Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
int64
sec
string
p_has_citation
int64
cites
string
citeids
list
pmid
int64
cited_id
string
sentences
string
all_sent_cites
list
sent_len
int64
sentence_batch_index
int64
sent_has_citation
float64
qc_fail
bool
cited_sentence
string
cites_in_sentence
list
cln_sentence
string
is_cap
bool
is_alpha
bool
ends_wp
bool
cit_qc
bool
lgtm
bool
__index_level_0__
int64
0
DISCUSSION
1
17
[ "b17" ]
16,982,646
pmid-14559182|pmid-11679670|pmid-15123812
This makes these parameters useful for determining free energy parameters at arbitrary temperature that are compatible with dynamic programming algorithms for secondary structure prediction.
[ "17" ]
190
4,900
0
false
This makes these parameters useful for determining free energy parameters at arbitrary temperature that are compatible with dynamic programming algorithms for secondary structure prediction.
[]
This makes these parameters useful for determining free energy parameters at arbitrary temperature that are compatible with dynamic programming algorithms for secondary structure prediction.
true
true
true
true
true
819
0
DISCUSSION
1
17
[ "b17" ]
16,982,646
pmid-14559182|pmid-11679670|pmid-15123812
Some of the enthalpy parameters have large percent standard errors as compared with the parameters of free energy.
[ "17" ]
114
4,901
0
false
Some of the enthalpy parameters have large percent standard errors as compared with the parameters of free energy.
[]
Some of the enthalpy parameters have large percent standard errors as compared with the parameters of free energy.
true
true
true
true
true
819
0
DISCUSSION
1
17
[ "b17" ]
16,982,646
pmid-14559182|pmid-11679670|pmid-15123812
This reflects the larger errors in the experimental results of enthalpy than free energy, but it also suggests that enthalpy may be more sequence dependent than free energy.
[ "17" ]
173
4,902
0
false
This reflects the larger errors in the experimental results of enthalpy than free energy, but it also suggests that enthalpy may be more sequence dependent than free energy.
[]
This reflects the larger errors in the experimental results of enthalpy than free energy, but it also suggests that enthalpy may be more sequence dependent than free energy.
true
true
true
true
true
819
0
DISCUSSION
1
17
[ "b17" ]
16,982,646
pmid-14559182|pmid-11679670|pmid-15123812
This sequence dependence cannot be determined using the currently available database of optical melting experiments and suggests a need for further optical melting experiments on model RNA systems.
[ "17" ]
197
4,903
0
false
This sequence dependence cannot be determined using the currently available database of optical melting experiments and suggests a need for further optical melting experiments on model RNA systems.
[]
This sequence dependence cannot be determined using the currently available database of optical melting experiments and suggests a need for further optical melting experiments on model RNA systems.
true
true
true
true
true
819
1
DISCUSSION
1
68
[ "b68", "b69" ]
16,982,646
pmid-15193319|pmid-8418835|pmid-10892344|pmid-2482415|pmid-6363901|pmid-12824338|pmid-15123812|pmid-15123812|pmid-9778347|pmid-15123812|pmid-15123812|pmid-10329189|pmid-15123812|pmid-15272118|pmid-1695107|pmid-15272118|pmid-15123812|pmid-15161262|pmid-15134461
Another source of error comes from the assumption that the enthalpy and entropy are independent of the temperature in both the model and in the analysis of optical melting experiments.
[ "68", "69" ]
184
4,904
0
false
Another source of error comes from the assumption that the enthalpy and entropy are independent of the temperature in both the model and in the analysis of optical melting experiments.
[]
Another source of error comes from the assumption that the enthalpy and entropy are independent of the temperature in both the model and in the analysis of optical melting experiments.
true
true
true
true
true
820
1
DISCUSSION
1
68
[ "b68", "b69" ]
16,982,646
pmid-15193319|pmid-8418835|pmid-10892344|pmid-2482415|pmid-6363901|pmid-12824338|pmid-15123812|pmid-15123812|pmid-9778347|pmid-15123812|pmid-15123812|pmid-10329189|pmid-15123812|pmid-15272118|pmid-1695107|pmid-15272118|pmid-15123812|pmid-15161262|pmid-15134461
When the temperature is too far from 37°C, the sensitivity of prediction is expected to be worse than 68.9% on average because of the approximation of ΔCp°=0.
[ "68", "69" ]
158
4,905
0
false
When the temperature is too far from 37°C, the sensitivity of prediction is expected to be worse than 68.9% on average because of the approximation of ΔCp°=0.
[]
When the temperature is too far from 37°C, the sensitivity of prediction is expected to be worse than 68.9% on average because of the approximation of ΔCp°=0.
true
true
true
true
true
820
1
DISCUSSION
1
68
[ "b68", "b69" ]
16,982,646
pmid-15193319|pmid-8418835|pmid-10892344|pmid-2482415|pmid-6363901|pmid-12824338|pmid-15123812|pmid-15123812|pmid-9778347|pmid-15123812|pmid-15123812|pmid-10329189|pmid-15123812|pmid-15272118|pmid-1695107|pmid-15272118|pmid-15123812|pmid-15161262|pmid-15134461
For example, experiments demonstrate cold denaturation of RNA (68,69), but the nearest neighbor model does not reproduce those results.
[ "68", "69" ]
135
4,906
0
false
For example, experiments demonstrate cold denaturation of RNA, but the nearest neighbor model does not reproduce those results.
[ "68,69" ]
For example, experiments demonstrate cold denaturation of RNA, but the nearest neighbor model does not reproduce those results.
true
true
true
true
true
820
1
DISCUSSION
1
68
[ "b68", "b69" ]
16,982,646
pmid-15193319|pmid-8418835|pmid-10892344|pmid-2482415|pmid-6363901|pmid-12824338|pmid-15123812|pmid-15123812|pmid-9778347|pmid-15123812|pmid-15123812|pmid-10329189|pmid-15123812|pmid-15272118|pmid-1695107|pmid-15272118|pmid-15123812|pmid-15161262|pmid-15134461
Further experiments by isothermal titration calorimetry would be needed to provide the data for a model that can include a non-zero heat capacity change.
[ "68", "69" ]
153
4,907
0
false
Further experiments by isothermal titration calorimetry would be needed to provide the data for a model that can include a non-zero heat capacity change.
[]
Further experiments by isothermal titration calorimetry would be needed to provide the data for a model that can include a non-zero heat capacity change.
true
true
true
true
true
820
2
DISCUSSION
0
null
null
16,982,646
pmid-8538457|pmid-15123812|pmid-15123812|pmid-10329189
There are common error sources that should be considered for the prediction of base pairs.
null
90
4,908
0
false
null
null
There are common error sources that should be considered for the prediction of base pairs.
true
true
true
true
true
821
2
DISCUSSION
0
null
null
16,982,646
pmid-8538457|pmid-15123812|pmid-15123812|pmid-10329189
Free energy minimization assumes that the secondary structure is at equilibrium.
null
80
4,909
0
false
null
null
Free energy minimization assumes that the secondary structure is at equilibrium.
true
true
true
true
true
821
2
DISCUSSION
0
null
null
16,982,646
pmid-8538457|pmid-15123812|pmid-15123812|pmid-10329189
The nearest neighbor model is an incomplete representation of structural free energy.
null
85
4,910
0
false
null
null
The nearest neighbor model is an incomplete representation of structural free energy.
true
true
true
true
true
821
2
DISCUSSION
0
null
null
16,982,646
pmid-8538457|pmid-15123812|pmid-15123812|pmid-10329189
The parameters average some sequence-specific effects and were derived from a limited set of experiments.
null
105
4,911
0
false
null
null
The parameters average some sequence-specific effects and were derived from a limited set of experiments.
true
true
true
true
true
821
2
DISCUSSION
0
null
null
16,982,646
pmid-8538457|pmid-15123812|pmid-15123812|pmid-10329189
Some RNA sequences, in particular mRNA, may sample multiple structures at equilibrium.
null
86
4,912
0
false
null
null
Some RNA sequences, in particular mRNA, may sample multiple structures at equilibrium.
true
true
true
true
true
821
2
DISCUSSION
0
null
null
16,982,646
pmid-8538457|pmid-15123812|pmid-15123812|pmid-10329189
The parameters are derived from experimental data at 1 M NaCl, whereas the salt concentration in different organisms may be very different.
null
139
4,913
0
false
null
null
The parameters are derived from experimental data at 1 M NaCl, whereas the salt concentration in different organisms may be very different.
true
true
true
true
true
821
3
DISCUSSION
1
17
[ "b17", "b75", "b22" ]
16,982,646
pmid-15123812|pmid-16023137|pmid-15272118
In spite of all these limitations, the nearest neighbor model predicts secondary structures with a 72.8% average sensitivity (17).
