ライフサイエンスコーパス: dsRBD

1 dsRBDs 1, 3 and 4 bind dsRNA in vitro, but dsRBDs 2 and

2 The Dicer-1 dsRBD and three Loqs-PB dsRBDs form a tight belt around

3 Similar behavior is observed for a dsRBD containing both dsRBM1 and dsRBM2 for sequences up

4 dsRNA in general, these do not explain how a dsRBD can recognize specific RNAs.

5 o varieties of dsRBD exist: canonical Type A dsRBDs interact with dsRNA, while non-canonical Type B d

6 dsRBD by assessing the binding of dsRBM1 and dsRBD to a series of dsRNA sequences ranging from 15 to

7 etect low-affinity binding of the kinase and dsRBD constructs in solution, indicating that these doma

8 region of the protein that contains a Type B dsRBD.

9 eract with dsRNA, while non-canonical Type B dsRBDs lack RNA-binding residues and instead interact wi

10 ein/protein interaction properties of Type B dsRBDs.

11 itory RNA mediates the interaction with both dsRBDs of PKR.

12 ynamics and structures of the free and bound dsRBD reveals that slow-timescale dynamics in the alpha1

13 dsRBDs 1, 3 and 4 bind dsRNA in vitro, but dsRBDs 2 and 5 do not, although dsRBD2 does bind dsRNA w

14 structural features modulate recognition by dsRBDs.

15 Thus, a highly conserved dsRBD-substrate interaction plays an important role in s

16 We show that the core dsRBD is sufficient for homodimerization and that mutati

17 contains an N-terminal dsRNA binding domain (dsRBD) and a C-terminal kinase domain.

18 quired a double-stranded RNA-binding domain (dsRBD) and a functional helicase motif I of REH2.

19 PKR contains a dsRNA-binding domain (dsRBD) and a kinase domain.

20 t the end of the Rnt1p dsRNA-binding domain (dsRBD) and the guanine nucleotide in the second position

21 KR has a double-stranded RNA-binding domain (dsRBD) composed of two copies of the dsRNA binding motif

22 7) in the Aa-RNase III dsRNA-binding domain (dsRBD) directly interacts with a proximal box base pair.

23 F90 is a member of the dsRNA binding domain (dsRBD) family of proteins.

24 functional domains: a dsRNA binding domain (dsRBD) for siRNA docking and a pH-dependent polyhistidin

25 s by its double-stranded RNA-binding domain (dsRBD) helix alpha1 to the tetraloop minor groove.

26 A dsRNA-binding domain (dsRBD) is a conserved feature of the superfamily and is

27 that its double-stranded RNA binding domain (dsRBD) is the limiting sequence required for this intera

28 with the double-stranded RNA-binding domain (dsRBD) motif although there is little (<10%) sequence ho

29 tructure of the 20 kDa dsRNA-binding domain (dsRBD) of human PKR, which provides the first three-dime

30 ding by the C-terminal dsRNA-binding domain (dsRBD) of RNase III, indicating that EB perturbs substra

31 tion mechanisms in two dsRNA-binding domain (dsRBD) paralogs, DRB2D1 and DRB3D1.

32 ate with double-stranded RNA-binding domain (dsRBD) proteins to convert precursor-microRNAs (pre-miRN

33 PKR has a dsRNA-binding domain (dsRBD) that contains two tandem copies of the dsRNA-bind

34 ein kinase (PKR) has a dsRNA-binding domain (dsRBD) that contains two tandem copies of the dsRNA-bind

35 terminal double-stranded RNA-binding domain (dsRBD), and are active as homodimers.

36 h as the double-stranded RNA binding domain (dsRBD), the hnRNP K homology (KH) domain and the RNP mot

37 tif referred to as the dsRNA-binding domain (dsRBD).

38 double-stranded RNA (dsRNA) binding domain (dsRBD).

39 nit domain comprises a dsRNA-binding domain (dsRBD, aa 377-448) whereas linker corresponds to the lon

40 ins two double-stranded RNA-binding domains (dsRBDs) and a C-terminal tail.

41 ultiple double-stranded RNA binding domains (dsRBDs) and a catalytic domain.

