzyme catalytic site.
[ "10,11" ]
During elongation, RNAP alternates between different conformational states that are defined by the position of 3′ end of the transcript relative to the enzyme catalytic site.
true
true
true
true
true
58
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13", "b14", "b16", "b17", "b11" ]
16,914,440
pmid-15016367|pmid-15016374|pmid-15610738|pmid-15016373|pmid-8995520|pmid-16284617|pmid-8085999|pmid-15016374|pmid-10860741|pmid-9094712|pmid-10915625
Following formation of the phosphodiester bond, the 3′ end of the RNA occupies the insertion site, and the complex is in the pretranslocated state.
[ "10", "11", "12", "13", "14", "16", "17", "11" ]
147
372
0
false
Following formation of the phosphodiester bond, the 3′ end of the RNA occupies the insertion site, and the complex is in the pretranslocated state.
[]
Following formation of the phosphodiester bond, the 3′ end of the RNA occupies the insertion site, and the complex is in the pretranslocated state.
true
true
true
true
true
58
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13", "b14", "b16", "b17", "b11" ]
16,914,440
pmid-15016367|pmid-15016374|pmid-15610738|pmid-15016373|pmid-8995520|pmid-16284617|pmid-8085999|pmid-15016374|pmid-10860741|pmid-9094712|pmid-10915625
Subsequent translocation of polymerase along the DNA template is required for the next round of the transcription cycle.
[ "10", "11", "12", "13", "14", "16", "17", "11" ]
120
373
0
false
Subsequent translocation of polymerase along the DNA template is required for the next round of the transcription cycle.
[]
Subsequent translocation of polymerase along the DNA template is required for the next round of the transcription cycle.
true
true
true
true
true
58
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13", "b14", "b16", "b17", "b11" ]
16,914,440
pmid-15016367|pmid-15016374|pmid-15610738|pmid-15016373|pmid-8995520|pmid-16284617|pmid-8085999|pmid-15016374|pmid-10860741|pmid-9094712|pmid-10915625
This transition results in the posttranslocated state of the complex, in which the 3′ end of the RNA is transferred to the product site, and the template acceptor base is available for substrate binding and selection (12,13).
[ "10", "11", "12", "13", "14", "16", "17", "11" ]
225
374
0
false
This transition results in the posttranslocated state of the complex, in which the 3′ end of the RNA is transferred to the product site, and the template acceptor base is available for substrate binding and selection.
[ "12,13" ]
This transition results in the posttranslocated state of the complex, in which the 3′ end of the RNA is transferred to the product site, and the template acceptor base is available for substrate binding and selection.
true
true
true
true
true
58
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13", "b14", "b16", "b17", "b11" ]
16,914,440
pmid-15016367|pmid-15016374|pmid-15610738|pmid-15016373|pmid-8995520|pmid-16284617|pmid-8085999|pmid-15016374|pmid-10860741|pmid-9094712|pmid-10915625
The manner in which RNAP oscillates between pre- and posttranslocated states during the nucleotide addition cycle, and what controls translocation, are poorly understood.
[ "10", "11", "12", "13", "14", "16", "17", "11" ]
170
375
0
false
The manner in which RNAP oscillates between pre- and posttranslocated states during the nucleotide addition cycle, and what controls translocation, are poorly understood.
[]
The manner in which RNAP oscillates between pre- and posttranslocated states during the nucleotide addition cycle, and what controls translocation, are poorly understood.
true
true
true
true
true
58
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13", "b14", "b16", "b17", "b11" ]
16,914,440
pmid-15016367|pmid-15016374|pmid-15610738|pmid-15016373|pmid-8995520|pmid-16284617|pmid-8085999|pmid-15016374|pmid-10860741|pmid-9094712|pmid-10915625
Several models have been proposed to explain RNAP translocation.
[ "10", "11", "12", "13", "14", "16", "17", "11" ]
64
376
0
false
Several models have been proposed to explain RNAP translocation.