[ "17", "75", "22" ]
130
4,914
1
false
In spite of all these limitations, the nearest neighbor model predicts secondary structures with a 72.8% average sensitivity.
[ "17" ]
In spite of all these limitations, the nearest neighbor model predicts secondary structures with a 72.8% average sensitivity.
true
true
true
true
true
822
3
DISCUSSION
1
75
[ "b17", "b75", "b22" ]
16,982,646
pmid-15123812|pmid-16023137|pmid-15272118
Recent experimental results on the self-folding of the 16S rRNA 5′ domain (75) support the assumption of thermodynamic control of folding pathway.
[ "17", "75", "22" ]
146
4,915
1
false
Recent experimental results on the self-folding of the 16S rRNA 5′ domain support the assumption of thermodynamic control of folding pathway.
[ "75" ]
Recent experimental results on the self-folding of the 16S rRNA 5′ domain support the assumption of thermodynamic control of folding pathway.
true
true
true
true
true
822
3
DISCUSSION
1
22
[ "b17", "b75", "b22" ]
16,982,646
pmid-15123812|pmid-16023137|pmid-15272118
Moreover, the base pair prediction with the partition function can be used to determine pairs predicted with greater confidence (22).
[ "17", "75", "22" ]
133
4,916
1
false
Moreover, the base pair prediction with the partition function can be used to determine pairs predicted with greater confidence.
[ "22" ]
Moreover, the base pair prediction with the partition function can be used to determine pairs predicted with greater confidence.
true
true
true
true
true
822
4
DISCUSSION
0
null
null
16,982,646
null
In spite of the fact that the enthalpy parameters have larger percent errors than the free energy parameters for 37°C, the enthalpy parameters are able to predict optical melting temperatures for small model sequences.
null
218
4,917
0
false
null
null
In spite of the fact that the enthalpy parameters have larger percent errors than the free energy parameters for 37°C, the enthalpy parameters are able to predict optical melting temperatures for small model sequences.
true
true
true
true
true
823
4
DISCUSSION
0
null
null
16,982,646
null
Predicted melting temperatures for structural RNA sequences correlate well with optimal growth temperature, suggesting that these parameters capture many of the sequence-dependent features of RNA folding enthalpy change.
null
220
4,918
0
false
null
null
Predicted melting temperatures for structural RNA sequences correlate well with optimal growth temperature, suggesting that these parameters capture many of the sequence-dependent features of RNA folding enthalpy change.
true
true
true
true
true
823
0
INTRODUCTION
1
1–3
[ "B1 B2 B3" ]
17,317,682
NA|pmid-12970556|pmid-15864262|pmid-14679244|pmid-16413033
Toxin–antitoxin systems in bacteria eliminate plasmid-free cells that emerge as a result of segregation or replication defects and they contribute to intra- and interspecies plasmid dissemination (1–3).
[ "1–3" ]
202
4,919
1
false
Toxin–antitoxin systems in bacteria eliminate plasmid-free cells that emerge as a result of segregation or replication defects and they contribute to intra- and interspecies plasmid dissemination.
[ "1–3" ]
Toxin–antitoxin systems in bacteria eliminate plasmid-free cells that emerge as a result of segregation or replication defects and they contribute to intra- and interspecies plasmid dissemination.
true
true
true
true
true
824
0
INTRODUCTION
1
1–3
[ "B1 B2 B3" ]
17,317,682
NA|pmid-12970556|pmid-15864262|pmid-14679244|pmid-16413033
Plasmid-encoded toxin–antitoxin systems and their chromosomal homologues are widespread in bacteria.
[ "1–3" ]
100
4,920
0
false
Plasmid-encoded toxin–antitoxin systems and their chromosomal homologues are widespread in bacteria.
[]
Plasmid-encoded toxin–antitoxin systems and their chromosomal homologues are widespread in bacteria.
true
true
true
true
true
824
0
INTRODUCTION
1
1–3
[ "B1 B2 B3" ]
17,317,682
NA|pmid-12970556|pmid-15864262|pmid-14679244|pmid-16413033
Chromosomal toxin–antitoxin systems have been proposed to induce reversible cell cycle arrest or plasmid stabilization in response to nutritional and/or environmental stress.
[ "1–3" ]
174
4,921
0
false
Chromosomal toxin–antitoxin systems have been proposed to induce reversible cell cycle arrest or plasmid stabilization in response to nutritional and/or environmental stress.
[]
Chromosomal toxin–antitoxin systems have been proposed to induce reversible cell cycle arrest or plasmid stabilization in response to nutritional and/or environmental stress.
true
true
true
true
true
824
0
INTRODUCTION
1
1–3
[ "B1 B2 B3" ]
17,317,682
NA|pmid-12970556|pmid-15864262|pmid-14679244|pmid-16413033
Toxin–antitoxin cassettes have a characteristic organization in which the gene encoding the toxin follows the gene encoding the antitoxin.
[ "1–3" ]
138
4,922
0
false
Toxin–antitoxin cassettes have a characteristic organization in which the gene encoding the toxin follows the gene encoding the antitoxin.
[]
Toxin–antitoxin cassettes have a characteristic organization in which the gene encoding the toxin follows the gene encoding the antitoxin.
true
true
true
true
true
824
0
INTRODUCTION
1
1–3
[ "B1 B2 B3" ]
17,317,682
NA|pmid-12970556|pmid-15864262|pmid-14679244|pmid-16413033
The two loci have often a common autoregulatory mechanism exerted by both components.
[ "1–3" ]
85
4,923
0
false
The two loci have often a common autoregulatory mechanism exerted by both components.
[]
The two loci have often a common autoregulatory mechanism exerted by both components.
true
true
true
true
true
824
0
INTRODUCTION
1
1–3
[ "B1 B2 B3" ]
17,317,682
NA|pmid-12970556|pmid-15864262|pmid-14679244|pmid-16413033
The toxin gene encodes a stable protein, whereas the antitoxin is either a non-translated, antisense RNA species (type I) or a labile protein (type II).
[ "1–3" ]
152
4,924
0
false
The toxin gene encodes a stable protein, whereas the antitoxin is either a non-translated, antisense RNA species (type I) or a labile protein (type II).
[]
The toxin gene encodes a stable protein, whereas the antitoxin is either a non-translated, antisense RNA species (type I) or a labile protein (type II).
true
true
true
true
true
824
1
INTRODUCTION
1
2
[ "B2", "B4", "B5", "B6", "B7 B8 B9 B10" ]
17,317,682
pmid-12970556|pmid-1324324|pmid-12010492|pmid-12526800|pmid-16109374|pmid-14580342|pmid-15178344|pmid-15838042|pmid-1779758|pmid-11454201|pmid-17007877|pmid-9829946
The majority of the plasmid and chromosome-encoded toxin–antitoxin loci is of the type II module (2).
[ "2", "4", "5", "6", "7–10" ]
101
4,925
1
false
The majority of the plasmid and chromosome-encoded toxin–antitoxin loci is of the type II module.
[ "2" ]
The majority of the plasmid and chromosome-encoded toxin–antitoxin loci is of the type II module.
true
true
true
true
true
825
1
INTRODUCTION
1
2
[ "B2", "B4", "B5", "B6", "B7 B8 B9 B10" ]
17,317,682
pmid-12970556|pmid-1324324|pmid-12010492|pmid-12526800|pmid-16109374|pmid-14580342|pmid-15178344|pmid-15838042|pmid-1779758|pmid-11454201|pmid-17007877|pmid-9829946
The toxin and antitoxin form a tight complex so that no free toxin is present in the cell.
[ "2", "4", "5", "6", "7–10" ]
90
4,926
0
false
The toxin and antitoxin form a tight complex so that no free toxin is present in the cell.
[]
The toxin and antitoxin form a tight complex so that no free toxin is present in the cell.
true
true
true
true
true
825
1
INTRODUCTION
1
2
[ "B2", "B4", "B5", "B6", "B7 B8 B9 B10" ]
17,317,682
pmid-12970556|pmid-1324324|pmid-12010492|pmid-12526800|pmid-16109374|pmid-14580342|pmid-15178344|pmid-15838042|pmid-1779758|pmid-11454201|pmid-17007877|pmid-9829946
When a plasmid-free daughter cell is produced, owing to a defect in plasmid replication or maintenance, the newborn cell will still inherit the toxin–antitoxin protein complex.
