Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
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1
INTRODUCTION
1
17
[ "B17", "B18", "B19 B20 B21 B22", "B16", "B23", "B24", "B25", "B26", "B27", "B17", "B19", "B22", "B19", "B28 B29 B30 B31" ]
17,395,637
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A larger, inactive form contains 7SK and HEXIM proteins that together sequester active P-TEFb (17,19,22).
[ "17", "18", "19–22", "16", "23", "24", "25", "26", "27", "17", "19", "22", "19", "28–31" ]
105
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false
A larger, inactive form contains 7SK and HEXIM proteins that together sequester active P-TEFb.
[ "17,19,22" ]
A larger, inactive form contains 7SK and HEXIM proteins that together sequester active P-TEFb.
true
true
true
true
true
1,300
1
INTRODUCTION
1
19
[ "B17", "B18", "B19 B20 B21 B22", "B16", "B23", "B24", "B25", "B26", "B27", "B17", "B19", "B22", "B19", "B28 B29 B30 B31" ]
17,395,637
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When cells are treated with P-TEFb inhibitors, such as DRB, or other agents that block transcription, P-TEFb is quickly released from the large form (19).
[ "17", "18", "19–22", "16", "23", "24", "25", "26", "27", "17", "19", "22", "19", "28–31" ]
154
8,001
1
false
When cells are treated with P-TEFb inhibitors, such as DRB, or other agents that block transcription, P-TEFb is quickly released from the large form.
[ "19" ]
When cells are treated with P-TEFb inhibitors, such as DRB, or other agents that block transcription, P-TEFb is quickly released from the large form.
true
true
true
true
true
1,300
1
INTRODUCTION
1
17
[ "B17", "B18", "B19 B20 B21 B22", "B16", "B23", "B24", "B25", "B26", "B27", "B17", "B19", "B22", "B19", "B28 B29 B30 B31" ]
17,395,637
pmid-11713533|pmid-11713532|pmid-12832472|pmid-14580347|pmid-15713661|pmid-15713662|pmid-11545735|pmid-12177005|pmid-12944920|pmid-12037670|pmid-16109377|pmid-16109376|pmid-11713533|pmid-12832472|pmid-15713662|pmid-12832472|pmid-15514168|pmid-12695656|pmid-12368904|pmid-14749500|pmid-16382153|pmid-1646389|pmid-1646389
This form of P-TEFb regulation is physiologically significant, because it has been shown that all signals that trigger cardiac hypertrophy converge at the critical step of activating P-TEFb through the dissociation of 7SK and HEXIM.
[ "17", "18", "19–22", "16", "23", "24", "25", "26", "27", "17", "19", "22", "19", "28–31" ]
232
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0
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This form of P-TEFb regulation is physiologically significant, because it has been shown that all signals that trigger cardiac hypertrophy converge at the critical step of activating P-TEFb through the dissociation of 7SK and HEXIM.
[]
This form of P-TEFb regulation is physiologically significant, because it has been shown that all signals that trigger cardiac hypertrophy converge at the critical step of activating P-TEFb through the dissociation of 7SK and HEXIM.
true
true
true
true
true
1,300
1
INTRODUCTION
1
28–31
[ "B17", "B18", "B19 B20 B21 B22", "B16", "B23", "B24", "B25", "B26", "B27", "B17", "B19", "B22", "B19", "B28 B29 B30 B31" ]
17,395,637
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This activation causes increased cellular transcription and an increase in the size of cardiomyocytes (28–31).
[ "17", "18", "19–22", "16", "23", "24", "25", "26", "27", "17", "19", "22", "19", "28–31" ]
110
8,003
1
false
This activation causes increased cellular transcription and an increase in the size of cardiomyocytes.
[ "28–31" ]
This activation causes increased cellular transcription and an increase in the size of cardiomyocytes.
true
true
true
true
true
1,300
1
INTRODUCTION
1
17
[ "B17", "B18", "B19 B20 B21 B22", "B16", "B23", "B24", "B25", "B26", "B27", "B17", "B19", "B22", "B19", "B28 B29 B30 B31" ]
17,395,637
pmid-11713533|pmid-11713532|pmid-12832472|pmid-14580347|pmid-15713661|pmid-15713662|pmid-11545735|pmid-12177005|pmid-12944920|pmid-12037670|pmid-16109377|pmid-16109376|pmid-11713533|pmid-12832472|pmid-15713662|pmid-12832472|pmid-15514168|pmid-12695656|pmid-12368904|pmid-14749500|pmid-16382153|pmid-1646389|pmid-1646389
Factors that release P-TEFb from the 7SK•HEXIM1•P-TEFb complex are currently unknown.
[ "17", "18", "19–22", "16", "23", "24", "25", "26", "27", "17", "19", "22", "19", "28–31" ]
85
8,004
0
false
Factors that release P-TEFb from the 7SK•HEXIM1•P-TEFb complex are currently unknown.
[]
Factors that release P-TEFb from the 7SK•HEXIM1•P-TEFb complex are currently unknown.
true
true
true
true
true
1,300
2
INTRODUCTION
1
32
[ "B32", "B33", "B33", "B34", "B33", "B32", "B21", "B32", "B35", "B36", "B32", "B33", "B32", "B37" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15201869|pmid-15169877|pmid-15201869|pmid-15965233|pmid-15713661|pmid-15965233|pmid-15994294|pmid-16377779|pmid-15965233|pmid-15201869|pmid-15965233|pmid-14627702|pmid-16382153
Several studies have uncovered some of the important interactions in the 7SK•HEXIM1•P-TEFb complex.
[ "32", "33", "33", "34", "33", "32", "21", "32", "35", "36", "32", "33", "32", "37" ]
99
8,005
0
false
Several studies have uncovered some of the important interactions in the 7SK•HEXIM1•P-TEFb complex.
[]
Several studies have uncovered some of the important interactions in the 7SK•HEXIM1•P-TEFb complex.
true
true
true
true
true
1,301
2
INTRODUCTION
1
32
[ "B32", "B33", "B33", "B34", "B33", "B32", "B21", "B32", "B35", "B36", "B32", "B33", "B32", "B37" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15201869|pmid-15169877|pmid-15201869|pmid-15965233|pmid-15713661|pmid-15965233|pmid-15994294|pmid-16377779|pmid-15965233|pmid-15201869|pmid-15965233|pmid-14627702|pmid-16382153
Functional domains of HEXIM1 have been identified.
[ "32", "33", "33", "34", "33", "32", "21", "32", "35", "36", "32", "33", "32", "37" ]
50
8,006
0
false
Functional domains of HEXIM1 have been identified.
[]
Functional domains of HEXIM1 have been identified.
true
true
true
true
true
1,301
2
INTRODUCTION
1
32
[ "B32", "B33", "B33", "B34", "B33", "B32", "B21", "B32", "B35", "B36", "B32", "B33", "B32", "B37" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15201869|pmid-15169877|pmid-15201869|pmid-15965233|pmid-15713661|pmid-15965233|pmid-15994294|pmid-16377779|pmid-15965233|pmid-15201869|pmid-15965233|pmid-14627702|pmid-16382153
The N-terminal region of HEXIM1 (amino acids 1–120) is found to be self-inhibitory, preventing HEXIM1 from interacting with P-TEFb in the absence of 7SK (32,33).
[ "32", "33", "33", "34", "33", "32", "21", "32", "35", "36", "32", "33", "32", "37" ]
161
8,007
0
false
The N-terminal region of HEXIM1 (amino acids 1–120) is found to be self-inhibitory, preventing HEXIM1 from interacting with P-TEFb in the absence of 7SK.
[ "32,33" ]
The N-terminal region of HEXIM1 is found to be self-inhibitory, preventing HEXIM1 from interacting with P-TEFb in the absence of 7SK.
true
true
true
true
true
1,301
2
INTRODUCTION
1
32
[ "B32", "B33", "B33", "B34", "B33", "B32", "B21", "B32", "B35", "B36", "B32", "B33", "B32", "B37" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15201869|pmid-15169877|pmid-15201869|pmid-15965233|pmid-15713661|pmid-15965233|pmid-15994294|pmid-16377779|pmid-15965233|pmid-15201869|pmid-15965233|pmid-14627702|pmid-16382153
The region centered upon KHRR (amino acids 152–155) is involved in the binding of 7SK, and nearby sequences comprise nuclear localization signals (33,34).
[ "32", "33", "33", "34", "33", "32", "21", "32", "35", "36", "32", "33", "32", "37" ]
154
8,008
0
false
The region centered upon KHRR (amino acids 152–155) is involved in the binding of 7SK, and nearby sequences comprise nuclear localization signals.
[ "33,34" ]
The region centered upon KHRR is involved in the binding of 7SK, and nearby sequences comprise nuclear localization signals.
true
true
true
true
true
1,301
2
INTRODUCTION
1
32
[ "B32", "B33", "B33", "B34", "B33", "B32", "B21", "B32", "B35", "B36", "B32", "B33", "B32", "B37" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15201869|pmid-15169877|pmid-15201869|pmid-15965233|pmid-15713661|pmid-15965233|pmid-15994294|pmid-16377779|pmid-15965233|pmid-15201869|pmid-15965233|pmid-14627702|pmid-16382153
An adjacent region centered upon PYNT (amino acids 202–205) is involved in interaction with P-TEFb (33), and a small region centered upon Y271 is involved in inhibition of P-TEFb (32).
