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
1
INTRODUCTION
1
14
[ "b14", "b17", "b14", "b18", "b19", "b20", "b21", "b22", "b23", "b24" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
The hexameric helicases studied to date bind both ssDNA and dsDNA as ring-shaped structures.
[ "14", "17", "14", "18", "19", "20", "21", "22", "23", "24" ]
92
8,900
0
false
The hexameric helicases studied to date bind both ssDNA and dsDNA as ring-shaped structures.
[]
The hexameric helicases studied to date bind both ssDNA and dsDNA as ring-shaped structures.
true
true
true
true
true
1,424
1
INTRODUCTION
1
14
[ "b14", "b17", "b14", "b18", "b19", "b20", "b21", "b22", "b23", "b24" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
In most cases ssDNA is the preferred substrate for DNA binding.
[ "14", "17", "14", "18", "19", "20", "21", "22", "23", "24" ]
63
8,901
0
false
In most cases ssDNA is the preferred substrate for DNA binding.
[]
In most cases ssDNA is the preferred substrate for DNA binding.
true
true
true
true
true
1,424
1
INTRODUCTION
1
14
[ "b14", "b17", "b14", "b18", "b19", "b20", "b21", "b22", "b23", "b24" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
As described above, the high affinity of T-antigen and E1 for dsDNA is primarily a manifestation of the presence of the OBD, and related to the assembly process for concentrating the proteins at ori.
[ "14", "17", "14", "18", "19", "20", "21", "22", "23", "24" ]
199
8,902
0
false
As described above, the high affinity of T-antigen and E1 for dsDNA is primarily a manifestation of the presence of the OBD, and related to the assembly process for concentrating the proteins at ori.
[]
As described above, the high affinity of T-antigen and E1 for dsDNA is primarily a manifestation of the presence of the OBD, and related to the assembly process for concentrating the proteins at ori.
true
true
true
true
true
1,424
1
INTRODUCTION
1
14
[ "b14", "b17", "b14", "b18", "b19", "b20", "b21", "b22", "b23", "b24" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
For T7 gp4, Escherichia coli DnaB helicase and other members of the DnaB family, ssDNA binds in a central cavity generated by oligomerization (14–17).
[ "14", "17", "14", "18", "19", "20", "21", "22", "23", "24" ]
150
8,903
0
false
For T7 gp4, Escherichia coli DnaB helicase and other members of the DnaB family, ssDNA binds in a central cavity generated by oligomerization.
[ "14–17" ]
For T7 gp4, Escherichia coli DnaB helicase and other members of the DnaB family, ssDNA binds in a central cavity generated by oligomerization.
true
true
true
true
true
1,424
1
INTRODUCTION
1
14
[ "b14", "b17", "b14", "b18", "b19", "b20", "b21", "b22", "b23", "b24" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
Binding appears unidirectional, consistent with the defined unwinding polarity of helicases (14).
[ "14", "17", "14", "18", "19", "20", "21", "22", "23", "24" ]
97
8,904
1
false
Binding appears unidirectional, consistent with the defined unwinding polarity of helicases.
[ "14" ]
Binding appears unidirectional, consistent with the defined unwinding polarity of helicases.
true
true
true
true
true
1,424
1
INTRODUCTION
1
14
[ "b14", "b17", "b14", "b18", "b19", "b20", "b21", "b22", "b23", "b24" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
Binding to replication forks, which is likely to reveal important features of the helicase mechanism, has been studied less extensively.
[ "14", "17", "14", "18", "19", "20", "21", "22", "23", "24" ]
136
8,905
0
false
Binding to replication forks, which is likely to reveal important features of the helicase mechanism, has been studied less extensively.
[]
Binding to replication forks, which is likely to reveal important features of the helicase mechanism, has been studied less extensively.
true
true
true
true
true
1,424
1
INTRODUCTION
1
14
[ "b14", "b17", "b14", "b18", "b19", "b20", "b21", "b22", "b23", "b24" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
However, DNA footprinting studies suggest that T-antigen encircle one DNA strand at a replication fork structure with interactions extending into the duplex region ahead of the fork.
[ "14", "17", "14", "18", "19", "20", "21", "22", "23", "24" ]
182
8,906
0
false
However, DNA footprinting studies suggest that T-antigen encircle one DNA strand at a replication fork structure with interactions extending into the duplex region ahead of the fork.
[]
However, DNA footprinting studies suggest that T-antigen encircle one DNA strand at a replication fork structure with interactions extending into the duplex region ahead of the fork.
true
true
true
true
true
1,424
1
INTRODUCTION
1
14
[ "b14", "b17", "b14", "b18", "b19", "b20", "b21", "b22", "b23", "b24" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
The other DNA strand is excluded from the protein complex (18,19).
[ "14", "17", "14", "18", "19", "20", "21", "22", "23", "24" ]
66
8,907
0
false
The other DNA strand is excluded from the protein complex.
[ "18,19" ]
The other DNA strand is excluded from the protein complex.
true
true
true
true
true
1,424
1
INTRODUCTION
1
20
[ "b14", "b17", "b14", "b18", "b19", "b20", "b21", "b22", "b23", "b24" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
Quantitative fluorescence titration studies with synthetic replication forks demonstrate that DnaB also excludes one strand of DNA when the substrate is engaged (20).
[ "14", "17", "14", "18", "19", "20", "21", "22", "23", "24" ]
166
8,908
1
false
Quantitative fluorescence titration studies with synthetic replication forks demonstrate that DnaB also excludes one strand of DNA when the substrate is engaged.
[ "20" ]
Quantitative fluorescence titration studies with synthetic replication forks demonstrate that DnaB also excludes one strand of DNA when the substrate is engaged.
true
true
true
true
true
1,424
1
INTRODUCTION
1
14
[ "b14", "b17", "b14", "b18", "b19", "b20", "b21", "b22", "b23", "b24" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
The requirements for oligomerization of hexameric helicases differ, although in most cases a nucleotide is required.
[ "14", "17", "14", "18", "19", "20", "21", "22", "23", "24" ]
116
8,909
0
false
The requirements for oligomerization of hexameric helicases differ, although in most cases a nucleotide is required.
[]
The requirements for oligomerization of hexameric helicases differ, although in most cases a nucleotide is required.
true
true
true
true
true
1,424
1
INTRODUCTION
1
21
[ "b14", "b17", "b14", "b18", "b19", "b20", "b21", "b22", "b23", "b24" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
T-antigen forms hexamers with ADP, ATP and non-hydrolysable analogues (21).
[ "14", "17", "14", "18", "19", "20", "21", "22", "23", "24" ]
75
8,910
1
false
T-antigen forms hexamers with ADP, ATP and non-hydrolysable analogues.
[ "21" ]
T-antigen forms hexamers with ADP, ATP and non-hydrolysable analogues.
true
true
true
true
true
1,424
1
INTRODUCTION
1
22
[ "b14", "b17", "b14", "b18", "b19", "b20", "b21", "b22", "b23", "b24" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
For bovine papillomavirus (BPV) E1 it has been reported that the enzyme purified from E.coli requires DNA for hexamerization, with or without ATP (22), but the enzyme purified from recombinant baculovirus-infected insect cells exists in a number of oligomeric states (23).
[ "14", "17", "14", "18", "19", "20", "21", "22", "23", "24" ]
272
8,911
1
false
For bovine papillomavirus (BPV) E1 it has been reported that the enzyme purified from E.coli requires DNA for hexamerization, with or without ATP, but the enzyme purified from recombinant baculovirus-infected insect cells exists in a number of oligomeric states.
[ "22", "23" ]
For bovine papillomavirus (BPV) E1 it has been reported that the enzyme purified from E.coli requires DNA for hexamerization, with or without ATP, but the enzyme purified from recombinant baculovirus-infected insect cells exists in a number of oligomeric states.
true
true
true
true
true
1,424
1
INTRODUCTION
1
24
[ "b14", "b17", "b14", "b18", "b19", "b20", "b21", "b22", "b23", "b24" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
Similar results have been reported for HPV 11 E1 from insect cells infected with a recombinant baculovirus (24).
[ "14", "17", "14", "18", "19", "20", "21", "22", "23", "24" ]
112
8,912
1
false
Similar results have been reported for HPV 11 E1 from insect cells infected with a recombinant baculovirus.
[ "24" ]
Similar results have been reported for HPV 11 E1 from insect cells infected with a recombinant baculovirus.
true
true
true
true
true
1,424
2
INTRODUCTION
1
25
[ "b25" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
The helicase mechanism can be viewed as a DNA translocase activity coupled to a base pair separation process.
[ "25" ]
109
8,913
0
false
The helicase mechanism can be viewed as a DNA translocase activity coupled to a base pair separation process.
[]
The helicase mechanism can be viewed as a DNA translocase activity coupled to a base pair separation process.
true
true
true
true
true
1,425
2
INTRODUCTION
1
25
[ "b25" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
However, how these processes proceed mechanistically and are coupled to each other and NTPase activity are largely unknown.
