Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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INTRODUCTION
1
1–6
[ "B1 B2 B3 B4 B5 B6", "B1", "B6 B7 B8 B9", "B10", "B7", "B8", "B11" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
We investigate here a euryarchaeal RPR that was reported to be inactive when tested alone (7,8) and examine the basis for its inactivity and its cooperation with cognate RPPs during catalysis.
[ "1–6", "1", "6–9", "10", "7", "8", "11" ]
192
37,716
0
false
We investigate here a euryarchaeal RPR that was reported to be inactive when tested alone and examine the basis for its inactivity and its cooperation with cognate RPPs during catalysis.
[ "7,8" ]
We investigate here a euryarchaeal RPR that was reported to be inactive when tested alone and examine the basis for its inactivity and its cooperation with cognate RPPs during catalysis.
true
true
true
true
true
6,465
0
INTRODUCTION
1
1–6
[ "B1 B2 B3 B4 B5 B6", "B1", "B6 B7 B8 B9", "B10", "B7", "B8", "B11" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
Figure 1.An RPR hybrid comprising an S and C domain from a bacterial and an archaeal type M RPR, respectively, is catalytically active and can accurately process ptRNATyr.
[ "1–6", "1", "6–9", "10", "7", "8", "11" ]
171
37,717
0
false
Figure 1.An RPR hybrid comprising an S and C domain from a bacterial and an archaeal type M RPR, respectively, is catalytically active and can accurately process ptRNATyr.
[]
Figure 1.An RPR hybrid comprising an S and C domain from a bacterial and an archaeal type M RPR, respectively, is catalytically active and can accurately process ptRNATyr.
true
true
true
true
true
6,465
0
INTRODUCTION
1
11
[ "B1 B2 B3 B4 B5 B6", "B1", "B6 B7 B8 B9", "B10", "B7", "B8", "B11" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
(A) The shaded circles, ovals, and black boxes depict known interactions between the Eco RPR and a ptRNA substrate (11).
[ "1–6", "1", "6–9", "10", "7", "8", "11" ]
120
37,718
1
false
(A) The shaded circles, ovals, and black boxes depict known interactions between the Eco RPR and a ptRNA substrate.
[ "11" ]
(A) The shaded circles, ovals, and black boxes depict known interactions between the Eco RPR and a ptRNA substrate.
false
false
true
true
false
6,465
0
INTRODUCTION
1
1–6
[ "B1 B2 B3 B4 B5 B6", "B1", "B6 B7 B8 B9", "B10", "B7", "B8", "B11" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
Arrow indicates the site of cleavage in the ptRNA.
[ "1–6", "1", "6–9", "10", "7", "8", "11" ]
50
37,719
0
false
Arrow indicates the site of cleavage in the ptRNA.
[]
Arrow indicates the site of cleavage in the ptRNA.
true
true
true
true
true
6,465
0
INTRODUCTION
1
1–6
[ "B1 B2 B3 B4 B5 B6", "B1", "B6 B7 B8 B9", "B10", "B7", "B8", "B11" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
In the RPR, the C and S domains are indicated in black and gray, respectively.
[ "1–6", "1", "6–9", "10", "7", "8", "11" ]
78
37,720
0
false
In the RPR, the C and S domains are indicated in black and gray, respectively.
[]
In the RPR, the C and S domains are indicated in black and gray, respectively.
true
true
true
true
true
6,465
0
INTRODUCTION
1
1–6
[ "B1 B2 B3 B4 B5 B6", "B1", "B6 B7 B8 B9", "B10", "B7", "B8", "B11" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
Thick dotted lines indicate tertiary interactions unique to the bacterial RPR.
[ "1–6", "1", "6–9", "10", "7", "8", "11" ]
78
37,721
0
false
Thick dotted lines indicate tertiary interactions unique to the bacterial RPR.
[]
Thick dotted lines indicate tertiary interactions unique to the bacterial RPR.
true
true
true
true
true
6,465
0
INTRODUCTION
1
1–6
[ "B1 B2 B3 B4 B5 B6", "B1", "B6 B7 B8 B9", "B10", "B7", "B8", "B11" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
(B and C) Secondary structures of representative archaeal type A and M RPRs, respectively.
[ "1–6", "1", "6–9", "10", "7", "8", "11" ]
90
37,722
0
false
(B and C) Secondary structures of representative archaeal type A and M RPRs, respectively.
[]
(B and C) Secondary structures of representative archaeal type A and M RPRs, respectively.
false
false
true
true
false
6,465
0
INTRODUCTION
1
1–6
[ "B1 B2 B3 B4 B5 B6", "B1", "B6 B7 B8 B9", "B10", "B7", "B8", "B11" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
The structural elements absent in type M RPR (C) are highlighted with dotted lines.
[ "1–6", "1", "6–9", "10", "7", "8", "11" ]
83
37,723
0
false
The structural elements absent in type M RPR (C) are highlighted with dotted lines.
[]
The structural elements absent in type M RPR (C) are highlighted with dotted lines.
true
true
true
true
true
6,465
0
INTRODUCTION
1
1–6
[ "B1 B2 B3 B4 B5 B6", "B1", "B6 B7 B8 B9", "B10", "B7", "B8", "B11" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
(D) Secondary structure of the bacterial/archaeal hybrid RPR (EcoS-MjaC RPR) used in this study.
[ "1–6", "1", "6–9", "10", "7", "8", "11" ]
96
37,724
0
false
(D) Secondary structure of the bacterial/archaeal hybrid RPR (EcoS-MjaC RPR) used in this study.
[]
(D) Secondary structure of the bacterial/archaeal hybrid RPR (EcoS-MjaC RPR) used in this study.
false
false
true
true
false
6,465
0
INTRODUCTION
1
1–6
[ "B1 B2 B3 B4 B5 B6", "B1", "B6 B7 B8 B9", "B10", "B7", "B8", "B11" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
The S domain of bacterial RPR is indicated in gray.
[ "1–6", "1", "6–9", "10", "7", "8", "11" ]
51
37,725
0
false
The S domain of bacterial RPR is indicated in gray.
[]
The S domain of bacterial RPR is indicated in gray.
true
true
true
true
true
6,465
0
INTRODUCTION
1
1–6
[ "B1 B2 B3 B4 B5 B6", "B1", "B6 B7 B8 B9", "B10", "B7", "B8", "B11" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
Universally conserved nucleotides are indicated in A–D.
[ "1–6", "1", "6–9", "10", "7", "8", "11" ]
55
37,726
0
false
Universally conserved nucleotides are indicated in A–D.
[]
Universally conserved nucleotides are indicated in A–D.
true
true
true
true
true
6,465
0
INTRODUCTION
1
1–6
[ "B1 B2 B3 B4 B5 B6", "B1", "B6 B7 B8 B9", "B10", "B7", "B8", "B11" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
(E) EcoS-MjaC RPR (2.5 ΞΌM) was tested for RNase P activity by incubating at 50Β°C for 15 min with 5β€² labeled ptRNATyr (∼1 pM) in 50 mM Tris-acetate (pH 8) and different NH4+ and Mg2+ concentrations as indicated.
[ "1–6", "1", "6–9", "10", "7", "8", "11" ]
210
37,727
0
false
(E) EcoS-MjaC RPR (2.5 ΞΌM) was tested for RNase P activity by incubating at 50Β°C for 15 min with 5β€² labeled ptRNATyr in 50 mM Tris-acetate and different NH4+ and Mg2+ concentrations as indicated.
[ "∼1 pM", "pH 8" ]
(E) EcoS-MjaC RPR (2.5 ΞΌM) was tested for RNase P activity by incubating at 50Β°C for 15 min with 5β€² labeled ptRNATyr in 50 mM Tris-acetate and different NH4+ and Mg2+ concentrations as indicated.
false
false
true
true
false
6,465
0
INTRODUCTION
1
1–6
[ "B1 B2 B3 B4 B5 B6", "B1", "B6 B7 B8 B9", "B10", "B7", "B8", "B11" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
M represents a size marker generated by processing of ptRNATyr by Eco RNase P.
[ "1–6", "1", "6–9", "10", "7", "8", "11" ]
78
37,728
0
false
M represents a size marker generated by processing of ptRNATyr by Eco RNase P.
[]
M represents a size marker generated by processing of ptRNATyr by Eco RNase P.
true
true
true
true
true
6,465
1
INTRODUCTION
1
11
[ "B11" ]
18,558,617
pmid-12431435|pmid-17081993
An RPR hybrid comprising an S and C domain from a bacterial and an archaeal type M RPR, respectively, is catalytically active and can accurately process ptRNATyr.
