ライフサイエンスコーパス: IDP

1 IDP consistently demonstrated the spatiotemporal co-exis

2 IDP-fusion is the first method to study gene fusion even

3 IDPs appear to have functional roles that diverge from t

4 IDPs can acquire tertiary structure when bound to their

5 IDPs do not adopt a single dominant structure in isolati

6 IDPs play important roles in a range of biological funct

7 IDPs, while structurally poor, are functionally rich by

8 h was tested using the experimental Rh of 22 IDPs covering a wide range of peptide lengths, net charg

9 by a confined chiral imidodiphosphoric acid (IDP).

10 ture and crowding agents consequently affect IDPs more than their folded counterparts.

11 Binding promiscuity and plasticity allow IDPs to interact with multiple partners in protein inter

12 f known IDP complexes reveals that, although IDP binding sites tend to be more hydrophobic compared t

13 xes (RNCs) of alpha-synuclein (alphaSyn), an IDP associated with Parkinson's disease (PD).

14 rRNase domain causes the enzyme to become an IDP (E3 rRNase(IDP)).

15 n insight into how a small molecule binds an IDP and emphasize the need to examine motions on the low

16 Overall, this study shows how an IDP can achieve very strong and structurally well-define

17 If an IDP could somehow be divided into smaller fragments and

18 e data lead to the hypothesis that FRQ is an IDP and that FRH acts nonenzymatically, stabilizing FRQ

19 PUMA, of the BCL-2 family, is an IDP in isolation but will form a single, contiguous alph

20 Prostate-Associated Gene 4 (PAGE4) is an IDP that acts as a potentiator of the Activator Protein-

21 ic and structural study of the binding of an IDP (antitoxin CcdA) to its molecular target (gyrase poi

22 The phase behavior of an IDP is sensitive to its amino acid sequence.

23 ring the biophysical binding mechanism of an IDP to a structured protein, whereby a local segment of

24 such modifications affect the binding of an IDP to its partner protein?

25 el system where the 'BH3 region' of PUMA, an IDP, forms a single, contiguous alpha-helix upon binding

26 Here, we show a mechanism by which an IDP can allosterically control function by simultaneousl

27 e, that inhibit the consumption of DMADP and IDP by prenyltransferases to gain insight into the exten

28 ostulated, but the extent to which DMADP and IDP can build up is not known.

29 courage comprehensive discussion of IDPs and IDP regions in biochemistry textbooks.

30 Intrinsically disordered proteins (IDPs) and IDP regions fail to form a stable structure, yet they ex

31 consist of phosphorylated intermediates and IDP.

32 for the dimensions of unfolded proteins and IDPs in the absence of chemical denaturants.

33 We applied IDP-fusion to PacBio data and Illumina data from the MCF

34 ed an innovative hybrid sequencing approach, IDP-fusion, to detect fusion genes, determine fusion sit

35 interpret the phase behaviour of archetypal IDP sequences and demonstrate the rational design of a v

36 ribe the dynamic behavior of this archetypal IDP.

37 kers from three bacterial species behaved as IDPs in vitro by circular dichroism and trypsin proteoly

38 protein families experimentally confirmed as IDPs.

39 hasis on inherently flexible systems such as IDPs.

40 (IDI) catalyzes the interconversion between IDP and DMADP.

41 ing its role in optimizing the ratio between IDP and DMADP as precursors for different downstream iso

42 conformational landscape of membrane-binding IDPs with multiple binding modes.

43 The direct association of both IDP-like organic matter with dominant C-O bonding enviro

44 The folded structure of the bound IDP appears to be defined largely by its own amino acid

45 e-dependent enzymes may often be affected by IDP and DMADP.

46 nge of physicochemical properties encoded by IDP sequences.

47 PtDXS was inhibited by IDP and DMADP.

48 The feedback inhibition of PtDXS by IDP and DMADP constitutes an important mechanism of meta

49 However, in some cases, IDPs such as the ones involved in neurodegenerative dise

50 s particularly helpful for repeat-containing IDPs and low-complexity regions.

51 assignment of challenging, repeat-containing IDPs.

52 We define IDPs as proteins that are disordered along their entire

53 discrimination among qualitatively different IDP ensembles for the amyloid-beta peptide.