[ "25" ]
123
8,914
0
false
However, how these processes proceed mechanistically and are coupled to each other and NTPase activity are largely unknown.
[]
However, how these processes proceed mechanistically and are coupled to each other and NTPase activity are largely unknown.
true
true
true
true
true
1,425
2
INTRODUCTION
1
25
[ "b25" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
Mechanisms based on active and passive unwinding have been proposed but differentiating between them is problematic since they share common features, principally the modulation of protein–protein and protein–DNA interactions in a nucleotide hydrolysis cycle (25).
[ "25" ]
263
8,915
1
false
Mechanisms based on active and passive unwinding have been proposed but differentiating between them is problematic since they share common features, principally the modulation of protein–protein and protein–DNA interactions in a nucleotide hydrolysis cycle.
[ "25" ]
Mechanisms based on active and passive unwinding have been proposed but differentiating between them is problematic since they share common features, principally the modulation of protein–protein and protein–DNA interactions in a nucleotide hydrolysis cycle.
true
true
true
true
true
1,425
2
INTRODUCTION
1
25
[ "b25" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
Here we report the characterization of the enzymatic, oligomerization and DNA-binding properties of a helicase protein derived from the C-terminal domain of BPV E1.
[ "25" ]
164
8,916
0
false
Here we report the characterization of the enzymatic, oligomerization and DNA-binding properties of a helicase protein derived from the C-terminal domain of BPV E1.
[]
Here we report the characterization of the enzymatic, oligomerization and DNA-binding properties of a helicase protein derived from the C-terminal domain of BPV E1.
true
true
true
true
true
1,425
2
INTRODUCTION
1
25
[ "b25" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
The E1HD is monomeric but assembles into hexamers with ssDNA or ATP but not ADP or AMP–PNP.
[ "25" ]
91
8,917
0
false
The E1HD is monomeric but assembles into hexamers with ssDNA or ATP but not ADP or AMP–PNP.
[]
The E1HD is monomeric but assembles into hexamers with ssDNA or ATP but not ADP or AMP–PNP.
true
true
true
true
true
1,425
2
INTRODUCTION
1
25
[ "b25" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
The minimal DNA-binding site sizefor efficient oligomerization is ∼16 bases.
[ "25" ]
76
8,918
0
false
The minimal DNA-binding site sizefor efficient oligomerization is ∼16 bases.
[]
The minimal DNA-binding site sizefor efficient oligomerization is ∼16 bases.
true
true
true
true
true
1,425
2
INTRODUCTION
1
25
[ "b25" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
With ADP, AMP–PNP or without a cofactor hexamers form an exceptionally tight complex with ssDNA.
[ "25" ]
96
8,919
0
false
With ADP, AMP–PNP or without a cofactor hexamers form an exceptionally tight complex with ssDNA.
[]
With ADP, AMP–PNP or without a cofactor hexamers form an exceptionally tight complex with ssDNA.
true
true
true
true
true
1,425
2
INTRODUCTION
1
25
[ "b25" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
However, in the presence of ATP the half-life of the protein–ssDNA interaction is, comparatively, exceptionally short.
[ "25" ]
118
8,920
0
false
However, in the presence of ATP the half-life of the protein–ssDNA interaction is, comparatively, exceptionally short.
[]
However, in the presence of ATP the half-life of the protein–ssDNA interaction is, comparatively, exceptionally short.
true
true
true
true
true
1,425
2
INTRODUCTION
1
25
[ "b25" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
These results suggest that during the ATP hydrolysis cycle an ssDNA-binding site ocillates from a high to a low-affinity state whereas protein–protein interactions change from a low- to high-affinity state.
[ "25" ]
206
8,921
0
false
These results suggest that during the ATP hydrolysis cycle an ssDNA-binding site ocillates from a high to a low-affinity state whereas protein–protein interactions change from a low- to high-affinity state.
[]
These results suggest that during the ATP hydrolysis cycle an ssDNA-binding site ocillates from a high to a low-affinity state whereas protein–protein interactions change from a low- to high-affinity state.
true
true
true
true
true
1,425
2
INTRODUCTION
1
25
[ "b25" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
These features are indicative of an ssDNA translocase activity, thus defining a component of the helicase mechanism for this important viral protein.
[ "25" ]
149
8,922
0
false
These features are indicative of an ssDNA translocase activity, thus defining a component of the helicase mechanism for this important viral protein.
[]
These features are indicative of an ssDNA translocase activity, thus defining a component of the helicase mechanism for this important viral protein.
true
true
true
true
true
1,425
0
DISCUSSION
1
29
[ "b29", "b22", "b23", "b31", "b32", "b33", "b34", "b35", "b35", "b21", "b24" ]
16,893,956
pmid-3025851|pmid-3035543|pmid-8389467|pmid-8380645|pmid-2846276|pmid-8090734|pmid-16061814|pmid-16738139|pmid-14504622|pmid-8557041|pmid-16285920|pmid-10652347|pmid-2539565|pmid-9843509|pmid-9658141|pmid-9933649|pmid-10535735|pmid-10892646|pmid-9302992|pmid-15454080|pmid-15289463|pmid-15289463|pmid-9149137|pmid-113045...
The C-terminal 307 residue domain of BPV E1 (E1HD) functions as a helicase with the unwinding polarity of native E1.
[ "29", "22", "23", "31", "32", "33", "34", "35", "35", "21", "24" ]
116
8,923
0
false
The C-terminal 307 residue domain of BPV E1 (E1HD) functions as a helicase with the unwinding polarity of native E1.
[]
The C-terminal 307 residue domain of BPV E1 (E1HD) functions as a helicase with the unwinding polarity of native E1.
true
true
true
true
true
1,426
0
DISCUSSION
1
29
[ "b29", "b22", "b23", "b31", "b32", "b33", "b34", "b35", "b35", "b21", "b24" ]
16,893,956
pmid-3025851|pmid-3035543|pmid-8389467|pmid-8380645|pmid-2846276|pmid-8090734|pmid-16061814|pmid-16738139|pmid-14504622|pmid-8557041|pmid-16285920|pmid-10652347|pmid-2539565|pmid-9843509|pmid-9658141|pmid-9933649|pmid-10535735|pmid-10892646|pmid-9302992|pmid-15454080|pmid-15289463|pmid-15289463|pmid-9149137|pmid-113045...
E1HD was capable of displacing long DNA strands from duplex DNA (Figure 1d), and based on our studies we propose below a mechanism for transclocase activity and processive unwinding by a hexameric protein complex.
[ "29", "22", "23", "31", "32", "33", "34", "35", "35", "21", "24" ]
213
8,924
0
false
E1HD was capable of displacing long DNA strands from duplex DNA (Figure 1d), and based on our studies we propose below a mechanism for transclocase activity and processive unwinding by a hexameric protein complex.
[]
E1HD was capable of displacing long DNA strands from duplex DNA (Figure 1d), and based on our studies we propose below a mechanism for transclocase activity and processive unwinding by a hexameric protein complex.
true
true
true
true
true
1,426
0
DISCUSSION
1
29
[ "b29", "b22", "b23", "b31", "b32", "b33", "b34", "b35", "b35", "b21", "b24" ]
16,893,956
pmid-3025851|pmid-3035543|pmid-8389467|pmid-8380645|pmid-2846276|pmid-8090734|pmid-16061814|pmid-16738139|pmid-14504622|pmid-8557041|pmid-16285920|pmid-10652347|pmid-2539565|pmid-9843509|pmid-9658141|pmid-9933649|pmid-10535735|pmid-10892646|pmid-9302992|pmid-15454080|pmid-15289463|pmid-15289463|pmid-9149137|pmid-113045...
The enzyme is monomeric at high-protein concentrations without cofactor or with ADP.
[ "29", "22", "23", "31", "32", "33", "34", "35", "35", "21", "24" ]
84
8,925
0
false
The enzyme is monomeric at high-protein concentrations without cofactor or with ADP.
[]
The enzyme is monomeric at high-protein concentrations without cofactor or with ADP.
true
true
true
true
true
1,426
0
DISCUSSION
1
29
[ "b29", "b22", "b23", "b31", "b32", "b33", "b34", "b35", "b35", "b21", "b24" ]
16,893,956
pmid-3025851|pmid-3035543|pmid-8389467|pmid-8380645|pmid-2846276|pmid-8090734|pmid-16061814|pmid-16738139|pmid-14504622|pmid-8557041|pmid-16285920|pmid-10652347|pmid-2539565|pmid-9843509|pmid-9658141|pmid-9933649|pmid-10535735|pmid-10892646|pmid-9302992|pmid-15454080|pmid-15289463|pmid-15289463|pmid-9149137|pmid-113045...
In the presence of ATP oligomerization is highly cooperative.