[ "11" ]
162
37,729
0
false
An RPR hybrid comprising an S and C domain from a bacterial and an archaeal type M RPR, respectively, is catalytically active and can accurately process ptRNATyr.
[]
An RPR hybrid comprising an S and C domain from a bacterial and an archaeal type M RPR, respectively, is catalytically active and can accurately process ptRNATyr.
true
true
true
true
true
6,466
1
INTRODUCTION
1
11
[ "B11" ]
18,558,617
pmid-12431435|pmid-17081993
(A) The shaded circles, ovals, and black boxes depict known interactions between the Eco RPR and a ptRNA substrate (11).
[ "11" ]
120
37,730
1
false
(A) The shaded circles, ovals, and black boxes depict known interactions between the Eco RPR and a ptRNA substrate.
[ "11" ]
(A) The shaded circles, ovals, and black boxes depict known interactions between the Eco RPR and a ptRNA substrate.
false
false
true
true
false
6,466
1
INTRODUCTION
1
11
[ "B11" ]
18,558,617
pmid-12431435|pmid-17081993
Arrow indicates the site of cleavage in the ptRNA.
[ "11" ]
50
37,731
0
false
Arrow indicates the site of cleavage in the ptRNA.
[]
Arrow indicates the site of cleavage in the ptRNA.
true
true
true
true
true
6,466
1
INTRODUCTION
1
11
[ "B11" ]
18,558,617
pmid-12431435|pmid-17081993
In the RPR, the C and S domains are indicated in black and gray, respectively.
[ "11" ]
78
37,732
0
false
In the RPR, the C and S domains are indicated in black and gray, respectively.
[]
In the RPR, the C and S domains are indicated in black and gray, respectively.
true
true
true
true
true
6,466
1
INTRODUCTION
1
11
[ "B11" ]
18,558,617
pmid-12431435|pmid-17081993
Thick dotted lines indicate tertiary interactions unique to the bacterial RPR.
[ "11" ]
78
37,733
0
false
Thick dotted lines indicate tertiary interactions unique to the bacterial RPR.
[]
Thick dotted lines indicate tertiary interactions unique to the bacterial RPR.
true
true
true
true
true
6,466
1
INTRODUCTION
1
11
[ "B11" ]
18,558,617
pmid-12431435|pmid-17081993
(B and C) Secondary structures of representative archaeal type A and M RPRs, respectively.
[ "11" ]
90
37,734
0
false
(B and C) Secondary structures of representative archaeal type A and M RPRs, respectively.
[]
(B and C) Secondary structures of representative archaeal type A and M RPRs, respectively.
false
false
true
true
false
6,466
1
INTRODUCTION
1
11
[ "B11" ]
18,558,617
pmid-12431435|pmid-17081993
The structural elements absent in type M RPR (C) are highlighted with dotted lines.
[ "11" ]
83
37,735
0
false
The structural elements absent in type M RPR (C) are highlighted with dotted lines.
[]
The structural elements absent in type M RPR (C) are highlighted with dotted lines.
true
true
true
true
true
6,466
1
INTRODUCTION
1
11
[ "B11" ]
18,558,617
pmid-12431435|pmid-17081993
(D) Secondary structure of the bacterial/archaeal hybrid RPR (EcoS-MjaC RPR) used in this study.
[ "11" ]
96
37,736
0
false
(D) Secondary structure of the bacterial/archaeal hybrid RPR (EcoS-MjaC RPR) used in this study.
[]
(D) Secondary structure of the bacterial/archaeal hybrid RPR (EcoS-MjaC RPR) used in this study.
false
false
true
true
false
6,466
1
INTRODUCTION
1
11
[ "B11" ]
18,558,617
pmid-12431435|pmid-17081993
The S domain of bacterial RPR is indicated in gray.
[ "11" ]
51
37,737
0
false
The S domain of bacterial RPR is indicated in gray.
[]
The S domain of bacterial RPR is indicated in gray.
true
true
true
true
true
6,466
1
INTRODUCTION
1
11
[ "B11" ]
18,558,617
pmid-12431435|pmid-17081993
Universally conserved nucleotides are indicated in A–D.
[ "11" ]
55
37,738
0
false
Universally conserved nucleotides are indicated in A–D.
[]
Universally conserved nucleotides are indicated in A–D.
true
true
true
true
true
6,466
1
INTRODUCTION
1
11
[ "B11" ]
18,558,617
pmid-12431435|pmid-17081993
(E) EcoS-MjaC RPR (2.5 ΞΌM) was tested for RNase P activity by incubating at 50Β°C for 15 min with 5β€² labeled ptRNATyr (∼1 pM) in 50 mM Tris-acetate (pH 8) and different NH4+ and Mg2+ concentrations as indicated.
[ "11" ]
210
37,739
0
false
(E) EcoS-MjaC RPR (2.5 ΞΌM) was tested for RNase P activity by incubating at 50Β°C for 15 min with 5β€² labeled ptRNATyr (∼1 pM) in 50 mM Tris-acetate (pH 8) and different NH4+ and Mg2+ concentrations as indicated.
[]
(E) EcoS-MjaC RPR (2.5 ΞΌM) was tested for RNase P activity by incubating at 50Β°C for 15 min with 5β€² labeled ptRNATyr in 50 mM Tris-acetate (pH 8) and different NH4+ and Mg2+ concentrations as indicated.
false
false
true
true
false
6,466
1
INTRODUCTION
1
11
[ "B11" ]
18,558,617
pmid-12431435|pmid-17081993
M represents a size marker generated by processing of ptRNATyr by Eco RNase P.
[ "11" ]
78
37,740
0
false
M represents a size marker generated by processing of ptRNATyr by Eco RNase P.
[]
M represents a size marker generated by processing of ptRNATyr by Eco RNase P.
true
true
true
true
true
6,466
2
INTRODUCTION
1
8
[ "B8", "B10", "B11", "B7" ]
18,558,617
pmid-11233979|pmid-9847214|pmid-12431435|pmid-10393902|pmid-16932744|pmid-17652407
Based on the conserved structural elements of the RPR, euryarchaeal RNase P is classified into types A and M (8).
[ "8", "10", "11", "7" ]
113
37,741
1
false
Based on the conserved structural elements of the RPR, euryarchaeal RNase P is classified into types A and M.
[ "8" ]
Based on the conserved structural elements of the RPR, euryarchaeal RNase P is classified into types A and M.
true
true
true
true
true
6,467
2
INTRODUCTION
1
8
[ "B8", "B10", "B11", "B7" ]
18,558,617
pmid-11233979|pmid-9847214|pmid-12431435|pmid-10393902|pmid-16932744|pmid-17652407
At the secondary structure level, type A RPRs resemble the ancestral bacterial RPRs while type M RPRs lack some of the structural elements implicated in substrate binding in bacterial RPRs (Figure 1A–C; 8,10,11).
[ "8", "10", "11", "7" ]
212
37,742
0
false
At the secondary structure level, type A RPRs resemble the ancestral bacterial RPRs while type M RPRs lack some of the structural elements implicated in substrate binding in bacterial RPRs.
[ "Figure 1A–C; 8,10,11" ]
At the secondary structure level, type A RPRs resemble the ancestral bacterial RPRs while type M RPRs lack some of the structural elements implicated in substrate binding in bacterial RPRs.
true
true
true
true
true
6,467
2
INTRODUCTION
1
7
[ "B8", "B10", "B11", "B7" ]
18,558,617
pmid-11233979|pmid-9847214|pmid-12431435|pmid-10393902|pmid-16932744|pmid-17652407
Consistent with this observation, only a few type A RPRs and none of the type M RPRs are catalytically active in vitro without their RPPs (7).
[ "8", "10", "11", "7" ]
142
37,743
1
false
Consistent with this observation, only a few type A RPRs and none of the type M RPRs are catalytically active in vitro without their RPPs.
[ "7" ]
Consistent with this observation, only a few type A RPRs and none of the type M RPRs are catalytically active in vitro without their RPPs.
true
true
true
true
true
6,467
2
INTRODUCTION
1
8
[ "B8", "B10", "B11", "B7" ]
18,558,617
pmid-11233979|pmid-9847214|pmid-12431435|pmid-10393902|pmid-16932744|pmid-17652407
In this study, we employ Methanocaldococcus jannaschii (Mja) RPR as a prototype for type M RPRs.
[ "8", "10", "11", "7" ]
96
37,744
0
false
In this study, we employ Methanocaldococcus jannaschii (Mja) RPR as a prototype for type M RPRs.