54 o gas-phase transfer of a range of different IDPs.

55 In plants, different IDPs involved in stress response have been identified an

56 the biosynthesis of isopentenyl diphosphate (IDP) and dimethylallyl diphosphate (DMADP), the precurso

57 5C building blocks isopentenyl diphosphate (IDP) and its isomer dimethylallyl diphosphate (DMADP).

58 osphate (DMADP) and isopentenyl diphosphate (IDP) was postulated, but the extent to which DMADP and I

59 in that promotes duplex formation of diverse IDP partners.

60 We show that FG repeats are highly dynamic IDPs, stabilized by the cellular environment.

61 The enzyme IDP isomerase (IDI) catalyzes the interconversion betwee

62 ure to a variety of IDPs and found that even IDPs with low net charge and high hydrophobicity remain

63 Finally, we propose future directions for IDP research.

64 This results in improved efficiency for IDP analysis and binding studies.

65 We present design rules for IDPs possessing SLCs that phase separate into diverse as

66 inferences based on RG and RE , whereas for IDPs under native conditions, we find substantial deviat

67 Amyloid-forming IDPs, unlike natively folded proteins, have folding traj

68 ch for the unbiased study of amyloid-forming IDPs.

69 FRAGFOLD-IDP enables better insight into backbone dynamics in IDP

70 FRAGFOLD-IDP produces very good predictions for 33.5% of cases an

71 e, we present a new de novo method, FRAGFOLD-IDP, which addresses this problem.

72 bles derived from NMR, we show that FRAGFOLD-IDP achieves superior results compared to methods which

73 of the inner part is similar to spectra from IDP organic grains and less aromatic with nitrogen below

74 Furthermore, IDPs/IDPRs are everywhere, and are ubiquitously engaged

75 e primary error for ranking or creating good IDP ensembles resides in the poor back-calculation from

76 scale relationships that encode hierarchical IDP assemblies, (2) design rules of such assemblies in c

77 How IDPs overcome such potential kinetic bottlenecks to viab

78 Thus, it is not clear how IDPs, lacking such well-defined structures, can alloster

79 1) (p27) as a model system to understand how IDPs might achieve efficient folding upon encounter for

80 We investigated the human IDP tau, which is involved in the pathogenic processes a

81 Length, however, was important: IDPs shorter than 43 or longer than 95 aa had compromise

82 key functional features to be identified in IDP structural ensembles.

83 les better insight into backbone dynamics in IDPs and opens exciting possibilities for the design of

84 secondary interactomes are also enriched in IDPs, most being cancer related, revealing that PTEN fun

85 However, how mutations in IDPs elicit diseases, remain elusive.

86 of experimental measurement of relaxation in IDPs, the physical origin of the measured relaxation rat

87 the same protein, may provide insights into IDP aggregation-a process that plays a role in several n

88 us analysis of charge distributions in known IDP complexes, our results support a prevalent role of e

89 is of charge distributions in a set of known IDP complexes reveals that, although IDP binding sites t

90 One of the most well-known IDPs is the microtubule-associated tau protein, which re

91 ly modified IDPs for studies of PTM-mediated IDP regulatory mechanisms.

92 ere we present a novel computational method, IDP-LZerD, which models the conformation of a disordered

93 Here, we investigate the model IDPs alpha-Synuclein (alphaS) and tau, that are involved

94 Here we describe an approach for modeling IDPs with similar sequences that simplifies the comparis

95 t tools for generating homogenously modified IDPs for studies of PTM-mediated IDP regulatory mechanis

96 Most IDPs are polyampholytes, with sequences that include bot

97 The protein NUPR1 is a multifunctional IDP involved in chromatin remodeling and in the developm

98 der functional networks operate via multiple IDP-IDP interactions facilitated by its C-tail IDR.

99 dly webserver that enables rapid analysis of IDP sequences.

100 to methodology development, applications of IDP-ASE to human embryonic stem cells and breast cancer

101 d structure was used to model the binding of IDP and DMADP and indicated that IDP and DMADP might bin

102 simulations for detailed characterization of IDP conformations, and at the same time reveals importan

103 s for deciphering the sequence dependence of IDP phase separation are discussed.