[ "32", "33", "33", "34", "33", "32", "21", "32", "35", "36", "32", "33", "32", "37" ]
184
8,009
1
false
An adjacent region centered upon PYNT (amino acids 202–205) is involved in interaction with P-TEFb, and a small region centered upon Y271 is involved in inhibition of P-TEFb.
[ "33", "32" ]
An adjacent region centered upon PYNT is involved in interaction with P-TEFb, and a small region centered upon Y271 is involved in inhibition of P-TEFb.
true
true
true
true
true
1,301
2
INTRODUCTION
1
32
[ "B32", "B33", "B33", "B34", "B33", "B32", "B21", "B32", "B35", "B36", "B32", "B33", "B32", "B37" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15201869|pmid-15169877|pmid-15201869|pmid-15965233|pmid-15713661|pmid-15965233|pmid-15994294|pmid-16377779|pmid-15965233|pmid-15201869|pmid-15965233|pmid-14627702|pmid-16382153
The C-terminal region of HEXIM1 (amino acids 281–359) mediates the dimerization of HEXIM1 via a leucine zipper motif (21,32,35,36).
[ "32", "33", "33", "34", "33", "32", "21", "32", "35", "36", "32", "33", "32", "37" ]
131
8,010
0
false
The C-terminal region of HEXIM1 mediates the dimerization of HEXIM1 via a leucine zipper motif.
[ "amino acids 281–359", "21,32,35,36" ]
The C-terminal region of HEXIM1 mediates the dimerization of HEXIM1 via a leucine zipper motif.
true
true
true
true
true
1,301
2
INTRODUCTION
1
32
[ "B32", "B33", "B33", "B34", "B33", "B32", "B21", "B32", "B35", "B36", "B32", "B33", "B32", "B37" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15201869|pmid-15169877|pmid-15201869|pmid-15965233|pmid-15713661|pmid-15965233|pmid-15994294|pmid-16377779|pmid-15965233|pmid-15201869|pmid-15965233|pmid-14627702|pmid-16382153
In addition, the regions involved in interactions have been narrowed down to amino acids 1–254 of 726 of cyclin T1, all of Cdk9 and nucleotide 1–172 of 7SK (32,33).
[ "32", "33", "33", "34", "33", "32", "21", "32", "35", "36", "32", "33", "32", "37" ]
164
8,011
0
false
In addition, the regions involved in interactions have been narrowed down to amino acids 1–254 of 726 of cyclin T1, all of Cdk9 and nucleotide 1–172 of 7SK.
[ "32,33" ]
In addition, the regions involved in interactions have been narrowed down to amino acids 1–254 of 726 of cyclin T1, all of Cdk9 and nucleotide 1–172 of 7SK.
true
true
true
true
true
1,301
2
INTRODUCTION
1
32
[ "B32", "B33", "B33", "B34", "B33", "B32", "B21", "B32", "B35", "B36", "B32", "B33", "B32", "B37" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15201869|pmid-15169877|pmid-15201869|pmid-15965233|pmid-15713661|pmid-15965233|pmid-15994294|pmid-16377779|pmid-15965233|pmid-15201869|pmid-15965233|pmid-14627702|pmid-16382153
Furthermore, phosphorylation of the T-loop of Cdk9 has been implicated in the activation of P-TEFb and is required for the formation of the 7SK•HEXIM1•P-TEFb complex (32,37).
[ "32", "33", "33", "34", "33", "32", "21", "32", "35", "36", "32", "33", "32", "37" ]
174
8,012
0
false
Furthermore, phosphorylation of the T-loop of Cdk9 has been implicated in the activation of P-TEFb and is required for the formation of the 7SK•HEXIM1•P-TEFb complex.
[ "32,37" ]
Furthermore, phosphorylation of the T-loop of Cdk9 has been implicated in the activation of P-TEFb and is required for the formation of the 7SK•HEXIM1•P-TEFb complex.
true
true
true
true
true
1,301
3
INTRODUCTION
0
null
null
17,395,637
pmid-15965233|pmid-15994294
In attempts to narrow down the minimal sequence of 7SK that is needed to form the 7SK•HEXIM1•P-TEFb complex in vitro, we serendipitously discovered that HEXIM1 is a potent dsRNA-binding protein.
null
194
8,013
0
false
null
null
In attempts to narrow down the minimal sequence of 7SK that is needed to form the 7SK•HEXIM1•P-TEFb complex in vitro, we serendipitously discovered that HEXIM1 is a potent dsRNA-binding protein.
true
true
true
true
true
1,302
3
INTRODUCTION
0
null
null
17,395,637
pmid-15965233|pmid-15994294
Further analysis revealed that dsRNA induces a conformational change in HEXIM1, so that it can interact with P-TEFb.
null
116
8,014
0
false
null
null
Further analysis revealed that dsRNA induces a conformational change in HEXIM1, so that it can interact with P-TEFb.
true
true
true
true
true
1,302
3
INTRODUCTION
0
null
null
17,395,637
pmid-15965233|pmid-15994294
In addition, in vivo studies demonstrated that endogenous HEXIM1 can be found in both the cytoplasm and nucleus, and most HEXIM1 in cells is associated with a variety of RNAs.
null
175
8,015
0
false
null
null
In addition, in vivo studies demonstrated that endogenous HEXIM1 can be found in both the cytoplasm and nucleus, and most HEXIM1 in cells is associated with a variety of RNAs.
true
true
true
true
true
1,302
3
INTRODUCTION
0
null
null
17,395,637
pmid-15965233|pmid-15994294
Interestingly, at least one microRNA was found to be associated with HEXIM1.
null
76
8,016
0
false
null
null
Interestingly, at least one microRNA was found to be associated with HEXIM1.
true
true
true
true
true
1,302
3
INTRODUCTION
0
null
null
17,395,637
pmid-15965233|pmid-15994294
These findings provide a mechanistic insight into the inhibition of P-TEFb by HEXIM1 and RNA, suggest a possible mechanism on how cells balance active and inactive forms of P-TEFb and indicate that HEXIM1 may play other roles besides inhibiting P-TEFb in vivo.
null
260
8,017
0
false
null
null
These findings provide a mechanistic insight into the inhibition of P-TEFb by HEXIM1 and RNA, suggest a possible mechanism on how cells balance active and inactive forms of P-TEFb and indicate that HEXIM1 may play other roles besides inhibiting P-TEFb in vivo.
true
true
true
true
true
1,302
0
DISCUSSION
0
null
null
17,395,637
pmid-16959964|pmid-16885020|pmid-16720337|pmid-9334325|pmid-12706900|pmid-9593731|pmid-10574912|pmid-8900211|pmid-7759473|pmid-9450929|pmid-16427012|pmid-9334325|pmid-9334326|pmid-9649438|pmid-10384302|pmid-9491887|pmid-11545735
In this article, we demonstrated that HEXIM1 is a dsRNA-binding protein, and this interaction is independent of RNA composition.
null
128
8,018
0
false
null
null
In this article, we demonstrated that HEXIM1 is a dsRNA-binding protein, and this interaction is independent of RNA composition.
true
true
true
true
true
1,303
0
DISCUSSION
0
null
null
17,395,637
pmid-16959964|pmid-16885020|pmid-16720337|pmid-9334325|pmid-12706900|pmid-9593731|pmid-10574912|pmid-8900211|pmid-7759473|pmid-9450929|pmid-16427012|pmid-9334325|pmid-9334326|pmid-9649438|pmid-10384302|pmid-9491887|pmid-11545735
Although dsDNA could interact with HEXIM1, dsRNA exhibited at least 100-fold higher affinity.
null
93
8,019
0
false
null
null
Although dsDNA could interact with HEXIM1, dsRNA exhibited at least 100-fold higher affinity.
true
true
true
true
true
1,303
0
DISCUSSION
0
null
null
17,395,637
pmid-16959964|pmid-16885020|pmid-16720337|pmid-9334325|pmid-12706900|pmid-9593731|pmid-10574912|pmid-8900211|pmid-7759473|pmid-9450929|pmid-16427012|pmid-9334325|pmid-9334326|pmid-9649438|pmid-10384302|pmid-9491887|pmid-11545735
We also provided evidence that dsRNA, but not dsDNA, binding induced a large conformational change in HEXIM1, which allows it to recruit P-TEFb.
null
144
8,020
0
false
null
null
We also provided evidence that dsRNA, but not dsDNA, binding induced a large conformational change in HEXIM1, which allows it to recruit P-TEFb.
true
true
true
true
true
1,303
0
DISCUSSION
0
null
null
17,395,637
pmid-16959964|pmid-16885020|pmid-16720337|pmid-9334325|pmid-12706900|pmid-9593731|pmid-10574912|pmid-8900211|pmid-7759473|pmid-9450929|pmid-16427012|pmid-9334325|pmid-9334326|pmid-9649438|pmid-10384302|pmid-9491887|pmid-11545735
Significantly, P-TEFb kinase activity was inhibited in this complex.
null
68
8,021
0
false
null
null
Significantly, P-TEFb kinase activity was inhibited in this complex.
true
true
true
true
true
1,303
0
DISCUSSION
0
null
null
17,395,637
pmid-16959964|pmid-16885020|pmid-16720337|pmid-9334325|pmid-12706900|pmid-9593731|pmid-10574912|pmid-8900211|pmid-7759473|pmid-9450929|pmid-16427012|pmid-9334325|pmid-9334326|pmid-9649438|pmid-10384302|pmid-9491887|pmid-11545735
Furthermore, we showed that endogenous HEXIM1 localized in both cytoplasm and the nucleus, and the majority of HEXIM1 in both locations was generally associated with RNA.
null
170
8,022
0
false
null
null
Furthermore, we showed that endogenous HEXIM1 localized in both cytoplasm and the nucleus, and the majority of HEXIM1 in both locations was generally associated with RNA.
true
true
true
true
true
1,303
1
DISCUSSION
1
40
[ "B40", "B41", "B41" ]
17,395,637
pmid-11713533|pmid-11713532|pmid-12832472|pmid-14580347|pmid-15713661|pmid-15713662|pmid-11545735|pmid-12177005|pmid-12944920|pmid-12037670|pmid-16109377|pmid-16109376|pmid-11713533|pmid-12832472|pmid-15713662|pmid-12832472|pmid-15514168|pmid-12695656|pmid-12368904|pmid-14749500|pmid-16382153|pmid-1646389|pmid-1646389
Several previous studies have analyzed the potential secondary structure of 7SK and the regions that support association with HEXIM1.