[ "29", "22", "23", "31", "32", "33", "34", "35", "35", "21", "24" ]
61
8,926
0
false
In the presence of ATP oligomerization is highly cooperative.
[]
In the presence of ATP oligomerization is highly cooperative.
true
true
true
true
true
1,426
0
DISCUSSION
1
29
[ "b29", "b22", "b23", "b31", "b32", "b33", "b34", "b35", "b35", "b21", "b24" ]
16,893,956
pmid-3025851|pmid-3035543|pmid-8389467|pmid-8380645|pmid-2846276|pmid-8090734|pmid-16061814|pmid-16738139|pmid-14504622|pmid-8557041|pmid-16285920|pmid-10652347|pmid-2539565|pmid-9843509|pmid-9658141|pmid-9933649|pmid-10535735|pmid-10892646|pmid-9302992|pmid-15454080|pmid-15289463|pmid-15289463|pmid-9149137|pmid-113045...
Consistent with the properties of other members of the same helicase family the complex appears to be hexameric, as its elution volume in gel filtration was similar to the hexameric complex with ssDNA whose size we determined accurately.
[ "29", "22", "23", "31", "32", "33", "34", "35", "35", "21", "24" ]
237
8,927
0
false
Consistent with the properties of other members of the same helicase family the complex appears to be hexameric, as its elution volume in gel filtration was similar to the hexameric complex with ssDNA whose size we determined accurately.
[]
Consistent with the properties of other members of the same helicase family the complex appears to be hexameric, as its elution volume in gel filtration was similar to the hexameric complex with ssDNA whose size we determined accurately.
true
true
true
true
true
1,426
0
DISCUSSION
1
29
[ "b29", "b22", "b23", "b31", "b32", "b33", "b34", "b35", "b35", "b21", "b24" ]
16,893,956
pmid-3025851|pmid-3035543|pmid-8389467|pmid-8380645|pmid-2846276|pmid-8090734|pmid-16061814|pmid-16738139|pmid-14504622|pmid-8557041|pmid-16285920|pmid-10652347|pmid-2539565|pmid-9843509|pmid-9658141|pmid-9933649|pmid-10535735|pmid-10892646|pmid-9302992|pmid-15454080|pmid-15289463|pmid-15289463|pmid-9149137|pmid-113045...
The nucleotide requirements for oligomerization therefore resemble those for full-length E1 binding to double-stranded ori DNA, where the complexes that form in the absence of hydrolysable ATP are relatively unstable (29).
[ "29", "22", "23", "31", "32", "33", "34", "35", "35", "21", "24" ]
222
8,928
1
false
The nucleotide requirements for oligomerization therefore resemble those for full-length E1 binding to double-stranded ori DNA, where the complexes that form in the absence of hydrolysable ATP are relatively unstable.
[ "29" ]
The nucleotide requirements for oligomerization therefore resemble those for full-length E1 binding to double-stranded ori DNA, where the complexes that form in the absence of hydrolysable ATP are relatively unstable.
true
true
true
true
true
1,426
0
DISCUSSION
1
29
[ "b29", "b22", "b23", "b31", "b32", "b33", "b34", "b35", "b35", "b21", "b24" ]
16,893,956
pmid-3025851|pmid-3035543|pmid-8389467|pmid-8380645|pmid-2846276|pmid-8090734|pmid-16061814|pmid-16738139|pmid-14504622|pmid-8557041|pmid-16285920|pmid-10652347|pmid-2539565|pmid-9843509|pmid-9658141|pmid-9933649|pmid-10535735|pmid-10892646|pmid-9302992|pmid-15454080|pmid-15289463|pmid-15289463|pmid-9149137|pmid-113045...
It is curious however that hexamerization of full-length E1 itself has not been observed with ATP (22,23).
[ "29", "22", "23", "31", "32", "33", "34", "35", "35", "21", "24" ]
106
8,929
0
false
It is curious however that hexamerization of full-length E1 itself has not been observed with ATP.
[ "22,23" ]
It is curious however that hexamerization of full-length E1 itself has not been observed with ATP.
true
true
true
true
true
1,426
0
DISCUSSION
1
29
[ "b29", "b22", "b23", "b31", "b32", "b33", "b34", "b35", "b35", "b21", "b24" ]
16,893,956
pmid-3025851|pmid-3035543|pmid-8389467|pmid-8380645|pmid-2846276|pmid-8090734|pmid-16061814|pmid-16738139|pmid-14504622|pmid-8557041|pmid-16285920|pmid-10652347|pmid-2539565|pmid-9843509|pmid-9658141|pmid-9933649|pmid-10535735|pmid-10892646|pmid-9302992|pmid-15454080|pmid-15289463|pmid-15289463|pmid-9149137|pmid-113045...
It is possible that the protein concentrations required for hexamerization were not achieved in previous studies or that the experimental conditions did not favour complex stabilization.
[ "29", "22", "23", "31", "32", "33", "34", "35", "35", "21", "24" ]
186
8,930
0
false
It is possible that the protein concentrations required for hexamerization were not achieved in previous studies or that the experimental conditions did not favour complex stabilization.
[]
It is possible that the protein concentrations required for hexamerization were not achieved in previous studies or that the experimental conditions did not favour complex stabilization.
true
true
true
true
true
1,426
0
DISCUSSION
1
29
[ "b29", "b22", "b23", "b31", "b32", "b33", "b34", "b35", "b35", "b21", "b24" ]
16,893,956
pmid-3025851|pmid-3035543|pmid-8389467|pmid-8380645|pmid-2846276|pmid-8090734|pmid-16061814|pmid-16738139|pmid-14504622|pmid-8557041|pmid-16285920|pmid-10652347|pmid-2539565|pmid-9843509|pmid-9658141|pmid-9933649|pmid-10535735|pmid-10892646|pmid-9302992|pmid-15454080|pmid-15289463|pmid-15289463|pmid-9149137|pmid-113045...
Hydrolysis of available ATP is a likely explanation for our inability to observe discrete peaks in glycerol gradients (data not shown), performed over hours rather than minutes in the case of gel filtration.
[ "29", "22", "23", "31", "32", "33", "34", "35", "35", "21", "24" ]
207
8,931
0
false
Hydrolysis of available ATP is a likely explanation for our inability to observe discrete peaks in glycerol gradients (data not shown), performed over hours rather than minutes in the case of gel filtration.
[]
Hydrolysis of available ATP is a likely explanation for our inability to observe discrete peaks in glycerol gradients (data not shown), performed over hours rather than minutes in the case of gel filtration.
true
true
true
true
true
1,426
0
DISCUSSION
1
29
[ "b29", "b22", "b23", "b31", "b32", "b33", "b34", "b35", "b35", "b21", "b24" ]
16,893,956
pmid-3025851|pmid-3035543|pmid-8389467|pmid-8380645|pmid-2846276|pmid-8090734|pmid-16061814|pmid-16738139|pmid-14504622|pmid-8557041|pmid-16285920|pmid-10652347|pmid-2539565|pmid-9843509|pmid-9658141|pmid-9933649|pmid-10535735|pmid-10892646|pmid-9302992|pmid-15454080|pmid-15289463|pmid-15289463|pmid-9149137|pmid-113045...
We have also shown that oligomerization in the presence of ATP is required to assemble a catalytically robust ATPase.
[ "29", "22", "23", "31", "32", "33", "34", "35", "35", "21", "24" ]
117
8,932
0
false
We have also shown that oligomerization in the presence of ATP is required to assemble a catalytically robust ATPase.
[]
We have also shown that oligomerization in the presence of ATP is required to assemble a catalytically robust ATPase.
true
true
true
true
true
1,426
0
DISCUSSION
1
33
[ "b29", "b22", "b23", "b31", "b32", "b33", "b34", "b35", "b35", "b21", "b24" ]
16,893,956
pmid-3025851|pmid-3035543|pmid-8389467|pmid-8380645|pmid-2846276|pmid-8090734|pmid-16061814|pmid-16738139|pmid-14504622|pmid-8557041|pmid-16285920|pmid-10652347|pmid-2539565|pmid-9843509|pmid-9658141|pmid-9933649|pmid-10535735|pmid-10892646|pmid-9302992|pmid-15454080|pmid-15289463|pmid-15289463|pmid-9149137|pmid-113045...
Many AAA+ helicases proteins possess an ‘arginine finger’ (31,32), first identified in GTPases (33).
[ "29", "22", "23", "31", "32", "33", "34", "35", "35", "21", "24" ]
100
8,933
1
false
Many AAA+ helicases proteins possess an ‘arginine finger’, first identified in GTPases.