104 nter topologies to enhance the efficiency of IDP folding upon encounter.

105 ggest that there is likely a co-evolution of IDP folded topology, charge characteristics, and coupled

106 lso reveal a greater motional flexibility of IDP compared with globular, folded proteins and more res

107 ly valuable in elucidating these pathways of IDP folding.

108 amine N-oxide (TMAO) shift the population of IDP monomer structures, but that no new conformational e

109 aracterization and functional annotations of IDPs/IDRs, and is intended to provide an invaluable reso

110 ciently lead to chemical shift assignment of IDPs, motivated by a case study of the C-terminal disord

111 implications for the biological behavior of IDPs in light of the evidence that a large fraction of t

112 inetic data suggest that specific binding of IDPs is generally no slower than that of globular protei

113 ter understanding of the modes of binding of IDPs, we combined statistical mechanics, calorimetry, an

114 here shown to share many characteristics of IDPs.

115 static forces exerted on enriched charges of IDPs could accelerate protein-protein encounter via "ele

116 We observe a compaction of IDPs not only with increasing concentration, but also wi

117 eveal that the residual structure content of IDPs is modulated both by ionic strength and by the type

118 indicate that the hydrodynamic dimensions of IDPs are evidence of considerable sequence-dependent bac

119 e will encourage comprehensive discussion of IDPs and IDP regions in biochemistry textbooks.

120 ual structure and conformational dynamics of IDPs are crucial for the mechanisms underlying their fun

121 information on the structure and dynamics of IDPs, but the fidelity to which these methods reflect th

122 The conformational ensembles of IDPs are encoded by their amino acid sequences.

123 olds information on more than 800 entries of IDPs/IDRs, i.e. intrinsically disordered proteins or reg

124 ins (HRGPs), have characteristic features of IDPs.

125 Owing to the inherent flexibility of IDPs, solution techniques are particularly appropriate f

126 nderstanding of the behavior and function of IDPs, adding a new and essential dimension to the descri

127 ence-ensemble relationships and functions of IDPs.

128 summarize the evidence for the importance of IDPs in plant biology and evaluate the functions associa

129 peptide folding in specific interactions of IDPs could impose a kinetic bottleneck, which could be o

130 We describe the diverse interactions of IDPs that can have unusual characteristics such as "ultr

131 sequence of the multipartner interactions of IDPs.

132 r facile binding and folding interactions of IDPs.

133 s and solvent quality (self-interactions) of IDPs from a single small-angle x-ray scattering measurem

134 are consistent with previous observation of IDPs under the influence of synthetic polymers.

135 the coupled folding and binding processes of IDPs.

136 elated dynamics are an intrinsic property of IDPs and offers a general physical mechanism of correlat

137 ions for describing the binding reactions of IDPs.

138 can be modified to optimize the recovery of IDPs from other organisms.

139 he structure, interaction, and regulation of IDPs in general.

140 al modifications in functional regulation of IDPs, molecular mechanisms behind the observed behaviors

141 sses that are dependent on PTM regulation of IDPs.

142 ffect the structure-function relationship of IDPs is a formidable task that requires detailed charact

143 physiological implications given the role of IDPs in signaling, the asymmetric ion profiles of differ

144 map the backbone conformational sampling of IDPs on a residue specific level.

145 his sensitivity to the marginal stability of IDPs, which could have physiological implications given

146 tially ordered regions in the bound state of IDPs.

147 The dynamical and fluctuating structures of IDPs or of disordered regions within proteins result in

148 all, our approach for comparative studies of IDPs with similar sequences provides a platform for futu

149 However, general study of IDPs by NMR spectroscopy is limited by the poor (1)H ami

150 The study of IDPs is a rapidly growing area as the crucial biological

151 gnized as enabling broad structural study of IDPs.

152 ning the diverse conformational substates of IDPs in their free states, in encounter complexes of bou

153 ion of the solution to gas-phase transfer of IDPs and provide a roadmap for future investigations int

154 Tuning of IDPs and IDPRs are mediated through post-translational m

155 We applied this procedure to a variety of IDPs and found that even IDPs with low net charge and hi

156 well as post-translational modifications on IDP structure and interaction.