[ "40", "41", "41" ]
133
8,023
0
false
Several previous studies have analyzed the potential secondary structure of 7SK and the regions that support association with HEXIM1.
[]
Several previous studies have analyzed the potential secondary structure of 7SK and the regions that support association with HEXIM1.
true
true
true
true
true
1,304
1
DISCUSSION
1
40
[ "B40", "B41", "B41" ]
17,395,637
pmid-11713533|pmid-11713532|pmid-12832472|pmid-14580347|pmid-15713661|pmid-15713662|pmid-11545735|pmid-12177005|pmid-12944920|pmid-12037670|pmid-16109377|pmid-16109376|pmid-11713533|pmid-12832472|pmid-15713662|pmid-12832472|pmid-15514168|pmid-12695656|pmid-12368904|pmid-14749500|pmid-16382153|pmid-1646389|pmid-1646389
In an extensive analysis of 7SK sequences required for association of HEXIM1 and P-TEFb in HeLa cells, Egloff et al.
[ "40", "41", "41" ]
116
8,024
0
false
In an extensive analysis of 7SK sequences required for association of HEXIM1 and P-TEFb in HeLa cells, Egloff et al.
[]
In an extensive analysis of 7SK sequences required for association of HEXIM1 and P-TEFb in HeLa cells, Egloff et al.
true
true
true
true
true
1,304
1
DISCUSSION
1
40
[ "B40", "B41", "B41" ]
17,395,637
pmid-11713533|pmid-11713532|pmid-12832472|pmid-14580347|pmid-15713661|pmid-15713662|pmid-11545735|pmid-12177005|pmid-12944920|pmid-12037670|pmid-16109377|pmid-16109376|pmid-11713533|pmid-12832472|pmid-15713662|pmid-12832472|pmid-15514168|pmid-12695656|pmid-12368904|pmid-14749500|pmid-16382153|pmid-1646389|pmid-1646389
found that many mutations within the first 100 nt of 7SK resulted in the loss of HEXIM1 binding (40).
[ "40", "41", "41" ]
101
8,025
1
false
found that many mutations within the first 100 nt of 7SK resulted in the loss of HEXIM1 binding.
[ "40" ]
found that many mutations within the first 100 nt of 7SK resulted in the loss of HEXIM1 binding.
false
true
true
true
false
1,304
1
DISCUSSION
1
41
[ "B40", "B41", "B41" ]
17,395,637
pmid-11713533|pmid-11713532|pmid-12832472|pmid-14580347|pmid-15713661|pmid-15713662|pmid-11545735|pmid-12177005|pmid-12944920|pmid-12037670|pmid-16109377|pmid-16109376|pmid-11713533|pmid-12832472|pmid-15713662|pmid-12832472|pmid-15514168|pmid-12695656|pmid-12368904|pmid-14749500|pmid-16382153|pmid-1646389|pmid-1646389
Their mutations were based on a structure proposed in a previous study (41) that mapped chemical and nuclease sensitivities of 7SK RNA and 7SK RNPs pulled out of cells.
[ "40", "41", "41" ]
168
8,026
1
false
Their mutations were based on a structure proposed in a previous study that mapped chemical and nuclease sensitivities of 7SK RNA and 7SK RNPs pulled out of cells.
[ "41" ]
Their mutations were based on a structure proposed in a previous study that mapped chemical and nuclease sensitivities of 7SK RNA and 7SK RNPs pulled out of cells.
true
true
true
true
true
1,304
1
DISCUSSION
1
41
[ "B40", "B41", "B41" ]
17,395,637
pmid-11713533|pmid-11713532|pmid-12832472|pmid-14580347|pmid-15713661|pmid-15713662|pmid-11545735|pmid-12177005|pmid-12944920|pmid-12037670|pmid-16109377|pmid-16109376|pmid-11713533|pmid-12832472|pmid-15713662|pmid-12832472|pmid-15514168|pmid-12695656|pmid-12368904|pmid-14749500|pmid-16382153|pmid-1646389|pmid-1646389
In that study, most of the results supported the proposed structure, but several sites of moderate modification (for example, U28, U30 and U66) were inexplicably found embedded in stems, not loops, as predicted from the known function of the modification reagents used (41).
[ "40", "41", "41" ]
274
8,027
1
false
In that study, most of the results supported the proposed structure, but several sites of moderate modification (for example, U28, U30 and U66) were inexplicably found embedded in stems, not loops, as predicted from the known function of the modification reagents used.
[ "41" ]
In that study, most of the results supported the proposed structure, but several sites of moderate modification (for example, U28, U30 and U66) were inexplicably found embedded in stems, not loops, as predicted from the known function of the modification reagents used.
true
true
true
true
true
1,304
1
DISCUSSION
1
40
[ "B40", "B41", "B41" ]
17,395,637
pmid-11713533|pmid-11713532|pmid-12832472|pmid-14580347|pmid-15713661|pmid-15713662|pmid-11545735|pmid-12177005|pmid-12944920|pmid-12037670|pmid-16109377|pmid-16109376|pmid-11713533|pmid-12832472|pmid-15713662|pmid-12832472|pmid-15514168|pmid-12695656|pmid-12368904|pmid-14749500|pmid-16382153|pmid-1646389|pmid-1646389
If mFold is used to predict the secondary structure of the first 100 nt of 7SK, two different structures are predicted that have similar thermodynamic stability (Supplementary Figure 1).
[ "40", "41", "41" ]
186
8,028
0
false
If mFold is used to predict the secondary structure of the first 100 nt of 7SK, two different structures are predicted that have similar thermodynamic stability (Supplementary Figure 1).
[]
If mFold is used to predict the secondary structure of the first 100 nt of 7SK, two different structures are predicted that have similar thermodynamic stability (Supplementary Figure 1).
true
true
true
true
true
1,304
1
DISCUSSION
1
40
[ "B40", "B41", "B41" ]
17,395,637
pmid-11713533|pmid-11713532|pmid-12832472|pmid-14580347|pmid-15713661|pmid-15713662|pmid-11545735|pmid-12177005|pmid-12944920|pmid-12037670|pmid-16109377|pmid-16109376|pmid-11713533|pmid-12832472|pmid-15713662|pmid-12832472|pmid-15514168|pmid-12695656|pmid-12368904|pmid-14749500|pmid-16382153|pmid-1646389|pmid-1646389
One (ΔG = −40.06 kcal/mole) is very similar to that proposed by Wasserman and Steitz, and the other (ΔG = −40.37 kcal/mole) is completely different.
[ "40", "41", "41" ]
148
8,029
0
false
One is very similar to that proposed by Wasserman and Steitz, and the other is completely different.
[ "ΔG = −40.06 kcal/mole", "ΔG = −40.37 kcal/mole" ]
One is very similar to that proposed by Wasserman and Steitz, and the other is completely different.
true
true
true
true
true
1,304
1
DISCUSSION
1
40
[ "B40", "B41", "B41" ]
17,395,637
pmid-11713533|pmid-11713532|pmid-12832472|pmid-14580347|pmid-15713661|pmid-15713662|pmid-11545735|pmid-12177005|pmid-12944920|pmid-12037670|pmid-16109377|pmid-16109376|pmid-11713533|pmid-12832472|pmid-15713662|pmid-12832472|pmid-15514168|pmid-12695656|pmid-12368904|pmid-14749500|pmid-16382153|pmid-1646389|pmid-1646389
In the slightly more stable second structure, U28, U30 and U66 are present in two prominent loops instead of stems.
[ "40", "41", "41" ]
115
8,030
0
false
In the slightly more stable second structure, U28, U30 and U66 are present in two prominent loops instead of stems.
[]
In the slightly more stable second structure, U28, U30 and U66 are present in two prominent loops instead of stems.
true
true
true
true
true
1,304
1
DISCUSSION
1
40
[ "B40", "B41", "B41" ]
17,395,637
pmid-11713533|pmid-11713532|pmid-12832472|pmid-14580347|pmid-15713661|pmid-15713662|pmid-11545735|pmid-12177005|pmid-12944920|pmid-12037670|pmid-16109377|pmid-16109376|pmid-11713533|pmid-12832472|pmid-15713662|pmid-12832472|pmid-15514168|pmid-12695656|pmid-12368904|pmid-14749500|pmid-16382153|pmid-1646389|pmid-1646389
The complete chemical and nuclease sensitivity data would be accommodated, if the isolated 7SK RNP contained a mixture of the two structures.