[ "31,32", "33" ]
Many AAA+ helicases proteins possess an ‘arginine finger’, first identified in GTPases.
true
true
true
true
true
1,426
0
DISCUSSION
1
29
[ "b29", "b22", "b23", "b31", "b32", "b33", "b34", "b35", "b35", "b21", "b24" ]
16,893,956
pmid-3025851|pmid-3035543|pmid-8389467|pmid-8380645|pmid-2846276|pmid-8090734|pmid-16061814|pmid-16738139|pmid-14504622|pmid-8557041|pmid-16285920|pmid-10652347|pmid-2539565|pmid-9843509|pmid-9658141|pmid-9933649|pmid-10535735|pmid-10892646|pmid-9302992|pmid-15454080|pmid-15289463|pmid-15289463|pmid-9149137|pmid-113045...
In some multimeric ATPase complexes the finger from one subunit extends into another to interact with the ATP tri-phosphate during hydrolysis.
[ "29", "22", "23", "31", "32", "33", "34", "35", "35", "21", "24" ]
142
8,934
0
false
In some multimeric ATPase complexes the finger from one subunit extends into another to interact with the ATP tri-phosphate during hydrolysis.
[]
In some multimeric ATPase complexes the finger from one subunit extends into another to interact with the ATP tri-phosphate during hydrolysis.
true
true
true
true
true
1,426
0
DISCUSSION
1
34
[ "b29", "b22", "b23", "b31", "b32", "b33", "b34", "b35", "b35", "b21", "b24" ]
16,893,956
pmid-3025851|pmid-3035543|pmid-8389467|pmid-8380645|pmid-2846276|pmid-8090734|pmid-16061814|pmid-16738139|pmid-14504622|pmid-8557041|pmid-16285920|pmid-10652347|pmid-2539565|pmid-9843509|pmid-9658141|pmid-9933649|pmid-10535735|pmid-10892646|pmid-9302992|pmid-15454080|pmid-15289463|pmid-15289463|pmid-9149137|pmid-113045...
T-antigen has an unusual finger motif in that a lysine as well as two arginines contact the phosphate directly or indirectly through a water molecule (34).
[ "29", "22", "23", "31", "32", "33", "34", "35", "35", "21", "24" ]
155
8,935
1
false
T-antigen has an unusual finger motif in that a lysine as well as two arginines contact the phosphate directly or indirectly through a water molecule.
[ "34" ]
T-antigen has an unusual finger motif in that a lysine as well as two arginines contact the phosphate directly or indirectly through a water molecule.
true
true
true
true
true
1,426
0
DISCUSSION
1
35
[ "b29", "b22", "b23", "b31", "b32", "b33", "b34", "b35", "b35", "b21", "b24" ]
16,893,956
pmid-3025851|pmid-3035543|pmid-8389467|pmid-8380645|pmid-2846276|pmid-8090734|pmid-16061814|pmid-16738139|pmid-14504622|pmid-8557041|pmid-16285920|pmid-10652347|pmid-2539565|pmid-9843509|pmid-9658141|pmid-9933649|pmid-10535735|pmid-10892646|pmid-9302992|pmid-15454080|pmid-15289463|pmid-15289463|pmid-9149137|pmid-113045...
A conserved arginine in HPV 18 E1 is required for robust ATPase activity and is possibly an arginine finger residue (35).
[ "29", "22", "23", "31", "32", "33", "34", "35", "35", "21", "24" ]
121
8,936
1
false
A conserved arginine in HPV 18 E1 is required for robust ATPase activity and is possibly an arginine finger residue.
[ "35" ]
A conserved arginine in HPV 18 E1 is required for robust ATPase activity and is possibly an arginine finger residue.
true
true
true
true
true
1,426
0
DISCUSSION
1
29
[ "b29", "b22", "b23", "b31", "b32", "b33", "b34", "b35", "b35", "b21", "b24" ]
16,893,956
pmid-3025851|pmid-3035543|pmid-8389467|pmid-8380645|pmid-2846276|pmid-8090734|pmid-16061814|pmid-16738139|pmid-14504622|pmid-8557041|pmid-16285920|pmid-10652347|pmid-2539565|pmid-9843509|pmid-9658141|pmid-9933649|pmid-10535735|pmid-10892646|pmid-9302992|pmid-15454080|pmid-15289463|pmid-15289463|pmid-9149137|pmid-113045...
The cooperative ATPase activity we observe therefore supports the notion that the papillomavirus helicase is an arginine finger ATPase.
[ "29", "22", "23", "31", "32", "33", "34", "35", "35", "21", "24" ]
135
8,937
0
false
The cooperative ATPase activity we observe therefore supports the notion that the papillomavirus helicase is an arginine finger ATPase.
[]
The cooperative ATPase activity we observe therefore supports the notion that the papillomavirus helicase is an arginine finger ATPase.
true
true
true
true
true
1,426
0
DISCUSSION
1
35
[ "b29", "b22", "b23", "b31", "b32", "b33", "b34", "b35", "b35", "b21", "b24" ]
16,893,956
pmid-3025851|pmid-3035543|pmid-8389467|pmid-8380645|pmid-2846276|pmid-8090734|pmid-16061814|pmid-16738139|pmid-14504622|pmid-8557041|pmid-16285920|pmid-10652347|pmid-2539565|pmid-9843509|pmid-9658141|pmid-9933649|pmid-10535735|pmid-10892646|pmid-9302992|pmid-15454080|pmid-15289463|pmid-15289463|pmid-9149137|pmid-113045...
Furthermore, since E1–E2 interactions are conserved between BPV and HPV, the ATP-driven oligomerization of BPV E1HD we describe could serve as a molecular mechanism for the displacement of E2 from E1 during initiator complex assembly, as in HPV (35).
[ "29", "22", "23", "31", "32", "33", "34", "35", "35", "21", "24" ]
250
8,938
1
false
Furthermore, since E1–E2 interactions are conserved between BPV and HPV, the ATP-driven oligomerization of BPV E1HD we describe could serve as a molecular mechanism for the displacement of E2 from E1 during initiator complex assembly, as in HPV.
[ "35" ]
Furthermore, since E1–E2 interactions are conserved between BPV and HPV, the ATP-driven oligomerization of BPV E1HD we describe could serve as a molecular mechanism for the displacement of E2 from E1 during initiator complex assembly, as in HPV.
true
true
true
true
true
1,426
0
DISCUSSION
1
21
[ "b29", "b22", "b23", "b31", "b32", "b33", "b34", "b35", "b35", "b21", "b24" ]
16,893,956
pmid-3025851|pmid-3035543|pmid-8389467|pmid-8380645|pmid-2846276|pmid-8090734|pmid-16061814|pmid-16738139|pmid-14504622|pmid-8557041|pmid-16285920|pmid-10652347|pmid-2539565|pmid-9843509|pmid-9658141|pmid-9933649|pmid-10535735|pmid-10892646|pmid-9302992|pmid-15454080|pmid-15289463|pmid-15289463|pmid-9149137|pmid-113045...
It is also noteworthy that SV40 T-antigen hexamerizes with ATP, ADP and non-hydrolysable ATP analogues (21), and that HPV 11 E1 apparently forms stable hexamers without cofactors or DNA (24).
[ "29", "22", "23", "31", "32", "33", "34", "35", "35", "21", "24" ]
191
8,939
1
false
It is also noteworthy that SV40 T-antigen hexamerizes with ATP, ADP and non-hydrolysable ATP analogues, and that HPV 11 E1 apparently forms stable hexamers without cofactors or DNA.
[ "21", "24" ]
It is also noteworthy that SV40 T-antigen hexamerizes with ATP, ADP and non-hydrolysable ATP analogues, and that HPV 11 E1 apparently forms stable hexamers without cofactors or DNA.
true
true
true
true
true
1,426
0
DISCUSSION
1
29
[ "b29", "b22", "b23", "b31", "b32", "b33", "b34", "b35", "b35", "b21", "b24" ]
16,893,956
pmid-3025851|pmid-3035543|pmid-8389467|pmid-8380645|pmid-2846276|pmid-8090734|pmid-16061814|pmid-16738139|pmid-14504622|pmid-8557041|pmid-16285920|pmid-10652347|pmid-2539565|pmid-9843509|pmid-9658141|pmid-9933649|pmid-10535735|pmid-10892646|pmid-9302992|pmid-15454080|pmid-15289463|pmid-15289463|pmid-9149137|pmid-113045...
Despite the sequence conservation and predicted structural similarity between T-antigen and E1, subtle differences may exist in the ATP hydrolysis cycle of these two viral helicases.
[ "29", "22", "23", "31", "32", "33", "34", "35", "35", "21", "24" ]
182
8,940
0
false
Despite the sequence conservation and predicted structural similarity between T-antigen and E1, subtle differences may exist in the ATP hydrolysis cycle of these two viral helicases.