[]
Several models have been proposed to explain RNAP translocation.
true
true
true
true
true
58
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13", "b14", "b16", "b17", "b11" ]
16,914,440
pmid-15016367|pmid-15016374|pmid-15610738|pmid-15016373|pmid-8995520|pmid-16284617|pmid-8085999|pmid-15016374|pmid-10860741|pmid-9094712|pmid-10915625
In the Brownian ratchet model, binding of the incoming substrate NTP stabilizes the oscillating RNAP in the posttranslocated state and serves as a pawl to prevent backward movement, as suggested by footprinting and single molecule studies (14–16).
[ "10", "11", "12", "13", "14", "16", "17", "11" ]
247
377
0
false
In the Brownian ratchet model, binding of the incoming substrate NTP stabilizes the oscillating RNAP in the posttranslocated state and serves as a pawl to prevent backward movement, as suggested by footprinting and single molecule studies.
[ "14–16" ]
In the Brownian ratchet model, binding of the incoming substrate NTP stabilizes the oscillating RNAP in the posttranslocated state and serves as a pawl to prevent backward movement, as suggested by footprinting and single molecule studies.
true
true
true
true
true
58
1
INTRODUCTION
1
17
[ "b10", "b11", "b12", "b13", "b14", "b16", "b17", "b11" ]
16,914,440
pmid-15016367|pmid-15016374|pmid-15610738|pmid-15016373|pmid-8995520|pmid-16284617|pmid-8085999|pmid-15016374|pmid-10860741|pmid-9094712|pmid-10915625
An alternative model (called the power stroke mechanism) suggests that motor proteins convert energy that derives from NTP hydrolysis into mechanical energy through conformational changes of the protein (17).
[ "10", "11", "12", "13", "14", "16", "17", "11" ]
208
378
1
false
An alternative model (called the power stroke mechanism) suggests that motor proteins convert energy that derives from NTP hydrolysis into mechanical energy through conformational changes of the protein.
[ "17" ]
An alternative model (called the power stroke mechanism) suggests that motor proteins convert energy that derives from NTP hydrolysis into mechanical energy through conformational changes of the protein.
true
true
true
true
true
58
1
INTRODUCTION
1
11
[ "b10", "b11", "b12", "b13", "b14", "b16", "b17", "b11" ]
16,914,440
pmid-15016367|pmid-15016374|pmid-15610738|pmid-15016373|pmid-8995520|pmid-16284617|pmid-8085999|pmid-15016374|pmid-10860741|pmid-9094712|pmid-10915625
An example of such a mechanism has been reported in the T7 RNAP system, where release of pyrophosphate after formation of the phosphodiester bond triggers a relaxation of a strained protein intermediate, which causes the transition from the pre- to posttranslocated state (11).
[ "10", "11", "12", "13", "14", "16", "17", "11" ]
277
379
1
false
An example of such a mechanism has been reported in the T7 RNAP system, where release of pyrophosphate after formation of the phosphodiester bond triggers a relaxation of a strained protein intermediate, which causes the transition from the pre- to posttranslocated state.
[ "11" ]
An example of such a mechanism has been reported in the T7 RNAP system, where release of pyrophosphate after formation of the phosphodiester bond triggers a relaxation of a strained protein intermediate, which causes the transition from the pre- to posttranslocated state.
true
true
true
true
true
58
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13", "b14", "b16", "b17", "b11" ]
16,914,440
pmid-15016367|pmid-15016374|pmid-15610738|pmid-15016373|pmid-8995520|pmid-16284617|pmid-8085999|pmid-15016374|pmid-10860741|pmid-9094712|pmid-10915625
In the latter case, it is the conformation of polymerase, not NTP-binding that determines the most stable position of the 3′ end of the RNA.
[ "10", "11", "12", "13", "14", "16", "17", "11" ]
140
380
0
false
In the latter case, it is the conformation of polymerase, not NTP-binding that determines the most stable position of the 3′ end of the RNA.
[]
In the latter case, it is the conformation of polymerase, not NTP-binding that determines the most stable position of the 3′ end of the RNA.
true
true
true
true
true
58
2
INTRODUCTION
1
18
[ "b18", "b22" ]
16,914,440
pmid-9050851|pmid-12727889|pmid-15610738|pmid-15610738|pmid-12242451|pmid-9843952
Elongation complexes (ECs) of bacterial RNAP halted downstream from a promoter differ significantly in their translocation conformations (18–22) which complicates studies of the mechanisms of transcription elongation.