[]
In this study, we employ Methanocaldococcus jannaschii (Mja) RPR as a prototype for type M RPRs.
true
true
true
true
true
6,467
2
INTRODUCTION
1
8
[ "B8", "B10", "B11", "B7" ]
18,558,617
pmid-11233979|pmid-9847214|pmid-12431435|pmid-10393902|pmid-16932744|pmid-17652407
Using a unimolecular enzyme-substrate conjugate expected to alleviate substrate-binding defects in Mja RPR, we establish that Mja RPR (in the absence of RPPs) supports cleavage in cis, thus reaffirming the RPR's pivotal catalytic role.
[ "8", "10", "11", "7" ]
235
37,745
0
false
Using a unimolecular enzyme-substrate conjugate expected to alleviate substrate-binding defects in Mja RPR, we establish that Mja RPR (in the absence of RPPs) supports cleavage in cis, thus reaffirming the RPR's pivotal catalytic role.
[]
Using a unimolecular enzyme-substrate conjugate expected to alleviate substrate-binding defects in Mja RPR, we establish that Mja RPR (in the absence of RPPs) supports cleavage in cis, thus reaffirming the RPR's pivotal catalytic role.
true
true
true
true
true
6,467
3
INTRODUCTION
1
12–15
[ "B12 B13 B14 B15", "B2", "B3", "B16" ]
18,558,617
pmid-14691942|pmid-9485387|pmid-16932744|pmid-17652407|pmid-11586922|pmid-12003490|pmid-17053064|pmid-17053064
If the RPR is the catalytic moiety in RNase P from all three domains of life, why do archaeal/eukaryal RNase P holoenzymes require multiple RPPs for function in vivo while bacterial RNase P employs a single RPP, which serves to normalize the binding affinity and rate of cleavage of different precursor tRNAs (ptRNAs) by...
[ "12–15", "2", "3", "16" ]
337
37,746
1
false
If the RPR is the catalytic moiety in RNase P from all three domains of life, why do archaeal/eukaryal RNase P holoenzymes require multiple RPPs for function in vivo while bacterial RNase P employs a single RPP, which serves to normalize the binding affinity and rate of cleavage of different precursor tRNAs (ptRNAs) by...
[ "12–15" ]
If the RPR is the catalytic moiety in RNase P from all three domains of life, why do archaeal/eukaryal RNase P holoenzymes require multiple RPPs for function in vivo while bacterial RNase P employs a single RPP, which serves to normalize the binding affinity and rate of cleavage of different precursor tRNAs (ptRNAs) by...
true
true
true
true
true
6,468
3
INTRODUCTION
1
12–15
[ "B12 B13 B14 B15", "B2", "B3", "B16" ]
18,558,617
pmid-14691942|pmid-9485387|pmid-16932744|pmid-17652407|pmid-11586922|pmid-12003490|pmid-17053064|pmid-17053064
Biochemical characterization of a partially purified archaeal RNase P holoenzyme demonstrated that the RPR is associated with at least four RPPs (POP5, RPP30, RPP21 and RPP29), which have eukaryal homologs (2,3).
[ "12–15", "2", "3", "16" ]
212
37,747
0
false
Biochemical characterization of a partially purified archaeal RNase P holoenzyme demonstrated that the RPR is associated with at least four RPPs, which have eukaryal homologs.
[ "POP5, RPP30, RPP21 and RPP29", "2,3" ]
Biochemical characterization of a partially purified archaeal RNase P holoenzyme demonstrated that the RPR is associated with at least four RPPs, which have eukaryal homologs.
true
true
true
true
true
6,468
3
INTRODUCTION
1
16
[ "B12 B13 B14 B15", "B2", "B3", "B16" ]
18,558,617
pmid-14691942|pmid-9485387|pmid-16932744|pmid-17652407|pmid-11586922|pmid-12003490|pmid-17053064|pmid-17053064
We recently reconstituted Pyrococcus furiosus (Pfu; type A) RNase P in vitro in an effort to develop archaeal RNase P as an experimental surrogate for the more complex eukaryal counterpart (16).
[ "12–15", "2", "3", "16" ]
194
37,748
1
false
We recently reconstituted Pyrococcus furiosus (Pfu; type A) RNase P in vitro in an effort to develop archaeal RNase P as an experimental surrogate for the more complex eukaryal counterpart.
[ "16" ]
We recently reconstituted Pyrococcus furiosus (Pfu; type A) RNase P in vitro in an effort to develop archaeal RNase P as an experimental surrogate for the more complex eukaryal counterpart.
true
true
true
true
true
6,468
3
INTRODUCTION
1
12–15
[ "B12 B13 B14 B15", "B2", "B3", "B16" ]
18,558,617
pmid-14691942|pmid-9485387|pmid-16932744|pmid-17652407|pmid-11586922|pmid-12003490|pmid-17053064|pmid-17053064
In this study, by examining the role of RPPs in aiding the self-processing of the type M RPR-ptRNA cis conjugate, we are beginning to uncover functional parallels between the archaeal RPPs and the sole bacterial RPP.
[ "12–15", "2", "3", "16" ]
216
37,749
0
false
In this study, by examining the role of RPPs in aiding the self-processing of the type M RPR-ptRNA cis conjugate, we are beginning to uncover functional parallels between the archaeal RPPs and the sole bacterial RPP.
[]
In this study, by examining the role of RPPs in aiding the self-processing of the type M RPR-ptRNA cis conjugate, we are beginning to uncover functional parallels between the archaeal RPPs and the sole bacterial RPP.
true
true
true
true
true
6,468
0
DISCUSSION
1
6–8
[ "B6 B7 B8", "B36", "B37", "B9" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
Although the bacterial RPR alone is catalytically active under in vitro conditions of high ionic strength, until recently RPRs from many archaeal and all eukaryal sources were reported as incapable of catalysis without their cognate RPPs.
[ "6–8", "36", "37", "9" ]
238
37,750
0
false
Although the bacterial RPR alone is catalytically active under in vitro conditions of high ionic strength, until recently RPRs from many archaeal and all eukaryal sources were reported as incapable of catalysis without their cognate RPPs.
[]
Although the bacterial RPR alone is catalytically active under in vitro conditions of high ionic strength, until recently RPRs from many archaeal and all eukaryal sources were reported as incapable of catalysis without their cognate RPPs.
true
true
true
true
true
6,469
0
DISCUSSION
1
6–8
[ "B6 B7 B8", "B36", "B37", "B9" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
These archaeal and eukaryal RPRs were not rendered active even in the presence of high concentrations of monovalent and divalent cations, which occasionally mitigate structural defects that prevent generation of an active RNA tertiary fold (6–8,36,37).
[ "6–8", "36", "37", "9" ]
252
37,751
0
false
These archaeal and eukaryal RPRs were not rendered active even in the presence of high concentrations of monovalent and divalent cations, which occasionally mitigate structural defects that prevent generation of an active RNA tertiary fold.
[ "6–8,36,37" ]
These archaeal and eukaryal RPRs were not rendered active even in the presence of high concentrations of monovalent and divalent cations, which occasionally mitigate structural defects that prevent generation of an active RNA tertiary fold.
true
true
true
true
true
6,469
0
DISCUSSION
1
6–8
[ "B6 B7 B8", "B36", "B37", "B9" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
The decreased activity in these RPRs might reflect a natural course towards a more complex RNP in which protein subunits provide functional groups that make up the active site.
[ "6–8", "36", "37", "9" ]
176
37,752
0
false
The decreased activity in these RPRs might reflect a natural course towards a more complex RNP in which protein subunits provide functional groups that make up the active site.
[]
The decreased activity in these RPRs might reflect a natural course towards a more complex RNP in which protein subunits provide functional groups that make up the active site.
true
true
true
true
true
6,469
0
DISCUSSION
1
6–8
[ "B6 B7 B8", "B36", "B37", "B9" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
However, results from a recent study and the data reported here do not support such a premise.
[ "6–8", "36", "37", "9" ]
94
37,753
0
false
However, results from a recent study and the data reported here do not support such a premise.
[]
However, results from a recent study and the data reported here do not support such a premise.
true
true
true
true
true
6,469
0
DISCUSSION
1
6–8
[ "B6 B7 B8", "B36", "B37", "B9" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
First, Kikovska et al.
[ "6–8", "36", "37", "9" ]
22
37,754
0
false
First, Kikovska et al.
[]
First, Kikovska et al.
true
true
true
true
true
6,469
0
DISCUSSION
1
9
[ "B6 B7 B8", "B36", "B37", "B9" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
(9) showed that the human RPR can process different ptRNAs and model substrates, albeit 106-fold slower than that of bacterial RPR.