[]
Despite the sequence conservation and predicted structural similarity between T-antigen and E1, subtle differences may exist in the ATP hydrolysis cycle of these two viral helicases.
true
true
true
true
true
1,426
0
DISCUSSION
1
29
[ "b29", "b22", "b23", "b31", "b32", "b33", "b34", "b35", "b35", "b21", "b24" ]
16,893,956
pmid-3025851|pmid-3035543|pmid-8389467|pmid-8380645|pmid-2846276|pmid-8090734|pmid-16061814|pmid-16738139|pmid-14504622|pmid-8557041|pmid-16285920|pmid-10652347|pmid-2539565|pmid-9843509|pmid-9658141|pmid-9933649|pmid-10535735|pmid-10892646|pmid-9302992|pmid-15454080|pmid-15289463|pmid-15289463|pmid-9149137|pmid-113045...
Within the papillomaviruses E1 proteins there may also be differences in the enzyme mechanism.
[ "29", "22", "23", "31", "32", "33", "34", "35", "35", "21", "24" ]
94
8,941
0
false
Within the papillomaviruses E1 proteins there may also be differences in the enzyme mechanism.
[]
Within the papillomaviruses E1 proteins there may also be differences in the enzyme mechanism.
true
true
true
true
true
1,426
1
DISCUSSION
1
36
[ "b36", "b36", "b38", "b15", "b18", "b20" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
E1HD binds ssDNA as a hexamer with only one molecule of an 18 base oligonucleotide (T18) per complex.
[ "36", "36", "38", "15", "18", "20" ]
101
8,942
0
false
E1HD binds ssDNA as a hexamer with only one molecule of an 18 base oligonucleotide per complex.
[ "T18" ]
E1HD binds ssDNA as a hexamer with only one molecule of an 18 base oligonucleotide per complex.
true
true
true
true
true
1,427
1
DISCUSSION
1
36
[ "b36", "b36", "b38", "b15", "b18", "b20" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
Thirty-three bases of ssDNA were protected from nuclease digestion by the helicase and only small differences in the binding affinity of poly(dT) oligonucleotides from 16 to 30 bases were observed.
[ "36", "36", "38", "15", "18", "20" ]
197
8,943
0
false
Thirty-three bases of ssDNA were protected from nuclease digestion by the helicase and only small differences in the binding affinity of poly(dT) oligonucleotides from 16 to 30 bases were observed.
[]
Thirty-three bases of ssDNA were protected from nuclease digestion by the helicase and only small differences in the binding affinity of poly(dT) oligonucleotides from 16 to 30 bases were observed.
true
true
true
true
true
1,427
1
DISCUSSION
1
36
[ "b36", "b36", "b38", "b15", "b18", "b20" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
Formation of the hexameric complex was significantly impaired for oligonucleotides of ≤14 bp.
[ "36", "36", "38", "15", "18", "20" ]
93
8,944
0
false
Formation of the hexameric complex was significantly impaired for oligonucleotides of ≤14 bp.
[]
Formation of the hexameric complex was significantly impaired for oligonucleotides of ≤14 bp.
true
true
true
true
true
1,427
1
DISCUSSION
1
36
[ "b36", "b36", "b38", "b15", "b18", "b20" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
The 16 base DNA sequence therefore defines the extent of the ssDNA required for hexamerization, whereas the length of protected DNA indicates passage of DNA through a protein complex larger than the minimal ssDNA-binding site.
[ "36", "36", "38", "15", "18", "20" ]
226
8,945
0
false
The 16 base DNA sequence therefore defines the extent of the ssDNA required for hexamerization, whereas the length of protected DNA indicates passage of DNA through a protein complex larger than the minimal ssDNA-binding site.
[]
The 16 base DNA sequence therefore defines the extent of the ssDNA required for hexamerization, whereas the length of protected DNA indicates passage of DNA through a protein complex larger than the minimal ssDNA-binding site.
true
true
true
true
true
1,427
1
DISCUSSION
1
36
[ "b36", "b36", "b38", "b15", "b18", "b20" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
Very stable hexameric complexes formed with an 18 base oligonucleotide (T18) but these were unstable under electrophoresis conditions compared with hexamers with a T30 oligonucleotide (Figure 2b).
[ "36", "36", "38", "15", "18", "20" ]
196
8,946
0
false
Very stable hexameric complexes formed with an 18 base oligonucleotide but these were unstable under electrophoresis conditions compared with hexamers with a T30 oligonucleotide (Figure 2b).
[ "T18" ]
Very stable hexameric complexes formed with an 18 base oligonucleotide but these were unstable under electrophoresis conditions compared with hexamers with a T30 oligonucleotide (Figure 2b).
true
true
true
true
true
1,427
1
DISCUSSION
1
36
[ "b36", "b36", "b38", "b15", "b18", "b20" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
Together with the results of the protection assay, this suggests that stabilizing contacts with nucleic acid may also occur outside an essential DNA-binding site.
[ "36", "36", "38", "15", "18", "20" ]
162
8,947
0
false
Together with the results of the protection assay, this suggests that stabilizing contacts with nucleic acid may also occur outside an essential DNA-binding site.
[]
Together with the results of the protection assay, this suggests that stabilizing contacts with nucleic acid may also occur outside an essential DNA-binding site.
true
true
true
true
true
1,427
1
DISCUSSION
1
36
[ "b36", "b36", "b38", "b15", "b18", "b20" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
These results are similar to those of other well-studied hexameric helicases such, as T7 gp4, that protect 25–30 bases of ssDNA (36).
[ "36", "36", "38", "15", "18", "20" ]
133
8,948
1
false
These results are similar to those of other well-studied hexameric helicases such, as T7 gp4, that protect 25–30 bases of ssDNA.
[ "36" ]
These results are similar to those of other well-studied hexameric helicases such, as T7 gp4, that protect 25–30 bases of ssDNA.
true
true
true
true
true
1,427
1
DISCUSSION
1
36
[ "b36", "b36", "b38", "b15", "b18", "b20" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
T7 gp4 and DnaB bind short oligonucleotides (10–30 bases) in the presence of non-hydrolysable ATP analogues with Kds of 10 and 60 nM, respectively (36–38).
[ "36", "36", "38", "15", "18", "20" ]
155
8,949
0
false
T7 gp4 and DnaB bind short oligonucleotides (10–30 bases) in the presence of non-hydrolysable ATP analogues with Kds of 10 and 60 nM, respectively.
[ "36–38" ]
T7 gp4 and DnaB bind short oligonucleotides in the presence of non-hydrolysable ATP analogues with Kds of 10 and 60 nM, respectively.
true
true
true
true
true
1,427
1
DISCUSSION
1
36
[ "b36", "b36", "b38", "b15", "b18", "b20" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
Both these helicases also bind a second DNA strand with a weaker Kd, ∼40 µM in the case of DnaB.
[ "36", "36", "38", "15", "18", "20" ]
96
8,950
0
false
Both these helicases also bind a second DNA strand with a weaker Kd, ∼40 µM in the case of DnaB.
[]
Both these helicases also bind a second DNA strand with a weaker Kd, ∼40 µM in the case of DnaB.
true
true
true
true
true
1,427
1
DISCUSSION
1
36
[ "b36", "b36", "b38", "b15", "b18", "b20" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
The binding constants (Kd) that we have obtained for E1, with or without ATP, are significantly higher, between those of the primary and secondary binding sites of DnaB.
[ "36", "36", "38", "15", "18", "20" ]
169
8,951
0
false
The binding constants (Kd) that we have obtained for E1, with or without ATP, are significantly higher, between those of the primary and secondary binding sites of DnaB.
[]
The binding constants (Kd) that we have obtained for E1, with or without ATP, are significantly higher, between those of the primary and secondary binding sites of DnaB.
true
true
true
true
true
1,427
1
DISCUSSION
1
36
[ "b36", "b36", "b38", "b15", "b18", "b20" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
However, the mechanism of helicase loading on DNA is different for these enzymes.
[ "36", "36", "38", "15", "18", "20" ]
81
8,952
0
false
However, the mechanism of helicase loading on DNA is different for these enzymes.
[]
However, the mechanism of helicase loading on DNA is different for these enzymes.
true
true
true
true
true
1,427
1
DISCUSSION
1
36
[ "b36", "b36", "b38", "b15", "b18", "b20" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
E1 and T-antigen bind and assemble on DNA via the sequence-specific OBD, while specific proteins load DnaB and T7 gp4 on to ssDNA.
[ "36", "36", "38", "15", "18", "20" ]
130
8,953
0
false
E1 and T-antigen bind and assemble on DNA via the sequence-specific OBD, while specific proteins load DnaB and T7 gp4 on to ssDNA.
[]
E1 and T-antigen bind and assemble on DNA via the sequence-specific OBD, while specific proteins load DnaB and T7 gp4 on to ssDNA.
true
true
true
true
true
1,427
1
DISCUSSION
1
36
[ "b36", "b36", "b38", "b15", "b18", "b20" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
The E1HD binding to dsDNA that we observe is complex, with no clear indication of the efficient and stable hexamerization seen with ssDNA.