42 ive double-stranded (ds)RNA-binding domains (dsRBDs) and a short region within an insertion that spli

43 Double-stranded RNA-binding domains (dsRBDs) are commonly found in modular proteins that inte

44 f viral dsRNAs to two dsRNA-binding domains (dsRBDs) in PKR leads to relief of an inhibitory region a

45 ein that contains two dsRNA-binding domains (dsRBDs) in tandem, is vital for nuclear maturation of pr

46 Two double-stranded RNA binding domains (dsRBDs) in the N-terminal half of PKR are thought to bin

47 , whose double-stranded RNA-binding domains (dsRBDs) interact with the A-form geometry of double-stra

48 randed RNA (dsRNA) by dsRNA-binding domains (dsRBDs) is involved in a large number of biological and

49 NAs (dsRNAs) with two dsRNA binding domains (dsRBDs) located in the N-terminus of PKR.

50 rboring double-stranded RNA binding domains (dsRBDs) play diverse functional roles such as RNA locali

51 s were created in the dsRNA binding domains (dsRBDs) that abolished all RNA binding, as tested for tw

52 of the double-stranded RNA-binding domains (dsRBDs) was identified.

53 to PKR double-stranded RNA-binding domains (dsRBDs) were determined by isothermal titration calorime

54 of its double-stranded RNA-binding domains (dsRBDs).

55 possess double-stranded RNA-binding domains (dsRBDs).

56 The nature of these interactions explains dsRBD specificity for dsRNA (over ssRNA or dsDNA) and th

57 Interestingly, the extra dsRBD in sqADAR2a conferred resistance to the high Cl(-)

58 The extra dsRBD of sqADAR2a increases its editing activity in vitr

59 ble to the RNA binding activity of the extra dsRBD.

60 To correlate free dsRBD dynamics with structural changes upon binding, we

61 etermined the solution structure of the free dsRBD used in the previously determined RNA-bound struct

62 dimers require two subunits with functional dsRBDs for binding to a dsRNA substrate and then for edi

63 to the mechanisms that govern specificity in dsRBD:dsRNA interactions.

64 The intervening dsRBD acts only as an RNA-sensing scaffold, allowing the

65 we ran extensive MD simulations of isolated dsRBDs (505-583 and 614-691) and the Core.

66 letely abolishes the RNA binding function of dsRBD.

67 The structure of dsRBD exhibits a dumb-bell shape comprising two tandem l

68 Crystal structures of dsRBD-dsRNA interactions suggest that the dsRNA helix mu

69 rticipates in the regulated translocation of dsRBD proteins to the cytoplasm where they interact with

70 Two varieties of dsRBD exist: canonical Type A dsRBDs interact with dsRNA

71 In NF90, a tandem pair of dsRBDs separated by a natively unstructured segment conf

72 anistic basis and functional significance of dsRBDs remain unclear.

73 Although structures of dsRBDs in complex with dsRNA have revealed how they can

74 operties of pY are not identical to those of dsRBDs, as the postulated RNA-binding site in pY does no

75 , these results suggest that this particular dsRBD-dsRNA interaction produces little to no change in

76 The Dicer-1 dsRBD and three Loqs-PB dsRBDs form a tight belt around the pre-miRNA, distortin

77 We report the solution structure of Rnt1p dsRBD complexed to the 5' terminal hairpin of one of its

78 The Rnt1p dsRBD has an extended hydrophobic core comprising helix

79 The Rnt1p dsRBD has been implicated in targeting this endonuclease

80 etermined the backbone dynamics of the Rnt1p dsRBD in the free and AGAA hairpin-bound states using NM

81 tant for binding site selection by the Rnt1p dsRBD.

82 PKR's dsRBD is involved in the regulation of the enzyme as dsR

83 fically modified each of the dsRBMs of PKR's dsRBD with the hydroxyl radical generator EDTA small mid

84 A resolution crystal structure of the second dsRBD of Xenopus laevis RNA-binding protein A complexed

85 These results show how a single dsRBD can convey specificity for particular RNA targets,

86 Purified, mutant proteins lacking single dsRBDs still bind RNA efficiently, demonstrating that no

87 ex shows surprising similarity to the tandem dsRBDs from an adenosine-to-inosine editing enzyme, ADAR

88 determined a crystal structure of the tandem dsRBDs of NF90 in complex with a synthetic dsRNA.

89 inant class of dsRNA-binding domains, termed dsRBDs, that are found in a large number of eukaryotic a

90 The dsRBD consists of two tandem copies of a conserved doubl

91 The dsRBD contacts the RNA at successive minor, major, and t

92 The dsRBD is composed of two tandem dsRNA-binding motifs.

93 ce electrostatic potential in HI0257 and the dsRBD family reveals significant differences in the loca

94 The most immediate differences between the dsRBD and HI0257 structures are that (1) HI0257 has a la

95 inding cleft of the kinase is blocked by the dsRBD.

