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
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ends_wp
bool
cit_qc
bool
lgtm
bool
__index_level_0__
int64
3
DISCUSSION
1
31
[ "b31", "b32", "b31", "b33", "b34", "b24", "b35" ]
17,145,717
pmid-9230460|pmid-2550456|pmid-15723043|pmid-16935303|pmid-15321724|pmid-16935303|pmid-16131486|pmid-16110343|pmid-16444738|pmid-15111064
All of the 372 MoRF-partner complexes exhibit these large surface areas for the monomers and interfaces; furthermore, nearly all of the MoRFs have substantial prediction of disorder in their flanking regions as well.
[ "31", "32", "31", "33", "34", "24", "35" ]
216
11,000
0
false
All of the 372 MoRF-partner complexes exhibit these large surface areas for the monomers and interfaces; furthermore, nearly all of the MoRFs have substantial prediction of disorder in their flanking regions as well.
[]
All of the 372 MoRF-partner complexes exhibit these large surface areas for the monomers and interfaces; furthermore, nearly all of the MoRFs have substantial prediction of disorder in their flanking regions as well.
true
true
true
true
true
1,757
3
DISCUSSION
1
31
[ "b31", "b32", "b31", "b33", "b34", "b24", "b35" ]
17,145,717
pmid-9230460|pmid-2550456|pmid-15723043|pmid-16935303|pmid-15321724|pmid-16935303|pmid-16131486|pmid-16110343|pmid-16444738|pmid-15111064
Both these observations support the concept that these interactions involve disorder-to-order transitions of the MoRFs (31).
[ "31", "32", "31", "33", "34", "24", "35" ]
124
11,001
1
false
Both these observations support the concept that these interactions involve disorder-to-order transitions of the MoRFs.
[ "31" ]
Both these observations support the concept that these interactions involve disorder-to-order transitions of the MoRFs.
true
true
true
true
true
1,757
3
DISCUSSION
1
33
[ "b31", "b32", "b31", "b33", "b34", "b24", "b35" ]
17,145,717
pmid-9230460|pmid-2550456|pmid-15723043|pmid-16935303|pmid-15321724|pmid-16935303|pmid-16131486|pmid-16110343|pmid-16444738|pmid-15111064
Direct experimental evidence in support of this concept has been presented in the case of deacetylation (33) and phosphorylation sites, SH3 interaction motifs (34) and recognition elements of 14-3-3 proteins (24), which all have been found in locally disordered regions of their parent proteins.
[ "31", "32", "31", "33", "34", "24", "35" ]
295
11,002
1
false
Direct experimental evidence in support of this concept has been presented in the case of deacetylation and phosphorylation sites, SH3 interaction motifs and recognition elements of 14-3-3 proteins, which all have been found in locally disordered regions of their parent proteins.
[ "33", "34", "24" ]
Direct experimental evidence in support of this concept has been presented in the case of deacetylation and phosphorylation sites, SH3 interaction motifs and recognition elements of 14-3-3 proteins, which all have been found in locally disordered regions of their parent proteins.
true
true
true
true
true
1,757
3
DISCUSSION
1
35
[ "b31", "b32", "b31", "b33", "b34", "b24", "b35" ]
17,145,717
pmid-9230460|pmid-2550456|pmid-15723043|pmid-16935303|pmid-15321724|pmid-16935303|pmid-16131486|pmid-16110343|pmid-16444738|pmid-15111064
The possible generality of this mode of protein–protein interactions has also been underlined by predicting the local structural preferences of interaction sites of IDPs (35).
[ "31", "32", "31", "33", "34", "24", "35" ]
175
11,003
1
false
The possible generality of this mode of protein–protein interactions has also been underlined by predicting the local structural preferences of interaction sites of IDPs.
[ "35" ]
The possible generality of this mode of protein–protein interactions has also been underlined by predicting the local structural preferences of interaction sites of IDPs.
true
true
true
true
true
1,757
4
DISCUSSION
1
20
[ "b20", "b21", "b36", "b20" ]
17,145,717
pmid-9405336|pmid-15943979|pmid-8303294|NA|pmid-12824381|pmid-15943979|pmid-12824383|pmid-12824381
Another approach, based on sequence comparison rather than analysis of structures in PDB, has been used to systematically identify short, linear motifs that bind to protein partners (20,21,36).
[ "20", "21", "36", "20" ]
193
11,004
0
false
Another approach, based on sequence comparison rather than analysis of structures in PDB, has been used to systematically identify short, linear motifs that bind to protein partners.
[ "20,21,36" ]
Another approach, based on sequence comparison rather than analysis of structures in PDB, has been used to systematically identify short, linear motifs that bind to protein partners.
true
true
true
true
true
1,758
4
DISCUSSION
1
20
[ "b20", "b21", "b36", "b20" ]
17,145,717
pmid-9405336|pmid-15943979|pmid-8303294|NA|pmid-12824381|pmid-15943979|pmid-12824383|pmid-12824381
These sequence-identified segments have been collected and are contained in the Eukaryotic Linear Motif (ELM) server () (20).
[ "20", "21", "36", "20" ]
125
11,005
1
false
These sequence-identified segments have been collected and are contained in the Eukaryotic Linear Motif (ELM) server ().
[ "20" ]
These sequence-identified segments have been collected and are contained in the Eukaryotic Linear Motif (ELM) server ().
true
true
true
true
true
1,758
4
DISCUSSION
1
20
[ "b20", "b21", "b36", "b20" ]
17,145,717
pmid-9405336|pmid-15943979|pmid-8303294|NA|pmid-12824381|pmid-15943979|pmid-12824383|pmid-12824381
Many of the sequence-based ELMs and the structure-based MoRFs are simply different descriptions of the same protein segments, and in these cases the ELMs likely undergo coupled binding and folding upon association with their partners (Fuxreiter, Tompa and Simon, work in progress).
[ "20", "21", "36", "20" ]
281
11,006
0
false
Many of the sequence-based ELMs and the structure-based MoRFs are simply different descriptions of the same protein segments, and in these cases the ELMs likely undergo coupled binding and folding upon association with their partners (Fuxreiter, Tompa and Simon, work in progress).
[]
Many of the sequence-based ELMs and the structure-based MoRFs are simply different descriptions of the same protein segments, and in these cases the ELMs likely undergo coupled binding and folding upon association with their partners (Fuxreiter, Tompa and Simon, work in progress).
true
true
true
true
true
1,758
4
DISCUSSION
1
20
[ "b20", "b21", "b36", "b20" ]
17,145,717
pmid-9405336|pmid-15943979|pmid-8303294|NA|pmid-12824381|pmid-15943979|pmid-12824383|pmid-12824381
The ELMs that have been experimentally verified to be unstructured in the absence of their partners and the ELM-MoRF matches will be added to DisProt with appropriate cross-references to the ELM collection.
[ "20", "21", "36", "20" ]
206
11,007
0
false
The ELMs that have been experimentally verified to be unstructured in the absence of their partners and the ELM-MoRF matches will be added to DisProt with appropriate cross-references to the ELM collection.