[ "2", "4", "5", "6", "7–10" ]
176
4,927
0
false
When a plasmid-free daughter cell is produced, owing to a defect in plasmid replication or maintenance, the newborn cell will still inherit the toxin–antitoxin protein complex.
[]
When a plasmid-free daughter cell is produced, owing to a defect in plasmid replication or maintenance, the newborn cell will still inherit the toxin–antitoxin protein complex.
true
true
true
true
true
825
1
INTRODUCTION
1
2
[ "B2", "B4", "B5", "B6", "B7 B8 B9 B10" ]
17,317,682
pmid-12970556|pmid-1324324|pmid-12010492|pmid-12526800|pmid-16109374|pmid-14580342|pmid-15178344|pmid-15838042|pmid-1779758|pmid-11454201|pmid-17007877|pmid-9829946
However, the antitoxin component is degraded easily by host proteases and is not refreshed because of the absence of the plasmid encoding for the toxin–antitoxin system.
[ "2", "4", "5", "6", "7–10" ]
169
4,928
0
false
However, the antitoxin component is degraded easily by host proteases and is not refreshed because of the absence of the plasmid encoding for the toxin–antitoxin system.
[]
However, the antitoxin component is degraded easily by host proteases and is not refreshed because of the absence of the plasmid encoding for the toxin–antitoxin system.
true
true
true
true
true
825
1
INTRODUCTION
1
2
[ "B2", "B4", "B5", "B6", "B7 B8 B9 B10" ]
17,317,682
pmid-12970556|pmid-1324324|pmid-12010492|pmid-12526800|pmid-16109374|pmid-14580342|pmid-15178344|pmid-15838042|pmid-1779758|pmid-11454201|pmid-17007877|pmid-9829946
The toxin will then act on an essential host target to cause growth impairment or cell death of the plasmid-free cell.
[ "2", "4", "5", "6", "7–10" ]
118
4,929
0
false
The toxin will then act on an essential host target to cause growth impairment or cell death of the plasmid-free cell.
[]
The toxin will then act on an essential host target to cause growth impairment or cell death of the plasmid-free cell.
true
true
true
true
true
825
1
INTRODUCTION
1
2
[ "B2", "B4", "B5", "B6", "B7 B8 B9 B10" ]
17,317,682
pmid-12970556|pmid-1324324|pmid-12010492|pmid-12526800|pmid-16109374|pmid-14580342|pmid-15178344|pmid-15838042|pmid-1779758|pmid-11454201|pmid-17007877|pmid-9829946
In spite of the many studies on type II toxin–antitoxin systems, only two intracellular targets have been identified.
[ "2", "4", "5", "6", "7–10" ]
117
4,930
0
false
In spite of the many studies on type II toxin–antitoxin systems, only two intracellular targets have been identified.
[]
In spite of the many studies on type II toxin–antitoxin systems, only two intracellular targets have been identified.
true
true
true
true
true
825
1
INTRODUCTION
1
6
[ "B2", "B4", "B5", "B6", "B7 B8 B9 B10" ]
17,317,682
pmid-12970556|pmid-1324324|pmid-12010492|pmid-12526800|pmid-16109374|pmid-14580342|pmid-15178344|pmid-15838042|pmid-1779758|pmid-11454201|pmid-17007877|pmid-9829946
CcdB and ParE are known to act on DNA gyrase (4,5), RelE mediates cleavage of mRNA in a ribosome-dependent manner, thereby affecting the level of protein synthesis (6) and MazF, Kid and YoeB proteins have been found to show ribosome-independent RNase activity (7–10).
[ "2", "4", "5", "6", "7–10" ]
267
4,931
1
false
CcdB and ParE are known to act on DNA gyrase, RelE mediates cleavage of mRNA in a ribosome-dependent manner, thereby affecting the level of protein synthesis and MazF, Kid and YoeB proteins have been found to show ribosome-independent RNase activity.
[ "4,5", "6", "7–10" ]
CcdB and ParE are known to act on DNA gyrase, RelE mediates cleavage of mRNA in a ribosome-dependent manner, thereby affecting the level of protein synthesis and MazF, Kid and YoeB proteins have been found to show ribosome-independent RNase activity.
true
true
true
true
true
825
2
INTRODUCTION
1
11–15
[ "B11 B12 B13 B14 B15" ]
17,317,682
pmid-1779758|pmid-2511422|pmid-9917385|pmid-2651399|pmid-9829946
Toxin–antitoxin systems that have been studied so far are autoregulated at the level of transcription by binding of the antitoxin to the operator-promoter region of the operon, however, the underlying molecular mechanism of this autoregulation is poorly understood.
[ "11–15" ]
265
4,932
0
false
Toxin–antitoxin systems that have been studied so far are autoregulated at the level of transcription by binding of the antitoxin to the operator-promoter region of the operon, however, the underlying molecular mechanism of this autoregulation is poorly understood.
[]
Toxin–antitoxin systems that have been studied so far are autoregulated at the level of transcription by binding of the antitoxin to the operator-promoter region of the operon, however, the underlying molecular mechanism of this autoregulation is poorly understood.
true
true
true
true
true
826
2
INTRODUCTION
1
11–15
[ "B11 B12 B13 B14 B15" ]
17,317,682
pmid-1779758|pmid-2511422|pmid-9917385|pmid-2651399|pmid-9829946
Several toxin–antitoxin pairs repress the transcription of their toxin–antitoxin operons, such as mazEF, relBE, kid–kis, ccd, higAB and doc-phd, indicating that an autoregulation process involving one or both proteins may be a common feature for these operons (11–15).
[ "11–15" ]
268
4,933
1
false
Several toxin–antitoxin pairs repress the transcription of their toxin–antitoxin operons, such as mazEF, relBE, kid–kis, ccd, higAB and doc-phd, indicating that an autoregulation process involving one or both proteins may be a common feature for these operons.
[ "11–15" ]
Several toxin–antitoxin pairs repress the transcription of their toxin–antitoxin operons, such as mazEF, relBE, kid–kis, ccd, higAB and doc-phd, indicating that an autoregulation process involving one or both proteins may be a common feature for these operons.
true
true
true
true
true
826
2
INTRODUCTION
1
11–15
[ "B11 B12 B13 B14 B15" ]
17,317,682
pmid-1779758|pmid-2511422|pmid-9917385|pmid-2651399|pmid-9829946
In most of the cases, the antitoxin is directly responsible for the repression, but the toxin can also assist by increasing the affinity of the regulatory complex.
[ "11–15" ]
163
4,934
0
false
In most of the cases, the antitoxin is directly responsible for the repression, but the toxin can also assist by increasing the affinity of the regulatory complex.
[]
In most of the cases, the antitoxin is directly responsible for the repression, but the toxin can also assist by increasing the affinity of the regulatory complex.
true
true
true
true
true
826
3
INTRODUCTION
1
16
[ "B16", "B17", "B18", "B19", "B11", "B18", "B20", "B21", "B22" ]
17,317,682
pmid-3071737|pmid-15024022|pmid-16413033|pmid-11786266|pmid-1779758|pmid-16413033|pmid-14679244|pmid-7476860|pmid-12514130|pmid-16413033|pmid-12718874|pmid-17007877|pmid-12718874|pmid-12377128|NA
In Escherichia coli, the parD operon of plasmid R1 encodes the toxin Kid (Killing determinant) and the antitoxin Kis (Killing suppressor) (16).
[ "16", "17", "18", "19", "11", "18", "20", "21", "22" ]
143
4,935
1
false
In Escherichia coli, the parD operon of plasmid R1 encodes the toxin Kid (Killing determinant) and the antitoxin Kis (Killing suppressor).
[ "16" ]
In Escherichia coli, the parD operon of plasmid R1 encodes the toxin Kid (Killing determinant) and the antitoxin Kis (Killing suppressor).
true
true
true
true
true
827
3
INTRODUCTION
1
16
[ "B16", "B17", "B18", "B19", "B11", "B18", "B20", "B21", "B22" ]
17,317,682
pmid-3071737|pmid-15024022|pmid-16413033|pmid-11786266|pmid-1779758|pmid-16413033|pmid-14679244|pmid-7476860|pmid-12514130|pmid-16413033|pmid-12718874|pmid-17007877|pmid-12718874|pmid-12377128|NA
Kid is a ribonuclease, which cleaves RNA preferentially at the 5′ side of the adenosine residue in the nucleotide sequence 5′-UA(A/C)-3′ of single-stranded regions, although cleavage in double-stranded regions and at the 3′ side of the adenosine has been observed as well (17,18).