[ "18", "22" ]
217
381
0
false
Elongation complexes (ECs) of bacterial RNAP halted downstream from a promoter differ significantly in their translocation conformations which complicates studies of the mechanisms of transcription elongation.
[ "18–22" ]
Elongation complexes (ECs) of bacterial RNAP halted downstream from a promoter differ significantly in their translocation conformations which complicates studies of the mechanisms of transcription elongation.
true
true
true
true
true
59
2
INTRODUCTION
1
18
[ "b18", "b22" ]
16,914,440
pmid-9050851|pmid-12727889|pmid-15610738|pmid-15610738|pmid-12242451|pmid-9843952
In this work, we demonstrate that ECs of Tth RNAP assembled on nucleic acid scaffolds that resemble the organization of the components of the EC have distinct translocation conformations.
[ "18", "22" ]
187
382
0
false
In this work, we demonstrate that ECs of Tth RNAP assembled on nucleic acid scaffolds that resemble the organization of the components of the EC have distinct translocation conformations.
[]
In this work, we demonstrate that ECs of Tth RNAP assembled on nucleic acid scaffolds that resemble the organization of the components of the EC have distinct translocation conformations.
true
true
true
true
true
59
2
INTRODUCTION
1
18
[ "b18", "b22" ]
16,914,440
pmid-9050851|pmid-12727889|pmid-15610738|pmid-15610738|pmid-12242451|pmid-9843952
Such complexes will be useful for functional and structural studies of ECs at different stages of the nucleotide addition cycle.
[ "18", "22" ]
128
383
0
false
Such complexes will be useful for functional and structural studies of ECs at different stages of the nucleotide addition cycle.
[]
Such complexes will be useful for functional and structural studies of ECs at different stages of the nucleotide addition cycle.
true
true
true
true
true
59
0
DISCUSSION
1
11
[ "b11", "b13", "b37", "b38", "b39", "b40", "b19" ]
16,914,440
pmid-16273103|pmid-16298991|pmid-12422209|pmid-15016374|pmid-15016373|pmid-15196470|pmid-10499798|pmid-8622917|pmid-12213654|pmid-14622598
During each catalytic cycle, transcription complexes must move along the DNA template, a process that is accompanied by conformational changes in the RNAP and the organization of the EC (11,13,37,38).
[ "11", "13", "37", "38", "39", "40", "19" ]
200
384
0
false
During each catalytic cycle, transcription complexes must move along the DNA template, a process that is accompanied by conformational changes in the RNAP and the organization of the EC.
[ "11,13,37,38" ]
During each catalytic cycle, transcription complexes must move along the DNA template, a process that is accompanied by conformational changes in the RNAP and the organization of the EC.
true
true
true
true
true
60
0
DISCUSSION
1
11
[ "b11", "b13", "b37", "b38", "b39", "b40", "b19" ]
16,914,440
pmid-16273103|pmid-16298991|pmid-12422209|pmid-15016374|pmid-15016373|pmid-15196470|pmid-10499798|pmid-8622917|pmid-12213654|pmid-14622598
Thus, the position of the active site of the enzyme relative to the 3′ end of the nascent RNA (pre and posttranslocated states) is variable, and, as shown in this study, is subject to various influences.
[ "11", "13", "37", "38", "39", "40", "19" ]
203
385
0
false
Thus, the position of the active site of the enzyme relative to the 3′ end of the nascent RNA (pre and posttranslocated states) is variable, and, as shown in this study, is subject to various influences.
[]
Thus, the position of the active site of the enzyme relative to the 3′ end of the nascent RNA (pre and posttranslocated states) is variable, and, as shown in this study, is subject to various influences.
true
true
true
true
true
60
0
DISCUSSION
1
11
[ "b11", "b13", "b37", "b38", "b39", "b40", "b19" ]
16,914,440
pmid-16273103|pmid-16298991|pmid-12422209|pmid-15016374|pmid-15016373|pmid-15196470|pmid-10499798|pmid-8622917|pmid-12213654|pmid-14622598
These factors and their effects on the equilibrium between the two states complicate the interpretation of a number of biochemical and structural studies.