[ "6–8", "36", "37", "9" ]
131
37,755
1
false
showed that the human RPR can process different ptRNAs and model substrates, albeit 106-fold slower than that of bacterial RPR.
[ "9" ]
showed that the human RPR can process different ptRNAs and model substrates, albeit 106-fold slower than that of bacterial RPR.
false
true
true
true
false
6,469
0
DISCUSSION
1
6–8
[ "B6 B7 B8", "B36", "B37", "B9" ]
18,558,617
pmid-6197186|pmid-11586922|pmid-12003490|pmid-16679018|NA|pmid-16595295|pmid-6197186|pmid-16595295|pmid-10393902|pmid-11233979|pmid-17284611|pmid-9847214|pmid-10393902|pmid-11233979|pmid-12431435|pmid-16595295|pmid-10393902|pmid-11233979|pmid-8022484|pmid-17081993|pmid-17284611
Second, we have demonstrated here through engineering strategies intended to overcome substrate-binding defects that a euryarchaeal type M RPR, thus far found to be incapable of ptRNA processing, can catalyze this reaction (Figures 1 and 2).
[ "6–8", "36", "37", "9" ]
241
37,756
0
false
Second, we have demonstrated here through engineering strategies intended to overcome substrate-binding defects that a euryarchaeal type M RPR, thus far found to be incapable of ptRNA processing, can catalyze this reaction (Figures 1 and 2).
[]
Second, we have demonstrated here through engineering strategies intended to overcome substrate-binding defects that a euryarchaeal type M RPR, thus far found to be incapable of ptRNA processing, can catalyze this reaction (Figures 1 and 2).
true
true
true
true
true
6,469
1
DISCUSSION
1
37
[ "B37" ]
18,558,617
pmid-12431435|pmid-17081993
Since the human and Mja (archaeal type M) RPRs can support ptRNA processing in the absence of RPPs when 150–500 mM Mg2+ is provided, it is evident that they possess the crucial structural elements required for generating the active site.
[ "37" ]
237
37,757
0
false
Since the human and Mja (archaeal type M) RPRs can support ptRNA processing in the absence of RPPs when 150–500 mM Mg2+ is provided, it is evident that they possess the crucial structural elements required for generating the active site.
[]
Since the human and Mja (archaeal type M) RPRs can support ptRNA processing in the absence of RPPs when 150–500 mM Mg2+ is provided, it is evident that they possess the crucial structural elements required for generating the active site.
true
true
true
true
true
6,470
1
DISCUSSION
1
37
[ "B37" ]
18,558,617
pmid-12431435|pmid-17081993
These findings together with the fact that all characterized RPPs, either individually or in combination, cannot promote ptRNA processing without their RPRs confirm that the RPR is the catalytic moiety in all three domains of life.
[ "37" ]
231
37,758
0
false
These findings together with the fact that all characterized RPPs, either individually or in combination, cannot promote ptRNA processing without their RPRs confirm that the RPR is the catalytic moiety in all three domains of life.
[]
These findings together with the fact that all characterized RPPs, either individually or in combination, cannot promote ptRNA processing without their RPRs confirm that the RPR is the catalytic moiety in all three domains of life.
true
true
true
true
true
6,470
1
DISCUSSION
1
37
[ "B37" ]
18,558,617
pmid-12431435|pmid-17081993
While such a broad inference might seem inconsistent with reports of failure to detect archaeal/eukaryal RPR-alone-catalyzed ptRNA processing, these results might reflect either an inability to form an active RPR fold in vitro or a masking of the cleavage capability due to extremely weak ptRNA binding (37).
[ "37" ]
308
37,759
1
false
While such a broad inference might seem inconsistent with reports of failure to detect archaeal/eukaryal RPR-alone-catalyzed ptRNA processing, these results might reflect either an inability to form an active RPR fold in vitro or a masking of the cleavage capability due to extremely weak ptRNA binding.
[ "37" ]
While such a broad inference might seem inconsistent with reports of failure to detect archaeal/eukaryal RPR-alone-catalyzed ptRNA processing, these results might reflect either an inability to form an active RPR fold in vitro or a masking of the cleavage capability due to extremely weak ptRNA binding.
true
true
true
true
true
6,470
2
DISCUSSION
1
14
[ "B14", "B15" ]
18,558,617
pmid-11233979|pmid-9847214|pmid-12431435|pmid-10393902|pmid-16932744|pmid-17652407
Addition of the sole bacterial RPP normalizes the binding affinity and rate of cleavage of different ptRNAs by the cognate RPR; moreover, it enhances the affinity for Mg2+ ions in the active site thereby making a vital contribution to rate enhancement at physiological Mg2+ concentrations (14,15).
[ "14", "15" ]
297
37,760
0
false
Addition of the sole bacterial RPP normalizes the binding affinity and rate of cleavage of different ptRNAs by the cognate RPR; moreover, it enhances the affinity for Mg2+ ions in the active site thereby making a vital contribution to rate enhancement at physiological Mg2+ concentrations.
[ "14,15" ]
Addition of the sole bacterial RPP normalizes the binding affinity and rate of cleavage of different ptRNAs by the cognate RPR; moreover, it enhances the affinity for Mg2+ ions in the active site thereby making a vital contribution to rate enhancement at physiological Mg2+ concentrations.
true
true
true
true
true
6,471
2
DISCUSSION
1
14
[ "B14", "B15" ]
18,558,617
pmid-11233979|pmid-9847214|pmid-12431435|pmid-10393902|pmid-16932744|pmid-17652407
What then are the roles played by the multiple archaeal/eukaryal RPPs?
[ "14", "15" ]
70
37,761
0
false
What then are the roles played by the multiple archaeal/eukaryal RPPs?
[]
What then are the roles played by the multiple archaeal/eukaryal RPPs?
true
true
true
true
true
6,471
3
DISCUSSION
1
16
[ "B16" ]
18,558,617
pmid-14691942|pmid-9485387|pmid-16932744|pmid-17652407|pmid-11586922|pmid-12003490|pmid-17053064|pmid-17053064
Our studies on Pfu RNase P, where we examined the trans cleavage of a ptRNA under multiple turnover conditions, revealed that POP5-RPP30 (but not RPP21-RPP29) enhances the kcat of the RPR by nearly 40-fold, in fact to the same extent observed with all four RPPs (16).
[ "16" ]
267
37,762
1
false
Our studies on Pfu RNase P, where we examined the trans cleavage of a ptRNA under multiple turnover conditions, revealed that POP5-RPP30 (but not RPP21-RPP29) enhances the kcat of the RPR by nearly 40-fold, in fact to the same extent observed with all four RPPs.
[ "16" ]
Our studies on Pfu RNase P, where we examined the trans cleavage of a ptRNA under multiple turnover conditions, revealed that POP5-RPP30 enhances the kcat of the RPR by nearly 40-fold, in fact to the same extent observed with all four RPPs.
true
true
true
true
true
6,472
3
DISCUSSION
1
16
[ "B16" ]
18,558,617
pmid-14691942|pmid-9485387|pmid-16932744|pmid-17652407|pmid-11586922|pmid-12003490|pmid-17053064|pmid-17053064
This finding indicated that POP5-RPP30 plays a vital role in cleavage and/or product release.
[ "16" ]
93
37,763
0
false
This finding indicated that POP5-RPP30 plays a vital role in cleavage and/or product release.
[]
This finding indicated that POP5-RPP30 plays a vital role in cleavage and/or product release.
true
true
true
true
true
6,472
3
DISCUSSION
1
16
[ "B16" ]
18,558,617
pmid-14691942|pmid-9485387|pmid-16932744|pmid-17652407|pmid-11586922|pmid-12003490|pmid-17053064|pmid-17053064
Although a comprehensive description of the kinetic scheme requires determining the rate constants for individual steps, we rationalized that studying the Mja RPR cis conjugate in the absence and presence of its cognate RPPs might permit us to focus on the chemical step (akin to a single-turnover reaction) without infl...
[ "16" ]
368
37,764
0
false
Although a comprehensive description of the kinetic scheme requires determining the rate constants for individual steps, we rationalized that studying the Mja RPR cis conjugate in the absence and presence of its cognate RPPs might permit us to focus on the chemical step (akin to a single-turnover reaction) without infl...
[]
Although a comprehensive description of the kinetic scheme requires determining the rate constants for individual steps, we rationalized that studying the Mja RPR cis conjugate in the absence and presence of its cognate RPPs might permit us to focus on the chemical step (akin to a single-turnover reaction) without infl...
true
true
true
true
true
6,472
3
DISCUSSION
1
16
[ "B16" ]
18,558,617
pmid-14691942|pmid-9485387|pmid-16932744|pmid-17652407|pmid-11586922|pmid-12003490|pmid-17053064|pmid-17053064
Even for a cis conjugate, however, kobs (the apparent rate of product formation) need not be the rate of the chemical step as steps prior to cleavage could be rate limiting (see scheme below).