[]
The ELMs that have been experimentally verified to be unstructured in the absence of their partners and the ELM-MoRF matches will be added to DisProt with appropriate cross-references to the ELM collection.
true
true
true
true
true
1,758
5
DISCUSSION
0
null
null
17,145,717
NA|NA|pmid-8876165|pmid-16444738
We recently carried out a bioinformatics study to determine which Swiss Protein keywords were associated with the prediction of long disordered regions and which keywords were associated with the absence of such predictions.
null
224
11,008
0
false
null
null
We recently carried out a bioinformatics study to determine which Swiss Protein keywords were associated with the prediction of long disordered regions and which keywords were associated with the absence of such predictions.
true
true
true
true
true
1,759
5
DISCUSSION
0
null
null
17,145,717
NA|NA|pmid-8876165|pmid-16444738
Of 711 function-associated keywords for which there were enough protein examples in Swiss Protein to make statistical inferences, 302 keywords were strongly associated with the absence of disorder prediction and 262 were strongly associated with the prediction of disorder.
null
273
11,009
0
false
null
null
Of 711 function-associated keywords for which there were enough protein examples in Swiss Protein to make statistical inferences, 302 keywords were strongly associated with the absence of disorder prediction and 262 were strongly associated with the prediction of disorder.
true
true
true
true
true
1,759
5
DISCUSSION
0
null
null
17,145,717
NA|NA|pmid-8876165|pmid-16444738
Manual literature searches provided numerous confirmatory examples for which laboratory experiments verified the direct involvement of disordered regions in carrying out the identified functions (H. Xie, S. Vucetic, L.M.
null
220
11,010
0
false
null
null
Manual literature searches provided numerous confirmatory examples for which laboratory experiments verified the direct involvement of disordered regions in carrying out the identified functions (H. Xie, S. Vucetic, L.M.
true
true
true
true
true
1,759
5
DISCUSSION
0
null
null
17,145,717
NA|NA|pmid-8876165|pmid-16444738
Iakoucheva, C.J.
null
16
11,011
0
false
null
null
Iakoucheva, C.J.
true
true
true
true
true
1,759
5
DISCUSSION
0
null
null
17,145,717
NA|NA|pmid-8876165|pmid-16444738
Oldfield, A.K.
null
14
11,012
0
false
null
null
Oldfield, A.K.
true
true
true
true
true
1,759
5
DISCUSSION
0
null
null
17,145,717
NA|NA|pmid-8876165|pmid-16444738
Dunker, Z. Obradovic and V.N.
null
29
11,013
0
false
null
null
Dunker, Z. Obradovic and V.N.
true
true
true
true
true
1,759
5
DISCUSSION
0
null
null
17,145,717
NA|NA|pmid-8876165|pmid-16444738
Uversky, submitted for publication).
null
36
11,014
0
false
null
null
Uversky, submitted for publication).
true
true
true
true
true
1,759
5
DISCUSSION
0
null
null
17,145,717
NA|NA|pmid-8876165|pmid-16444738
In the coming year, we will focus our annotation efforts on finding papers that determine whether or not IDPs are directly responsible for carrying out the 262 functions that were indicated to be IDP-associated.
null
211
11,015
0
false
null
null
In the coming year, we will focus our annotation efforts on finding papers that determine whether or not IDPs are directly responsible for carrying out the 262 functions that were indicated to be IDP-associated.
true
true
true
true
true
1,759
5
DISCUSSION
0
null
null
17,145,717
NA|NA|pmid-8876165|pmid-16444738
This bioinformatics-directed DisProt expansion will enable us to rapidly increase the number of experimentally verified disordered protein–function relationships.
null
162
11,016
0
false
null
null
This bioinformatics-directed DisProt expansion will enable us to rapidly increase the number of experimentally verified disordered protein–function relationships.
true
true
true
true
true
1,759
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,439,962
pmid-8469282|pmid-15568983|pmid-9920940|pmid-10585471|pmid-14563842
The accurate transmission of genetic information of an organism from one generation to the next is a crucial step during the lifespan of an organism.
[ "1", "2" ]
149
11,017
0
false
The accurate transmission of genetic information of an organism from one generation to the next is a crucial step during the lifespan of an organism.
[]
The accurate transmission of genetic information of an organism from one generation to the next is a crucial step during the lifespan of an organism.
true
true
true
true
true
1,760
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,439,962
pmid-8469282|pmid-15568983|pmid-9920940|pmid-10585471|pmid-14563842
In order to ensure the absolute precision required in DNA synthesis and transmission, eukaryotic cells have derived a complex system of genome quality control to maximize accuracy and minimize mistakes resulting from DNA damage and inaccurate DNA synthesis.
[ "1", "2" ]
257
11,018
0
false
In order to ensure the absolute precision required in DNA synthesis and transmission, eukaryotic cells have derived a complex system of genome quality control to maximize accuracy and minimize mistakes resulting from DNA damage and inaccurate DNA synthesis.
[]
In order to ensure the absolute precision required in DNA synthesis and transmission, eukaryotic cells have derived a complex system of genome quality control to maximize accuracy and minimize mistakes resulting from DNA damage and inaccurate DNA synthesis.
true
true
true
true
true
1,760
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,439,962
pmid-8469282|pmid-15568983|pmid-9920940|pmid-10585471|pmid-14563842
One of the best-known and best-described systems of DNA repair in eukaryotic cells is the base excision repair (BER) pathway.
[ "1", "2" ]
125
11,019
0
false
One of the best-known and best-described systems of DNA repair in eukaryotic cells is the base excision repair (BER) pathway.
[]
One of the best-known and best-described systems of DNA repair in eukaryotic cells is the base excision repair (BER) pathway.
true
true
true
true
true
1,760
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,439,962
pmid-8469282|pmid-15568983|pmid-9920940|pmid-10585471|pmid-14563842
BER has been estimated to provide repairs for ∼10 000 lesions per cell per day from spontaneous oxidative and alkylation damage (1,2).
[ "1", "2" ]
134
11,020
0
false
BER has been estimated to provide repairs for ∼10 000 lesions per cell per day from spontaneous oxidative and alkylation damage.
[ "1,2" ]
BER has been estimated to provide repairs for ∼10 000 lesions per cell per day from spontaneous oxidative and alkylation damage.
true
true
true
true
true
1,760
1
INTRODUCTION
1
4
[ "B3", "B4", "B5", "B6", "B7", "B8" ]
17,439,962
NA|pmid-7979257|pmid-8538772|pmid-8978692|pmid-7624801|pmid-10946235|pmid-9920940|pmid-10585471|pmid-14563842
During BER, a specific DNA glycosylase recognizes its target DNA damage and excises the damaged base, leaving an abasic site (for review see 3); an apurinic/apyrimidinic endonuclease nicks the sugar–phosphate backbone and leaves a gap at the original DNA damage site (4).
[ "3", "4", "5", "6", "7", "8" ]
271
11,021
1
false
During BER, a specific DNA glycosylase recognizes its target DNA damage and excises the damaged base, leaving an abasic site ; an apurinic/apyrimidinic endonuclease nicks the sugar–phosphate backbone and leaves a gap at the original DNA damage site.
[ "for review see 3", "4" ]
During BER, a specific DNA glycosylase recognizes its target DNA damage and excises the damaged base, leaving an abasic site ; an apurinic/apyrimidinic endonuclease nicks the sugar–phosphate backbone and leaves a gap at the original DNA damage site.
true
true
true
true
true
1,761
1
INTRODUCTION
1
3
[ "B3", "B4", "B5", "B6", "B7", "B8" ]
17,439,962
NA|pmid-7979257|pmid-8538772|pmid-8978692|pmid-7624801|pmid-10946235|pmid-9920940|pmid-10585471|pmid-14563842
It is the role of DNA polymerase beta (pol β) to fill in this gap in a template-directed manner (5,6).
[ "3", "4", "5", "6", "7", "8" ]
102
11,022
0
false
It is the role of DNA polymerase beta (pol β) to fill in this gap in a template-directed manner.
[ "5,6" ]
It is the role of DNA polymerase beta (pol β) to fill in this gap in a template-directed manner.
true
true
true
true
true
1,761
1
INTRODUCTION
1
7
[ "B3", "B4", "B5", "B6", "B7", "B8" ]
17,439,962
NA|pmid-7979257|pmid-8538772|pmid-8978692|pmid-7624801|pmid-10946235|pmid-9920940|pmid-10585471|pmid-14563842
Along with its polymerase function, pol β utilizes its 5′-deoxyribose phosphate lyase activity (7) to remove the 5′-deoxyribose phosphate moiety on the DNA substrate, and ready the product for ligation by a DNA ligase.
[ "3", "4", "5", "6", "7", "8" ]
218
11,023
1
false
Along with its polymerase function, pol β utilizes its 5′-deoxyribose phosphate lyase activity to remove the 5′-deoxyribose phosphate moiety on the DNA substrate, and ready the product for ligation by a DNA ligase.