[ "11", "13", "37", "38", "39", "40", "19" ]
154
386
0
false
These factors and their effects on the equilibrium between the two states complicate the interpretation of a number of biochemical and structural studies.
[]
These factors and their effects on the equilibrium between the two states complicate the interpretation of a number of biochemical and structural studies.
true
true
true
true
true
60
0
DISCUSSION
1
39
[ "b11", "b13", "b37", "b38", "b39", "b40", "b19" ]
16,914,440
pmid-16273103|pmid-16298991|pmid-12422209|pmid-15016374|pmid-15016373|pmid-15196470|pmid-10499798|pmid-8622917|pmid-12213654|pmid-14622598
For example, a number of E.coli ECs exhibited different sensitivity to exonuclease cleavage and pyrophosphorolysis and produced quite distinct patterns of cross-linking when reactive analogs were placed at the 3′ end of RNA (39).
[ "11", "13", "37", "38", "39", "40", "19" ]
229
387
1
false
For example, a number of E.coli ECs exhibited different sensitivity to exonuclease cleavage and pyrophosphorolysis and produced quite distinct patterns of cross-linking when reactive analogs were placed at the 3′ end of RNA.
[ "39" ]
For example, a number of E.coli ECs exhibited different sensitivity to exonuclease cleavage and pyrophosphorolysis and produced quite distinct patterns of cross-linking when reactive analogs were placed at the 3′ end of RNA.
true
true
true
true
true
60
0
DISCUSSION
1
40
[ "b11", "b13", "b37", "b38", "b39", "b40", "b19" ]
16,914,440
pmid-16273103|pmid-16298991|pmid-12422209|pmid-15016374|pmid-15016373|pmid-15196470|pmid-10499798|pmid-8622917|pmid-12213654|pmid-14622598
Thus, biochemical experiments have suggested that halted E.coli ECs represent a mixed population of pre and posttranslocated complexes (40).
[ "11", "13", "37", "38", "39", "40", "19" ]
140
388
1
false
Thus, biochemical experiments have suggested that halted E.coli ECs represent a mixed population of pre and posttranslocated complexes.
[ "40" ]
Thus, biochemical experiments have suggested that halted E.coli ECs represent a mixed population of pre and posttranslocated complexes.
true
true
true
true
true
60
0
DISCUSSION
1
19
[ "b11", "b13", "b37", "b38", "b39", "b40", "b19" ]
16,914,440
pmid-16273103|pmid-16298991|pmid-12422209|pmid-15016374|pmid-15016373|pmid-15196470|pmid-10499798|pmid-8622917|pmid-12213654|pmid-14622598
The heterogeneity of ECs has also been revealed in single molecule experiments (19).
[ "11", "13", "37", "38", "39", "40", "19" ]
84
389
1
false
The heterogeneity of ECs has also been revealed in single molecule experiments.
[ "19" ]
The heterogeneity of ECs has also been revealed in single molecule experiments.
true
true
true
true
true
60
1
DISCUSSION
1
41
[ "b41", "b21", "b42" ]
16,914,440
pmid-15016367|pmid-15016374|pmid-15610738|pmid-15016373|pmid-8995520|pmid-16284617|pmid-8085999|pmid-15016374|pmid-10860741|pmid-9094712|pmid-10915625
Successful crystallization of ECs, however, requires homogeneous populations of complexes.
[ "41", "21", "42" ]
90
390
0
false
Successful crystallization of ECs, however, requires homogeneous populations of complexes.
[]
Successful crystallization of ECs, however, requires homogeneous populations of complexes.
true
true
true
true
true
61
1
DISCUSSION
1
41
[ "b41", "b21", "b42" ]
16,914,440
pmid-15016367|pmid-15016374|pmid-15610738|pmid-15016373|pmid-8995520|pmid-16284617|pmid-8085999|pmid-15016374|pmid-10860741|pmid-9094712|pmid-10915625
One of the important goals of this work, therefore, was to determine conditions that would allow the formation of homogeneous populations of ECs.
[ "41", "21", "42" ]
145
391
0
false
One of the important goals of this work, therefore, was to determine conditions that would allow the formation of homogeneous populations of ECs.