[ "40", "41", "41" ]
141
8,031
0
false
The complete chemical and nuclease sensitivity data would be accommodated, if the isolated 7SK RNP contained a mixture of the two structures.
[]
The complete chemical and nuclease sensitivity data would be accommodated, if the isolated 7SK RNP contained a mixture of the two structures.
true
true
true
true
true
1,304
1
DISCUSSION
1
40
[ "B40", "B41", "B41" ]
17,395,637
pmid-11713533|pmid-11713532|pmid-12832472|pmid-14580347|pmid-15713661|pmid-15713662|pmid-11545735|pmid-12177005|pmid-12944920|pmid-12037670|pmid-16109377|pmid-16109376|pmid-11713533|pmid-12832472|pmid-15713662|pmid-12832472|pmid-15514168|pmid-12695656|pmid-12368904|pmid-14749500|pmid-16382153|pmid-1646389|pmid-1646389
The structure predicted for 7SK 10–48 used in our study is present in the alternative structure predicted for the entire 1–100 nt of 7SK (compare Figure 1 with Supplementary Figure 1).
[ "40", "41", "41" ]
184
8,032
0
false
The structure predicted for 7SK 10–48 used in our study is present in the alternative structure predicted for the entire 1–100 nt of 7SK (compare Figure 1 with Supplementary Figure 1).
[]
The structure predicted for 7SK 10–48 used in our study is present in the alternative structure predicted for the entire 1–100 nt of 7SK (compare Figure 1 with Supplementary Figure 1).
true
true
true
true
true
1,304
1
DISCUSSION
1
40
[ "B40", "B41", "B41" ]
17,395,637
pmid-11713533|pmid-11713532|pmid-12832472|pmid-14580347|pmid-15713661|pmid-15713662|pmid-11545735|pmid-12177005|pmid-12944920|pmid-12037670|pmid-16109377|pmid-16109376|pmid-11713533|pmid-12832472|pmid-15713662|pmid-12832472|pmid-15514168|pmid-12695656|pmid-12368904|pmid-14749500|pmid-16382153|pmid-1646389|pmid-1646389
Our results clearly demonstrate that HEXIM1 can bind to 7SK 10–48 or other short dsRNAs in vitro.
[ "40", "41", "41" ]
97
8,033
0
false
Our results clearly demonstrate that HEXIM1 can bind to 7SK 10–48 or other short dsRNAs in vitro.
[]
Our results clearly demonstrate that HEXIM1 can bind to 7SK 10–48 or other short dsRNAs in vitro.
true
true
true
true
true
1,304
1
DISCUSSION
1
40
[ "B40", "B41", "B41" ]
17,395,637
pmid-11713533|pmid-11713532|pmid-12832472|pmid-14580347|pmid-15713661|pmid-15713662|pmid-11545735|pmid-12177005|pmid-12944920|pmid-12037670|pmid-16109377|pmid-16109376|pmid-11713533|pmid-12832472|pmid-15713662|pmid-12832472|pmid-15514168|pmid-12695656|pmid-12368904|pmid-14749500|pmid-16382153|pmid-1646389|pmid-1646389
However, determination of what 7SK structure is present when HEXIM1 and P-TEFb are associated in vivo will require chemical modification analysis of the RNA in 7SK RNPs pulled down with antibodies to HEXIM1 or P-TEFb.
[ "40", "41", "41" ]
217
8,034
0
false
However, determination of what 7SK structure is present when HEXIM1 and P-TEFb are associated in vivo will require chemical modification analysis of the RNA in 7SK RNPs pulled down with antibodies to HEXIM1 or P-TEFb.
[]
However, determination of what 7SK structure is present when HEXIM1 and P-TEFb are associated in vivo will require chemical modification analysis of the RNA in 7SK RNPs pulled down with antibodies to HEXIM1 or P-TEFb.
true
true
true
true
true
1,304
2
DISCUSSION
1
40
[ "B40" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15201869|pmid-15169877|pmid-15201869|pmid-15965233|pmid-15713661|pmid-15965233|pmid-15994294|pmid-16377779|pmid-15965233|pmid-15201869|pmid-15965233|pmid-14627702|pmid-16382153
Here, we demonstrated that dsRNA can functionally replace 7SK in vitro, and that most HEXIM1 is associated with RNAs in vivo, yet in cells, 7SK is the only identified RNA that allows formation of a complex with both HEXIM1 and P-TEFb.
[ "40" ]
234
8,035
0
false
Here, we demonstrated that dsRNA can functionally replace 7SK in vitro, and that most HEXIM1 is associated with RNAs in vivo, yet in cells, 7SK is the only identified RNA that allows formation of a complex with both HEXIM1 and P-TEFb.
[]
Here, we demonstrated that dsRNA can functionally replace 7SK in vitro, and that most HEXIM1 is associated with RNAs in vivo, yet in cells, 7SK is the only identified RNA that allows formation of a complex with both HEXIM1 and P-TEFb.
true
true
true
true
true
1,305
2
DISCUSSION
1
40
[ "B40" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15201869|pmid-15169877|pmid-15201869|pmid-15965233|pmid-15713661|pmid-15965233|pmid-15994294|pmid-16377779|pmid-15965233|pmid-15201869|pmid-15965233|pmid-14627702|pmid-16382153
A small stem and loop near the 3′ end of 7SK has been shown to be essential for P-TEFb association in vivo (40).
[ "40" ]
112
8,036
1
false
A small stem and loop near the 3′ end of 7SK has been shown to be essential for P-TEFb association in vivo.
[ "40" ]
A small stem and loop near the 3′ end of 7SK has been shown to be essential for P-TEFb association in vivo.
true
true
true
true
true
1,305
2
DISCUSSION
1
40
[ "B40" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15201869|pmid-15169877|pmid-15201869|pmid-15965233|pmid-15713661|pmid-15965233|pmid-15994294|pmid-16377779|pmid-15965233|pmid-15201869|pmid-15965233|pmid-14627702|pmid-16382153
However, our results indicate that that region of 7SK is not needed in vitro and, in fact, that no region of 7SK is needed for the dsRNA-dependent conformational change that results in recruitment and inhibition of P-TEFb.
[ "40" ]
222
8,037
0
false
However, our results indicate that that region of 7SK is not needed in vitro and, in fact, that no region of 7SK is needed for the dsRNA-dependent conformational change that results in recruitment and inhibition of P-TEFb.
[]
However, our results indicate that that region of 7SK is not needed in vitro and, in fact, that no region of 7SK is needed for the dsRNA-dependent conformational change that results in recruitment and inhibition of P-TEFb.
true
true
true
true
true
1,305
2
DISCUSSION
1
40
[ "B40" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15201869|pmid-15169877|pmid-15201869|pmid-15965233|pmid-15713661|pmid-15965233|pmid-15994294|pmid-16377779|pmid-15965233|pmid-15201869|pmid-15965233|pmid-14627702|pmid-16382153
Because the two studies measured HEXIM1 and P-TEFb binding under very different conditions, the results are not contradictory.
[ "40" ]
126
8,038
0
false
Because the two studies measured HEXIM1 and P-TEFb binding under very different conditions, the results are not contradictory.
[]
Because the two studies measured HEXIM1 and P-TEFb binding under very different conditions, the results are not contradictory.
true
true
true
true
true
1,305
2
DISCUSSION
1
40
[ "B40" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15201869|pmid-15169877|pmid-15201869|pmid-15965233|pmid-15713661|pmid-15965233|pmid-15994294|pmid-16377779|pmid-15965233|pmid-15201869|pmid-15965233|pmid-14627702|pmid-16382153
However, they suggest an interesting possibility.
[ "40" ]
49
8,039
0
false
However, they suggest an interesting possibility.
[]
However, they suggest an interesting possibility.
true
true
true
true
true
1,305
2
DISCUSSION
1
40
[ "B40" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15201869|pmid-15169877|pmid-15201869|pmid-15965233|pmid-15713661|pmid-15965233|pmid-15994294|pmid-16377779|pmid-15965233|pmid-15201869|pmid-15965233|pmid-14627702|pmid-16382153
There could be a modification in HEXIM1, for example in its P-TEFb interaction domain, which prevents it from interacting with P-TEFb even when bound with RNAs.
[ "40" ]
160
8,040
0
false
There could be a modification in HEXIM1, for example in its P-TEFb interaction domain, which prevents it from interacting with P-TEFb even when bound with RNAs.
[]
There could be a modification in HEXIM1, for example in its P-TEFb interaction domain, which prevents it from interacting with P-TEFb even when bound with RNAs.
true
true
true
true
true
1,305
2
DISCUSSION
1
40
[ "B40" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15201869|pmid-15169877|pmid-15201869|pmid-15965233|pmid-15713661|pmid-15965233|pmid-15994294|pmid-16377779|pmid-15965233|pmid-15201869|pmid-15965233|pmid-14627702|pmid-16382153
This modification would not be present on the recombinant HEXIM1 utilized for the in vitro experiments here, but could be present on the endogenous HEXIM1.
[ "40" ]
155
8,041
0
false
This modification would not be present on the recombinant HEXIM1 utilized for the in vitro experiments here, but could be present on the endogenous HEXIM1.