[ "7" ]
Along with its polymerase function, pol β utilizes its 5′-deoxyribose phosphate lyase activity to remove the 5′-deoxyribose phosphate moiety on the DNA substrate, and ready the product for ligation by a DNA ligase.
true
true
true
true
true
1,761
1
INTRODUCTION
1
8
[ "B3", "B4", "B5", "B6", "B7", "B8" ]
17,439,962
NA|pmid-7979257|pmid-8538772|pmid-8978692|pmid-7624801|pmid-10946235|pmid-9920940|pmid-10585471|pmid-14563842
The XRCC1- DNA ligase IIIα complex seals the nick during short-patch BER, while the same duty is thought to be performed by DNA ligase I during long-patch BER (8).
[ "3", "4", "5", "6", "7", "8" ]
163
11,024
1
false
The XRCC1- DNA ligase IIIα complex seals the nick during short-patch BER, while the same duty is thought to be performed by DNA ligase I during long-patch BER.
[ "8" ]
The XRCC1- DNA ligase IIIα complex seals the nick during short-patch BER, while the same duty is thought to be performed by DNA ligase I during long-patch BER.
true
true
true
true
true
1,761
2
INTRODUCTION
1
9
[ "B9", "B10 B11 B12 B13 B14" ]
17,439,962
pmid-3988773|pmid-16615916|pmid-7516580|pmid-8841118|pmid-9287163|pmid-11330999
While all of the proteins involved in BER contribute an important and specialized role, it is pol β
[ "9", "10–14" ]
99
11,025
0
false
While all of the proteins involved in BER contribute an important and specialized role, it is pol β
[]
While all of the proteins involved in BER contribute an important and specialized role, it is pol β
true
true
false
true
false
1,762
2
INTRODUCTION
1
9
[ "B9", "B10 B11 B12 B13 B14" ]
17,439,962
pmid-3988773|pmid-16615916|pmid-7516580|pmid-8841118|pmid-9287163|pmid-11330999
that is responsible for restoring the genetic information of the damaged DNA substrate back to its original state.
[ "9", "10–14" ]
114
11,026
0
false
that is responsible for restoring the genetic information of the damaged DNA substrate back to its original state.
[]
that is responsible for restoring the genetic information of the damaged DNA substrate back to its original state.
false
true
true
true
false
1,762
2
INTRODUCTION
1
9
[ "B9", "B10 B11 B12 B13 B14" ]
17,439,962
pmid-3988773|pmid-16615916|pmid-7516580|pmid-8841118|pmid-9287163|pmid-11330999
Pol β is not as accurate as replicative DNA polymerases (9) because it lacks proofreading capability.
[ "9", "10–14" ]
101
11,027
1
false
Pol β is not as accurate as replicative DNA polymerases because it lacks proofreading capability.
[ "9" ]
Pol β is not as accurate as replicative DNA polymerases because it lacks proofreading capability.
true
true
true
true
true
1,762
2
INTRODUCTION
1
9
[ "B9", "B10 B11 B12 B13 B14" ]
17,439,962
pmid-3988773|pmid-16615916|pmid-7516580|pmid-8841118|pmid-9287163|pmid-11330999
However, this intrinsic lack of proofreading makes pol β an excellent candidate to study the mechanism of polymerization fidelity directly.
[ "9", "10–14" ]
139
11,028
0
false
However, this intrinsic lack of proofreading makes pol β an excellent candidate to study the mechanism of polymerization fidelity directly.
[]
However, this intrinsic lack of proofreading makes pol β an excellent candidate to study the mechanism of polymerization fidelity directly.
true
true
true
true
true
1,762
2
INTRODUCTION
1
9
[ "B9", "B10 B11 B12 B13 B14" ]
17,439,962
pmid-3988773|pmid-16615916|pmid-7516580|pmid-8841118|pmid-9287163|pmid-11330999
Advantages in using pol β to study polymerization fidelity include the abundance of structural data (for example 10–14), and the small size of this protein resulting in ease of purification.
[ "9", "10–14" ]
190
11,029
0
false
Advantages in using pol β to study polymerization fidelity include the abundance of structural data, and the small size of this protein resulting in ease of purification.
[ "for example 10–14" ]
Advantages in using pol β to study polymerization fidelity include the abundance of structural data, and the small size of this protein resulting in ease of purification.
true
true
true
true
true
1,762
3
INTRODUCTION
1
15
[ "B15", "B16", "B17", "B18 B19 B20 B21 B22 B23 B24 B25 B26" ]
17,439,962
pmid-6214209|pmid-10409611|pmid-11756435|NA|pmid-10200168|pmid-10449735|pmid-11154692|pmid-11560485|pmid-12962495|pmid-15751954|pmid-15901725|pmid-16313169|pmid-9920940|pmid-10585471|pmid-14563842|pmid-10946231|pmid-9287163|pmid-11330999|pmid-8137427|pmid-12517346|pmid-11823435|pmid-14992725|NA
Like other template-directed polymerases, pol β selects the correct complementary base from a pool of four nucleotides.
[ "15", "16", "17", "18–26" ]
119
11,030
0
false
Like other template-directed polymerases, pol β selects the correct complementary base from a pool of four nucleotides.
[]
Like other template-directed polymerases, pol β selects the correct complementary base from a pool of four nucleotides.
true
true
true
true
true
1,763
3
INTRODUCTION
1
15
[ "B15", "B16", "B17", "B18 B19 B20 B21 B22 B23 B24 B25 B26" ]
17,439,962
pmid-6214209|pmid-10409611|pmid-11756435|NA|pmid-10200168|pmid-10449735|pmid-11154692|pmid-11560485|pmid-12962495|pmid-15751954|pmid-15901725|pmid-16313169|pmid-9920940|pmid-10585471|pmid-14563842|pmid-10946231|pmid-9287163|pmid-11330999|pmid-8137427|pmid-12517346|pmid-11823435|pmid-14992725|NA
While the complementary nature of Watson–Crick base pairs lies at the heart of a template-directed polymerase's ability to select the correct incoming nucleotide opposite the templating base, the accuracy by which a DNA polymerase is able to perform its function delineates the fact that a polymerase's nucleotide discri...
[ "15", "16", "17", "18–26" ]
418
11,031
1
false
While the complementary nature of Watson–Crick base pairs lies at the heart of a template-directed polymerase's ability to select the correct incoming nucleotide opposite the templating base, the accuracy by which a DNA polymerase is able to perform its function delineates the fact that a polymerase's nucleotide discri...
[ "15" ]
While the complementary nature of Watson–Crick base pairs lies at the heart of a template-directed polymerase's ability to select the correct incoming nucleotide opposite the templating base, the accuracy by which a DNA polymerase is able to perform its function delineates the fact that a polymerase's nucleotide discri...
true
true
true
true
true
1,763
3
INTRODUCTION
1
15
[ "B15", "B16", "B17", "B18 B19 B20 B21 B22 B23 B24 B25 B26" ]
17,439,962
pmid-6214209|pmid-10409611|pmid-11756435|NA|pmid-10200168|pmid-10449735|pmid-11154692|pmid-11560485|pmid-12962495|pmid-15751954|pmid-15901725|pmid-16313169|pmid-9920940|pmid-10585471|pmid-14563842|pmid-10946231|pmid-9287163|pmid-11330999|pmid-8137427|pmid-12517346|pmid-11823435|pmid-14992725|NA
Therefore in order to gain a better understanding of how a polymerase achieves its fidelity, a detailed study of the structure–function relationship is imperative.
[ "15", "16", "17", "18–26" ]
163
11,032
0
false
Therefore in order to gain a better understanding of how a polymerase achieves its fidelity, a detailed study of the structure–function relationship is imperative.
[]
Therefore in order to gain a better understanding of how a polymerase achieves its fidelity, a detailed study of the structure–function relationship is imperative.
true
true
true
true
true
1,763
3
INTRODUCTION
1
15
[ "B15", "B16", "B17", "B18 B19 B20 B21 B22 B23 B24 B25 B26" ]
17,439,962
pmid-6214209|pmid-10409611|pmid-11756435|NA|pmid-10200168|pmid-10449735|pmid-11154692|pmid-11560485|pmid-12962495|pmid-15751954|pmid-15901725|pmid-16313169|pmid-9920940|pmid-10585471|pmid-14563842|pmid-10946231|pmid-9287163|pmid-11330999|pmid-8137427|pmid-12517346|pmid-11823435|pmid-14992725|NA
Intuitively, the region of interest for fidelity would be amino acid residues near the active site region, as demonstrated by others (16,17).