[]
One of the important goals of this work, therefore, was to determine conditions that would allow the formation of homogeneous populations of ECs.
true
true
true
true
true
61
1
DISCUSSION
1
41
[ "b41", "b21", "b42" ]
16,914,440
pmid-15016367|pmid-15016374|pmid-15610738|pmid-15016373|pmid-8995520|pmid-16284617|pmid-8085999|pmid-15016374|pmid-10860741|pmid-9094712|pmid-10915625
Characterization of ECs assembled on nucleic acid scaffolds, as described in this work, offers a number of advantages over promoter-originated ECs in terms of manipulation, convenience and, particularly, homogeneity.
[ "41", "21", "42" ]
216
392
0
false
Characterization of ECs assembled on nucleic acid scaffolds, as described in this work, offers a number of advantages over promoter-originated ECs in terms of manipulation, convenience and, particularly, homogeneity.
[]
Characterization of ECs assembled on nucleic acid scaffolds, as described in this work, offers a number of advantages over promoter-originated ECs in terms of manipulation, convenience and, particularly, homogeneity.
true
true
true
true
true
61
1
DISCUSSION
1
41
[ "b41", "b21", "b42" ]
16,914,440
pmid-15016367|pmid-15016374|pmid-15610738|pmid-15016373|pmid-8995520|pmid-16284617|pmid-8085999|pmid-15016374|pmid-10860741|pmid-9094712|pmid-10915625
Interestingly, Tth RNAP ECs assembled on a 8 bp RNA:DNA hybrid scaffold appear to be in a pretranslocated form, while ECs that were assembled on a 9 bp RNA:DNA scaffold, or obtained by extension of EC8 by 1 nt, were in a posttranslocated state.
[ "41", "21", "42" ]
244
393
0
false
Interestingly, Tth RNAP ECs assembled on a 8 bp RNA:DNA hybrid scaffold appear to be in a pretranslocated form, while ECs that were assembled on a 9 bp RNA:DNA scaffold, or obtained by extension of EC8 by 1 nt, were in a posttranslocated state.
[]
Interestingly, Tth RNAP ECs assembled on a 8 bp RNA:DNA hybrid scaffold appear to be in a pretranslocated form, while ECs that were assembled on a 9 bp RNA:DNA scaffold, or obtained by extension of EC8 by 1 nt, were in a posttranslocated state.
true
true
true
true
true
61
1
DISCUSSION
1
41
[ "b41", "b21", "b42" ]
16,914,440
pmid-15016367|pmid-15016374|pmid-15610738|pmid-15016373|pmid-8995520|pmid-16284617|pmid-8085999|pmid-15016374|pmid-10860741|pmid-9094712|pmid-10915625
This difference most clearly observed during pyrophosphorolysis—posttranslocated EC9 are extremely resistant to PPi (Figure 1).
[ "41", "21", "42" ]
127
394
0
false
This difference most clearly observed during pyrophosphorolysis—posttranslocated EC9 are extremely resistant to PPi (Figure 1).
[]
This difference most clearly observed during pyrophosphorolysis—posttranslocated EC9 are extremely resistant to PPi.
true
true
true
true
true
61
1
DISCUSSION
1
41
[ "b41", "b21", "b42" ]
16,914,440
pmid-15016367|pmid-15016374|pmid-15610738|pmid-15016373|pmid-8995520|pmid-16284617|pmid-8085999|pmid-15016374|pmid-10860741|pmid-9094712|pmid-10915625
EC10 obtained by extension of EC8 by 2 nt (or by direct assembly) is highly sensitive to PPi and rapidly cleaves RNA to 9 nt.
[ "41", "21", "42" ]
125
395
0
false
EC10 obtained by extension of EC8 by 2 nt (or by direct assembly) is highly sensitive to PPi and rapidly cleaves RNA to 9 nt.