157 y, there has been an explosion of studies on IDP regions and their functions, yet the discovery and i

158 en extensively studied, experimental data on IDPs at the air/water (A/W) and water/lipid interfaces a

159 enriched with charges to complement those on IDPs.

160 y important in explaining signaling in other IDPs.

161 As with many other IDPs, KID undergoes coupled folding and binding to form

162 lpha-synuclein as well as a variety of other IDPs undergoes slow reorientations at time scales compar

163 o our knowledge) approach for studying other IDPs.

164 Overall, IDP-associated biological activities complement those of

165 rites and two interplanetary dust particles (IDPs) originating from comets.

166 t to be an intrinsically disordered peptide (IDP).

167 Plant IDPs play critical roles in plant biology and often act

168 we propose various modes of action for plant IDPs that may provide insight for future experimental ap

169 In plants, IDP is synthesized in the cytoplasm from mevalonic acid

170 In plants, IDPs are implicated in plant stress responses, signaling

171 conformational preferences of polyampholytic IDPs, and this ability could become a useful tool for en

172 nce-ensemble relationships of polyampholytic IDPs.

173 sing the integrative disease predictability (IDP) criterion: if TC-BC association is part of the dise

174 The ability to predict and program IDP-rich assemblies in this fashion offers new insights

175 ments of the histone proteins, are prominent IDPs that are implicated in a variety of signaling proce

176 PTEN as an intrinsically disordered protein (IDP) and elucidated the molecular principles by which it

177 Intrinsically disordered protein (IDP) conformers occupy large regions of conformational s

178 cine rich, intrinsically disordered protein (IDP) domain of LAF-1 is necessary and sufficient for bot

179 Intrinsically disordered protein (IDP) duplexes composed of two IDP chains cross-linked by

180 The intrinsically disordered protein (IDP), alpha-synuclein (alphaS), is well-known for phosph

181 ein and an intrinsically disordered protein (IDP), are prevalent in the cell, including important sig

182 become an intrinsically disordered protein (IDP).

183 ily, is an intrinsically disordered protein (IDP).

184 otions in intrinsically disordered proteins (IDP), a largely unexplored class of proteins that, in co

185 Intrinsically disordaered proteins (IDPs) are a prevalent phenomenon with over 30% of human

186 cognized as intrinsically disorder proteins (IDPs) or partially disordered segments known as intrinsi

187 proteins, intrinsically disordered proteins (IDPs) and catalytic residues.

188 These intrinsically disordered proteins (IDPs) and hybrid proteins containing ordered and intrins

189 Intrinsically disordered proteins (IDPs) and IDP regions fail to form a stable structure, y

190 embles of intrinsically disordered proteins (IDPs) and of denatured proteins based on nuclear magneti

191 Many intrinsically disordered proteins (IDPs) and protein regions (IDRs) engage in transient, ye

192 ce of the intrinsically disordered proteins (IDPs) and regions (IDRs) in the human proteome together

193 roles of intrinsically disordered proteins (IDPs) and regions (IDRs), which represent approximately

194 Intrinsically disordered proteins (IDPs) are a set of proteins that lack a definite seconda

195 Intrinsically disordered proteins (IDPs) are a unique class of proteins that have no stable

196 Intrinsically disordered proteins (IDPs) are characterized by a lack of defined structure.

197 Intrinsically disordered proteins (IDPs) are characterized by a lack of persistent structur

198 Intrinsically disordered proteins (IDPs) are frequently associated with human diseases such

199 Intrinsically disordered proteins (IDPs) are functional proteins that lack a well-defined t

200 ctions of intrinsically disordered proteins (IDPs) are governed by relationships between information