[ "15", "16", "17", "18–26" ]
141
11,033
0
false
Intuitively, the region of interest for fidelity would be amino acid residues near the active site region, as demonstrated by others.
[ "16,17" ]
Intuitively, the region of interest for fidelity would be amino acid residues near the active site region, as demonstrated by others.
true
true
true
true
true
1,763
3
INTRODUCTION
1
18–26
[ "B15", "B16", "B17", "B18 B19 B20 B21 B22 B23 B24 B25 B26" ]
17,439,962
pmid-6214209|pmid-10409611|pmid-11756435|NA|pmid-10200168|pmid-10449735|pmid-11154692|pmid-11560485|pmid-12962495|pmid-15751954|pmid-15901725|pmid-16313169|pmid-9920940|pmid-10585471|pmid-14563842|pmid-10946231|pmid-9287163|pmid-11330999|pmid-8137427|pmid-12517346|pmid-11823435|pmid-14992725|NA
However, other studies have shown that regions that are located away from the active site and do not come into direct contact with either DNA substrate or incoming dNTP such as the hydrophobic hinge region, play a critical role in maintaining the fidelity of polymerization (18–26).
[ "15", "16", "17", "18–26" ]
282
11,034
1
false
However, other studies have shown that regions that are located away from the active site and do not come into direct contact with either DNA substrate or incoming dNTP such as the hydrophobic hinge region, play a critical role in maintaining the fidelity of polymerization.
[ "18–26" ]
However, other studies have shown that regions that are located away from the active site and do not come into direct contact with either DNA substrate or incoming dNTP such as the hydrophobic hinge region, play a critical role in maintaining the fidelity of polymerization.
true
true
true
true
true
1,763
4
INTRODUCTION
1
27
[ "B27" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
One region that is likely to be important for accurate DNA synthesis in pol β is the 14-amino acid loop II that spans residues 240–253 as shown in Figure 1.
[ "27" ]
156
11,035
0
false
One region that is likely to be important for accurate DNA synthesis in pol β is the 14-amino acid loop II that spans residues 240–253 as shown in Figure 1.
[]
One region that is likely to be important for accurate DNA synthesis in pol β is the 14-amino acid loop II that spans residues 240–253 as shown in Figure 1.
true
true
true
true
true
1,764
4
INTRODUCTION
1
27
[ "B27" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
It is located on the outskirts of the palm domain, the domain in which the active site residues are located.
[ "27" ]
108
11,036
0
false
It is located on the outskirts of the palm domain, the domain in which the active site residues are located.
[]
It is located on the outskirts of the palm domain, the domain in which the active site residues are located.
true
true
true
true
true
1,764
4
INTRODUCTION
1
27
[ "B27" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
As was first shown in the work presented by Garcia-Diaz et al.
[ "27" ]
62
11,037
0
false
As was first shown in the work presented by Garcia-Diaz et al.
[]
As was first shown in the work presented by Garcia-Diaz et al.
true
true
true
true
true
1,764
4
INTRODUCTION
1
27
[ "B27" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
(27), structural comparison of the loop II region of two members of the Pol X family, pol β and DNA polymerase lambda (pol λ) revealed that there were some identical amino acid residues on each end of the loop as shown in Figure 2.
[ "27" ]
231
11,038
1
false
, structural comparison of the loop II region of two members of the Pol X family, pol β and DNA polymerase lambda (pol λ) revealed that there were some identical amino acid residues on each end of the loop as shown in Figure 2.
[ "27" ]
, structural comparison of the loop II region of two members of the Pol X family, pol β and DNA polymerase lambda (pol λ) revealed that there were some identical amino acid residues on each end of the loop as shown in Figure 2.
false
false
true
true
false
1,764
4
INTRODUCTION
1
27
[ "B27" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
Amino acid residues G-V-C-Q-L-P and G-V-C-R-L-P for pol β and pol λ, respectively, appear to anchor one end of loop II, whereas residues H-R-R appear to anchor the end of the loop region for both of these members of the pol X family (Figure 2).
[ "27" ]
244
11,039
0
false
Amino acid residues G-V-C-Q-L-P and G-V-C-R-L-P for pol β and pol λ, respectively, appear to anchor one end of loop II, whereas residues H-R-R appear to anchor the end of the loop region for both of these members of the pol X family (Figure 2).
[]
Amino acid residues G-V-C-Q-L-P and G-V-C-R-L-P for pol β and pol λ, respectively, appear to anchor one end of loop II, whereas residues H-R-R appear to anchor the end of the loop region for both of these members of the pol X family.
true
true
true
true
true
1,764
4
INTRODUCTION
1
27
[ "B27" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
Figure 1.Pol β ribbon diagram of the loop region.
[ "27" ]
49
11,040
0
false
Figure 1.Pol β ribbon diagram of the loop region.
[]
Figure 1.Pol β ribbon diagram of the loop region.
true
true
true
true
true
1,764
4
INTRODUCTION
1
27
[ "B27" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
Loop II, containing amino acid residues R253, E249 and D246, and the subdomains of pol β are labeled.
[ "27" ]
101
11,041
0
false
Loop II, containing amino acid residues R253, E249 and D246, and the subdomains of pol β are labeled.
[]
Loop II, containing amino acid residues R253, E249 and D246, and the subdomains of pol β are labeled.
true
true
true
true
true
1,764
4
INTRODUCTION
1
27
[ "B27" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
Figure 2.Comparison of the loop II region of pol β and pol λ.
[ "27" ]
61
11,042
0
false
Figure 2.Comparison of the loop II region of pol β and pol λ.
[]
Figure 2.Comparison of the loop II region of pol β and pol λ.
true
true
true
true
true
1,764
4
INTRODUCTION
1
27
[ "B27" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
Amino acid sequence surrounding and including loop II of mammalian pol β and mammalian pol λ is shown.
[ "27" ]
102
11,043
0
false
Amino acid sequence surrounding and including loop II of mammalian pol β and mammalian pol λ is shown.
[]
Amino acid sequence surrounding and including loop II of mammalian pol β and mammalian pol λ is shown.
true
true
true
true
true
1,764
4
INTRODUCTION
1
27
[ "B27" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
The loop sequence of pol β is from residues 240–253, and the loop sequence of pol λ is from residues 476–485.
[ "27" ]
109
11,044
0
false
The loop sequence of pol β is from residues 240–253, and the loop sequence of pol λ is from residues 476–485.
[]
The loop sequence of pol β is from residues 240–253, and the loop sequence of pol λ is from residues 476–485.
true
true
true
true
true
1,764
4
INTRODUCTION
1
27
[ "B27" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
The amino acid residues of the pol β loop that were altered in this study are in bold.
[ "27" ]
86
11,045
0
false
The amino acid residues of the pol β loop that were altered in this study are in bold.
[]
The amino acid residues of the pol β loop that were altered in this study are in bold.
true
true
true
true
true
1,764
4
INTRODUCTION
1
27
[ "B27" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
The amino acids near the beginning and end of the loop that are conserved between pol β and pol λ are italicized and indicated by the two arrows in between the beginning and the end of both sequences.
[ "27" ]
200
11,046
0
false
The amino acids near the beginning and end of the loop that are conserved between pol β and pol λ are italicized and indicated by the two arrows in between the beginning and the end of both sequences.