[ "16", "17", "18", "19", "11", "18", "20", "21", "22" ]
280
4,936
0
false
Kid is a ribonuclease, which cleaves RNA preferentially at the 5′ side of the adenosine residue in the nucleotide sequence 5′-UA(A/C)-3′ of single-stranded regions, although cleavage in double-stranded regions and at the 3′ side of the adenosine has been observed as well.
[ "17,18" ]
Kid is a ribonuclease, which cleaves RNA preferentially at the 5′ side of the adenosine residue in the nucleotide sequence 5′-UA(A/C)-3′ of single-stranded regions, although cleavage in double-stranded regions and at the 3′ side of the adenosine has been observed as well.
true
true
true
true
true
827
3
INTRODUCTION
1
16
[ "B16", "B17", "B18", "B19", "B11", "B18", "B20", "B21", "B22" ]
17,317,682
pmid-3071737|pmid-15024022|pmid-16413033|pmid-11786266|pmid-1779758|pmid-16413033|pmid-14679244|pmid-7476860|pmid-12514130|pmid-16413033|pmid-12718874|pmid-17007877|pmid-12718874|pmid-12377128|NA
Kis prevents the inhibition of E. coli cell growth caused by Kid.
[ "16", "17", "18", "19", "11", "18", "20", "21", "22" ]
65
4,937
0
false
Kis prevents the inhibition of E. coli cell growth caused by Kid.
[]
Kis prevents the inhibition of E. coli cell growth caused by Kid.
true
true
true
true
true
827
3
INTRODUCTION
1
19
[ "B16", "B17", "B18", "B19", "B11", "B18", "B20", "B21", "B22" ]
17,317,682
pmid-3071737|pmid-15024022|pmid-16413033|pmid-11786266|pmid-1779758|pmid-16413033|pmid-14679244|pmid-7476860|pmid-12514130|pmid-16413033|pmid-12718874|pmid-17007877|pmid-12718874|pmid-12377128|NA
Kis autoregulates parD transcription to a limited extent and this activity can be allocated to the N-terminal region of the protein (19).
[ "16", "17", "18", "19", "11", "18", "20", "21", "22" ]
137
4,938
1
false
Kis autoregulates parD transcription to a limited extent and this activity can be allocated to the N-terminal region of the protein.
[ "19" ]
Kis autoregulates parD transcription to a limited extent and this activity can be allocated to the N-terminal region of the protein.
true
true
true
true
true
827
3
INTRODUCTION
1
16
[ "B16", "B17", "B18", "B19", "B11", "B18", "B20", "B21", "B22" ]
17,317,682
pmid-3071737|pmid-15024022|pmid-16413033|pmid-11786266|pmid-1779758|pmid-16413033|pmid-14679244|pmid-7476860|pmid-12514130|pmid-16413033|pmid-12718874|pmid-17007877|pmid-12718874|pmid-12377128|NA
The coordinate action of the Kid–Kis complexes has been shown to efficiently repress parD transcription (11,18,20).
[ "16", "17", "18", "19", "11", "18", "20", "21", "22" ]
115
4,939
0
false
The coordinate action of the Kid–Kis complexes has been shown to efficiently repress parD transcription.
[ "11,18,20" ]
The coordinate action of the Kid–Kis complexes has been shown to efficiently repress parD transcription.
true
true
true
true
true
827
3
INTRODUCTION
1
21
[ "B16", "B17", "B18", "B19", "B11", "B18", "B20", "B21", "B22" ]
17,317,682
pmid-3071737|pmid-15024022|pmid-16413033|pmid-11786266|pmid-1779758|pmid-16413033|pmid-14679244|pmid-7476860|pmid-12514130|pmid-16413033|pmid-12718874|pmid-17007877|pmid-12718874|pmid-12377128|NA
In addition, synthesis of the Kid toxin is coupled to the synthesis of the Kis antitoxin and the intracellular levels of these proteins are also controlled by limited degradation of a polycistronic messenger (21).
[ "16", "17", "18", "19", "11", "18", "20", "21", "22" ]
213
4,940
1
false
In addition, synthesis of the Kid toxin is coupled to the synthesis of the Kis antitoxin and the intracellular levels of these proteins are also controlled by limited degradation of a polycistronic messenger.
[ "21" ]
In addition, synthesis of the Kid toxin is coupled to the synthesis of the Kis antitoxin and the intracellular levels of these proteins are also controlled by limited degradation of a polycistronic messenger.
true
true
true
true
true
827
3
INTRODUCTION
1
22
[ "B16", "B17", "B18", "B19", "B11", "B18", "B20", "B21", "B22" ]
17,317,682
pmid-3071737|pmid-15024022|pmid-16413033|pmid-11786266|pmid-1779758|pmid-16413033|pmid-14679244|pmid-7476860|pmid-12514130|pmid-16413033|pmid-12718874|pmid-17007877|pmid-12718874|pmid-12377128|NA
These regulatory mechanisms avoid the synthesis of the toxic component in case its antitoxin has not been translated previously and ensures a balanced production of the antitoxin relative to the toxin (22).
[ "16", "17", "18", "19", "11", "18", "20", "21", "22" ]
206
4,941
1
false
These regulatory mechanisms avoid the synthesis of the toxic component in case its antitoxin has not been translated previously and ensures a balanced production of the antitoxin relative to the toxin.
[ "22" ]
These regulatory mechanisms avoid the synthesis of the toxic component in case its antitoxin has not been translated previously and ensures a balanced production of the antitoxin relative to the toxin.
true
true
true
true
true
827
4
INTRODUCTION
1
23–25
[ "B23 B24 B25", "B23" ]
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
For mazEF and ccd addiction complexes it has been shown that the toxin and antitoxin can form various assemblies with different stoichiometries (23–25).
[ "23–25", "23" ]
152
4,942
1
false
For mazEF and ccd addiction complexes it has been shown that the toxin and antitoxin can form various assemblies with different stoichiometries.
[ "23–25" ]
For mazEF and ccd addiction complexes it has been shown that the toxin and antitoxin can form various assemblies with different stoichiometries.
true
true
true
true
true
828
4
INTRODUCTION
1
23–25
[ "B23 B24 B25", "B23" ]
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
Dao-Thi et al.
[ "23–25", "23" ]
14
4,943
0
false
Dao-Thi et al.
[]
Dao-Thi et al.
true
true
true
true
true
828
4
INTRODUCTION
1
23
[ "B23 B24 B25", "B23" ]
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
(23) have proposed a model in which (CcdA2-CcdB2)n complexes interact with multiple DNA-binding sites and spiral around the 120-bp promoter region.
[ "23–25", "23" ]
147
4,944
1
false
have proposed a model in which (CcdA2-CcdB2)n complexes interact with multiple DNA-binding sites and spiral around the 120-bp promoter region.
[ "23" ]
have proposed a model in which n complexes interact with multiple DNA-binding sites and spiral around the 120-bp promoter region.
false
true
true
true
false
828
4
INTRODUCTION
1
23–25
[ "B23 B24 B25", "B23" ]
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
Kis and Kid also form various complexes.
[ "23–25", "23" ]
40
4,945
0
false
Kis and Kid also form various complexes.
[]
Kis and Kid also form various complexes.
true
true
true
true
true
828
4
INTRODUCTION
1
23–25
[ "B23 B24 B25", "B23" ]
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
The Kid2–Kis2–Kid2 heterohexamer is the most abundant species when Kid is in excess of Kis, whereas at higher concentrations of Kis, various complexes are present ranging from Kid2–Kis2 tetramer up to heterodecamers, however, the function of these complexes and especially the interactions with operator-promoter DNA has...
[ "23–25", "23" ]
346
4,946
0
false
The Kid2–Kis2–Kid2 heterohexamer is the most abundant species when Kid is in excess of Kis, whereas at higher concentrations of Kis, various complexes are present ranging from Kid2–Kis2 tetramer up to heterodecamers, however, the function of these complexes and especially the interactions with operator-promoter DNA has...
[]
The Kid2–Kis2–Kid2 heterohexamer is the most abundant species when Kid is in excess of Kis, whereas at higher concentrations of Kis, various complexes are present ranging from Kid2–Kis2 tetramer up to heterodecamers, however, the function of these complexes and especially the interactions with operator-promoter DNA has...
true
true
true
true
true
828
4
INTRODUCTION
1
23–25
[ "B23 B24 B25", "B23" ]
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
Kamphuis et al., submitted for publication).
[ "23–25", "23" ]
44
4,947
0
false
Kamphuis et al., submitted for publication).