[ "16" ]
192
37,765
0
false
Even for a cis conjugate, however, kobs (the apparent rate of product formation) need not be the rate of the chemical step as steps prior to cleavage could be rate limiting (see scheme below).
[]
Even for a cis conjugate, however, kobs (the apparent rate of product formation) need not be the rate of the chemical step as steps prior to cleavage could be rate limiting (see scheme below).
true
true
true
true
true
6,472
4
DISCUSSION
1
16
[ "B16" ]
18,558,617
pmid-17053064
The maximal kobs for self-cleavage of ptTyr-S3-M RPR is accelerated ∼100-fold by Mja POP5-RPP30
[ "16" ]
95
37,766
0
false
The maximal kobs for self-cleavage of ptTyr-S3-M RPR is accelerated ∼100-fold by Mja POP5-RPP30
[]
The maximal kobs for self-cleavage of ptTyr-S3-M RPR is accelerated ∼100-fold by Mja POP5-RPP30
true
true
false
true
false
6,473
4
DISCUSSION
1
16
[ "B16" ]
18,558,617
pmid-17053064
but not at all by RPP21-RPP29 (Table 1).
[ "16" ]
40
37,767
0
false
but not at all by RPP21-RPP29 (Table 1).
[]
but not at all by RPP21-RPP29.
false
true
true
true
false
6,473
4
DISCUSSION
1
16
[ "B16" ]
18,558,617
pmid-17053064
Similarly, only POP5-RPP30 promotes the trans cleavage of ptRNA by Mja RPR under multiple turnover conditions (unpublished observations).
[ "16" ]
137
37,768
0
false
Similarly, only POP5-RPP30 promotes the trans cleavage of ptRNA by Mja RPR under multiple turnover conditions (unpublished observations).
[]
Similarly, only POP5-RPP30 promotes the trans cleavage of ptRNA by Mja RPR under multiple turnover conditions (unpublished observations).
true
true
true
true
true
6,473
4
DISCUSSION
1
16
[ "B16" ]
18,558,617
pmid-17053064
These findings are also consistent with our earlier observation that Pfu RPP21-RPP29 leaves the kcat of the Pfu RPR-catalyzed reaction unaltered while decreasing the Km five-fold and lowering the Mg2+ requirement (16).
[ "16" ]
218
37,769
1
false
These findings are also consistent with our earlier observation that Pfu RPP21-RPP29 leaves the kcat of the Pfu RPR-catalyzed reaction unaltered while decreasing the Km five-fold and lowering the Mg2+ requirement.
[ "16" ]
These findings are also consistent with our earlier observation that Pfu RPP21-RPP29 leaves the kcat of the Pfu RPR-catalyzed reaction unaltered while decreasing the Km five-fold and lowering the Mg2+ requirement.
true
true
true
true
true
6,473
5
DISCUSSION
1
14
[ "B14", "B38", "B39", "B14", "B40", "B41", "B16", "B42 B43 B44" ]
18,558,617
pmid-16932744|pmid-9665718|pmid-10445877|pmid-16932744|pmid-16430919|pmid-16418270|pmid-17053064|pmid-12507471|pmid-16228004|pmid-17299131
We interpret our current results within a framework based on the kinetic scheme put forth by Harris and coworkers for trans cleavage of ptRNAs by Eco RNase P (14).
[ "14", "38", "39", "14", "40", "41", "16", "42–44" ]
163
37,770
1
false
We interpret our current results within a framework based on the kinetic scheme put forth by Harris and coworkers for trans cleavage of ptRNAs by Eco RNase P.
[ "14" ]
We interpret our current results within a framework based on the kinetic scheme put forth by Harris and coworkers for trans cleavage of ptRNAs by Eco RNase P.
true
true
true
true
true
6,474
5
DISCUSSION
1
14
[ "B14", "B38", "B39", "B14", "B40", "B41", "B16", "B42 B43 B44" ]
18,558,617
pmid-16932744|pmid-9665718|pmid-10445877|pmid-16932744|pmid-16430919|pmid-16418270|pmid-17053064|pmid-12507471|pmid-16228004|pmid-17299131
When the role of the Eco RPP in RPR-mediated cleavage of ptRNAs with and without consensus recognition sequences was examined in single-turnover reactions, the RPP increased by 100- to 1000-fold the kobs for non-consensus ptRNA processing by the cognate RPR.
[ "14", "38", "39", "14", "40", "41", "16", "42–44" ]
258
37,771
0
false
When the role of the Eco RPP in RPR-mediated cleavage of ptRNAs with and without consensus recognition sequences was examined in single-turnover reactions, the RPP increased by 100- to 1000-fold the kobs for non-consensus ptRNA processing by the cognate RPR.
[]
When the role of the Eco RPP in RPR-mediated cleavage of ptRNAs with and without consensus recognition sequences was examined in single-turnover reactions, the RPP increased by 100- to 1000-fold the kobs for non-consensus ptRNA processing by the cognate RPR.
true
true
true
true
true
6,474
5
DISCUSSION
1
14
[ "B14", "B38", "B39", "B14", "B40", "B41", "B16", "B42 B43 B44" ]
18,558,617
pmid-16932744|pmid-9665718|pmid-10445877|pmid-16932744|pmid-16430919|pmid-16418270|pmid-17053064|pmid-12507471|pmid-16228004|pmid-17299131
The scheme below was used to explain the role of the bacterial RPP in catalysis.
[ "14", "38", "39", "14", "40", "41", "16", "42–44" ]
80
37,772
0
false
The scheme below was used to explain the role of the bacterial RPP in catalysis.
[]
The scheme below was used to explain the role of the bacterial RPP in catalysis.
true
true
true
true
true
6,474
5
DISCUSSION
1
14
[ "B14", "B38", "B39", "B14", "B40", "B41", "B16", "B42 B43 B44" ]
18,558,617
pmid-16932744|pmid-9665718|pmid-10445877|pmid-16932744|pmid-16430919|pmid-16418270|pmid-17053064|pmid-12507471|pmid-16228004|pmid-17299131
Subsequent to substrate binding, a conformational change from ES to ES*, which helps position the ptRNA and catalytic metal ions optimally for cleavage, had already been proposed based on results from various kinetic and structural studies (38,39).
[ "14", "38", "39", "14", "40", "41", "16", "42–44" ]
248
37,773
0
false
Subsequent to substrate binding, a conformational change from ES to ES*, which helps position the ptRNA and catalytic metal ions optimally for cleavage, had already been proposed based on results from various kinetic and structural studies.
[ "38,39" ]
Subsequent to substrate binding, a conformational change from ES to ES*, which helps position the ptRNA and catalytic metal ions optimally for cleavage, had already been proposed based on results from various kinetic and structural studies.
true
true
true
true
true
6,474
5
DISCUSSION
1
14
[ "B14", "B38", "B39", "B14", "B40", "B41", "B16", "B42 B43 B44" ]
18,558,617
pmid-16932744|pmid-9665718|pmid-10445877|pmid-16932744|pmid-16430919|pmid-16418270|pmid-17053064|pmid-12507471|pmid-16228004|pmid-17299131
Because the bacterial RPR's kobs with tight-binding, consensus ptRNAs increases only three fold by the RPP, the possibility of the RPP contributing functional groups to catalysis and thereby increasing kc (the rate of the chemical step) was discounted.
[ "14", "38", "39", "14", "40", "41", "16", "42–44" ]
252
37,774
0
false
Because the bacterial RPR's kobs with tight-binding, consensus ptRNAs increases only three fold by the RPP, the possibility of the RPP contributing functional groups to catalysis and thereby increasing kc (the rate of the chemical step) was discounted.
[]
Because the bacterial RPR's kobs with tight-binding, consensus ptRNAs increases only three fold by the RPP, the possibility of the RPP contributing functional groups to catalysis and thereby increasing kc (the rate of the chemical step) was discounted.
true
true
true
true
true
6,474
5
DISCUSSION
1
14
[ "B14", "B38", "B39", "B14", "B40", "B41", "B16", "B42 B43 B44" ]
18,558,617
pmid-16932744|pmid-9665718|pmid-10445877|pmid-16932744|pmid-16430919|pmid-16418270|pmid-17053064|pmid-12507471|pmid-16228004|pmid-17299131
What then accounts for the dramatic RPP-facilitated increase in kobs with non-consensus substrates?