[]
The amino acids near the beginning and end of the loop that are conserved between pol β and pol λ are italicized and indicated by the two arrows in between the beginning and the end of both sequences.
true
true
true
true
true
1,764
5
INTRODUCTION
0
null
null
17,439,962
null
Pol β ribbon diagram of the loop region.
null
40
11,047
0
false
null
null
Pol β ribbon diagram of the loop region.
true
true
true
true
true
1,765
5
INTRODUCTION
0
null
null
17,439,962
null
Loop II, containing amino acid residues R253, E249 and D246, and the subdomains of pol β are labeled.
null
101
11,048
0
false
null
null
Loop II, containing amino acid residues R253, E249 and D246, and the subdomains of pol β are labeled.
true
true
true
true
true
1,765
6
INTRODUCTION
0
null
null
17,439,962
null
Comparison of the loop II region of pol β and pol λ.
null
52
11,049
0
false
null
null
Comparison of the loop II region of pol β and pol λ.
true
true
true
true
true
1,766
6
INTRODUCTION
0
null
null
17,439,962
null
Amino acid sequence surrounding and including loop II of mammalian pol β and mammalian pol λ is shown.
null
102
11,050
0
false
null
null
Amino acid sequence surrounding and including loop II of mammalian pol β and mammalian pol λ is shown.
true
true
true
true
true
1,766
6
INTRODUCTION
0
null
null
17,439,962
null
The loop sequence of pol β is from residues 240–253, and the loop sequence of pol λ is from residues 476–485.
null
109
11,051
0
false
null
null
The loop sequence of pol β is from residues 240–253, and the loop sequence of pol λ is from residues 476–485.
true
true
true
true
true
1,766
6
INTRODUCTION
0
null
null
17,439,962
null
The amino acid residues of the pol β loop that were altered in this study are in bold.
null
86
11,052
0
false
null
null
The amino acid residues of the pol β loop that were altered in this study are in bold.
true
true
true
true
true
1,766
6
INTRODUCTION
0
null
null
17,439,962
null
The amino acids near the beginning and end of the loop that are conserved between pol β and pol λ are italicized and indicated by the two arrows in between the beginning and the end of both sequences.
null
200
11,053
0
false
null
null
The amino acids near the beginning and end of the loop that are conserved between pol β and pol λ are italicized and indicated by the two arrows in between the beginning and the end of both sequences.
true
true
true
true
true
1,766
7
INTRODUCTION
1
28
[ "B28", "B29", "B30", "B29", "B30" ]
17,439,962
pmid-9920940|pmid-10585471|pmid-14563842|pmid-10585471|pmid-14563842|pmid-15794655|pmid-11330999
Three different single amino acid alterations of loop II, R253M, D246V and E249K confer AZT resistance as depicted in Figure 1 (28).
[ "28", "29", "30", "29", "30" ]
132
11,054
1
false
Three different single amino acid alterations of loop II, R253M, D246V and E249K confer AZT resistance as depicted in Figure 1.
[ "28" ]
Three different single amino acid alterations of loop II, R253M, D246V and E249K confer AZT resistance as depicted in Figure 1.
true
true
true
true
true
1,767
7
INTRODUCTION
1
28
[ "B28", "B29", "B30", "B29", "B30" ]
17,439,962
pmid-9920940|pmid-10585471|pmid-14563842|pmid-10585471|pmid-14563842|pmid-15794655|pmid-11330999
Two of these mutants, E249K and D246V, were characterized through detailed kinetic analyses (29,30).
[ "28", "29", "30", "29", "30" ]
100
11,055
0
false
Two of these mutants, E249K and D246V, were characterized through detailed kinetic analyses.
[ "29,30" ]
Two of these mutants, E249K and D246V, were characterized through detailed kinetic analyses.
true
true
true
true
true
1,767
7
INTRODUCTION
1
29
[ "B28", "B29", "B30", "B29", "B30" ]
17,439,962
pmid-9920940|pmid-10585471|pmid-14563842|pmid-10585471|pmid-14563842|pmid-15794655|pmid-11330999
The mutant E249K was shown to have lower fidelity than wild-type pol β due to its tendency to extend mispaired bases at catalytic efficiencies greater than wild-type pol β (29).
[ "28", "29", "30", "29", "30" ]
177
11,056
1
false
The mutant E249K was shown to have lower fidelity than wild-type pol β due to its tendency to extend mispaired bases at catalytic efficiencies greater than wild-type pol β.
[ "29" ]
The mutant E249K was shown to have lower fidelity than wild-type pol β due to its tendency to extend mispaired bases at catalytic efficiencies greater than wild-type pol β.
true
true
true
true
true
1,767
7
INTRODUCTION
1
30
[ "B28", "B29", "B30", "B29", "B30" ]
17,439,962
pmid-9920940|pmid-10585471|pmid-14563842|pmid-10585471|pmid-14563842|pmid-15794655|pmid-11330999
The lowered fidelity of D246V was attributed to its tendency to misincorporate T opposite template bases G and C, but the misincorporation was greatly influenced by the identity of the base 5′ to the templating base (30).
[ "28", "29", "30", "29", "30" ]
221
11,057
1
false
The lowered fidelity of D246V was attributed to its tendency to misincorporate T opposite template bases G and C, but the misincorporation was greatly influenced by the identity of the base 5′ to the templating base.
[ "30" ]
The lowered fidelity of D246V was attributed to its tendency to misincorporate T opposite template bases G and C, but the misincorporation was greatly influenced by the identity of the base 5′ to the templating base.
true
true
true
true
true
1,767
7
INTRODUCTION
1
28
[ "B28", "B29", "B30", "B29", "B30" ]
17,439,962
pmid-9920940|pmid-10585471|pmid-14563842|pmid-10585471|pmid-14563842|pmid-15794655|pmid-11330999
Kinetic investigations of these two mutants suggest that loop II of pol β exerts a distinct influence on the primer position of the DNA substrate.
[ "28", "29", "30", "29", "30" ]
146
11,058
0
false
Kinetic investigations of these two mutants suggest that loop II of pol β exerts a distinct influence on the primer position of the DNA substrate.
[]
Kinetic investigations of these two mutants suggest that loop II of pol β exerts a distinct influence on the primer position of the DNA substrate.
true
true
true
true
true
1,767
8
INTRODUCTION
0
null
null
17,439,962
pmid-8538772
Loop II itself is solvent-exposed and highly flexible.
null
54
11,059
0
false
null
null
Loop II itself is solvent-exposed and highly flexible.
true
true
true
true
true
1,768
8
INTRODUCTION
0
null
null
17,439,962
pmid-8538772
While it is not completely disordered in known pol β crystal structures, its flexibility masks our ability to obtain a good structural understanding of this region.
null
164
11,060
0
false
null
null
While it is not completely disordered in known pol β crystal structures, its flexibility masks our ability to obtain a good structural understanding of this region.
true
true
true
true
true
1,768
8
INTRODUCTION
0
null
null
17,439,962
pmid-8538772
In order to gain a better, comprehensive understanding of its role in pol β polymerization fidelity, we constructed pol β mutants with shorter or chemically different types of loops, and characterized the resultant variants for DNA synthesis efficiencies and fidelity.
null
268
11,061
0
false
null
null
In order to gain a better, comprehensive understanding of its role in pol β polymerization fidelity, we constructed pol β mutants with shorter or chemically different types of loops, and characterized the resultant variants for DNA synthesis efficiencies and fidelity.
true
true
true
true
true
1,768
8
INTRODUCTION
0
null
null
17,439,962
pmid-8538772
Our data suggest that the length of loop II plays an important role in maintaining the activity and fidelity of polymerization.
null
127
11,062
0
false
null
null
Our data suggest that the length of loop II plays an important role in maintaining the activity and fidelity of polymerization.
true
true
true
true
true
1,768
0
DISCUSSION
1
28–30
[ "B28 B29 B30" ]
17,439,962
pmid-8469282|pmid-15568983|pmid-9920940|pmid-10585471|pmid-14563842
The goal of the work presented here was to determine if loop II of pol β is essential for activity and accurate DNA synthesis.
[ "28–30" ]
126
11,063
0
false
The goal of the work presented here was to determine if loop II of pol β is essential for activity and accurate DNA synthesis.
[]
The goal of the work presented here was to determine if loop II of pol β is essential for activity and accurate DNA synthesis.
true
true
true
true
true
1,769
0
DISCUSSION
1
28–30
[ "B28 B29 B30" ]
17,439,962
pmid-8469282|pmid-15568983|pmid-9920940|pmid-10585471|pmid-14563842
This study was prompted by previous work from our laboratory in which we demonstrated that loop II was important for substrate specificity and the prevention of mispair extension (28–30).
[ "28–30" ]
187
11,064
1
false
This study was prompted by previous work from our laboratory in which we demonstrated that loop II was important for substrate specificity and the prevention of mispair extension.