[]
Kamphuis et al., submitted for publication).
true
true
true
true
true
828
5
INTRODUCTION
1
26
[ "B26", "B27", "B28 B29 B30" ]
17,317,682
pmid-15056667|NA|pmid-16869714|pmid-17073415|pmid-16594706
In this study, we aimed to unravel the mechanism of autoregulation at the transcriptional level of the type II toxin–antitoxin system kid–kis by analyzing the Kid–Kis complexes formed at the parD operon.
[ "26", "27", "28–30" ]
203
4,948
0
false
In this study, we aimed to unravel the mechanism of autoregulation at the transcriptional level of the type II toxin–antitoxin system kid–kis by analyzing the Kid–Kis complexes formed at the parD operon.
[]
In this study, we aimed to unravel the mechanism of autoregulation at the transcriptional level of the type II toxin–antitoxin system kid–kis by analyzing the Kid–Kis complexes formed at the parD operon.
true
true
true
true
true
829
5
INTRODUCTION
1
26
[ "B26", "B27", "B28 B29 B30" ]
17,317,682
pmid-15056667|NA|pmid-16869714|pmid-17073415|pmid-16594706
We focused on the dynamic changes of the stoichiometry of Kid–Kis oligomers induced by binding of the parD operon and on their different binding affinity by using electrophoretic mobility shift assays, hydroxyl radical footprinting and macromolecular mass spectrometry.
[ "26", "27", "28–30" ]
269
4,949
0
false
We focused on the dynamic changes of the stoichiometry of Kid–Kis oligomers induced by binding of the parD operon and on their different binding affinity by using electrophoretic mobility shift assays, hydroxyl radical footprinting and macromolecular mass spectrometry.
[]
We focused on the dynamic changes of the stoichiometry of Kid–Kis oligomers induced by binding of the parD operon and on their different binding affinity by using electrophoretic mobility shift assays, hydroxyl radical footprinting and macromolecular mass spectrometry.
true
true
true
true
true
829
5
INTRODUCTION
1
26
[ "B26", "B27", "B28 B29 B30" ]
17,317,682
pmid-15056667|NA|pmid-16869714|pmid-17073415|pmid-16594706
Mass spectrometry is a relatively new player in the field of structural biology of non-covalent protein–nucleic acid complexes, which allows for the analysis of multiple species in a single experiment (26,27).
[ "26", "27", "28–30" ]
209
4,950
0
false
Mass spectrometry is a relatively new player in the field of structural biology of non-covalent protein–nucleic acid complexes, which allows for the analysis of multiple species in a single experiment.
[ "26,27" ]
Mass spectrometry is a relatively new player in the field of structural biology of non-covalent protein–nucleic acid complexes, which allows for the analysis of multiple species in a single experiment.
true
true
true
true
true
829
5
INTRODUCTION
1
28–30
[ "B26", "B27", "B28 B29 B30" ]
17,317,682
pmid-15056667|NA|pmid-16869714|pmid-17073415|pmid-16594706
Moreover, in combination with gas-phase dissociation experiments, the data also provide insight in the global organization of complexes (28–30).
[ "26", "27", "28–30" ]
144
4,951
1
false
Moreover, in combination with gas-phase dissociation experiments, the data also provide insight in the global organization of complexes.
[ "28–30" ]
Moreover, in combination with gas-phase dissociation experiments, the data also provide insight in the global organization of complexes.
true
true
true
true
true
829
5
INTRODUCTION
1
26
[ "B26", "B27", "B28 B29 B30" ]
17,317,682
pmid-15056667|NA|pmid-16869714|pmid-17073415|pmid-16594706
Based on our results, we present a detailed model, which explains the transcriptional autoregulation process of the parD operon.
[ "26", "27", "28–30" ]
128
4,952
0
false
Based on our results, we present a detailed model, which explains the transcriptional autoregulation process of the parD operon.
[]
Based on our results, we present a detailed model, which explains the transcriptional autoregulation process of the parD operon.
true
true
true
true
true
829
0
DISCUSSION
1
20
[ "B20", "B18" ]
17,317,682
NA|pmid-12970556|pmid-15864262|pmid-14679244|pmid-16413033
The parD operon of plasmid R1 encodes the toxin Kid and the antitoxin Kis.
[ "20", "18" ]
74
4,953
0
false
The parD operon of plasmid R1 encodes the toxin Kid and the antitoxin Kis.
[]
The parD operon of plasmid R1 encodes the toxin Kid and the antitoxin Kis.
true
true
true
true
true
830
0
DISCUSSION
1
20
[ "B20", "B18" ]
17,317,682
NA|pmid-12970556|pmid-15864262|pmid-14679244|pmid-16413033
It has been demonstrated that in vivo efficient autoregulation of the parD operon requires the consorted action of both proteins (20).
[ "20", "18" ]
134
4,954
1
false
It has been demonstrated that in vivo efficient autoregulation of the parD operon requires the consorted action of both proteins.
[ "20" ]
It has been demonstrated that in vivo efficient autoregulation of the parD operon requires the consorted action of both proteins.
true
true
true
true
true
830
0
DISCUSSION
1
18
[ "B20", "B18" ]
17,317,682
NA|pmid-12970556|pmid-15864262|pmid-14679244|pmid-16413033
Recent in vitro studies have shown that Kid and Kis can form multiple complexes with different stoichiometries and oligomeric states, depending on the molar ratio between Kid and Kis (18).
[ "20", "18" ]
188
4,955
1
false
Recent in vitro studies have shown that Kid and Kis can form multiple complexes with different stoichiometries and oligomeric states, depending on the molar ratio between Kid and Kis.
[ "18" ]
Recent in vitro studies have shown that Kid and Kis can form multiple complexes with different stoichiometries and oligomeric states, depending on the molar ratio between Kid and Kis.
true
true
true
true
true
830
0
DISCUSSION
1
20
[ "B20", "B18" ]
17,317,682
NA|pmid-12970556|pmid-15864262|pmid-14679244|pmid-16413033
The Kid2–Kis2–Kid2 hexamer is the most abundant species when Kid exceeds the concentration of Kis, whereas various Kid–Kis complexes are present when the concentration of Kis equals or exceeds the concentration of Kid.
[ "20", "18" ]
218
4,956
0
false
The Kid2–Kis2–Kid2 hexamer is the most abundant species when Kid exceeds the concentration of Kis, whereas various Kid–Kis complexes are present when the concentration of Kis equals or exceeds the concentration of Kid.
[]
The Kid2–Kis2–Kid2 hexamer is the most abundant species when Kid exceeds the concentration of Kis, whereas various Kid–Kis complexes are present when the concentration of Kis equals or exceeds the concentration of Kid.
true
true
true
true
true
830
1
DISCUSSION
1
11
[ "B11", "B25", "B37", "B15" ]
17,317,682
pmid-12970556|pmid-1324324|pmid-12010492|pmid-12526800|pmid-16109374|pmid-14580342|pmid-15178344|pmid-15838042|pmid-1779758|pmid-11454201|pmid-17007877|pmid-9829946
Our DNA binding and mass spectrometry data presented here show that the antitoxin Kis interacts with the parD operon with low affinity.
[ "11", "25", "37", "15" ]
135
4,957
0
false
Our DNA binding and mass spectrometry data presented here show that the antitoxin Kis interacts with the parD operon with low affinity.
[]
Our DNA binding and mass spectrometry data presented here show that the antitoxin Kis interacts with the parD operon with low affinity.
true
true
true
true
true
831
1
DISCUSSION
1
11
[ "B11", "B25", "B37", "B15" ]
17,317,682
pmid-12970556|pmid-1324324|pmid-12010492|pmid-12526800|pmid-16109374|pmid-14580342|pmid-15178344|pmid-15838042|pmid-1779758|pmid-11454201|pmid-17007877|pmid-9829946
These data are in line with previous studies, which have shown that Kis alone is a poor repressor in vivo (11).
[ "11", "25", "37", "15" ]
111
4,958
1
false
These data are in line with previous studies, which have shown that Kis alone is a poor repressor in vivo.
[ "11" ]
These data are in line with previous studies, which have shown that Kis alone is a poor repressor in vivo.
true
true
true
true
true
831
1
DISCUSSION
1
11
[ "B11", "B25", "B37", "B15" ]
17,317,682
pmid-12970556|pmid-1324324|pmid-12010492|pmid-12526800|pmid-16109374|pmid-14580342|pmid-15178344|pmid-15838042|pmid-1779758|pmid-11454201|pmid-17007877|pmid-9829946
The addition of toxin Kid to Kis enhances the binding affinity with parD DNA, however, the tightness of this interaction with parD DNA is determined by the molar ratio between Kid and Kis.