[]
This modification would not be present on the recombinant HEXIM1 utilized for the in vitro experiments here, but could be present on the endogenous HEXIM1.
true
true
true
true
true
1,305
2
DISCUSSION
1
40
[ "B40" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15201869|pmid-15169877|pmid-15201869|pmid-15965233|pmid-15713661|pmid-15965233|pmid-15994294|pmid-16377779|pmid-15965233|pmid-15201869|pmid-15965233|pmid-14627702|pmid-16382153
A factor associated with the 3′ end of 7SK, but not other RNAs, could be responsible for removing this negative modification from HEXIM1, thereby allowing only 7SK•HEXIM1 but not other RNA•HEXIM1 complexes to recruit P-TEFb.
[ "40" ]
224
8,042
0
false
A factor associated with the 3′ end of 7SK, but not other RNAs, could be responsible for removing this negative modification from HEXIM1, thereby allowing only 7SK•HEXIM1 but not other RNA•HEXIM1 complexes to recruit P-TEFb.
[]
A factor associated with the 3′ end of 7SK, but not other RNAs, could be responsible for removing this negative modification from HEXIM1, thereby allowing only 7SK•HEXIM1 but not other RNA•HEXIM1 complexes to recruit P-TEFb.
true
true
true
true
true
1,305
3
DISCUSSION
1
32
[ "B32", "B35" ]
17,395,637
pmid-15965233|pmid-15994294
The finding that HEXIM1 is a dsRNA-binding protein is surprising because 7SK has been previously regarded as the only RNA associated with HEXIM1.
[ "32", "35" ]
145
8,043
0
false
The finding that HEXIM1 is a dsRNA-binding protein is surprising because 7SK has been previously regarded as the only RNA associated with HEXIM1.
[]
The finding that HEXIM1 is a dsRNA-binding protein is surprising because 7SK has been previously regarded as the only RNA associated with HEXIM1.
true
true
true
true
true
1,306
3
DISCUSSION
1
32
[ "B32", "B35" ]
17,395,637
pmid-15965233|pmid-15994294
Although dsDNA could interact with HEXIM1 (Figure 2A), this interaction can be readily displaced by dsRNA (Figure 3C).
[ "32", "35" ]
118
8,044
0
false
Although dsDNA could interact with HEXIM1 (Figure 2A), this interaction can be readily displaced by dsRNA (Figure 3C).
[]
Although dsDNA could interact with HEXIM1, this interaction can be readily displaced by dsRNA.
true
true
true
true
true
1,306
3
DISCUSSION
1
32
[ "B32", "B35" ]
17,395,637
pmid-15965233|pmid-15994294
On the contrary, dsRNA•HEXIM1 interaction is very stable and cannot be disrupted by dsDNA (Figure 3B).
[ "32", "35" ]
102
8,045
0
false
On the contrary, dsRNA•HEXIM1 interaction is very stable and cannot be disrupted by dsDNA (Figure 3B).
[]
On the contrary, dsRNA•HEXIM1 interaction is very stable and cannot be disrupted by dsDNA.
true
true
true
true
true
1,306
3
DISCUSSION
1
32
[ "B32", "B35" ]
17,395,637
pmid-15965233|pmid-15994294
Our results demonstrate that HEXIM1 prefers to bind A-form nucleic acids, and also suggest that dsDNA•HEXIM1 interaction may not be physiologically relevant.
[ "32", "35" ]
157
8,046
0
false
Our results demonstrate that HEXIM1 prefers to bind A-form nucleic acids, and also suggest that dsDNA•HEXIM1 interaction may not be physiologically relevant.
[]
Our results demonstrate that HEXIM1 prefers to bind A-form nucleic acids, and also suggest that dsDNA•HEXIM1 interaction may not be physiologically relevant.
true
true
true
true
true
1,306
3
DISCUSSION
1
32
[ "B32", "B35" ]
17,395,637
pmid-15965233|pmid-15994294
Our unpublished data indicated that the minimal length of dsRNA for HEXIM1 interaction is 12 bp.
[ "32", "35" ]
96
8,047
0
false
Our unpublished data indicated that the minimal length of dsRNA for HEXIM1 interaction is 12 bp.
[]
Our unpublished data indicated that the minimal length of dsRNA for HEXIM1 interaction is 12 bp.
true
true
true
true
true
1,306
3
DISCUSSION
1
32
[ "B32", "B35" ]
17,395,637
pmid-15965233|pmid-15994294
However, there are no uninterrupted helices of >10 nt in 7SK and 7SK (10–48) (Figure 1B).
[ "32", "35" ]
89
8,048
0
false
However, there are no uninterrupted helices of >10 nt in 7SK and 7SK (10–48) (Figure 1B).
[]
However, there are no uninterrupted helices of >10 nt in 7SK and 7SK (10–48) (Figure 1B).
true
true
true
true
true
1,306
3
DISCUSSION
1
32
[ "B32", "B35" ]
17,395,637
pmid-15965233|pmid-15994294
Taking into consideration that HEXIM1 is a dimer with two RNA-interaction regions (32,35) and HEXIM1 monomer does not bind RNA (data not shown), each HEXIM1 RNA-interaction region may bind a short stretch of dsRNA, and the distance between the two RNA-interaction regions has to be at least the length of a 12-bp dsRNA.
[ "32", "35" ]
319
8,049
0
false
Taking into consideration that HEXIM1 is a dimer with two RNA-interaction regions and HEXIM1 monomer does not bind RNA (data not shown), each HEXIM1 RNA-interaction region may bind a short stretch of dsRNA, and the distance between the two RNA-interaction regions has to be at least the length of a 12-bp dsRNA.
[ "32,35" ]
Taking into consideration that HEXIM1 is a dimer with two RNA-interaction regions and HEXIM1 monomer does not bind RNA (data not shown), each HEXIM1 RNA-interaction region may bind a short stretch of dsRNA, and the distance between the two RNA-interaction regions has to be at least the length of a 12-bp dsRNA.
true
true
true
true
true
1,306
3
DISCUSSION
1
32
[ "B32", "B35" ]
17,395,637
pmid-15965233|pmid-15994294
It is not clear if structures in between the two short stretches of dsRNA regions contribute significantly to the dsRNA•HEXIM1 interaction.
[ "32", "35" ]
139
8,050
0
false
It is not clear if structures in between the two short stretches of dsRNA regions contribute significantly to the dsRNA•HEXIM1 interaction.
[]
It is not clear if structures in between the two short stretches of dsRNA regions contribute significantly to the dsRNA•HEXIM1 interaction.
true
true
true
true
true
1,306
4
DISCUSSION
1
32
[ "B32", "B33", "B21", "B22", "B35" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15713661|pmid-15713662|pmid-15994294
We provide two lines of evidence to support the previous hypothesis that RNA binding induces a conformational change in N-terminal self-inhibitory domain of HEXIM1 (32,33).
[ "32", "33", "21", "22", "35" ]
172
8,051
0
false
We provide two lines of evidence to support the previous hypothesis that RNA binding induces a conformational change in N-terminal self-inhibitory domain of HEXIM1.
[ "32,33" ]
We provide two lines of evidence to support the previous hypothesis that RNA binding induces a conformational change in N-terminal self-inhibitory domain of HEXIM1.
true
true
true
true
true
1,307
4
DISCUSSION
1
32
[ "B32", "B33", "B21", "B22", "B35" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15713661|pmid-15713662|pmid-15994294
The first line of evidence came from the observation that dsRNA reduced the mobility of HEXIM1 dramatically.
[ "32", "33", "21", "22", "35" ]
108
8,052
0
false
The first line of evidence came from the observation that dsRNA reduced the mobility of HEXIM1 dramatically.
[]
The first line of evidence came from the observation that dsRNA reduced the mobility of HEXIM1 dramatically.
true
true
true
true
true
1,307
4
DISCUSSION
1
32
[ "B32", "B33", "B21", "B22", "B35" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15713661|pmid-15713662|pmid-15994294
There are two major determinants for a protein's mobility on a native gel, i.e.
[ "32", "33", "21", "22", "35" ]
79
8,053
0
false
There are two major determinants for a protein's mobility on a native gel, i.e.
[]
There are two major determinants for a protein's mobility on a native gel, i.e.
true
true
true
true
true
1,307
4
DISCUSSION
1
32
[ "B32", "B33", "B21", "B22", "B35" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15713661|pmid-15713662|pmid-15994294
its overall negative charges and its shape.
[ "32", "33", "21", "22", "35" ]
43
8,054
0
false
its overall negative charges and its shape.
[]
its overall negative charges and its shape.
false
true
true
true
false
1,307
4
DISCUSSION
1
32
[ "B32", "B33", "B21", "B22", "B35" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15713661|pmid-15713662|pmid-15994294
More negative charges and a compact conformation would give rise to a faster migration than a less negative charged and extended conformation.
[ "32", "33", "21", "22", "35" ]
142
8,055
0
false
More negative charges and a compact conformation would give rise to a faster migration than a less negative charged and extended conformation.
[]
More negative charges and a compact conformation would give rise to a faster migration than a less negative charged and extended conformation.
true
true
true
true
true
1,307
4
DISCUSSION
1
32
[ "B32", "B33", "B21", "B22", "B35" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15713661|pmid-15713662|pmid-15994294
Considering that the overall negative charge of the dsRNA•HEXIM1 complex is increased significantly, one would expect that the mobility of HEXIM1 should increase.
[ "32", "33", "21", "22", "35" ]
162
8,056
0
false
Considering that the overall negative charge of the dsRNA•HEXIM1 complex is increased significantly, one would expect that the mobility of HEXIM1 should increase.