96 to a truncated version of PKR containing the dsRBD.

97 e long a-helix (aa 460-512) that follows the dsRBD.

98 line-tyrosine-NLS, which is missing from the dsRBD-NLS.

99 te whether conformational flexibility in the dsRBD regulates the binding specificity, we determined t

100 gle of about 30 degrees to each other in the dsRBD, and (3) HI0257 lacks the extended loop commonly s

101 Interestingly, the dsRBD fold resembles a portion of the conserved core str

102 rm of Escherichia coli RNase III lacking the dsRBD (RNase III[DeltadsRBD]) can accurately cleave smal

103 e but not obligatorily linked actions of the dsRBD and the catalytic domain.

104 The dynamic behavior of the dsRBD bound to a longer AGAA hairpin reveals that dynami

105 We have characterized the function of the dsRBD by assessing the binding of dsRBM1 and dsRBD to a

106 for HI0257 may be distinct from that of the dsRBD family of proteins.

107 ond-to-millisecond timescale dynamics of the dsRBD suggests that helix alpha1 undergoes conformationa

108 oscopy was used to define the regions of the dsRBD that interact with dsRNA.

109 n that is mediated by the interaction of the dsRBD with the kinase.

110 domain (i) can function independently of the dsRBD, (ii) is dsRNA-specific, and (iii) participates in

111 Structural comparisons of the dsRBD-dsRNA complex and models proposed for polynucleoti

112 Here, we report the structure of the dsRBD-NLS, which reveals an unusual dsRBD fold extended

113 een the first and second beta-strands of the dsRBD.

114 ral model showing how Trn1 can recognize the dsRBD-NLS and how dsRNA binding can interfere with Trn1

115 wn whether the catalytic domain requires the dsRBD for activity.

116 n are non-equivalent; regions other than the dsRBD stem-loops of inhibitory RNA are required for inhi

117 l and biochemical analyses indicate that the dsRBD and N-terminal domains (NTDs) of Rnt1p function as

118 We find that the dsRBD of ILF3 functions as a novel nuclear export sequen

119 alpha1-beta1 hinge result in changes to the dsRBD stability and RNA-binding affinity and cause defec

120 t its major groove expands to conform to the dsRBD's binding surface.

121 As of cellular and viral origins bind to the dsRBD, leading to either activation or inhibition of PKR

122 The dsRBDs also mediate ribosome association and we proposed

123 The binding sites on inhibitor RNAs and the dsRBDs of PKR have been mapped by NMR chemical shift per

124 r entire N-terminal sequences, including the dsRBDs.

125 The specific organization of the dsRBDs near the apical junction is independent of Drosha

126 coincide with the RNA-binding surface of the dsRBDs.

127 Pre-miRNA cleavage shifts the dsRBDs and partially closes Dicer-1, which may promote p

128 nction of double-stranded RNA binding to the dsRBDs of native PKR is to promote dimerization and acti

129 We report that these dsRBD homodimers display structural asymmetry and that t

130 e essential for diffusion, whereas the third dsRBD is dispensable.

131 This dsRBD-NLS is recognized by the nuclear import receptor t

132 A binding protein (TRBP) consisting of three dsRBDs, which functions in HIV replication, protein kina

133 Two dsRBDs form a molecular ruler to measure the stem length

134 The first two dsRBDs of TRBP are essential for diffusion, whereas the

135 from the flexible linker connecting the two dsRBDs in the antiviral response protein, PKR.

136 ructure of the linker region between the two dsRBDs that differs from the flexible linker connecting

137 the interfacial interactions between the two dsRBDs, we ran extensive MD simulations of isolated dsRB

138 flexible linker domain that connects the two dsRBDs.

139 Binding of dsRNA to two dsRBDs (double-stranded RNA binding domains) of PKR modu

140 loops, have an effect on the binding to two dsRBDs of PKR still remains unclear.

141 e of the dsRBD-NLS, which reveals an unusual dsRBD fold extended by an additional N-terminal alpha-he

142 d by molecular-dynamics simulations in which dsRBD-dsRNA interactions generate only modest bending of

143 While dsRBD binding is understood, little is known about ADAR

144 Importantly, the Kap interacts with dsRBDs found in several other proteins and binding is bl