[ "11", "25", "37", "15" ]
188
4,959
0
false
The addition of toxin Kid to Kis enhances the binding affinity with parD DNA, however, the tightness of this interaction with parD DNA is determined by the molar ratio between Kid and Kis.
[]
The addition of toxin Kid to Kis enhances the binding affinity with parD DNA, however, the tightness of this interaction with parD DNA is determined by the molar ratio between Kid and Kis.
true
true
true
true
true
831
1
DISCUSSION
1
11
[ "B11", "B25", "B37", "B15" ]
17,317,682
pmid-12970556|pmid-1324324|pmid-12010492|pmid-12526800|pmid-16109374|pmid-14580342|pmid-15178344|pmid-15838042|pmid-1779758|pmid-11454201|pmid-17007877|pmid-9829946
We demonstrated that when Kid and Kis were mixed in a molar ratio of 2:1, the interaction between the resulting Kid2–Kis2–Kid2 hexamer and the parD DNA is weak.
[ "11", "25", "37", "15" ]
160
4,960
0
false
We demonstrated that when Kid and Kis were mixed in a molar ratio of 2:1, the interaction between the resulting Kid2–Kis2–Kid2 hexamer and the parD DNA is weak.
[]
We demonstrated that when Kid and Kis were mixed in a molar ratio of 2:1, the interaction between the resulting Kid2–Kis2–Kid2 hexamer and the parD DNA is weak.
true
true
true
true
true
831
1
DISCUSSION
1
11
[ "B11", "B25", "B37", "B15" ]
17,317,682
pmid-12970556|pmid-1324324|pmid-12010492|pmid-12526800|pmid-16109374|pmid-14580342|pmid-15178344|pmid-15838042|pmid-1779758|pmid-11454201|pmid-17007877|pmid-9829946
Thus, in these conditions transcriptional repression is expected to be limited.
[ "11", "25", "37", "15" ]
79
4,961
0
false
Thus, in these conditions transcriptional repression is expected to be limited.
[]
Thus, in these conditions transcriptional repression is expected to be limited.
true
true
true
true
true
831
1
DISCUSSION
1
11
[ "B11", "B25", "B37", "B15" ]
17,317,682
pmid-12970556|pmid-1324324|pmid-12010492|pmid-12526800|pmid-16109374|pmid-14580342|pmid-15178344|pmid-15838042|pmid-1779758|pmid-11454201|pmid-17007877|pmid-9829946
On the contrary, when the complex mixture of Kid–Kis oligomers, obtained at an equimolar ratio of Kid and Kis, was added to the parD DNA a strong cooperative effect of DNA binding and Kid2–Kis2–Kid2–Kis2 octamerization was observed and the parD DNA interacted tightly to this octamer.
[ "11", "25", "37", "15" ]
284
4,962
0
false
On the contrary, when the complex mixture of Kid–Kis oligomers, obtained at an equimolar ratio of Kid and Kis, was added to the parD DNA a strong cooperative effect of DNA binding and Kid2–Kis2–Kid2–Kis2 octamerization was observed and the parD DNA interacted tightly to this octamer.
[]
On the contrary, when the complex mixture of Kid–Kis oligomers, obtained at an equimolar ratio of Kid and Kis, was added to the parD DNA a strong cooperative effect of DNA binding and Kid2–Kis2–Kid2–Kis2 octamerization was observed and the parD DNA interacted tightly to this octamer.
true
true
true
true
true
831
1
DISCUSSION
1
11
[ "B11", "B25", "B37", "B15" ]
17,317,682
pmid-12970556|pmid-1324324|pmid-12010492|pmid-12526800|pmid-16109374|pmid-14580342|pmid-15178344|pmid-15838042|pmid-1779758|pmid-11454201|pmid-17007877|pmid-9829946
We also observed that the addition of extra toxin (up to a 2-fold molar excess of Kid) to the Kid–Kis octamer–parD DNA complex weakened the interaction with the DNA.
[ "11", "25", "37", "15" ]
165
4,963
0
false
We also observed that the addition of extra toxin (up to a 2-fold molar excess of Kid) to the Kid–Kis octamer–parD DNA complex weakened the interaction with the DNA.
[]
We also observed that the addition of extra toxin (up to a 2-fold molar excess of Kid) to the Kid–Kis octamer–parD DNA complex weakened the interaction with the DNA.
true
true
true
true
true
831
1
DISCUSSION
1
11
[ "B11", "B25", "B37", "B15" ]
17,317,682
pmid-12970556|pmid-1324324|pmid-12010492|pmid-12526800|pmid-16109374|pmid-14580342|pmid-15178344|pmid-15838042|pmid-1779758|pmid-11454201|pmid-17007877|pmid-9829946
From these data we conclude that different molar ratios of Kid and Kis can either enhance or diminish the parD DNA-binding activity of Kis.
[ "11", "25", "37", "15" ]
139
4,964
0
false
From these data we conclude that different molar ratios of Kid and Kis can either enhance or diminish the parD DNA-binding activity of Kis.
[]
From these data we conclude that different molar ratios of Kid and Kis can either enhance or diminish the parD DNA-binding activity of Kis.
true
true
true
true
true
831
1
DISCUSSION
1
11
[ "B11", "B25", "B37", "B15" ]
17,317,682
pmid-12970556|pmid-1324324|pmid-12010492|pmid-12526800|pmid-16109374|pmid-14580342|pmid-15178344|pmid-15838042|pmid-1779758|pmid-11454201|pmid-17007877|pmid-9829946
Therefore, the transcriptional repression of the parD operon and thus the expression of Kid and Kis is critically dependent on the molar ratio of Kid and Kis.
[ "11", "25", "37", "15" ]
158
4,965
0
false
Therefore, the transcriptional repression of the parD operon and thus the expression of Kid and Kis is critically dependent on the molar ratio of Kid and Kis.
[]
Therefore, the transcriptional repression of the parD operon and thus the expression of Kid and Kis is critically dependent on the molar ratio of Kid and Kis.
true
true
true
true
true
831
1
DISCUSSION
1
11
[ "B11", "B25", "B37", "B15" ]
17,317,682
pmid-12970556|pmid-1324324|pmid-12010492|pmid-12526800|pmid-16109374|pmid-14580342|pmid-15178344|pmid-15838042|pmid-1779758|pmid-11454201|pmid-17007877|pmid-9829946
It should be noted here that the Kid–Kis octamer can interact with the two half-sites of the specific operator region (region I and II) using the two dimers of the antitoxin, whereas the Kid–Kis hexameric can interact with the two half-sites using only one dimer.
[ "11", "25", "37", "15" ]
263
4,966
0
false
It should be noted here that the Kid–Kis octamer can interact with the two half-sites of the specific operator region (region I and II) using the two dimers of the antitoxin, whereas the Kid–Kis hexameric can interact with the two half-sites using only one dimer.
[]
It should be noted here that the Kid–Kis octamer can interact with the two half-sites of the specific operator region (region I and II) using the two dimers of the antitoxin, whereas the Kid–Kis hexameric can interact with the two half-sites using only one dimer.
true
true
true
true
true
831
1
DISCUSSION
1
11
[ "B11", "B25", "B37", "B15" ]
17,317,682
pmid-12970556|pmid-1324324|pmid-12010492|pmid-12526800|pmid-16109374|pmid-14580342|pmid-15178344|pmid-15838042|pmid-1779758|pmid-11454201|pmid-17007877|pmid-9829946
This is likely to explain the more efficient binding of the octamer.
[ "11", "25", "37", "15" ]
68
4,967
0
false
This is likely to explain the more efficient binding of the octamer.
[]
This is likely to explain the more efficient binding of the octamer.
true
true
true
true
true
831
1
DISCUSSION
1
15
[ "B11", "B25", "B37", "B15" ]
17,317,682
pmid-12970556|pmid-1324324|pmid-12010492|pmid-12526800|pmid-16109374|pmid-14580342|pmid-15178344|pmid-15838042|pmid-1779758|pmid-11454201|pmid-17007877|pmid-9829946
Alleviation of the repression modulated by toxin and antitoxin complexes in excess of the toxin has also been reported for the ccd system (25,37) as well as for the phD-doc system (15).
[ "11", "25", "37", "15" ]
185
4,968
1
false
Alleviation of the repression modulated by toxin and antitoxin complexes in excess of the toxin has also been reported for the ccd system as well as for the phD-doc system.