[]
Considering that the overall negative charge of the dsRNA•HEXIM1 complex is increased significantly, one would expect that the mobility of HEXIM1 should increase.
true
true
true
true
true
1,307
4
DISCUSSION
1
32
[ "B32", "B33", "B21", "B22", "B35" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15713661|pmid-15713662|pmid-15994294
Instead, dsRNA•HEXIM1 showed slower mobility than HEXIM1, suggesting that it adapts a more expanded conformation.
[ "32", "33", "21", "22", "35" ]
113
8,057
0
false
Instead, dsRNA•HEXIM1 showed slower mobility than HEXIM1, suggesting that it adapts a more expanded conformation.
[]
Instead, dsRNA•HEXIM1 showed slower mobility than HEXIM1, suggesting that it adapts a more expanded conformation.
true
true
true
true
true
1,307
4
DISCUSSION
1
32
[ "B32", "B33", "B21", "B22", "B35" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15713661|pmid-15713662|pmid-15994294
In fact, HEXIM2 (21,22,35), a HEXIM1 homolog that has a much shorter N-terminal domain, but otherwise shares high sequence identity with HEXIM1, showed increased mobility upon dsRNA binding (data not shown).
[ "32", "33", "21", "22", "35" ]
207
8,058
0
false
In fact, HEXIM2, a HEXIM1 homolog that has a much shorter N-terminal domain, but otherwise shares high sequence identity with HEXIM1, showed increased mobility upon dsRNA binding (data not shown).
[ "21,22,35" ]
In fact, HEXIM2, a HEXIM1 homolog that has a much shorter N-terminal domain, but otherwise shares high sequence identity with HEXIM1, showed increased mobility upon dsRNA binding (data not shown).
true
true
true
true
true
1,307
4
DISCUSSION
1
32
[ "B32", "B33", "B21", "B22", "B35" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15713661|pmid-15713662|pmid-15994294
The second line of evidence came from a large decrease in intrinsic tryptophan fluorescence and a slight shift of the emission peak upon dsRNA, but not dsDNA binding.
[ "32", "33", "21", "22", "35" ]
166
8,059
0
false
The second line of evidence came from a large decrease in intrinsic tryptophan fluorescence and a slight shift of the emission peak upon dsRNA, but not dsDNA binding.
[]
The second line of evidence came from a large decrease in intrinsic tryptophan fluorescence and a slight shift of the emission peak upon dsRNA, but not dsDNA binding.
true
true
true
true
true
1,307
4
DISCUSSION
1
32
[ "B32", "B33", "B21", "B22", "B35" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15713661|pmid-15713662|pmid-15994294
Although a decrease in intrinsic fluorescence could be caused by the quenching of tryptophan fluorescence by nucleic acids, only dsRNA, but not dsDNA, reduced the intrinsic fluorescence of HEXIM1 dramatically.
[ "32", "33", "21", "22", "35" ]
209
8,060
0
false
Although a decrease in intrinsic fluorescence could be caused by the quenching of tryptophan fluorescence by nucleic acids, only dsRNA, but not dsDNA, reduced the intrinsic fluorescence of HEXIM1 dramatically.
[]
Although a decrease in intrinsic fluorescence could be caused by the quenching of tryptophan fluorescence by nucleic acids, only dsRNA, but not dsDNA, reduced the intrinsic fluorescence of HEXIM1 dramatically.
true
true
true
true
true
1,307
4
DISCUSSION
1
32
[ "B32", "B33", "B21", "B22", "B35" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15713661|pmid-15713662|pmid-15994294
In addition, only dsRNA, but not dsDNA, caused a shift of the emission wavelength.
[ "32", "33", "21", "22", "35" ]
82
8,061
0
false
In addition, only dsRNA, but not dsDNA, caused a shift of the emission wavelength.
[]
In addition, only dsRNA, but not dsDNA, caused a shift of the emission wavelength.
true
true
true
true
true
1,307
4
DISCUSSION
1
32
[ "B32", "B33", "B21", "B22", "B35" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15713661|pmid-15713662|pmid-15994294
This is consistent with the observation, obtained from the native gel analysis, that only dsRNA but not dsDNA, reduces the mobility of HEXIM1 dramatically.
[ "32", "33", "21", "22", "35" ]
155
8,062
0
false
This is consistent with the observation, obtained from the native gel analysis, that only dsRNA but not dsDNA, reduces the mobility of HEXIM1 dramatically.
[]
This is consistent with the observation, obtained from the native gel analysis, that only dsRNA but not dsDNA, reduces the mobility of HEXIM1 dramatically.
true
true
true
true
true
1,307
4
DISCUSSION
1
32
[ "B32", "B33", "B21", "B22", "B35" ]
17,395,637
pmid-15965233|pmid-15201869|pmid-15713661|pmid-15713662|pmid-15994294
Taking all the evidence into account, it is likely that, upon dsRNA binding, there is a conformational change in HEXIM1 that exposes the P-TEFb-binding site.
[ "32", "33", "21", "22", "35" ]
157
8,063
0
false
Taking all the evidence into account, it is likely that, upon dsRNA binding, there is a conformational change in HEXIM1 that exposes the P-TEFb-binding site.
[]
Taking all the evidence into account, it is likely that, upon dsRNA binding, there is a conformational change in HEXIM1 that exposes the P-TEFb-binding site.
true
true
true
true
true
1,307
5
DISCUSSION
1
32
[ "B32", "B35" ]
17,395,637
pmid-15965233|pmid-15994294
Another interesting observation is that after RNase A treatment, both cytoplasmic and nuclear HEXIM1 migrated the same as the recombinant HEXIM1 protein on a native gel.
[ "32", "35" ]
169
8,064
0
false
Another interesting observation is that after RNase A treatment, both cytoplasmic and nuclear HEXIM1 migrated the same as the recombinant HEXIM1 protein on a native gel.
[]
Another interesting observation is that after RNase A treatment, both cytoplasmic and nuclear HEXIM1 migrated the same as the recombinant HEXIM1 protein on a native gel.
true
true
true
true
true
1,308
5
DISCUSSION
1
32
[ "B32", "B35" ]
17,395,637
pmid-15965233|pmid-15994294
Recombinant HEXIM1 has been shown to be a dimer (32) under the same condition.
[ "32", "35" ]
78
8,065
1
false
Recombinant HEXIM1 has been shown to be a dimer under the same condition.
[ "32" ]
Recombinant HEXIM1 has been shown to be a dimer under the same condition.
true
true
true
true
true
1,308
5
DISCUSSION
1
32
[ "B32", "B35" ]
17,395,637
pmid-15965233|pmid-15994294
Therefore, endogenous HEXIM1 is likely to be a dimer as well.
[ "32", "35" ]
61
8,066
0
false
Therefore, endogenous HEXIM1 is likely to be a dimer as well.
[]
Therefore, endogenous HEXIM1 is likely to be a dimer as well.
true
true
true
true
true
1,308
5
DISCUSSION
1
32
[ "B32", "B35" ]
17,395,637
pmid-15965233|pmid-15994294
The calculated molecular weight for a HEXIM1 dimer is 80 kDa.
[ "32", "35" ]
61
8,067
0
false
The calculated molecular weight for a HEXIM1 dimer is 80 kDa.
[]
The calculated molecular weight for a HEXIM1 dimer is 80 kDa.
true
true
true
true
true
1,308
5
DISCUSSION
1
35
[ "B32", "B35" ]
17,395,637
pmid-15965233|pmid-15994294
However, biophysical studies estimated that endogenous HEXIM1, free of 7SK and P-TEFb, has a size of 95–130 kDa (35).
[ "32", "35" ]
117
8,068
1
false
However, biophysical studies estimated that endogenous HEXIM1, free of 7SK and P-TEFb, has a size of 95–130 kDa.
[ "35" ]
However, biophysical studies estimated that endogenous HEXIM1, free of 7SK and P-TEFb, has a size of 95–130 kDa.
true
true
true
true
true
1,308
5
DISCUSSION
1
32
[ "B32", "B35" ]
17,395,637
pmid-15965233|pmid-15994294
Our observation that most endogenous HEXIM1 has RNAs associated could explain this apparent discrepancy.
[ "32", "35" ]
104
8,069
0
false
Our observation that most endogenous HEXIM1 has RNAs associated could explain this apparent discrepancy.
[]
Our observation that most endogenous HEXIM1 has RNAs associated could explain this apparent discrepancy.
true
true
true
true
true
1,308
6
DISCUSSION
1
42
[ "B42", "B42 B43 B44" ]
17,395,637
pmid-15573138|pmid-15573138|pmid-15853796|pmid-10782096
dsRNA-binding proteins are involved in a variety of cellular processes such as RNA editing, RNAi, viral defense and transcription (42).
[ "42", "42–44" ]
135
8,070
1
false
dsRNA-binding proteins are involved in a variety of cellular processes such as RNA editing, RNAi, viral defense and transcription.
[ "42" ]
dsRNA-binding proteins are involved in a variety of cellular processes such as RNA editing, RNAi, viral defense and transcription.
false
true
true
true
false
1,309
6
DISCUSSION
1
42
[ "B42", "B42 B43 B44" ]
17,395,637
pmid-15573138|pmid-15573138|pmid-15853796|pmid-10782096
Unlike most dsRNA-binding proteins, HEXIM1 lacks the characteristic 50–100 amino acid dsRNA-binding motif (dsRBM).
[ "42", "42–44" ]
114
8,071
0
false
Unlike most dsRNA-binding proteins, HEXIM1 lacks the characteristic 50–100 amino acid dsRNA-binding motif (dsRBM).