[ "36", "36", "38", "15", "18", "20" ]
138
8,954
0
false
The E1HD binding to dsDNA that we observe is complex, with no clear indication of the efficient and stable hexamerization seen with ssDNA.
[]
The E1HD binding to dsDNA that we observe is complex, with no clear indication of the efficient and stable hexamerization seen with ssDNA.
true
true
true
true
true
1,427
1
DISCUSSION
1
36
[ "b36", "b36", "b38", "b15", "b18", "b20" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
Although T-antigen and E1 encircle their respective ori dsDNAs as hexamers, this is performed in conjunction with the OBD.
[ "36", "36", "38", "15", "18", "20" ]
122
8,955
0
false
Although T-antigen and E1 encircle their respective ori dsDNAs as hexamers, this is performed in conjunction with the OBD.
[]
Although T-antigen and E1 encircle their respective ori dsDNAs as hexamers, this is performed in conjunction with the OBD.
true
true
true
true
true
1,427
1
DISCUSSION
1
36
[ "b36", "b36", "b38", "b15", "b18", "b20" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
T7 gp4, DnaB and T-antigen both exclude one ssDNA strand during helicase unwinding (15,18,20), and E1 is likely to function similarly.
[ "36", "36", "38", "15", "18", "20" ]
134
8,956
0
false
T7 gp4, DnaB and T-antigen both exclude one ssDNA strand during helicase unwinding, and E1 is likely to function similarly.
[ "15,18,20" ]
T7 gp4, DnaB and T-antigen both exclude one ssDNA strand during helicase unwinding, and E1 is likely to function similarly.
true
true
true
true
true
1,427
1
DISCUSSION
1
36
[ "b36", "b36", "b38", "b15", "b18", "b20" ]
16,893,956
pmid-7731998|pmid-12034814|pmid-7731998|pmid-1319087|pmid-9765408|pmid-9254631|pmid-9149137|pmid-9658141|pmid-9933649|pmid-11304544|pmid-8241139|pmid-8241139|pmid-8626772|pmid-9369480|pmid-1319087|pmid-9254631
Together with the inability of E1HD to unwind DNA of pure duplex character, our dsDNA-binding data suggest that E1 is unlikely to translocate on dsDNA as a base pair separation machine.
[ "36", "36", "38", "15", "18", "20" ]
185
8,957
0
false
Together with the inability of E1HD to unwind DNA of pure duplex character, our dsDNA-binding data suggest that E1 is unlikely to translocate on dsDNA as a base pair separation machine.
[]
Together with the inability of E1HD to unwind DNA of pure duplex character, our dsDNA-binding data suggest that E1 is unlikely to translocate on dsDNA as a base pair separation machine.
true
true
true
true
true
1,427
2
DISCUSSION
1
36
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
E1HD forms an exceptionally stable complex with ssDNA oligonucleotides without cofactor, with ADP or with AMP–PNP.
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
114
8,958
0
false
E1HD forms an exceptionally stable complex with ssDNA oligonucleotides without cofactor, with ADP or with AMP–PNP.
[]
E1HD forms an exceptionally stable complex with ssDNA oligonucleotides without cofactor, with ADP or with AMP–PNP.
true
true
true
true
true
1,428
2
DISCUSSION
1
36
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
However, upon ATP addition the affinity for ssDNA is significantly reduced.
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
75
8,959
0
false
However, upon ATP addition the affinity for ssDNA is significantly reduced.
[]
However, upon ATP addition the affinity for ssDNA is significantly reduced.
true
true
true
true
true
1,428
2
DISCUSSION
1
36
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
The ATP-dependent kinetics of (E1HD)6–ssDNA complex dissociation we observed (Figure 6) showed an immediate phase of rapid dissociation followed by a slower rate of decay.
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
171
8,960
0
false
The ATP-dependent kinetics of (E1HD)6–ssDNA complex dissociation we observed (Figure 6) showed an immediate phase of rapid dissociation followed by a slower rate of decay.
[]
The ATP-dependent kinetics of (E1HD)6–ssDNA complex dissociation we observed showed an immediate phase of rapid dissociation followed by a slower rate of decay.
true
true
true
true
true
1,428
2
DISCUSSION
1
36
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
These observations are notable since ATP stimulates formation of the hexameric protein–DNA complex.
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
99
8,961
0
false
These observations are notable since ATP stimulates formation of the hexameric protein–DNA complex.
[]
These observations are notable since ATP stimulates formation of the hexameric protein–DNA complex.
true
true
true
true
true
1,428
2
DISCUSSION
1
36
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
With NTP compared with NDP or no cofactor T7 gp4
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
48
8,962
0
false
With NTP compared with NDP or no cofactor T7 gp4
[]
With NTP compared with NDP or no cofactor T7 gp4
true
true
false
true
false
1,428
2
DISCUSSION
1
39
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
and DnaB also bind ssDNA more tightly, by orders of magnitude (36,38), and in the case of DnaB, nucleotide is not required for hexamerization (39).
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
147
8,963
1
false
and DnaB also bind ssDNA more tightly, by orders of magnitude, and in the case of DnaB, nucleotide is not required for hexamerization.
[ "36,38", "39" ]
and DnaB also bind ssDNA more tightly, by orders of magnitude, and in the case of DnaB, nucleotide is not required for hexamerization.
false
true
true
true
false
1,428
2
DISCUSSION
1
36
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
The immediate questions that arise are how is ssDNA affinity modulated and can these results be rationalized in terms of current models for DNA unwinding?
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
154
8,964
0
false
The immediate questions that arise are how is ssDNA affinity modulated and can these results be rationalized in terms of current models for DNA unwinding?
[]
The immediate questions that arise are how is ssDNA affinity modulated and can these results be rationalized in terms of current models for DNA unwinding?
true
true
true
true
true
1,428
2
DISCUSSION
1
36
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
ssDNA complex dissociation could occur if the hexameric ring were to open or disassemble.
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
89
8,965
0
false
ssDNA complex dissociation could occur if the hexameric ring were to open or disassemble.
[]
ssDNA complex dissociation could occur if the hexameric ring were to open or disassemble.
false
true
true
true
false
1,428
2
DISCUSSION
1
36
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
We consider these possibilities unlikely since we show that ATP promotes protein complex assembly.
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
98
8,966
0
false
We consider these possibilities unlikely since we show that ATP promotes protein complex assembly.
[]
We consider these possibilities unlikely since we show that ATP promotes protein complex assembly.
true
true
true
true
true
1,428
2
DISCUSSION
1
36
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
Furthermore, the mechanism of E1 helicase loading occurs by stepwise binding to ori rather than loading of a preformed hexamer requiring a ring-opening step.
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
157
8,967
0
false
Furthermore, the mechanism of E1 helicase loading occurs by stepwise binding to ori rather than loading of a preformed hexamer requiring a ring-opening step.
[]
Furthermore, the mechanism of E1 helicase loading occurs by stepwise binding to ori rather than loading of a preformed hexamer requiring a ring-opening step.
true
true
true
true
true
1,428
2
DISCUSSION
1
36
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
Our favoured interpretation is that we have observed the ATP-dependent modulation of ssDNA-binding site affinity that is a component of the helicase transloction mechanism.
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
172
8,968
0
false
Our favoured interpretation is that we have observed the ATP-dependent modulation of ssDNA-binding site affinity that is a component of the helicase transloction mechanism.
[]
Our favoured interpretation is that we have observed the ATP-dependent modulation of ssDNA-binding site affinity that is a component of the helicase transloction mechanism.
true
true
true
true
true
1,428
2
DISCUSSION
1
34
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
The recent structures of T-antigen hexamers with and without bound nucleotide have shown large longitudinal ATP-dependent movements of a β-hairpin structure (the pre-sensor 1 β hairpin, PS1βH) within the central channel of the complex (34).
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
240
8,969
1
false
The recent structures of T-antigen hexamers with and without bound nucleotide have shown large longitudinal ATP-dependent movements of a β-hairpin structure (the pre-sensor 1 β hairpin, PS1βH) within the central channel of the complex.
[ "34" ]
The recent structures of T-antigen hexamers with and without bound nucleotide have shown large longitudinal ATP-dependent movements of a β-hairpin structure (the pre-sensor 1 β hairpin, PS1βH) within the central channel of the complex.
true
true
true
true
true
1,428
2
DISCUSSION
1
36
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
This structure is critical for ssDNA binding in both T-antigen and E1 hexamers (7,8), and along with an aromatic loop constitutes the primary ssDNA-binding site.
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
161
8,970
0
false
This structure is critical for ssDNA binding in both T-antigen and E1 hexamers, and along with an aromatic loop constitutes the primary ssDNA-binding site.
[ "7,8" ]
This structure is critical for ssDNA binding in both T-antigen and E1 hexamers, and along with an aromatic loop constitutes the primary ssDNA-binding site.
true
true
true
true
true
1,428
2
DISCUSSION
1
34
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
PS1βH movement is accompanied by changes in the dimensions of the hexameric channel, rotation of the two tiers of the hexamer relative to each other, and a large increase in the buried surface area between protomers with ATP (34).