[ "25,37", "15" ]
Alleviation of the repression modulated by toxin and antitoxin complexes in excess of the toxin has also been reported for the ccd system as well as for the phD-doc system.
true
true
true
true
true
831
2
DISCUSSION
0
null
null
17,317,682
pmid-1779758|pmid-2511422|pmid-9917385|pmid-2651399|pmid-9829946
Our data also show that Kis and Kid–Kis complexes interact in two imperfect inverted repeats (region I and II).
null
111
4,969
0
false
null
null
Our data also show that Kis and Kid–Kis complexes interact in two imperfect inverted repeats (region I and II).
true
true
true
true
true
832
2
DISCUSSION
0
null
null
17,317,682
pmid-1779758|pmid-2511422|pmid-9917385|pmid-2651399|pmid-9829946
Region I contains an 18-bp symmetric element and region II a pseudo-symmetric element.
null
86
4,970
0
false
null
null
Region I contains an 18-bp symmetric element and region II a pseudo-symmetric element.
true
true
true
true
true
832
2
DISCUSSION
0
null
null
17,317,682
pmid-1779758|pmid-2511422|pmid-9917385|pmid-2651399|pmid-9829946
Moreover, by using separated fragments containing parD regions I or II, we found that Kis and Kid–Kis complexes interact with higher affinity to region I.
null
154
4,971
0
false
null
null
Moreover, by using separated fragments containing parD regions I or II, we found that Kis and Kid–Kis complexes interact with higher affinity to region I.
true
true
true
true
true
832
2
DISCUSSION
0
null
null
17,317,682
pmid-1779758|pmid-2511422|pmid-9917385|pmid-2651399|pmid-9829946
The lower affinity to region II is probably due to the four non-conserved bases in this element (5′-GTTATATTTTTATTAAAC-3′, in italic non-conserved residues).
null
157
4,972
0
false
null
null
The lower affinity to region II is probably due to the four non-conserved bases in this element (5′-GTTATATTTTTATTAAAC-3′, in italic non-conserved residues).
true
true
true
true
true
832
2
DISCUSSION
0
null
null
17,317,682
pmid-1779758|pmid-2511422|pmid-9917385|pmid-2651399|pmid-9829946
However, cooperative interactions between regions I and II potentially play an important role in the transcriptional regulation of the parD operon.
null
147
4,973
0
false
null
null
However, cooperative interactions between regions I and II potentially play an important role in the transcriptional regulation of the parD operon.
true
true
true
true
true
832
3
DISCUSSION
1
18
[ "B18", "B24", "B37", "B24", "B31", "B1" ]
17,317,682
pmid-3071737|pmid-15024022|pmid-16413033|pmid-11786266|pmid-1779758|pmid-16413033|pmid-14679244|pmid-7476860|pmid-12514130|pmid-16413033|pmid-12718874|pmid-17007877|pmid-12718874|pmid-12377128|NA
Are the physical parameters of the Kid–Kis complexes sufficient to form multiple interactions over the full length of the 30-bp parD DNA region I?
[ "18", "24", "37", "24", "31", "1" ]
146
4,974
0
false
Are the physical parameters of the Kid–Kis complexes sufficient to form multiple interactions over the full length of the 30-bp parD DNA region I?
[]
Are the physical parameters of the Kid–Kis complexes sufficient to form multiple interactions over the full length of the 30-bp parD DNA region I?
true
true
true
true
true
833
3
DISCUSSION
1
18
[ "B18", "B24", "B37", "B24", "B31", "B1" ]
17,317,682
pmid-3071737|pmid-15024022|pmid-16413033|pmid-11786266|pmid-1779758|pmid-16413033|pmid-14679244|pmid-7476860|pmid-12514130|pmid-16413033|pmid-12718874|pmid-17007877|pmid-12718874|pmid-12377128|NA
Calculation of the length of the 30-bp parD region I and the Kid–Kis octamer, assuming a similar topology as the MazF–MazE hexamer (18,24), revealed lengths of ∼100 Å for the DNA and ∼150 Å for the Kid–Kis octameric complex.
[ "18", "24", "37", "24", "31", "1" ]
224
4,975
0
false
Calculation of the length of the 30-bp parD region I and the Kid–Kis octamer, assuming a similar topology as the MazF–MazE hexamer, revealed lengths of ∼100 Å for the DNA and ∼150 Å for the Kid–Kis octameric complex.
[ "18,24" ]
Calculation of the length of the 30-bp parD region I and the Kid–Kis octamer, assuming a similar topology as the MazF–MazE hexamer, revealed lengths of ∼100 Å for the DNA and ∼150 Å for the Kid–Kis octameric complex.
true
true
true
true
true
833
3
DISCUSSION
1
18
[ "B18", "B24", "B37", "B24", "B31", "B1" ]
17,317,682
pmid-3071737|pmid-15024022|pmid-16413033|pmid-11786266|pmid-1779758|pmid-16413033|pmid-14679244|pmid-7476860|pmid-12514130|pmid-16413033|pmid-12718874|pmid-17007877|pmid-12718874|pmid-12377128|NA
Although no 3D structural model is available for a Kid–Kis–DNA complex or a related toxin–antitoxin–DNA complex, it can be speculated that the octamer can fully cover the 30-bp DNA, which is in line with the DNA footprinting and tandem mass spectrometry data.
[ "18", "24", "37", "24", "31", "1" ]
259
4,976
0
false
Although no 3D structural model is available for a Kid–Kis–DNA complex or a related toxin–antitoxin–DNA complex, it can be speculated that the octamer can fully cover the 30-bp DNA, which is in line with the DNA footprinting and tandem mass spectrometry data.
[]
Although no 3D structural model is available for a Kid–Kis–DNA complex or a related toxin–antitoxin–DNA complex, it can be speculated that the octamer can fully cover the 30-bp DNA, which is in line with the DNA footprinting and tandem mass spectrometry data.
true
true
true
true
true
833
3
DISCUSSION
1
37
[ "B18", "B24", "B37", "B24", "B31", "B1" ]
17,317,682
pmid-3071737|pmid-15024022|pmid-16413033|pmid-11786266|pmid-1779758|pmid-16413033|pmid-14679244|pmid-7476860|pmid-12514130|pmid-16413033|pmid-12718874|pmid-17007877|pmid-12718874|pmid-12377128|NA
Very recent nuclear magnetic resonance chemical-shift mapping data have revealed that the antitoxin CcdA alone interacts with duplex DNA comprising a 6-bp palindromic sequence (37).
[ "18", "24", "37", "24", "31", "1" ]
181
4,977
1
false
Very recent nuclear magnetic resonance chemical-shift mapping data have revealed that the antitoxin CcdA alone interacts with duplex DNA comprising a 6-bp palindromic sequence.
[ "37" ]
Very recent nuclear magnetic resonance chemical-shift mapping data have revealed that the antitoxin CcdA alone interacts with duplex DNA comprising a 6-bp palindromic sequence.
true
true
true
true
true
833
3
DISCUSSION
1
18
[ "B18", "B24", "B37", "B24", "B31", "B1" ]
17,317,682
pmid-3071737|pmid-15024022|pmid-16413033|pmid-11786266|pmid-1779758|pmid-16413033|pmid-14679244|pmid-7476860|pmid-12514130|pmid-16413033|pmid-12718874|pmid-17007877|pmid-12718874|pmid-12377128|NA
In here, it is also shown that a 33-bp DNA fragment, containing three potential CcdA binding sites, can bind in a cooperate manner with three CcdA dimers.
[ "18", "24", "37", "24", "31", "1" ]
154
4,978
0
false
In here, it is also shown that a 33-bp DNA fragment, containing three potential CcdA binding sites, can bind in a cooperate manner with three CcdA dimers.
[]
In here, it is also shown that a 33-bp DNA fragment, containing three potential CcdA binding sites, can bind in a cooperate manner with three CcdA dimers.
true
true
true
true
true
833
3
DISCUSSION
1
18
[ "B18", "B24", "B37", "B24", "B31", "B1" ]
17,317,682
pmid-3071737|pmid-15024022|pmid-16413033|pmid-11786266|pmid-1779758|pmid-16413033|pmid-14679244|pmid-7476860|pmid-12514130|pmid-16413033|pmid-12718874|pmid-17007877|pmid-12718874|pmid-12377128|NA
The antitoxins of the ccd and mazEF systems have amino terminal regions that dimerize to form the DNA-binding region, and contain an unstructured C-terminal part, which interacts with the toxins.
[ "18", "24", "37", "24", "31", "1" ]
195
4,979
0
false
The antitoxins of the ccd and mazEF systems have amino terminal regions that dimerize to form the DNA-binding region, and contain an unstructured C-terminal part, which interacts with the toxins.