[ "28–30" ]
This study was prompted by previous work from our laboratory in which we demonstrated that loop II was important for substrate specificity and the prevention of mispair extension.
true
true
true
true
true
1,769
1
DISCUSSION
1
28–30
[ "B28 B29 B30" ]
17,439,962
NA|pmid-7979257|pmid-8538772|pmid-8978692|pmid-7624801|pmid-10946235|pmid-9920940|pmid-10585471|pmid-14563842
In the study described here, we characterized a number of different variants of loop II for their ability to function in and maintain fidelity during DNA synthesis.
[ "28–30" ]
164
11,065
0
false
In the study described here, we characterized a number of different variants of loop II for their ability to function in and maintain fidelity during DNA synthesis.
[]
In the study described here, we characterized a number of different variants of loop II for their ability to function in and maintain fidelity during DNA synthesis.
true
true
true
true
true
1,770
1
DISCUSSION
1
28–30
[ "B28 B29 B30" ]
17,439,962
NA|pmid-7979257|pmid-8538772|pmid-8978692|pmid-7624801|pmid-10946235|pmid-9920940|pmid-10585471|pmid-14563842
Remarkably, we found that loops consisting of three to nine alanine residues were as or nearly as active as wild-type pol β and exhibited burst kinetics, suggesting that the overall rate-limiting step of these variants is the same as that of wild type.
[ "28–30" ]
252
11,066
0
false
Remarkably, we found that loops consisting of three to nine alanine residues were as or nearly as active as wild-type pol β and exhibited burst kinetics, suggesting that the overall rate-limiting step of these variants is the same as that of wild type.
[]
Remarkably, we found that loops consisting of three to nine alanine residues were as or nearly as active as wild-type pol β and exhibited burst kinetics, suggesting that the overall rate-limiting step of these variants is the same as that of wild type.
true
true
true
true
true
1,770
1
DISCUSSION
1
28–30
[ "B28 B29 B30" ]
17,439,962
NA|pmid-7979257|pmid-8538772|pmid-8978692|pmid-7624801|pmid-10946235|pmid-9920940|pmid-10585471|pmid-14563842
In addition, each of these loop variants appear to synthesize DNA with fidelity that is similar to wild-type pol β.
[ "28–30" ]
115
11,067
0
false
In addition, each of these loop variants appear to synthesize DNA with fidelity that is similar to wild-type pol β.
[]
In addition, each of these loop variants appear to synthesize DNA with fidelity that is similar to wild-type pol β.
true
true
true
true
true
1,770
1
DISCUSSION
1
28–30
[ "B28 B29 B30" ]
17,439,962
NA|pmid-7979257|pmid-8538772|pmid-8978692|pmid-7624801|pmid-10946235|pmid-9920940|pmid-10585471|pmid-14563842
Replacement of the nine residue loop II with either four or five residues other alanine also resulted in a polymerase that could catalyze DNA synthesis with similar activity as wild-type pol β.
[ "28–30" ]
193
11,068
0
false
Replacement of the nine residue loop II with either four or five residues other alanine also resulted in a polymerase that could catalyze DNA synthesis with similar activity as wild-type pol β.
[]
Replacement of the nine residue loop II with either four or five residues other alanine also resulted in a polymerase that could catalyze DNA synthesis with similar activity as wild-type pol β.
true
true
true
true
true
1,770
1
DISCUSSION
1
28–30
[ "B28 B29 B30" ]
17,439,962
NA|pmid-7979257|pmid-8538772|pmid-8978692|pmid-7624801|pmid-10946235|pmid-9920940|pmid-10585471|pmid-14563842
Loops consisting of 0–2 alanines were also able to catalyze DNA synthesis, but at much slower rates and with altered kinetics in comparison to wild-type pol β.
[ "28–30" ]
159
11,069
0
false
Loops consisting of 0–2 alanines were also able to catalyze DNA synthesis, but at much slower rates and with altered kinetics in comparison to wild-type pol β.
[]
Loops consisting of 0–2 alanines were also able to catalyze DNA synthesis, but at much slower rates and with altered kinetics in comparison to wild-type pol β.
true
true
true
true
true
1,770
1
DISCUSSION
1
28–30
[ "B28 B29 B30" ]
17,439,962
NA|pmid-7979257|pmid-8538772|pmid-8978692|pmid-7624801|pmid-10946235|pmid-9920940|pmid-10585471|pmid-14563842
Taken together, our results lead us to conclude that the length of the loop, rather than its chemical nature, is critical for pol β polymerase activity.
[ "28–30" ]
152
11,070
0
false
Taken together, our results lead us to conclude that the length of the loop, rather than its chemical nature, is critical for pol β polymerase activity.
[]
Taken together, our results lead us to conclude that the length of the loop, rather than its chemical nature, is critical for pol β polymerase activity.
true
true
true
true
true
1,770
1
DISCUSSION
1
28–30
[ "B28 B29 B30" ]
17,439,962
NA|pmid-7979257|pmid-8538772|pmid-8978692|pmid-7624801|pmid-10946235|pmid-9920940|pmid-10585471|pmid-14563842
Surprisingly, although loops consisting of five amino acid residues of various chemical natures were active, the resulting polymerases catalyze DNA synthesis with lower fidelity than wild-type pol β.
[ "28–30" ]
199
11,071
0
false
Surprisingly, although loops consisting of five amino acid residues of various chemical natures were active, the resulting polymerases catalyze DNA synthesis with lower fidelity than wild-type pol β.
[]
Surprisingly, although loops consisting of five amino acid residues of various chemical natures were active, the resulting polymerases catalyze DNA synthesis with lower fidelity than wild-type pol β.
true
true
true
true
true
1,770
1
DISCUSSION
1
28–30
[ "B28 B29 B30" ]
17,439,962
NA|pmid-7979257|pmid-8538772|pmid-8978692|pmid-7624801|pmid-10946235|pmid-9920940|pmid-10585471|pmid-14563842
Based upon these observations and our previous results (28–30), we conclude that loop II is important for the fidelity of pol β.
[ "28–30" ]
128
11,072
1
false
Based upon these observations and our previous results, we conclude that loop II is important for the fidelity of pol β.
[ "28–30" ]
Based upon these observations and our previous results, we conclude that loop II is important for the fidelity of pol β.
true
true
true
true
true
1,770
2
DISCUSSION
0
null
null
17,439,962
pmid-3988773|pmid-16615916|pmid-7516580|pmid-8841118|pmid-9287163|pmid-11330999
Surprisingly, we found that a pol β variant with a loop consisting of nine Ala residues was just as active as wild-type pol β, and exhibited burst kinetics, suggesting that it followed a kinetic pathway quite similar to wild-type pol β.
null
236
11,073
0
false
null
null
Surprisingly, we found that a pol β variant with a loop consisting of nine Ala residues was just as active as wild-type pol β, and exhibited burst kinetics, suggesting that it followed a kinetic pathway quite similar to wild-type pol β.
true
true
true
true
true
1,771
2
DISCUSSION
0
null
null
17,439,962
pmid-3988773|pmid-16615916|pmid-7516580|pmid-8841118|pmid-9287163|pmid-11330999
Pol β variants with loops of 5, 4 and 3 Ala residues were also found to exhibit burst kinetics.
null
95
11,074
0
false
null
null
Pol β variants with loops of 5, 4 and 3 Ala residues were also found to exhibit burst kinetics.
true
true
true
true
true
1,771
2
DISCUSSION
0
null
null
17,439,962
pmid-3988773|pmid-16615916|pmid-7516580|pmid-8841118|pmid-9287163|pmid-11330999
These results suggest that the chemical nature and size of loop II are not important for activity until the loop is comprised of less than three residues.
null
154
11,075
0
false
null
null
These results suggest that the chemical nature and size of loop II are not important for activity until the loop is comprised of less than three residues.
true
true
true
true
true
1,771
3
DISCUSSION
1
28–30
[ "B28 B29 B30", "B43", "B13", "B14", "B44", "B45", "B46", "B47", "B48" ]
17,439,962
pmid-6214209|pmid-10409611|pmid-11756435|NA|pmid-10200168|pmid-10449735|pmid-11154692|pmid-11560485|pmid-12962495|pmid-15751954|pmid-15901725|pmid-16313169|pmid-9920940|pmid-10585471|pmid-14563842|pmid-10946231|pmid-9287163|pmid-11330999|pmid-8137427|pmid-12517346|pmid-11823435|pmid-14992725|NA
We and others (28–30,43) have proposed that loop II may somehow contribute to the formation of a gate that regulates access of dNTPs to the active site, and that the length and mobility of the loop controls the size of such a channel.