201 Intrinsically disordered proteins (IDPs) are highly abundant in eukaryotic proteomes.

202 Intrinsically disordered proteins (IDPs) are important for health and disease, yet their la

203 Intrinsically disordered proteins (IDPs) are increasingly recognized for their important ro

204 Intrinsically disordered proteins (IDPs) are involved in a wide range of regulatory process

205 Intrinsically disordered proteins (IDPs) are involved in a wide variety of physiological an

206 Intrinsically disordered proteins (IDPs) are known to undergo a range of posttranslational

207 Intrinsically disordered proteins (IDPs) are now recognized to be prevalent in biology, and

208 Intrinsically disordered proteins (IDPs) are proteins that lack a unique three-dimensional

209 Intrinsically disordered proteins (IDPs) are proteins that lack secondary and/or tertiary s

210 Many intrinsically disordered proteins (IDPs) are significantly unstructured under physiological

211 Intrinsically disordered proteins (IDPs) are ubiquitous in eukaryotes, and they are often a

212 Intrinsically disordered proteins (IDPs) are widespread and important in biology but defy t

213 erties of intrinsically disordered proteins (IDPs) by affecting their energy landscapes.

214 study of intrinsically disordered proteins (IDPs) by NMR often suffers from highly overlapped resona

215 of these intrinsically disordered proteins (IDPs) can, upon binding another molecule, fold to a well

216 separated intrinsically disordered proteins (IDPs) composed of sequences of low complexity (SLC) have

217 Intrinsically disordered proteins (IDPs) containing phenylalanyl-glycyl (FG)-rich repeats l

218 ampled by intrinsically disordered proteins (IDPs) define their function.

219 ctures of intrinsically disordered proteins (IDPs) due to their role in various biological processes

220 havior in intrinsically disordered proteins (IDPs) has not been established.

221 Intrinsically disordered proteins (IDPs) have roles in myriad biological processes and nume

222 e (HX) of intrinsically disordered proteins (IDPs) in solutions containing high concentrations of mac

223 ration of intrinsically disordered proteins (IDPs) is a major undergirding factor in the regulated fo

224 zation of intrinsically disordered proteins (IDPs) is challenging, in part because of a lack of accur

225 zation of intrinsically disordered proteins (IDPs) is complicated by their conformational heterogenei

226 inding of intrinsically disordered proteins (IDPs) is prevalent in biology.

227 Intrinsically disordered proteins (IDPs) lack stable secondary and tertiary structure under

228 rature on intrinsically disordered proteins (IDPs) led scientists to rethink the structure-function p

229 ration of intrinsically disordered proteins (IDPs) or regions (IDRs).

230 Intrinsically disordered proteins (IDPs) perform their physiological role without possessin

231 emblage." Intrinsically disordered proteins (IDPs) play an important role in forming a subset of cell

232 Intrinsically disordered proteins (IDPs) play central roles in many biological processes.

233 states of intrinsically disordered proteins (IDPs) populate heterogeneous conformational ensembles in

234 Intrinsically disordered proteins (IDPs) present a functional paradox because they lack sta

235 hich such intrinsically disordered proteins (IDPs) recognize their targets are not well understood.

236 ntial for intrinsically disordered proteins (IDPs) that are involved in cellular signaling and regula

237 Intrinsically disordered proteins (IDPs) that lack a unique 3D structure and comprise a lar

238 tures for intrinsically disordered proteins (IDPs) that takes full advantage of NMR chemical shifts a

239 risons of intrinsically disordered proteins (IDPs) with similar sequences, such as mutant forms of th

240 s, termed intrinsically disordered proteins (IDPs), demonstrates that flexibility in structure can be

241 s such as intrinsically disordered proteins (IDPs), globular proteins in the unfolded basin and durin

242 s than on intrinsically disordered proteins (IDPs), peptides, and liposomes.

243 lexity or intrinsically disordered proteins (IDPs).

244 e case of intrinsically disordered proteins (IDPs).

245 embles of intrinsically disordered proteins (IDPs).

246 erties of intrinsically disordered proteins (IDPs); however, the characterization of these states rem

247 t the D2 domain of p27(Kip1), a prototypical IDP, samples multiple discrete, rapidly exchanging confo

248 feasible for alpha-synuclein, a prototypical IDP.

249 We then apply the EISD method to rank IDP ensembles most consistent with the NMR data and show

250 el engineering of self-assembled recombinant IDP-rich materials.