[]
The antitoxins of the ccd and mazEF systems have amino terminal regions that dimerize to form the DNA-binding region, and contain an unstructured C-terminal part, which interacts with the toxins.
true
true
true
true
true
833
3
DISCUSSION
1
18
[ "B18", "B24", "B37", "B24", "B31", "B1" ]
17,317,682
pmid-3071737|pmid-15024022|pmid-16413033|pmid-11786266|pmid-1779758|pmid-16413033|pmid-14679244|pmid-7476860|pmid-12514130|pmid-16413033|pmid-12718874|pmid-17007877|pmid-12718874|pmid-12377128|NA
The toxins of these systems have also substantial structural homology (24,31), however the N-terminal domains of the CcdA and MazE antitoxin adopt different protein folds.
[ "18", "24", "37", "24", "31", "1" ]
171
4,980
0
false
The toxins of these systems have also substantial structural homology, however the N-terminal domains of the CcdA and MazE antitoxin adopt different protein folds.
[ "24,31" ]
The toxins of these systems have also substantial structural homology, however the N-terminal domains of the CcdA and MazE antitoxin adopt different protein folds.
true
true
true
true
true
833
3
DISCUSSION
1
1
[ "B18", "B24", "B37", "B24", "B31", "B1" ]
17,317,682
pmid-3071737|pmid-15024022|pmid-16413033|pmid-11786266|pmid-1779758|pmid-16413033|pmid-14679244|pmid-7476860|pmid-12514130|pmid-16413033|pmid-12718874|pmid-17007877|pmid-12718874|pmid-12377128|NA
As pointed by these authors, this surprising result confirms the proposal that gene shuffling or partner switching has been important in the evolution of the toxin–antitoxin systems (1).
[ "18", "24", "37", "24", "31", "1" ]
186
4,981
1
false
As pointed by these authors, this surprising result confirms the proposal that gene shuffling or partner switching has been important in the evolution of the toxin–antitoxin systems.
[ "1" ]
As pointed by these authors, this surprising result confirms the proposal that gene shuffling or partner switching has been important in the evolution of the toxin–antitoxin systems.
true
true
true
true
true
833
4
DISCUSSION
0
null
null
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
Our results lead us to propose a model in which the repression of the parD operon is tightly regulated by the molar ratio of the toxin and the antitoxin present in the cell (Figure 8).
null
184
4,982
0
false
null
null
Our results lead us to propose a model in which the repression of the parD operon is tightly regulated by the molar ratio of the toxin and the antitoxin present in the cell (Figure 8).
true
true
true
true
true
834
4
DISCUSSION
0
null
null
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
When the level of the toxin exceeds the one of the antitoxin, stable (Kid2–Kis)n non-covalent complexes are formed, which are able to completely neutralize Kid lethal activity (M.B.
null
181
4,983
0
false
null
null
When the level of the toxin exceeds the one of the antitoxin, stable (Kid2–Kis)n non-covalent complexes are formed, which are able to completely neutralize Kid lethal activity (M.B.
true
true
true
true
true
834
4
DISCUSSION
0
null
null
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
Kamphuis et al., submitted for publication), but do not tightly interact with the parD operator-promoter region.
null
112
4,984
0
false
null
null
Kamphuis et al., submitted for publication), but do not tightly interact with the parD operator-promoter region.
true
true
true
true
true
834
4
DISCUSSION
0
null
null
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
On the contrary, when the concentration of Kis is enhanced relative to Kid, such that both proteins have similar concentrations, (Kid2–Kis2)n or (Kid2–Kis2–Kid2–Kis2)n oligomers are formed capable of strongly interacting with the parD operator-promoter region.
null
260
4,985
0
false
null
null
On the contrary, when the concentration of Kis is enhanced relative to Kid, such that both proteins have similar concentrations, (Kid2–Kis2)n or (Kid2–Kis2–Kid2–Kis2)n oligomers are formed capable of strongly interacting with the parD operator-promoter region.
true
true
true
true
true
834
4
DISCUSSION
0
null
null
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
These stoichiometric complexes have a very strong capacity to interact with the specific parD sequences and to repress the transcription pathway.
null
145
4,986
0
false
null
null
These stoichiometric complexes have a very strong capacity to interact with the specific parD sequences and to repress the transcription pathway.
true
true
true
true
true
834
4
DISCUSSION
0
null
null
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
When the expression is repressed, no replacement can occur of the labile Kis antitoxin, which is prone to degradation by Lon protease.
null
134
4,987
0
false
null
null
When the expression is repressed, no replacement can occur of the labile Kis antitoxin, which is prone to degradation by Lon protease.
true
true
true
true
true
834
4
DISCUSSION
0
null
null
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
The level of the toxin will, therefore, exceed the one of the antitoxin.
null
72
4,988
0
false
null
null
The level of the toxin will, therefore, exceed the one of the antitoxin.
true
true
true
true
true
834
4
DISCUSSION
0
null
null
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
At this stage, the equilibrium between (Kid2–Kis2)n oligomers will shift towards (Kid2–Kis)n oligomers, thereby reducing the affinity for the parD operon.
null
154
4,989
0
false
null
null
At this stage, the equilibrium between (Kid2–Kis2)n oligomers will shift towards (Kid2–Kis)n oligomers, thereby reducing the affinity for the parD operon.
true
true
true
true
true
834
4
DISCUSSION
0
null
null
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
Subsequently, the inhibition of transcription will be alleviated.
null
65
4,990
0
false
null
null
Subsequently, the inhibition of transcription will be alleviated.
true
true
true
true
true
834
4
DISCUSSION
0
null
null
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
The tight interaction with parD region I suggests that this region plays a prominent role in the regulation of parD repression, however, interactions in region II could be required for fine adjustment in this regulation.
null
220
4,991
0
false
null
null
The tight interaction with parD region I suggests that this region plays a prominent role in the regulation of parD repression, however, interactions in region II could be required for fine adjustment in this regulation.
true
true
true
true
true
834
4
DISCUSSION
0
null
null
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
As mentioned above, cooperative interactions between the two regions could introduce additional complexity in this regulation.
null
126
4,992
0
false
null
null
As mentioned above, cooperative interactions between the two regions could introduce additional complexity in this regulation.
true
true
true
true
true
834
4
DISCUSSION
0
null
null
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
The neutralization of the negative charges of the antitoxin by the toxin may stabilize interaction of the repressor complexes with the DNA.
null
139
4,993
0
false
null
null
The neutralization of the negative charges of the antitoxin by the toxin may stabilize interaction of the repressor complexes with the DNA.
true
true
true
true
true
834
4
DISCUSSION
0
null
null
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
How this particular configuration contributes to the efficient binding of the repressor complex and thus to the fine-tuning of the promoter activity remains to be established.
null
175
4,994
0
false
null
null
How this particular configuration contributes to the efficient binding of the repressor complex and thus to the fine-tuning of the promoter activity remains to be established.
true
true
true
true
true
834
4
DISCUSSION
0
null
null
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
Figure 8.Schematic model of the transcription autoregulation of the parD operon.
null
80
4,995
0
false
null
null
Figure 8.Schematic model of the transcription autoregulation of the parD operon.
true
true
true
true
true
834
4
DISCUSSION
0
null
null
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
The kid gene and the Kid protein are shown in blue and the kis gene and the Kis protein in orange.
null
98
4,996
0
false
null
null
The kid gene and the Kid protein are shown in blue and the kis gene and the Kis protein in orange.
true
true
true
true
true
834
4
DISCUSSION
0
null
null
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
Each protein complex is represented by an appropriate combination of blue rectangles (Kid) and orange ellipses (Kis).
null
117
4,997
0
false
null
null
Each protein complex is represented by an appropriate combination of blue rectangles (Kid) and orange ellipses (Kis).
true
true
true
true
true
834
4
DISCUSSION
0
null
null
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
Free Kid inhibits cell growth.
null
30
4,998
0
false
null
null
Free Kid inhibits cell growth.
true
true
true
true
true
834
4
DISCUSSION
0
null
null
17,317,682
pmid-11741897|pmid-12718874|pmid-11454201|pmid-11741897
In conditions in which the concentration of Kid is higher than that of Kis Kid2–Kis1 and Kid2–Kis2–Kid2 complexes are formed.
null
125
4,999
0
false
null
null
In conditions in which the concentration of Kid is higher than that of Kis Kid2–Kis1 and Kid2–Kis2–Kid2 complexes are formed.
true
true
true
true
true
834