[ "14", "38", "39", "14", "40", "41", "16", "42–44" ]
99
37,775
0
false
What then accounts for the dramatic RPP-facilitated increase in kobs with non-consensus substrates?
[]
What then accounts for the dramatic RPP-facilitated increase in kobs with non-consensus substrates?
true
true
true
true
true
6,474
5
DISCUSSION
1
14
[ "B14", "B38", "B39", "B14", "B40", "B41", "B16", "B42 B43 B44" ]
18,558,617
pmid-16932744|pmid-9665718|pmid-10445877|pmid-16932744|pmid-16430919|pmid-16418270|pmid-17053064|pmid-12507471|pmid-16228004|pmid-17299131
Since only Kconf and kc contribute to kobs in a single-turnover trans cleavage reaction, the RPP was then inferred to influence the equilibrium (Kconf) that precedes the slower bond-breaking step.
[ "14", "38", "39", "14", "40", "41", "16", "42–44" ]
196
37,776
0
false
Since only Kconf and kc contribute to kobs in a single-turnover trans cleavage reaction, the RPP was then inferred to influence the equilibrium (Kconf) that precedes the slower bond-breaking step.
[]
Since only Kconf and kc contribute to kobs in a single-turnover trans cleavage reaction, the RPP was then inferred to influence the equilibrium (Kconf) that precedes the slower bond-breaking step.
true
true
true
true
true
6,474
5
DISCUSSION
1
14
[ "B14", "B38", "B39", "B14", "B40", "B41", "B16", "B42 B43 B44" ]
18,558,617
pmid-16932744|pmid-9665718|pmid-10445877|pmid-16932744|pmid-16430919|pmid-16418270|pmid-17053064|pmid-12507471|pmid-16228004|pmid-17299131
By shifting the equilibrium from ES to ES* for the atypical ptRNAs, the bacterial RPP was postulated to stabilize ES* and enhance catalysis (14).
[ "14", "38", "39", "14", "40", "41", "16", "42–44" ]
145
37,777
1
false
By shifting the equilibrium from ES to ES* for the atypical ptRNAs, the bacterial RPP was postulated to stabilize ES* and enhance catalysis.
[ "14" ]
By shifting the equilibrium from ES to ES* for the atypical ptRNAs, the bacterial RPP was postulated to stabilize ES* and enhance catalysis.
true
true
true
true
true
6,474
5
DISCUSSION
1
14
[ "B14", "B38", "B39", "B14", "B40", "B41", "B16", "B42 B43 B44" ]
18,558,617
pmid-16932744|pmid-9665718|pmid-10445877|pmid-16932744|pmid-16430919|pmid-16418270|pmid-17053064|pmid-12507471|pmid-16228004|pmid-17299131
In the case of ptTyr-S3-M RPR, the tethered substrate renders it similar to the ES complex in the trans cleavage scheme.
[ "14", "38", "39", "14", "40", "41", "16", "42–44" ]
120
37,778
0
false
In the case of ptTyr-S3-M RPR, the tethered substrate renders it similar to the ES complex in the trans cleavage scheme.
[]
In the case of ptTyr-S3-M RPR, the tethered substrate renders it similar to the ES complex in the trans cleavage scheme.
true
true
true
true
true
6,474
5
DISCUSSION
1
14
[ "B14", "B38", "B39", "B14", "B40", "B41", "B16", "B42 B43 B44" ]
18,558,617
pmid-16932744|pmid-9665718|pmid-10445877|pmid-16932744|pmid-16430919|pmid-16418270|pmid-17053064|pmid-12507471|pmid-16228004|pmid-17299131
Mja POP5-RPP30 (but not RPP21-RPP29) enhances kobs for self-cleavage of ptTyr-S3-M RPR with a concomitant reduction in the requirement for Mg2+.
[ "14", "38", "39", "14", "40", "41", "16", "42–44" ]
144
37,779
0
false
Mja POP5-RPP30 (but not RPP21-RPP29) enhances kobs for self-cleavage of ptTyr-S3-M RPR with a concomitant reduction in the requirement for Mg2+.
[]
Mja POP5-RPP30 enhances kobs for self-cleavage of ptTyr-S3-M RPR with a concomitant reduction in the requirement for Mg2+.
true
true
true
true
true
6,474
5
DISCUSSION
1
14
[ "B14", "B38", "B39", "B14", "B40", "B41", "B16", "B42 B43 B44" ]
18,558,617
pmid-16932744|pmid-9665718|pmid-10445877|pmid-16932744|pmid-16430919|pmid-16418270|pmid-17053064|pmid-12507471|pmid-16228004|pmid-17299131
The kobs for the cis conjugate is dictated only by Kconf and kc.
[ "14", "38", "39", "14", "40", "41", "16", "42–44" ]
64
37,780
0
false
The kobs for the cis conjugate is dictated only by Kconf and kc.
[]
The kobs for the cis conjugate is dictated only by Kconf and kc.
true
true
true
true
true
6,474
5
DISCUSSION
1
14
[ "B14", "B38", "B39", "B14", "B40", "B41", "B16", "B42 B43 B44" ]
18,558,617
pmid-16932744|pmid-9665718|pmid-10445877|pmid-16932744|pmid-16430919|pmid-16418270|pmid-17053064|pmid-12507471|pmid-16228004|pmid-17299131
A direct increase in kc upon addition of Mja POP5-RPP30 is unlikely since it would necessitate an alternative mechanism from that employed by the Mja RPR, for which there is no evidence.
[ "14", "38", "39", "14", "40", "41", "16", "42–44" ]
186
37,781
0
false
A direct increase in kc upon addition of Mja POP5-RPP30 is unlikely since it would necessitate an alternative mechanism from that employed by the Mja RPR, for which there is no evidence.
[]
A direct increase in kc upon addition of Mja POP5-RPP30 is unlikely since it would necessitate an alternative mechanism from that employed by the Mja RPR, for which there is no evidence.
true
true
true
true
true
6,474
5
DISCUSSION
1
14
[ "B14", "B38", "B39", "B14", "B40", "B41", "B16", "B42 B43 B44" ]
18,558,617
pmid-16932744|pmid-9665718|pmid-10445877|pmid-16932744|pmid-16430919|pmid-16418270|pmid-17053064|pmid-12507471|pmid-16228004|pmid-17299131
Moreover, both Mja and Eco RPR cis conjugates exhibit a comparable efficiency suggesting that the functional groups for catalysis are present in the RPR (31).
[ "14", "38", "39", "14", "40", "41", "16", "42–44" ]
158
37,782
0
false
Moreover, both Mja and Eco RPR cis conjugates exhibit a comparable efficiency suggesting that the functional groups for catalysis are present in the RPR (31).
[]
Moreover, both Mja and Eco RPR cis conjugates exhibit a comparable efficiency suggesting that the functional groups for catalysis are present in the RPR.
true
true
true
true
true
6,474
5
DISCUSSION
1
14
[ "B14", "B38", "B39", "B14", "B40", "B41", "B16", "B42 B43 B44" ]
18,558,617
pmid-16932744|pmid-9665718|pmid-10445877|pmid-16932744|pmid-16430919|pmid-16418270|pmid-17053064|pmid-12507471|pmid-16228004|pmid-17299131
Therefore, the 100-fold increase in kobs upon addition of POP5-RPP30 must arise from increased conversion of ES to ES*.
[ "14", "38", "39", "14", "40", "41", "16", "42–44" ]
119
37,783
0
false
Therefore, the 100-fold increase in kobs upon addition of POP5-RPP30 must arise from increased conversion of ES to ES*.
[]
Therefore, the 100-fold increase in kobs upon addition of POP5-RPP30 must arise from increased conversion of ES to ES*.
true
true
true
true
true
6,474
5
DISCUSSION
1
14
[ "B14", "B38", "B39", "B14", "B40", "B41", "B16", "B42 B43 B44" ]
18,558,617
pmid-16932744|pmid-9665718|pmid-10445877|pmid-16932744|pmid-16430919|pmid-16418270|pmid-17053064|pmid-12507471|pmid-16228004|pmid-17299131
Additional support for this functional parallel between POP5-RPP30 and bacterial RPP stems from the findings that the tertiary structures of archaeal POP5 and bacterial RPP are strikingly similar (40,41), and POP5-RPP30 and Eco RPP footprint at similar locations in the C domains of their respective RPRs (16,42–44).
[ "14", "38", "39", "14", "40", "41", "16", "42–44" ]
316
37,784
0
false
Additional support for this functional parallel between POP5-RPP30 and bacterial RPP stems from the findings that the tertiary structures of archaeal POP5 and bacterial RPP are strikingly similar, and POP5-RPP30 and Eco RPP footprint at similar locations in the C domains of their respective RPRs.