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
230
8,971
1
false
PS1βH movement is accompanied by changes in the dimensions of the hexameric channel, rotation of the two tiers of the hexamer relative to each other, and a large increase in the buried surface area between protomers with ATP.
[ "34" ]
PS1βH movement is accompanied by changes in the dimensions of the hexameric channel, rotation of the two tiers of the hexamer relative to each other, and a large increase in the buried surface area between protomers with ATP.
true
true
true
true
true
1,428
2
DISCUSSION
1
36
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
These data also suggested that the ATP hydrolysis cycle was all-or-none, with all protomers transducing the energy of ATP hydrolysis in a concerted step.
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
153
8,972
0
false
These data also suggested that the ATP hydrolysis cycle was all-or-none, with all protomers transducing the energy of ATP hydrolysis in a concerted step.
[]
These data also suggested that the ATP hydrolysis cycle was all-or-none, with all protomers transducing the energy of ATP hydrolysis in a concerted step.
true
true
true
true
true
1,428
2
DISCUSSION
1
36
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
The initial rapid dissociation of ssDNA, we observed, upon ATP addition may represent PS1βH movement, ssDNA translocation, and its consequential release from the binding site at the end of the hydrolysis cycle.
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
210
8,973
0
false
The initial rapid dissociation of ssDNA, we observed, upon ATP addition may represent PS1βH movement, ssDNA translocation, and its consequential release from the binding site at the end of the hydrolysis cycle.
[]
The initial rapid dissociation of ssDNA, we observed, upon ATP addition may represent PS1βH movement, ssDNA translocation, and its consequential release from the binding site at the end of the hydrolysis cycle.
true
true
true
true
true
1,428
2
DISCUSSION
1
36
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
Changes in the DNA-binding site from high to low affinity must occur or the helicase would not move.
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
100
8,974
0
false
Changes in the DNA-binding site from high to low affinity must occur or the helicase would not move.
[]
Changes in the DNA-binding site from high to low affinity must occur or the helicase would not move.
true
true
true
true
true
1,428
2
DISCUSSION
1
36
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
The subsequent decrease in the ssDNA complex dissociation rate is not consistent with the rapid turnover of ATP by E1HD that we measured, albeit that ATPase activity is reduced in the prersence of ssDNA (Figure 7).
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
214
8,975
0
false
The subsequent decrease in the ssDNA complex dissociation rate is not consistent with the rapid turnover of ATP by E1HD that we measured, albeit that ATPase activity is reduced in the prersence of ssDNA.
[ "Figure 7" ]
The subsequent decrease in the ssDNA complex dissociation rate is not consistent with the rapid turnover of ATP by E1HD that we measured, albeit that ATPase activity is reduced in the prersence of ssDNA.
true
true
true
true
true
1,428
2
DISCUSSION
1
36
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
However, this may be the result of accumulating ADP, or a slow rate of ADP release from the helicase–ssDNA complex, suggesting that translocase activity itself cannot be effectively reconstituted on ssDNA alone.
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
211
8,976
0
false
However, this may be the result of accumulating ADP, or a slow rate of ADP release from the helicase–ssDNA complex, suggesting that translocase activity itself cannot be effectively reconstituted on ssDNA alone.
[]
However, this may be the result of accumulating ADP, or a slow rate of ADP release from the helicase–ssDNA complex, suggesting that translocase activity itself cannot be effectively reconstituted on ssDNA alone.
true
true
true
true
true
1,428
2
DISCUSSION
1
36
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
With T-antigen, the excluded ssDNA and a small region of dsDNA ahead of a replication fork also interact with the helicase, and all ATP modulated interactions may require coupling for efficient use of ATP and unwinding/translocation.
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
233
8,977
0
false
With T-antigen, the excluded ssDNA and a small region of dsDNA ahead of a replication fork also interact with the helicase, and all ATP modulated interactions may require coupling for efficient use of ATP and unwinding/translocation.
[]
With T-antigen, the excluded ssDNA and a small region of dsDNA ahead of a replication fork also interact with the helicase, and all ATP modulated interactions may require coupling for efficient use of ATP and unwinding/translocation.
true
true
true
true
true
1,428
2
DISCUSSION
1
19
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
With T-antigen, the excluded ssDNA has been shown to load on the outside of the helicase at high ATP concentrations (19).
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
121
8,978
1
false
With T-antigen, the excluded ssDNA has been shown to load on the outside of the helicase at high ATP concentrations.
[ "19" ]
With T-antigen, the excluded ssDNA has been shown to load on the outside of the helicase at high ATP concentrations.
true
true
true
true
true
1,428
2
DISCUSSION
1
36
[ "b36", "b38", "b39", "b34", "b7", "b8", "b34", "b19" ]
16,893,956
pmid-10966472|pmid-8241139|pmid-8626772|pmid-7989299|pmid-15454080|pmid-16061814|pmid-16738139|pmid-15454080|pmid-9765408
Our observation that a small mobility difference in gel-shifts is seen for E1HD complexes loaded onto large ssDNA probes with or without ATP (Figure 5a), may indicate that ssDNA can also interact with the exterior of the E1 hexamer in a cofactor dependent manner.
[ "36", "38", "39", "34", "7", "8", "34", "19" ]
263
8,979
0
false
Our observation that a small mobility difference in gel-shifts is seen for E1HD complexes loaded onto large ssDNA probes with or without ATP (Figure 5a), may indicate that ssDNA can also interact with the exterior of the E1 hexamer in a cofactor dependent manner.
[]
Our observation that a small mobility difference in gel-shifts is seen for E1HD complexes loaded onto large ssDNA probes with or without ATP (Figure 5a), may indicate that ssDNA can also interact with the exterior of the E1 hexamer in a cofactor dependent manner.
true
true
true
true
true
1,428
3
DISCUSSION
0
null
null
16,893,956
null
In summary, our data suggest that during the ATP-hydrolysis cycle an internal ssDNA-binding site in an E1 hexamer oscillates from a high to a low-affinity state while protein–protein interactions change from a low- to high-affinity state.
null
238
8,980
0
false
null
null
In summary, our data suggest that during the ATP-hydrolysis cycle an internal ssDNA-binding site in an E1 hexamer oscillates from a high to a low-affinity state while protein–protein interactions change from a low- to high-affinity state.
true
true
true
true
true
1,429
3
DISCUSSION
0
null
null
16,893,956
null
This mechanism would ensure that the complex remains tethered to DNA while processive movement along DNA proceeds.
null
114
8,981
0
false
null
null
This mechanism would ensure that the complex remains tethered to DNA while processive movement along DNA proceeds.
true
true
true
true
true
1,429
3
DISCUSSION
0
null
null
16,893,956
null
A complete evaluation of this proposal awaits the determination of the crystal structures of E1 or T-antigen with DNA.
null
118
8,982
0
false
null
null
A complete evaluation of this proposal awaits the determination of the crystal structures of E1 or T-antigen with DNA.
true
true
true
true
true
1,429
3
DISCUSSION
0
null
null
16,893,956
null
These data would also provide an answer to the intriguing question of how the path of DNA through the complex impacts on the assembly of stable hexameric structures.
null
165
8,983
0
false
null
null
These data would also provide an answer to the intriguing question of how the path of DNA through the complex impacts on the assembly of stable hexameric structures.
true
true
true
true
true
1,429
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,483,517
pmid-16600018|NA
The identification of transcription factor binding sites (TFBSs) in the promoters of genes is a critical step in the delineation of the genetic regulatory network of an organism.
[ "1", "2" ]
178
8,984
0
false
The identification of transcription factor binding sites (TFBSs) in the promoters of genes is a critical step in the delineation of the genetic regulatory network of an organism.
[]
The identification of transcription factor binding sites (TFBSs) in the promoters of genes is a critical step in the delineation of the genetic regulatory network of an organism.
true
true
true
true
true
1,430
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,483,517
pmid-16600018|NA
A number of motif discovery algorithms have been developed over the past decade and a half, for the detection of cis-regulatory sites (1).
[ "1", "2" ]
138
8,985
1
false
A number of motif discovery algorithms have been developed over the past decade and a half, for the detection of cis-regulatory sites.
[ "1" ]
A number of motif discovery algorithms have been developed over the past decade and a half, for the detection of cis-regulatory sites.
true
true
true
true
true
1,430
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,483,517
pmid-16600018|NA
Most of these algorithms depend, in one way or another, on finding an optimal alignment of motif sites.
[ "1", "2" ]
103
8,986
0
false
Most of these algorithms depend, in one way or another, on finding an optimal alignment of motif sites.