[]
EC10 obtained by extension of EC8 by 2 nt (or by direct assembly) is highly sensitive to PPi and rapidly cleaves RNA to 9 nt.
true
true
true
true
true
61
1
DISCUSSION
1
41
[ "b41", "b21", "b42" ]
16,914,440
pmid-15016367|pmid-15016374|pmid-15610738|pmid-15016373|pmid-8995520|pmid-16284617|pmid-8085999|pmid-15016374|pmid-10860741|pmid-9094712|pmid-10915625
An immediate conclusion is that RNAP in the EC10 failed to translocate upon substrate incorporation, likely due to inability to displace the 5′ end of the RNA in the hybrid in the absence of a fully complementary NT strand (41).
[ "41", "21", "42" ]
228
396
1
false
An immediate conclusion is that RNAP in the EC10 failed to translocate upon substrate incorporation, likely due to inability to displace the 5′ end of the RNA in the hybrid in the absence of a fully complementary NT strand.
[ "41" ]
An immediate conclusion is that RNAP in the EC10 failed to translocate upon substrate incorporation, likely due to inability to displace the 5′ end of the RNA in the hybrid in the absence of a fully complementary NT strand.
true
true
true
true
true
61
1
DISCUSSION
1
41
[ "b41", "b21", "b42" ]
16,914,440
pmid-15016367|pmid-15016374|pmid-15610738|pmid-15016373|pmid-8995520|pmid-16284617|pmid-8085999|pmid-15016374|pmid-10860741|pmid-9094712|pmid-10915625
This suggests that the length of RNA:DNA hybrid that gives rise to the most stable conformation for Tth RNAP is 9 bp (in the posttranslocated state) as both 8 and 10 bp scaffold ECs exhibit high sensitivity to pyrophosphorolysis.
[ "41", "21", "42" ]
229
397
0
false
This suggests that the length of RNA:DNA hybrid that gives rise to the most stable conformation for Tth RNAP is 9 bp (in the posttranslocated state) as both 8 and 10 bp scaffold ECs exhibit high sensitivity to pyrophosphorolysis.
[]
This suggests that the length of RNA:DNA hybrid that gives rise to the most stable conformation for Tth RNAP is 9 bp (in the posttranslocated state) as both 8 and 10 bp scaffold ECs exhibit high sensitivity to pyrophosphorolysis.
true
true
true
true
true
61
1
DISCUSSION
1
21
[ "b41", "b21", "b42" ]
16,914,440
pmid-15016367|pmid-15016374|pmid-15610738|pmid-15016373|pmid-8995520|pmid-16284617|pmid-8085999|pmid-15016374|pmid-10860741|pmid-9094712|pmid-10915625
This conclusion is in agreement with cross-linking data on the length of the RNA:DNA hybrid in a bacterial EC (21) and the fact, that additional interaction(s) with the transcript in the EC involve contacts with the RNA base that is 9 nt away from RNAP active site, as revealed by photo cross-linking studies (42).
[ "41", "21", "42" ]
314
398
1
false
This conclusion is in agreement with cross-linking data on the length of the RNA:DNA hybrid in a bacterial EC and the fact, that additional interaction(s) with the transcript in the EC involve contacts with the RNA base that is 9 nt away from RNAP active site, as revealed by photo cross-linking studies.
[ "21", "42" ]
This conclusion is in agreement with cross-linking data on the length of the RNA:DNA hybrid in a bacterial EC and the fact, that additional interaction(s) with the transcript in the EC involve contacts with the RNA base that is 9 nt away from RNAP active site, as revealed by photo cross-linking studies.
true
true
true
true
true
61
2
DISCUSSION
1
12
[ "b12", "b12", "b43", "b31" ]
16,914,440
pmid-9050851|pmid-12727889|pmid-15610738|pmid-15610738|pmid-12242451|pmid-9843952
In all assays used in this work assembled ECs having the same length RNA:DNA hybrid behaved similarly, regardless of scaffold topology, however, we cannot exclude that the absence of a particular DNA component affects complex conformation.
[ "12", "12", "43", "31" ]
239
399
0
false
In all assays used in this work assembled ECs having the same length RNA:DNA hybrid behaved similarly, regardless of scaffold topology, however, we cannot exclude that the absence of a particular DNA component affects complex conformation.
[]
In all assays used in this work assembled ECs having the same length RNA:DNA hybrid behaved similarly, regardless of scaffold topology, however, we cannot exclude that the absence of a particular DNA component affects complex conformation.
true
true
true
true
true
62