[]
Unlike most dsRNA-binding proteins, HEXIM1 lacks the characteristic 50–100 amino acid dsRNA-binding motif (dsRBM).
true
true
true
true
true
1,309
6
DISCUSSION
1
42
[ "B42", "B42 B43 B44" ]
17,395,637
pmid-15573138|pmid-15573138|pmid-15853796|pmid-10782096
The RNA-binding ability of HEXIM1 largely depends on KHRR (amino acids 152–155).
[ "42", "42–44" ]
80
8,072
0
false
The RNA-binding ability of HEXIM1 largely depends on KHRR (amino acids 152–155).
[]
The RNA-binding ability of HEXIM1 largely depends on KHRR.
true
true
true
true
true
1,309
6
DISCUSSION
1
42
[ "B42", "B42 B43 B44" ]
17,395,637
pmid-15573138|pmid-15573138|pmid-15853796|pmid-10782096
On the other hand, like most, if not all, characterized dsRNA-binding proteins, HEXIM1 binds to any dsRNA, regardless of its primary sequence in vitro.
[ "42", "42–44" ]
151
8,073
0
false
On the other hand, like most, if not all, characterized dsRNA-binding proteins, HEXIM1 binds to any dsRNA, regardless of its primary sequence in vitro.
[]
On the other hand, like most, if not all, characterized dsRNA-binding proteins, HEXIM1 binds to any dsRNA, regardless of its primary sequence in vitro.
true
true
true
true
true
1,309
6
DISCUSSION
1
42
[ "B42", "B42 B43 B44" ]
17,395,637
pmid-15573138|pmid-15573138|pmid-15853796|pmid-10782096
Given this, a dsRNA substrate of one dsRNA-binding protein could easily be bound by other dsRNA proteins in the cell, resulting in crosstalk between different dsRNA-mediated pathways.
[ "42", "42–44" ]
183
8,074
0
false
Given this, a dsRNA substrate of one dsRNA-binding protein could easily be bound by other dsRNA proteins in the cell, resulting in crosstalk between different dsRNA-mediated pathways.
[]
Given this, a dsRNA substrate of one dsRNA-binding protein could easily be bound by other dsRNA proteins in the cell, resulting in crosstalk between different dsRNA-mediated pathways.
true
true
true
true
true
1,309
6
DISCUSSION
1
42–44
[ "B42", "B42 B43 B44" ]
17,395,637
pmid-15573138|pmid-15573138|pmid-15853796|pmid-10782096
However, some dsRNA-binding proteins do recognize specific dsRNA substrates in cells, and how this specificity is achieved remains elusive (42–44).
[ "42", "42–44" ]
147
8,075
1
false
However, some dsRNA-binding proteins do recognize specific dsRNA substrates in cells, and how this specificity is achieved remains elusive.
[ "42–44" ]
However, some dsRNA-binding proteins do recognize specific dsRNA substrates in cells, and how this specificity is achieved remains elusive.
true
true
true
true
true
1,309
6
DISCUSSION
1
42
[ "B42", "B42 B43 B44" ]
17,395,637
pmid-15573138|pmid-15573138|pmid-15853796|pmid-10782096
Our results do not at present demonstrate conclusively that HEXIM1 is involved in cellular processes other than controlling P-TEFb.
[ "42", "42–44" ]
131
8,076
0
false
Our results do not at present demonstrate conclusively that HEXIM1 is involved in cellular processes other than controlling P-TEFb.
[]
Our results do not at present demonstrate conclusively that HEXIM1 is involved in cellular processes other than controlling P-TEFb.
true
true
true
true
true
1,309
6
DISCUSSION
1
42
[ "B42", "B42 B43 B44" ]
17,395,637
pmid-15573138|pmid-15573138|pmid-15853796|pmid-10782096
However, future studies including the identification of other HEXIM1-bound RNAs may shed light on the function of the HEXIM1•RNA complexes found in the cytoplasm and the nucleus.
[ "42", "42–44" ]
178
8,077
0
false
However, future studies including the identification of other HEXIM1-bound RNAs may shed light on the function of the HEXIM1•RNA complexes found in the cytoplasm and the nucleus.
[]
However, future studies including the identification of other HEXIM1-bound RNAs may shed light on the function of the HEXIM1•RNA complexes found in the cytoplasm and the nucleus.
true
true
true
true
true
1,309
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b9" ]
16,738,132
pmid-9383185|pmid-8022289|pmid-10369778|pmid-7715723|pmid-8419914|pmid-7544009|pmid-14687568
In Bacillus subtilis, genes involved in tryptophan biosynthesis and transport are regulated by a tryptophan-activated RNA binding protein called TRAP (trp RNA binding attenuation protein) (1,2).
[ "1", "2", "3", "4", "5", "9" ]
194
8,078
0
false
In Bacillus subtilis, genes involved in tryptophan biosynthesis and transport are regulated by a tryptophan-activated RNA binding protein called TRAP (trp RNA binding attenuation protein).
[ "1,2" ]
In Bacillus subtilis, genes involved in tryptophan biosynthesis and transport are regulated by a tryptophan-activated RNA binding protein called TRAP (trp RNA binding attenuation protein).
true
true
true
true
true
1,310
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b9" ]
16,738,132
pmid-9383185|pmid-8022289|pmid-10369778|pmid-7715723|pmid-8419914|pmid-7544009|pmid-14687568
TRAP regulates both transcription and translation of these genes in response to changes in intracellular levels of l-tryptophan.
[ "1", "2", "3", "4", "5", "9" ]
128
8,079
0
false
TRAP regulates both transcription and translation of these genes in response to changes in intracellular levels of l-tryptophan.
[]
TRAP regulates both transcription and translation of these genes in response to changes in intracellular levels of l-tryptophan.
true
true
true
true
true
1,310
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b9" ]
16,738,132
pmid-9383185|pmid-8022289|pmid-10369778|pmid-7715723|pmid-8419914|pmid-7544009|pmid-14687568
TRAP is composed of eleven identical subunits arranged in a symmetric ring (3,4).
[ "1", "2", "3", "4", "5", "9" ]
81
8,080
0
false
TRAP is composed of eleven identical subunits arranged in a symmetric ring.
[ "3,4" ]
TRAP is composed of eleven identical subunits arranged in a symmetric ring.
true
true
true
true
true
1,310
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b9" ]
16,738,132
pmid-9383185|pmid-8022289|pmid-10369778|pmid-7715723|pmid-8419914|pmid-7544009|pmid-14687568
TRAP is activated to bind RNA by binding up to 11 molecules of l-tryptophan in pockets formed by adjacent subunits.
[ "1", "2", "3", "4", "5", "9" ]
115
8,081
0
false
TRAP is activated to bind RNA by binding up to 11 molecules of l-tryptophan in pockets formed by adjacent subunits.
[]
TRAP is activated to bind RNA by binding up to 11 molecules of l-tryptophan in pockets formed by adjacent subunits.
true
true
true
true
true
1,310
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b9" ]
16,738,132
pmid-9383185|pmid-8022289|pmid-10369778|pmid-7715723|pmid-8419914|pmid-7544009|pmid-14687568
The natural RNA targets of TRAP contain 9–11 NAG (where N = G ≈ U >
[ "1", "2", "3", "4", "5", "9" ]
67
8,082
0
false
The natural RNA targets of TRAP contain 9–11 NAG (where N = G ≈ U >
[]
The natural RNA targets of TRAP contain 9–11 NAG (where N = G ≈ U >
true
true
false
true
false
1,310
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b9" ]
16,738,132
pmid-9383185|pmid-8022289|pmid-10369778|pmid-7715723|pmid-8419914|pmid-7544009|pmid-14687568
A > C) triplet repeats separated by several nonconserved spacer residues (5–9).
[ "1", "2", "3", "4", "5", "9" ]
79
8,083
0
false
A > C) triplet repeats separated by several nonconserved spacer residues.
[ "5–9" ]
A > C) triplet repeats separated by several nonconserved spacer residues.
true
true
true
true
true
1,310
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b9" ]
16,738,132
pmid-9383185|pmid-8022289|pmid-10369778|pmid-7715723|pmid-8419914|pmid-7544009|pmid-14687568
As a result of TRAP binding to several RNA targets, expression of the trp genes is down regulated.
[ "1", "2", "3", "4", "5", "9" ]
98
8,084
0
false
As a result of TRAP binding to several RNA targets, expression of the trp genes is down regulated.
[]
As a result of TRAP binding to several RNA targets, expression of the trp genes is down regulated.
true
true
true
true
true
1,310
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b9" ]
16,738,132
pmid-9383185|pmid-8022289|pmid-10369778|pmid-7715723|pmid-8419914|pmid-7544009|pmid-14687568
Alternatively, when the tryptophan level is growth limiting, TRAP is not activated to bind RNA, which allows elevated expression of the tryptophan synthesis genes.
[ "1", "2", "3", "4", "5", "9" ]
163
8,085
0
false
Alternatively, when the tryptophan level is growth limiting, TRAP is not activated to bind RNA, which allows elevated expression of the tryptophan synthesis genes.
[]
Alternatively, when the tryptophan level is growth limiting, TRAP is not activated to bind RNA, which allows elevated expression of the tryptophan synthesis genes.
true
true
true
true
true
1,310
1
INTRODUCTION
1
10
[ "b10", "b12", "b3" ]
16,738,132
pmid-15050822|pmid-9245598|pmid-10369778|pmid-7715723|pmid-14687568
Several crystal structures of tryptophan-activated TRAP in complex with RNAs containing 11 GAG or UAG repeats revealed that the RNA binds by wrapping around the outer periphery of the protein ring.