[ "40,41", "16,42–44" ]
Additional support for this functional parallel between POP5-RPP30 and bacterial RPP stems from the findings that the tertiary structures of archaeal POP5 and bacterial RPP are strikingly similar, and POP5-RPP30 and Eco RPP footprint at similar locations in the C domains of their respective RPRs.
true
true
true
true
true
6,474
6
DISCUSSION
1
36
[ "B36", "B45" ]
18,558,617
pmid-8022484|pmid-18172503
RPP21-RPP29 does not impact the kobs for self-cleavage but probably stabilizes the RPR's tertiary fold and substitutes for some of the RNA–RNA tertiary interactions that strengthen the structural core in bacterial RPRs.
[ "36", "45" ]
219
37,785
0
false
RPP21-RPP29 does not impact the kobs for self-cleavage but probably stabilizes the RPR's tertiary fold and substitutes for some of the RNA–RNA tertiary interactions that strengthen the structural core in bacterial RPRs.
[]
RPP21-RPP29 does not impact the kobs for self-cleavage but probably stabilizes the RPR's tertiary fold and substitutes for some of the RNA–RNA tertiary interactions that strengthen the structural core in bacterial RPRs.
true
true
true
true
true
6,475
6
DISCUSSION
1
36
[ "B36", "B45" ]
18,558,617
pmid-8022484|pmid-18172503
In this fashion, it might mirror protein cofactors that facilitate the self-splicing reactions of certain group I introns by tertiary structure capture (36,45; for a comparison of models of the bacterial and archaeal RNase P holoenzymes, see Supplementary Data).
[ "36", "45" ]
262
37,786
0
false
In this fashion, it might mirror protein cofactors that facilitate the self-splicing reactions of certain group I introns by tertiary structure capture.
[ "36,45; for a comparison of models of the bacterial and archaeal RNase P holoenzymes, see Supplementary Data" ]
In this fashion, it might mirror protein cofactors that facilitate the self-splicing reactions of certain group I introns by tertiary structure capture.
true
true
true
true
true
6,475
7
DISCUSSION
0
null
null
18,558,617
null
Although RPP21-RPP29 does not contribute to the kobs for self-processing of ptTyr-S3-M RPR, it renders ptTyr-S3-M RPR active at 100 mM Mg2+ (Figure 4A, lanes 2 and 3).
null
167
37,787
0
false
null
null
Although RPP21-RPP29 does not contribute to the kobs for self-processing of ptTyr-S3-M RPR, it renders ptTyr-S3-M RPR active at 100 mM Mg2+ (Figure 4A, lanes 2 and 3).
true
true
true
true
true
6,476
7
DISCUSSION
0
null
null
18,558,617
null
The maximal kobs determined for this reaction is similar to that observed for the RPR-alone reaction in the presence of its optimal Mg2+ concentration of 500 mM (0.06 versus 0.05 minβˆ’1; Table 1).
null
195
37,788
0
false
null
null
The maximal kobs determined for this reaction is similar to that observed for the RPR-alone reaction in the presence of its optimal Mg2+ concentration of 500 mM (0.06 versus 0.05 minβˆ’1; Table 1).
true
true
true
true
true
6,476
7
DISCUSSION
0
null
null
18,558,617
null
Therefore, RPP21-RPP29 enables the RPR to attain its maximal kobs at a lower Mg2+ concentration perhaps by enhancing the affinity of the RNP for Mg2+ without affecting ES*.
null
172
37,789
0
false
null
null
Therefore, RPP21-RPP29 enables the RPR to attain its maximal kobs at a lower Mg2+ concentration perhaps by enhancing the affinity of the RNP for Mg2+ without affecting ES*.
true
true
true
true
true
6,476
7
DISCUSSION
0
null
null
18,558,617
null
If these RPPs and Mg2+ bind to the folded state of the RPR, their binding will be thermodynamically coupled.
null
108
37,790
0
false
null
null
If these RPPs and Mg2+ bind to the folded state of the RPR, their binding will be thermodynamically coupled.
true
true
true
true
true
6,476
8
DISCUSSION
0
null
null
18,558,617
null
Since the Mja RPR does not exhibit trans cleavage, we used the rate of self-processing of a cis conjugate as the baseline for its catalytic potential and then determined how RPPs influenced this rate.
null
200
37,791
0
false
null
null
Since the Mja RPR does not exhibit trans cleavage, we used the rate of self-processing of a cis conjugate as the baseline for its catalytic potential and then determined how RPPs influenced this rate.
true
true
true
true
true
6,477
8
DISCUSSION
0
null
null
18,558,617
null
In the cis construct, the substrate is docked on the enzyme though likely not optimally positioned.
null
99
37,792
0
false
null
null
In the cis construct, the substrate is docked on the enzyme though likely not optimally positioned.
true
true
true
true
true
6,477
8
DISCUSSION
0
null
null
18,558,617
null
If RPP21-RPP29 plays a role in substrate binding, its effect on the catalytic efficiency of a trans cleavage reaction might be more pronounced than in a cis reaction where the substrate is already docked.
null
204
37,793
0
false
null
null
If RPP21-RPP29 plays a role in substrate binding, its effect on the catalytic efficiency of a trans cleavage reaction might be more pronounced than in a cis reaction where the substrate is already docked.
true
true
true
true
true
6,477
8
DISCUSSION
0
null
null
18,558,617
null
In fact, RPP21-RPP29 enhances by two fold the kobs for self-cleavage of a cis conjugate with a 5-nt spacer in contrast to a 3-nt-spacer construct where it has no effect (Table 1; data not shown).
null
195
37,794
0
false
null
null
In fact, RPP21-RPP29 enhances by two fold the kobs for self-cleavage of a cis conjugate with a 5-nt spacer in contrast to a 3-nt-spacer construct where it has no effect (Table 1; data not shown).
true
true
true
true
true
6,477
8
DISCUSSION
0
null
null
18,558,617
null
We are investigating if the pattern of activation by RPPs differs between a cis and a trans cleavage reaction.
null
110
37,795
0
false
null
null
We are investigating if the pattern of activation by RPPs differs between a cis and a trans cleavage reaction.
true
true
true
true
true
6,477
9
DISCUSSION
1
22
[ "B22", "B34", "B35", "B35" ]
18,558,617
pmid-1741379|pmid-8628683|pmid-10393536|pmid-10393536
Despite the identification of a conserved C domain in all RPRs, previous studies suggested that this domain by itself was either not functional in the absence of cognate RPPs or that its activity was nearly 25 000-fold weaker than the wild type (22,34,35).
[ "22", "34", "35", "35" ]
256
37,796
0
false
Despite the identification of a conserved C domain in all RPRs, previous studies suggested that this domain by itself was either not functional in the absence of cognate RPPs or that its activity was nearly 25 000-fold weaker than the wild type.
[ "22,34,35" ]
Despite the identification of a conserved C domain in all RPRs, previous studies suggested that this domain by itself was either not functional in the absence of cognate RPPs or that its activity was nearly 25 000-fold weaker than the wild type.
true
true
true
true
true
6,478
9
DISCUSSION
1
22
[ "B22", "B34", "B35", "B35" ]
18,558,617
pmid-1741379|pmid-8628683|pmid-10393536|pmid-10393536
If this defect is attributable to weak substrate binding, covalent attachment of the substrate should remedy it.
[ "22", "34", "35", "35" ]
112
37,797
0
false
If this defect is attributable to weak substrate binding, covalent attachment of the substrate should remedy it.
[]
If this defect is attributable to weak substrate binding, covalent attachment of the substrate should remedy it.
true
true
true
true
true
6,478
9
DISCUSSION
1
22
[ "B22", "B34", "B35", "B35" ]
18,558,617
pmid-1741379|pmid-8628683|pmid-10393536|pmid-10393536
Indeed, our study shows that self-cleavage of ptTyr-S3-Ξ”S M RPR is only 12-fold slower than ptTyr-S3-M RPR at pH 5.1 (Table 1); moreover, the decreased activity suggests that the S domain does play a role in cleavage even in the cis conjugate (perhaps, by influencing Kconf).
[ "22", "34", "35", "35" ]
275
37,798
0
false
Indeed, our study shows that self-cleavage of ptTyr-S3-Ξ”S M RPR is only 12-fold slower than ptTyr-S3-M RPR at pH 5.1 (Table 1); moreover, the decreased activity suggests that the S domain does play a role in cleavage even in the cis conjugate (perhaps, by influencing Kconf).