251 trinsically disordered proteins and regions (IDPs) represent a large class of proteins that are defin

252 trinsically disordered proteins and regions (IDPs/IDRs) that do not adopt a dominant well-folded stru

253 Intrinsically disordered proteins/regions (IDPs/IDRs) are proteins or peptide segments that fail to

254 e interaction and subsequently the remaining IDP regions explore and coalesce around the initial bind

255 E3 rRNase(IDP) binds stoichiometrically to Im3 and forms a structu

256 However, binding of E3 rRNase(IDP) to Im3 is 4 orders of magnitude weaker than that of

257 auses the enzyme to become an IDP (E3 rRNase(IDP)).

258 eady-state kinetic analysis of the E3 rRNase(IDP)-Im3 complex demonstrates that the decrease in affin

259 spite their simplified amino acid sequences, IDPs/IDPRs are complex entities often resembling chaotic

260 requirement of protein folding for specific IDP recognition could lead to kinetic bottlenecks.

261 These findings reveal how specific IDPs can phase separate to form permeable, low-density (

262 mputational methods are widely used to study IDPs, however, nearly all treat disorder in a binary fas

263 recently studied and became a model to study IDPs.

264 iscusses biophysical approaches for studying IDPs and illuminates their importance to critical functi

265 dynein intermediate chain (N-IC) is one such IDP that forms a bivalent scaffold with multiple dynein

266 We investigate this question using one such IDP, the kinase inducible domain (KID) of the transcript

267 binding of IDP and DMADP and indicated that IDP and DMADP might bind with the enzyme in a manner ver

268 The results show that IDP-fusion will be useful for unraveling the complexity

269 We show that IDPs undergo a vast conformational space expansion in th

270 e characteristics, it is not surprising that IDPs serve as important hubs in signaling networks, scaf

271 The IDP analyzed the same images at a predetermined and fixe

272 The IDP has high sensitivity and specificity to detect RDR.

273 The IDP sensitivity was 96.8% (95% CI, 94.4%-99.3%) and spec

274 aisy chain connections to be built along the IDP backbone, facilitated by acquisition of amino acid-s

275 gth of TC-BC association was measured by the IDP coefficients and incidence prediction accuracy.

276 , we directly measured slow kinetics for the IDP domains ( approximately 1 s(-1) at 277 K) related to

277 Organic matter in the IDP samples is less aromatic than that in the CR chondri

278 onally generated structural ensembles of the IDP amyloid-beta42 (Abeta42) to an alternative sequence

279 ll division, suggesting that sequence of the IDP did not matter.

280 ured protein, whereby a local segment of the IDP initiates the interaction and subsequently the remai

281 nd, determine the hydrodynamic radius of the IDP, and thus the distance over which the protein can ca

282 ins and more restricted water motions on the IDP surface.

283 While the need to represent the IDP structures is clear, methods for determining and eva

284 elaxation measurements we here show that the IDP alpha-synuclein as well as a variety of other IDPs u

285 tatively if the polymeric nature of both the IDPs and the crowding molecules is taken into account ex

286 lly heterogeneous, unbound ensemble of these IDPs, conformations are likely to exist that, in part, r

287 ectrostatic forces in the formation of three IDP complexes with more complex folded topologies.

288 enables a wide range of analyses relevant to IDP sequences.

289 This approach is applicable to IDPs of varying sizes and complexity, and is particularl

290 nance energy transfer experiments applied to IDPs.

291 d that small molecules bind promiscuously to IDPs, causing expansion of their conformational landscap

292 We developed a tool, IDP-ASE, for full ASE analysis.

293 Compared with the existing tools, IDP-fusion detects fusion genes at higher precision and

294 dered protein (IDP) duplexes composed of two IDP chains cross-linked by bivalent partner proteins for

295 om other bacteria, and even for an unrelated IDP from human alpha-adducin.

296 rom hepatitis C virus (HCV), a typical viral IDP with multiple functions during the viral life cycle.

297 thesis to rationalize the mechanism by which IDP structure and aggregation is regulated in the cell.

298 provide insight into the mechanism by which IDP-driven molecular interactions give rise to liquid ph

299 l early examples and the mechanisms by which IDPs contribute to function, which we hope will encourag

300 On a dataset of 22 disordered PPIs with IDPs up to 69 amino acids, successful predictions were m

301 als new elements of dynamic structure within IDP linker regions.

302 Short interaction-prone segments within IDPs, termed molecular recognition features, represent p