[ "28–30", "43", "13", "14", "44", "45", "46", "47", "48" ]
234
11,076
0
false
We and others have proposed that loop II may somehow contribute to the formation of a gate that regulates access of dNTPs to the active site, and that the length and mobility of the loop controls the size of such a channel.
[ "28–30,43" ]
We and others have proposed that loop II may somehow contribute to the formation of a gate that regulates access of dNTPs to the active site, and that the length and mobility of the loop controls the size of such a channel.
true
true
true
true
true
1,772
3
DISCUSSION
1
28–30
[ "B28 B29 B30", "B43", "B13", "B14", "B44", "B45", "B46", "B47", "B48" ]
17,439,962
pmid-6214209|pmid-10409611|pmid-11756435|NA|pmid-10200168|pmid-10449735|pmid-11154692|pmid-11560485|pmid-12962495|pmid-15751954|pmid-15901725|pmid-16313169|pmid-9920940|pmid-10585471|pmid-14563842|pmid-10946231|pmid-9287163|pmid-11330999|pmid-8137427|pmid-12517346|pmid-11823435|pmid-14992725|NA
The mobility of loop II is well documented through X-ray crystallographic studies (13,14,44,45).
[ "28–30", "43", "13", "14", "44", "45", "46", "47", "48" ]
96
11,077
0
false
The mobility of loop II is well documented through X-ray crystallographic studies.
[ "13,14,44,45" ]
The mobility of loop II is well documented through X-ray crystallographic studies.
true
true
true
true
true
1,772
3
DISCUSSION
1
28–30
[ "B28 B29 B30", "B43", "B13", "B14", "B44", "B45", "B46", "B47", "B48" ]
17,439,962
pmid-6214209|pmid-10409611|pmid-11756435|NA|pmid-10200168|pmid-10449735|pmid-11154692|pmid-11560485|pmid-12962495|pmid-15751954|pmid-15901725|pmid-16313169|pmid-9920940|pmid-10585471|pmid-14563842|pmid-10946231|pmid-9287163|pmid-11330999|pmid-8137427|pmid-12517346|pmid-11823435|pmid-14992725|NA
None of the structures published to date show any side-chain or main-chain interactions of any kind that would stabilize a certain loop conformation.
[ "28–30", "43", "13", "14", "44", "45", "46", "47", "48" ]
149
11,078
0
false
None of the structures published to date show any side-chain or main-chain interactions of any kind that would stabilize a certain loop conformation.
[]
None of the structures published to date show any side-chain or main-chain interactions of any kind that would stabilize a certain loop conformation.
true
true
true
true
true
1,772
3
DISCUSSION
1
28–30
[ "B28 B29 B30", "B43", "B13", "B14", "B44", "B45", "B46", "B47", "B48" ]
17,439,962
pmid-6214209|pmid-10409611|pmid-11756435|NA|pmid-10200168|pmid-10449735|pmid-11154692|pmid-11560485|pmid-12962495|pmid-15751954|pmid-15901725|pmid-16313169|pmid-9920940|pmid-10585471|pmid-14563842|pmid-10946231|pmid-9287163|pmid-11330999|pmid-8137427|pmid-12517346|pmid-11823435|pmid-14992725|NA
Model building of short loop II mutants followed by molecular dynamics calculations and comparison to other members of the pol X family suggest that only the longest variants of loops could theoretically play a role in gating dNTP access not through direct steric interference but through long-range electrostatic intera...
[ "28–30", "43", "13", "14", "44", "45", "46", "47", "48" ]
327
11,079
0
false
Model building of short loop II mutants followed by molecular dynamics calculations and comparison to other members of the pol X family suggest that only the longest variants of loops could theoretically play a role in gating dNTP access not through direct steric interference but through long-range electrostatic intera...
[]
Model building of short loop II mutants followed by molecular dynamics calculations and comparison to other members of the pol X family suggest that only the longest variants of loops could theoretically play a role in gating dNTP access not through direct steric interference but through long-range electrostatic intera...
true
true
true
true
true
1,772
3
DISCUSSION
1
46
[ "B28 B29 B30", "B43", "B13", "B14", "B44", "B45", "B46", "B47", "B48" ]
17,439,962
pmid-6214209|pmid-10409611|pmid-11756435|NA|pmid-10200168|pmid-10449735|pmid-11154692|pmid-11560485|pmid-12962495|pmid-15751954|pmid-15901725|pmid-16313169|pmid-9920940|pmid-10585471|pmid-14563842|pmid-10946231|pmid-9287163|pmid-11330999|pmid-8137427|pmid-12517346|pmid-11823435|pmid-14992725|NA
In terminal transferase co-crystal structures (46), for example, where the loop equivalent to loop II in pol β consists of 17 residues, the geometry of the dNTP channel is not visibly affected by the loop.
[ "28–30", "43", "13", "14", "44", "45", "46", "47", "48" ]
205
11,080
1
false
In terminal transferase co-crystal structures, for example, where the loop equivalent to loop II in pol β consists of 17 residues, the geometry of the dNTP channel is not visibly affected by the loop.
[ "46" ]
In terminal transferase co-crystal structures, for example, where the loop equivalent to loop II in pol β consists of 17 residues, the geometry of the dNTP channel is not visibly affected by the loop.
true
true
true
true
true
1,772
3
DISCUSSION
1
28–30
[ "B28 B29 B30", "B43", "B13", "B14", "B44", "B45", "B46", "B47", "B48" ]
17,439,962
pmid-6214209|pmid-10409611|pmid-11756435|NA|pmid-10200168|pmid-10449735|pmid-11154692|pmid-11560485|pmid-12962495|pmid-15751954|pmid-15901725|pmid-16313169|pmid-9920940|pmid-10585471|pmid-14563842|pmid-10946231|pmid-9287163|pmid-11330999|pmid-8137427|pmid-12517346|pmid-11823435|pmid-14992725|NA
Pol λ, in which loop II consists of five residues, shows an increased affinity for the dNTP substrate when compared to pol β (47,48).
[ "28–30", "43", "13", "14", "44", "45", "46", "47", "48" ]
133
11,081
0
false
Pol λ, in which loop II consists of five residues, shows an increased affinity for the dNTP substrate when compared to pol β.
[ "47,48" ]
Pol λ, in which loop II consists of five residues, shows an increased affinity for the dNTP substrate when compared to pol β.
true
true
true
true
true
1,772
3
DISCUSSION
1
28–30
[ "B28 B29 B30", "B43", "B13", "B14", "B44", "B45", "B46", "B47", "B48" ]
17,439,962
pmid-6214209|pmid-10409611|pmid-11756435|NA|pmid-10200168|pmid-10449735|pmid-11154692|pmid-11560485|pmid-12962495|pmid-15751954|pmid-15901725|pmid-16313169|pmid-9920940|pmid-10585471|pmid-14563842|pmid-10946231|pmid-9287163|pmid-11330999|pmid-8137427|pmid-12517346|pmid-11823435|pmid-14992725|NA
Taken together, these results indicate that the loop and its proposed contribution to a gating function are unlikely to affect the movement of dNTP substrates in and PPi product out of the active site in a major way.
[ "28–30", "43", "13", "14", "44", "45", "46", "47", "48" ]
216
11,082
0
false
Taken together, these results indicate that the loop and its proposed contribution to a gating function are unlikely to affect the movement of dNTP substrates in and PPi product out of the active site in a major way.
[]
Taken together, these results indicate that the loop and its proposed contribution to a gating function are unlikely to affect the movement of dNTP substrates in and PPi product out of the active site in a major way.
true
true
true
true
true
1,772
4
DISCUSSION
1
49
[ "B49", "B50", "B22" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
Shorter loop II mutants, however, exhibit significant kinetic effects.
[ "49", "50", "22" ]
70
11,083
0
false
Shorter loop II mutants, however, exhibit significant kinetic effects.