[]
Most of these algorithms depend, in one way or another, on finding an optimal alignment of motif sites.
true
true
true
true
true
1,430
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,483,517
pmid-16600018|NA
In this article, we describe the web server for an improved motif discovery algorithm, the Gibbs Centroid Sampler, which finds a centroid alignment.
[ "1", "2" ]
148
8,987
0
false
In this article, we describe the web server for an improved motif discovery algorithm, the Gibbs Centroid Sampler, which finds a centroid alignment.
[]
In this article, we describe the web server for an improved motif discovery algorithm, the Gibbs Centroid Sampler, which finds a centroid alignment.
true
true
true
true
true
1,430
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,483,517
pmid-16600018|NA
The centroid alignment is the alignment that has the minimum total distance to the set of samples chosen from the a posteriori probability distribution of TFBS alignments.
[ "1", "2" ]
171
8,988
0
false
The centroid alignment is the alignment that has the minimum total distance to the set of samples chosen from the a posteriori probability distribution of TFBS alignments.
[]
The centroid alignment is the alignment that has the minimum total distance to the set of samples chosen from the a posteriori probability distribution of TFBS alignments.
true
true
true
true
true
1,430
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,483,517
pmid-16600018|NA
By focusing on the region of solution space containing the most posterior probability, rather than on the single solution that is most probable, this approach significantly enhances the predictive power of the algorithm.
[ "1", "2" ]
220
8,989
0
false
By focusing on the region of solution space containing the most posterior probability, rather than on the single solution that is most probable, this approach significantly enhances the predictive power of the algorithm.
[]
By focusing on the region of solution space containing the most posterior probability, rather than on the single solution that is most probable, this approach significantly enhances the predictive power of the algorithm.
true
true
true
true
true
1,430
0
INTRODUCTION
1
2
[ "B1", "B2" ]
17,483,517
pmid-16600018|NA
In computational experiments using simulated proteobacterial and yeast data (2), the centroid sampler showed improved specificity and positive predictive value over algorithms that report an optimal solution.
[ "1", "2" ]
208
8,990
1
false
In computational experiments using simulated proteobacterial and yeast data, the centroid sampler showed improved specificity and positive predictive value over algorithms that report an optimal solution.
[ "2" ]
In computational experiments using simulated proteobacterial and yeast data, the centroid sampler showed improved specificity and positive predictive value over algorithms that report an optimal solution.
true
true
true
true
true
1,430
1
INTRODUCTION
1
3
[ "B3", "B4 B5 B6 B7 B8", "B3", "B9", "B3" ]
17,483,517
pmid-12824370|pmid-16269786|pmid-11160901|pmid-12368244|pmid-15466295|pmid-12933881|pmid-12824370|NA|pmid-12824370
The Gibbs Centroid Sampler is an improved version of the Gibbs Recursive Sampler (3), which has been used extensively in the identification of TFBSs (4–8), and has been available at our Web site for some time (3,9).
[ "3", "4–8", "3", "9", "3" ]
215
8,991
1
false
The Gibbs Centroid Sampler is an improved version of the Gibbs Recursive Sampler, which has been used extensively in the identification of TFBSs, and has been available at our Web site for some time.
[ "3", "4–8", "3,9" ]
The Gibbs Centroid Sampler is an improved version of the Gibbs Recursive Sampler, which has been used extensively in the identification of TFBSs, and has been available at our Web site for some time.
true
true
true
true
true
1,431
1
INTRODUCTION
1
3
[ "B3", "B4 B5 B6 B7 B8", "B3", "B9", "B3" ]
17,483,517
pmid-12824370|pmid-16269786|pmid-11160901|pmid-12368244|pmid-15466295|pmid-12933881|pmid-12824370|NA|pmid-12824370
The software currently available at the Web site retains all of the features of the previous versions, including searches for multiple motif types, multiple instances (sites) of a motif, palindromic motifs, motifs of varying widths and a heterogeneous background frequency model (see (3) for descriptions of these and ot...
[ "3", "4–8", "3", "9", "3" ]
334
8,992
0
false
The software currently available at the Web site retains all of the features of the previous versions, including searches for multiple motif types, multiple instances (sites) of a motif, palindromic motifs, motifs of varying widths and a heterogeneous background frequency model for descriptions of these and other featu...
[ "see (3" ]
The software currently available at the Web site retains all of the features of the previous versions, including searches for multiple motif types, multiple instances (sites) of a motif, palindromic motifs, motifs of varying widths and a heterogeneous background frequency model for descriptions of these and other featu...
true
true
true
true
true
1,431
1
INTRODUCTION
1
3
[ "B3", "B4 B5 B6 B7 B8", "B3", "B9", "B3" ]
17,483,517
pmid-12824370|pmid-16269786|pmid-11160901|pmid-12368244|pmid-15466295|pmid-12933881|pmid-12824370|NA|pmid-12824370
The users’ choices of options are entered through a web form, described below, and the output is returned to the user via e-mail.
[ "3", "4–8", "3", "9", "3" ]
129
8,993
0
false
The users’ choices of options are entered through a web form, described below, and the output is returned to the user via e-mail.
[]
The users’ choices of options are entered through a web form, described below, and the output is returned to the user via e-mail.
true
true
true
true
true
1,431
1
INTRODUCTION
1
3
[ "B3", "B4 B5 B6 B7 B8", "B3", "B9", "B3" ]
17,483,517
pmid-12824370|pmid-16269786|pmid-11160901|pmid-12368244|pmid-15466295|pmid-12933881|pmid-12824370|NA|pmid-12824370
In addition to the new algorithmic features, the Web site has been updated to include extensive tutorials on the use of the Gibbs sampling software for prokaryotic phylogenetic footprinting and for the analysis of prokaryotic co-expression data.
[ "3", "4–8", "3", "9", "3" ]
245
8,994
0
false
In addition to the new algorithmic features, the Web site has been updated to include extensive tutorials on the use of the Gibbs sampling software for prokaryotic phylogenetic footprinting and for the analysis of prokaryotic co-expression data.
[]
In addition to the new algorithmic features, the Web site has been updated to include extensive tutorials on the use of the Gibbs sampling software for prokaryotic phylogenetic footprinting and for the analysis of prokaryotic co-expression data.
true
true
true
true
true
1,431
2
INTRODUCTION
1
10
[ "B10", "B11", "B12" ]
17,483,517
NA|pmid-2184437|NA
A key feature of most sequence-based Gibbs sampling and expectation maximization algorithms (10,11), is the use of a probabilistic score that is maximized.
[ "10", "11", "12" ]
155
8,995
0
false
A key feature of most sequence-based Gibbs sampling and expectation maximization algorithms, is the use of a probabilistic score that is maximized.
[ "10,11" ]
A key feature of most sequence-based Gibbs sampling and expectation maximization algorithms, is the use of a probabilistic score that is maximized.
true
true
true
true
true
1,432
2
INTRODUCTION
1
10
[ "B10", "B11", "B12" ]
17,483,517
NA|pmid-2184437|NA
Typically, the alignment that has the maximum of this score is reported to the user.
[ "10", "11", "12" ]
84
8,996
0
false
Typically, the alignment that has the maximum of this score is reported to the user.
[]
Typically, the alignment that has the maximum of this score is reported to the user.
true
true
true
true
true
1,432
2
INTRODUCTION
1
12
[ "B10", "B11", "B12" ]
17,483,517
NA|pmid-2184437|NA
Previous versions of the Gibbs Sampler used the posterior probability of the alignment, called the MAP (maximum a posteriori probability) (12), as a measure of the quality of the alignment, and thus the alignment that produced the highest posterior probability (i.e.
[ "10", "11", "12" ]
266
8,997
1
false
Previous versions of the Gibbs Sampler used the posterior probability of the alignment, called the MAP (maximum a posteriori probability), as a measure of the quality of the alignment, and thus the alignment that produced the highest posterior probability (i.e.
[ "12" ]
Previous versions of the Gibbs Sampler used the posterior probability of the alignment, called the MAP (maximum a posteriori probability), as a measure of the quality of the alignment, and thus the alignment that produced the highest posterior probability (i.e.
true
true
true
true
true
1,432
2
INTRODUCTION
1
10
[ "B10", "B11", "B12" ]
17,483,517
NA|pmid-2184437|NA
the MAP alignment) was returned.
[ "10", "11", "12" ]
32
8,998
0
false
the MAP alignment) was returned.
[]
the MAP alignment) was returned.
false
true
true
true
false
1,432
2
INTRODUCTION
1
10
[ "B10", "B11", "B12" ]
17,483,517
NA|pmid-2184437|NA
The reported MAP was calculated as the logarithm of the alignment probability minus the logarithm of an empty or background alignment.
[ "10", "11", "12" ]
134
8,999
0
false
The reported MAP was calculated as the logarithm of the alignment probability minus the logarithm of an empty or background alignment.
[]
The reported MAP was calculated as the logarithm of the alignment probability minus the logarithm of an empty or background alignment.
true
true
true
true
true
1,432