[]
Indeed, our study shows that self-cleavage of ptTyr-S3-Ξ”S M RPR is only 12-fold slower than ptTyr-S3-M RPR at pH 5.1 (Table 1); moreover, the decreased activity suggests that the S domain does play a role in cleavage even in the cis conjugate (perhaps, by influencing Kconf).
true
true
true
true
true
6,478
9
DISCUSSION
1
22
[ "B22", "B34", "B35", "B35" ]
18,558,617
pmid-1741379|pmid-8628683|pmid-10393536|pmid-10393536
Such a function of the S domain is clearly redundant with POP5-RPP30 since both ptTyr-S3-M RPR and ptTyr-S3-Ξ”S M RPR display near identical rates of self-cleavage in the presence of POP5-RPP30 (Table 1).
[ "22", "34", "35", "35" ]
203
37,799
0
false
Such a function of the S domain is clearly redundant with POP5-RPP30 since both ptTyr-S3-M RPR and ptTyr-S3-Ξ”S M RPR display near identical rates of self-cleavage in the presence of POP5-RPP30 (Table 1).
[]
Such a function of the S domain is clearly redundant with POP5-RPP30 since both ptTyr-S3-M RPR and ptTyr-S3-Ξ”S M RPR display near identical rates of self-cleavage in the presence of POP5-RPP30 (Table 1).
true
true
true
true
true
6,478
9
DISCUSSION
1
35
[ "B22", "B34", "B35", "B35" ]
18,558,617
pmid-1741379|pmid-8628683|pmid-10393536|pmid-10393536
This result parallels the rescue of the bacterial RPR's C domain by its RPP (35) and once again reveals similarities in the functioning of bacterial and archaeal RNase P.
[ "22", "34", "35", "35" ]
170
37,800
1
false
This result parallels the rescue of the bacterial RPR's C domain by its RPP and once again reveals similarities in the functioning of bacterial and archaeal RNase P.
[ "35" ]
This result parallels the rescue of the bacterial RPR's C domain by its RPP and once again reveals similarities in the functioning of bacterial and archaeal RNase P.
true
true
true
true
true
6,478
0
INTRODUCTION
0
null
null
20,460,459
null
Most of the activities of living cells are performed by protein–protein interactions that form molecular complexes.
null
115
37,801
0
false
null
null
Most of the activities of living cells are performed by protein–protein interactions that form molecular complexes.
true
true
true
true
true
6,479
0
INTRODUCTION
0
null
null
20,460,459
null
Accurate modeling of the 3D structure of a complex assists in understanding its function in the cell.
null
101
37,802
0
false
null
null
Accurate modeling of the 3D structure of a complex assists in understanding its function in the cell.
true
true
true
true
true
6,479
0
INTRODUCTION
0
null
null
20,460,459
null
Additionally, atomic structures of molecular complexes are used in the field of drug design, permitting the design of small molecules that prevent or induce the formation of certain complexes.
null
192
37,803
0
false
null
null
Additionally, atomic structures of molecular complexes are used in the field of drug design, permitting the design of small molecules that prevent or induce the formation of certain complexes.
true
true
true
true
true
6,479
0
INTRODUCTION
0
null
null
20,460,459
null
In some cases, the 3D structure of protein–protein complexes can be determined experimentally by X-ray crystallography or NMR spectroscopy.
null
139
37,804
0
false
null
null
In some cases, the 3D structure of protein–protein complexes can be determined experimentally by X-ray crystallography or NMR spectroscopy.
true
true
true
true
true
6,479
0
INTRODUCTION
0
null
null
20,460,459
null
However, it is an extremely difficult and time-consuming task.
null
62
37,805
0
false
null
null
However, it is an extremely difficult and time-consuming task.
true
true
true
true
true
6,479
0
INTRODUCTION
0
null
null
20,460,459
null
Therefore, the ability to predict the structure of complexes by computational means is essential.
null
97
37,806
0
false
null
null
Therefore, the ability to predict the structure of complexes by computational means is essential.
true
true
true
true
true
6,479
1
INTRODUCTION
1
1
[ "B1" ]
20,460,459
pmid-18655061
Protein–protein docking algorithms aim to predict the structure of a complex given the atomic structures of the proteins that assemble it.
[ "1" ]
138
37,807
0
false
Protein–protein docking algorithms aim to predict the structure of a complex given the atomic structures of the proteins that assemble it.
[]
Protein–protein docking algorithms aim to predict the structure of a complex given the atomic structures of the proteins that assemble it.
true
true
true
true
true
6,480
1
INTRODUCTION
1
1
[ "B1" ]
20,460,459
pmid-18655061
Due to protein flexibility, the structure of each individual protein (unbound conformation) is often rather different from its structure in the complex (bound conformation).
[ "1" ]
173
37,808
0
false
Due to protein flexibility, the structure of each individual protein (unbound conformation) is often rather different from its structure in the complex (bound conformation).
[]
Due to protein flexibility, the structure of each individual protein (unbound conformation) is often rather different from its structure in the complex (bound conformation).
true
true
true
true
true
6,480
1
INTRODUCTION
1
1
[ "B1" ]
20,460,459
pmid-18655061
Docking algorithms must therefore take the protein flexibility into account (1).
[ "1" ]
80
37,809
1
false
Docking algorithms must therefore take the protein flexibility into account.
[ "1" ]
Docking algorithms must therefore take the protein flexibility into account.
true
true
true
true
true
6,480
1
INTRODUCTION
1
1
[ "B1" ]
20,460,459
pmid-18655061
This is currently the major challenge in the docking field.
[ "1" ]
59
37,810
0
false
This is currently the major challenge in the docking field.
[]
This is currently the major challenge in the docking field.
true
true
true
true
true
6,480
1
INTRODUCTION
1
1
[ "B1" ]
20,460,459
pmid-18655061
Protein flexibility, which includes both backbone and side-chains movements, adds a huge number of degrees of freedom to the search space, making it impossible for naΓ―ve search algorithms to find the native structure of the complex.
[ "1" ]
232
37,811
0
false
Protein flexibility, which includes both backbone and side-chains movements, adds a huge number of degrees of freedom to the search space, making it impossible for naΓ―ve search algorithms to find the native structure of the complex.
[]
Protein flexibility, which includes both backbone and side-chains movements, adds a huge number of degrees of freedom to the search space, making it impossible for naΓ―ve search algorithms to find the native structure of the complex.
true
true
true
true
true
6,480
1
INTRODUCTION
1
1
[ "B1" ]
20,460,459
pmid-18655061
Thus, a two-stage docking protocol is often used: performing a fast soft rigid docking (rigid docking that allows a certain amount of steric clashes), followed by flexible refinement of the results.
[ "1" ]
198
37,812
0
false
Thus, a two-stage docking protocol is often used: performing a fast soft rigid docking (rigid docking that allows a certain amount of steric clashes), followed by flexible refinement of the results.
[]
Thus, a two-stage docking protocol is often used: performing a fast soft rigid docking (rigid docking that allows a certain amount of steric clashes), followed by flexible refinement of the results.
true
true
true
true
true
6,480
1
INTRODUCTION
1
1
[ "B1" ]
20,460,459
pmid-18655061
Applying a soft rigid-docking method on the unbound structures of two proteins often results in a near-native solution that is poorly ranked due to steric clashes and bad shape complementarity.
[ "1" ]
193
37,813
0
false
Applying a soft rigid-docking method on the unbound structures of two proteins often results in a near-native solution that is poorly ranked due to steric clashes and bad shape complementarity.
[]
Applying a soft rigid-docking method on the unbound structures of two proteins often results in a near-native solution that is poorly ranked due to steric clashes and bad shape complementarity.
true
true
true
true
true
6,480
1
INTRODUCTION
1
1
[ "B1" ]
20,460,459
pmid-18655061
The goal of the flexible refinement stage is to model the conformational changes that the proteins undergo, and thus to resolve the clashes and improve their shape complementarity.
[ "1" ]
180
37,814
0
false
The goal of the flexible refinement stage is to model the conformational changes that the proteins undergo, and thus to resolve the clashes and improve their shape complementarity.
[]
The goal of the flexible refinement stage is to model the conformational changes that the proteins undergo, and thus to resolve the clashes and improve their shape complementarity.
true
true
true
true
true
6,480
1
INTRODUCTION
1
1
[ "B1" ]
20,460,459
pmid-18655061
Re-scoring the refined solutions by a binding energy score significantly improves the ranking of near-native models.
[ "1" ]
116
37,815
0
false
Re-scoring the refined solutions by a binding energy score significantly improves the ranking of near-native models.
[]
Re-scoring the refined solutions by a binding energy score significantly improves the ranking of near-native models.
true
true
true
true
true
6,480