[]
Shorter loop II mutants, however, exhibit significant kinetic effects.
true
true
true
true
true
1,773
4
DISCUSSION
1
49
[ "B49", "B50", "B22" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
These are conceivably caused by strain and distortions in the main-chain geometry of residues adjacent to or within strands 4 and 5.
[ "49", "50", "22" ]
132
11,084
0
false
These are conceivably caused by strain and distortions in the main-chain geometry of residues adjacent to or within strands 4 and 5.
[]
These are conceivably caused by strain and distortions in the main-chain geometry of residues adjacent to or within strands 4 and 5.
true
true
true
true
true
1,773
4
DISCUSSION
1
49
[ "B49", "B50", "B22" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
Computer modeling and molecular dynamics of the Loopless model of pol β indicate that the position and backbone angles of Leu241, Pro242 and His252 have to be altered significantly (data not shown).
[ "49", "50", "22" ]
198
11,085
0
false
Computer modeling and molecular dynamics of the Loopless model of pol β indicate that the position and backbone angles of Leu241, Pro242 and His252 have to be altered significantly (data not shown).
[]
Computer modeling and molecular dynamics of the Loopless model of pol β indicate that the position and backbone angles of Leu241, Pro242 and His252 have to be altered significantly (data not shown).
true
true
true
true
true
1,773
4
DISCUSSION
1
49
[ "B49", "B50", "B22" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
The changes in alpha carbon positions required to reconnect the main chain of pol β occur only 13 Å away from Asp256 and the metal-ion-binding site in the catalytic domain.
[ "49", "50", "22" ]
172
11,086
0
false
The changes in alpha carbon positions required to reconnect the main chain of pol β occur only 13 Å away from Asp256 and the metal-ion-binding site in the catalytic domain.
[]
The changes in alpha carbon positions required to reconnect the main chain of pol β occur only 13 Å away from Asp256 and the metal-ion-binding site in the catalytic domain.
true
true
true
true
true
1,773
4
DISCUSSION
1
49
[ "B49", "B50", "B22" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
Mutations in loop residues can have wide-ranging effects, even on rigid structures as those found in beta alpha barrels (49,50).
[ "49", "50", "22" ]
128
11,087
0
false
Mutations in loop residues can have wide-ranging effects, even on rigid structures as those found in beta alpha barrels.
[ "49,50" ]
Mutations in loop residues can have wide-ranging effects, even on rigid structures as those found in beta alpha barrels.
true
true
true
true
true
1,773
4
DISCUSSION
1
49
[ "B49", "B50", "B22" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
It is possible that drastic changes in the composition and length of loop II have similar effects on the stability of adjacent beta strands in the pol β active site.
[ "49", "50", "22" ]
165
11,088
0
false
It is possible that drastic changes in the composition and length of loop II have similar effects on the stability of adjacent beta strands in the pol β active site.
[]
It is possible that drastic changes in the composition and length of loop II have similar effects on the stability of adjacent beta strands in the pol β active site.
true
true
true
true
true
1,773
4
DISCUSSION
1
22
[ "B49", "B50", "B22" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
An increase in domain rigidity of pol β is known to affect the accuracy of DNA synthesis as observed in the case of the Met282Leu mutator mutant (22).
[ "49", "50", "22" ]
150
11,089
1
false
An increase in domain rigidity of pol β is known to affect the accuracy of DNA synthesis as observed in the case of the Met282Leu mutator mutant.
[ "22" ]
An increase in domain rigidity of pol β is known to affect the accuracy of DNA synthesis as observed in the case of the Met282Leu mutator mutant.
true
true
true
true
true
1,773
4
DISCUSSION
1
49
[ "B49", "B50", "B22" ]
17,439,962
pmid-10966791|pmid-2188262|pmid-1304881|pmid-11560485
We suggest that a loop II consisting of three amino acid residues is sufficient to maintain the backbone angles and positions of Leu241, Pro242 and His252 that are required for efficient catalysis.
[ "49", "50", "22" ]
197
11,090
0
false
We suggest that a loop II consisting of three amino acid residues is sufficient to maintain the backbone angles and positions of Leu241, Pro242 and His252 that are required for efficient catalysis.
[]
We suggest that a loop II consisting of three amino acid residues is sufficient to maintain the backbone angles and positions of Leu241, Pro242 and His252 that are required for efficient catalysis.
true
true
true
true
true
1,773
5
DISCUSSION
0
null
null
17,439,962
null
We have also proposed that loop II functions to position the primer strand of the DNA by buttressing against helix I of pol β.
null
126
11,091
0
false
null
null
We have also proposed that loop II functions to position the primer strand of the DNA by buttressing against helix I of pol β.
true
true
true
true
true
1,774
5
DISCUSSION
0
null
null
17,439,962
null
In initiating these studies, we assumed that a smaller loop II would have diminished its ability to support helix I and the thumb domain of pol β would affect the primer position.
null
179
11,092
0
false
null
null
In initiating these studies, we assumed that a smaller loop II would have diminished its ability to support helix I and the thumb domain of pol β would affect the primer position.
true
true
true
true
true
1,774
5
DISCUSSION
0
null
null
17,439,962
null
In terms of catalytic activity, this proposal seems questionable since loops of four and three amino acid residues still exhibit burst kinetics.
null
144
11,093
0
false
null
null
In terms of catalytic activity, this proposal seems questionable since loops of four and three amino acid residues still exhibit burst kinetics.
true
true
true
true
true
1,774
6
DISCUSSION
0
null
null
17,439,962
null
We were surprised to find that variants with loops consisting of five amino acid residues, irrespective of a specific sequence context or side-chain character, synthesized DNA with lower fidelity than wild-type pol β.
null
217
11,094
0
false
null
null
We were surprised to find that variants with loops consisting of five amino acid residues, irrespective of a specific sequence context or side-chain character, synthesized DNA with lower fidelity than wild-type pol β.
true
true
true
true
true
1,775
6
DISCUSSION
0
null
null
17,439,962
null
The simplest explanation for this result is that a loop of five residues assumes a structure that somehow impairs the accurate synthesis of DNA.
null
144
11,095
0
false
null
null
The simplest explanation for this result is that a loop of five residues assumes a structure that somehow impairs the accurate synthesis of DNA.
true
true
true
true
true
1,775
6
DISCUSSION
0
null
null
17,439,962
null
It is likely that the backbone angles and positions of Leu241, Pro242 and His252 are maintained in the five residue loop variants because they are active, but that the length of these loops induces subtle alterations in the protein that result in inaccurate DNA synthesis.
null
272
11,096
0
false
null
null
It is likely that the backbone angles and positions of Leu241, Pro242 and His252 are maintained in the five residue loop variants because they are active, but that the length of these loops induces subtle alterations in the protein that result in inaccurate DNA synthesis.
true
true
true
true
true
1,775
6
DISCUSSION
0
null
null
17,439,962
null
These subtle alterations could result in a lack of template or primer stabilization, or alteration in the dNTP-binding pocket.
null
126
11,097
0
false
null
null
These subtle alterations could result in a lack of template or primer stabilization, or alteration in the dNTP-binding pocket.
true
true
true
true
true
1,775
6
DISCUSSION
0
null
null
17,439,962
null
Characterization of the types of mutations induced by the five residue loop variants should be informative regarding their mechanisms of inaccurate DNA synthesis.
null
162
11,098
0
false
null
null
Characterization of the types of mutations induced by the five residue loop variants should be informative regarding their mechanisms of inaccurate DNA synthesis.
true
true
true
true
true
1,775
7
DISCUSSION
1
51
[ "B51", "B14" ]
17,439,962
pmid-9920940|pmid-10585471|pmid-14563842|pmid-10585471|pmid-14563842|pmid-15794655|pmid-11330999
Another possible explanation for the lack fidelity of the five residue loop variants is that the position of Asp256 may be affected.
[ "51", "14" ]
132
11,099
0
false
Another possible explanation for the lack fidelity of the five residue loop variants is that the position of Asp256 may be affected.
[]
Another possible explanation for the lack fidelity of the five residue loop variants is that the position of Asp256 may be affected.
true
true
true
true
true
1,776