[ "10", "12", "3" ]
197
8,086
0
false
Several crystal structures of tryptophan-activated TRAP in complex with RNAs containing 11 GAG or UAG repeats revealed that the RNA binds by wrapping around the outer periphery of the protein ring.
[]
Several crystal structures of tryptophan-activated TRAP in complex with RNAs containing 11 GAG or UAG repeats revealed that the RNA binds by wrapping around the outer periphery of the protein ring.
true
true
true
true
true
1,311
1
INTRODUCTION
1
10
[ "b10", "b12", "b3" ]
16,738,132
pmid-15050822|pmid-9245598|pmid-10369778|pmid-7715723|pmid-14687568
The bound RNA interacts primarily with four amino acids of each subunit:
[ "10", "12", "3" ]
72
8,087
0
false
The bound RNA interacts primarily with four amino acids of each subunit:
[]
The bound RNA interacts primarily with four amino acids of each subunit:
true
true
false
true
false
1,311
1
INTRODUCTION
1
10
[ "b10", "b12", "b3" ]
16,738,132
pmid-15050822|pmid-9245598|pmid-10369778|pmid-7715723|pmid-14687568
Glu36, Lys37, Lys56 and Arg58 (10–12).
[ "10", "12", "3" ]
38
8,088
0
false
Glu36, Lys37, Lys56 and Arg58.
[ "10–12" ]
Glu36, Lys37, Lys56 and Arg58.
true
true
true
true
true
1,311
1
INTRODUCTION
1
10
[ "b10", "b12", "b3" ]
16,738,132
pmid-15050822|pmid-9245598|pmid-10369778|pmid-7715723|pmid-14687568
These residues as well as those involved in binding tryptophan (see below), are completely conserved in all currently available TRAP sequences, which have 64–86% identity to B.subtilis TRAP
[ "10", "12", "3" ]
189
8,089
0
false
These residues as well as those involved in binding tryptophan (see below), are completely conserved in all currently available TRAP sequences, which have 64–86% identity to B.subtilis TRAP
[]
These residues as well as those involved in binding tryptophan (see below), are completely conserved in all currently available TRAP sequences, which have 64–86% identity to B.subtilis TRAP
true
true
false
true
false
1,311
1
INTRODUCTION
1
10
[ "b10", "b12", "b3" ]
16,738,132
pmid-15050822|pmid-9245598|pmid-10369778|pmid-7715723|pmid-14687568
[(3) and P. Gollnick unpublished data].
[ "10", "12", "3" ]
39
8,090
0
false
.
[ "(3) and P. Gollnick unpublished data" ]
.
false
false
true
true
false
1,311
2
INTRODUCTION
1
13
[ "b13", "b14", "b14", "b15" ]
16,738,132
pmid-15099736|pmid-11805104|pmid-11805104|pmid-12381302|pmid-10660627|NA|NA
In comparison to the interaction with RNA, relatively little is known about the mechanism by which tryptophan binding activates TRAP to bind RNA.
[ "13", "14", "14", "15" ]
145
8,091
0
false
In comparison to the interaction with RNA, relatively little is known about the mechanism by which tryptophan binding activates TRAP to bind RNA.
[]
In comparison to the interaction with RNA, relatively little is known about the mechanism by which tryptophan binding activates TRAP to bind RNA.
true
true
true
true
true
1,312
2
INTRODUCTION
1
13
[ "b13", "b14", "b14", "b15" ]
16,738,132
pmid-15099736|pmid-11805104|pmid-11805104|pmid-12381302|pmid-10660627|NA|NA
There is currently no high resolution structure of TRAP in the absence of tryptophan.
[ "13", "14", "14", "15" ]
85
8,092
0
false
There is currently no high resolution structure of TRAP in the absence of tryptophan.
[]
There is currently no high resolution structure of TRAP in the absence of tryptophan.
true
true
true
true
true
1,312
2
INTRODUCTION
1
13
[ "b13", "b14", "b14", "b15" ]
16,738,132
pmid-15099736|pmid-11805104|pmid-11805104|pmid-12381302|pmid-10660627|NA|NA
TRAP is an 11mer in the absence or presence of tryptophan, which rules out a mechanism of activation involving altering oligomerization of the protein (13,14).
[ "13", "14", "14", "15" ]
159
8,093
0
false
TRAP is an 11mer in the absence or presence of tryptophan, which rules out a mechanism of activation involving altering oligomerization of the protein.
[ "13,14" ]
TRAP is an 11mer in the absence or presence of tryptophan, which rules out a mechanism of activation involving altering oligomerization of the protein.
true
true
true
true
true
1,312
2
INTRODUCTION
1
14
[ "b13", "b14", "b14", "b15" ]
16,738,132
pmid-15099736|pmid-11805104|pmid-11805104|pmid-12381302|pmid-10660627|NA|NA
Although each TRAP 11mer can bind up to 11 molecules of l-tryptophan, studies of hetero-11mers containing varying ratios of WT and mutant subunits (defective in tryptophan binding) have shown that the presence of just one or two bound tryptophans significantly activates TRAP to bind RNA (14).
[ "13", "14", "14", "15" ]
293
8,094
1
false
Although each TRAP 11mer can bind up to 11 molecules of l-tryptophan, studies of hetero-11mers containing varying ratios of WT and mutant subunits (defective in tryptophan binding) have shown that the presence of just one or two bound tryptophans significantly activates TRAP to bind RNA.
[ "14" ]
Although each TRAP 11mer can bind up to 11 molecules of l-tryptophan, studies of hetero-11mers containing varying ratios of WT and mutant subunits (defective in tryptophan binding) have shown that the presence of just one or two bound tryptophans significantly activates TRAP to bind RNA.
true
true
true
true
true
1,312
2
INTRODUCTION
1
13
[ "b13", "b14", "b14", "b15" ]
16,738,132
pmid-15099736|pmid-11805104|pmid-11805104|pmid-12381302|pmid-10660627|NA|NA
NMR studies have shown that tryptophan binding alters the dynamic properties of TRAP.
[ "13", "14", "14", "15" ]
85
8,095
0
false
NMR studies have shown that tryptophan binding alters the dynamic properties of TRAP.
[]
NMR studies have shown that tryptophan binding alters the dynamic properties of TRAP.
true
true
true
true
true
1,312
2
INTRODUCTION
1
15
[ "b13", "b14", "b14", "b15" ]
16,738,132
pmid-15099736|pmid-11805104|pmid-11805104|pmid-12381302|pmid-10660627|NA|NA
In particular, tryptophan binding reduces the flexibility of the tryptophan- and RNA-binding regions of TRAP, which is likely an important feature of the activation mechanism (15).
[ "13", "14", "14", "15" ]
180
8,096
1
false
In particular, tryptophan binding reduces the flexibility of the tryptophan- and RNA-binding regions of TRAP, which is likely an important feature of the activation mechanism.
[ "15" ]
In particular, tryptophan binding reduces the flexibility of the tryptophan- and RNA-binding regions of TRAP, which is likely an important feature of the activation mechanism.
true
true
true
true
true
1,312
2
INTRODUCTION
1
13
[ "b13", "b14", "b14", "b15" ]
16,738,132
pmid-15099736|pmid-11805104|pmid-11805104|pmid-12381302|pmid-10660627|NA|NA
The observation that apo-TRAP is quite flexible and contains regions that are dynamically disordered likely explains why it has not been possible to obtain good quality crystals of TRAP in the absence of tryptophan.
[ "13", "14", "14", "15" ]
215
8,097
0
false
The observation that apo-TRAP is quite flexible and contains regions that are dynamically disordered likely explains why it has not been possible to obtain good quality crystals of TRAP in the absence of tryptophan.
[]
The observation that apo-TRAP is quite flexible and contains regions that are dynamically disordered likely explains why it has not been possible to obtain good quality crystals of TRAP in the absence of tryptophan.
true
true
true
true
true
1,312
3
INTRODUCTION
1
4
[ "b4", "b16", "b12", "b16" ]
16,738,132
pmid-7715723|pmid-10660627|pmid-9245598|pmid-10660627|pmid-10499579
Each bound tryptophan is completely buried in a pocket between adjacent subunits, and it forms one hydrogen bond with the side chains of four TRAP residues (4).
[ "4", "16", "12", "16" ]
160
8,098
1
false
Each bound tryptophan is completely buried in a pocket between adjacent subunits, and it forms one hydrogen bond with the side chains of four TRAP residues.
[ "4" ]
Each bound tryptophan is completely buried in a pocket between adjacent subunits, and it forms one hydrogen bond with the side chains of four TRAP residues.
true
true
true
true
true
1,313
3
INTRODUCTION
1
4
[ "b4", "b16", "b12", "b16" ]
16,738,132
pmid-7715723|pmid-10660627|pmid-9245598|pmid-10660627|pmid-10499579
These include Thr49 and Thr52 from one subunit and Thr30 and Ser53 from the adjacent subunit.
[ "4", "16", "12", "16" ]
93
8,099
0
false
These include Thr49 and Thr52 from one subunit and Thr30 and Ser53 from the adjacent subunit.
[]
These include Thr49 and Thr52 from one subunit and Thr30 and Ser53 from the adjacent subunit.
true
true
true
true
true
1,313