ライフサイエンスコーパス: protein domain

1 ated protein FeoB, which has an N-terminal G-protein domain.

2 Phenotypic severity varies by protein domain.

3 nsation domain to recognize the acyl carrier protein domain.

4 adation tag through the light-sensitive LOV2 protein domain.

5 dation occur, they affect the unfolding of a protein domain.

6 leavage activities that are dominated by one protein domain.

7 s on expansion and contraction of the entire protein domain.

8 chain fatty acids and a CD36-binding PfEMP1 protein domain.

9 hotspot regions, rather than a whole gene or protein domain.

10 g that the phosphoinositide destabilizes the protein domain.

11 haracterized 'enhancer of microexons' (eMIC) protein domain.

12 Ras C terminus for lipid anchoring and its G-protein domain.

13 ncies are suggested for individual tricalbin protein domains.

14 egions and 0.91 using sub-regions defined by protein domains.

15 otide, amino acid, amino acid properties and protein domains.

16 traint and suggest unannotated or incomplete protein domains.

17 on when fusing it to specifically localising protein domains.

18 ences and sites located within cysteine-rich protein domains.

19 power strokes are sufficient to unfold some protein domains.

20 inases that phosphorylate residues in folded protein domains.

21 the level of single evolutionary families of protein domains.

22 RMs) in the absence of other clearly defined protein domains.

23 scalable strategy for assigning functions to protein domains.

24 ctor and separation of the N- and C-terminal protein domains.

25 Data Bank (PDB) into evolutionary groups of protein domains.

26 classifications for over 100 000 additional protein domains.

27 tutive exons and exons that encode conserved protein domains.

28 rvature-generating activity present in other protein domains.

29 e presence and coordination between multiple protein domains.

30 ral elements, or linkers that connect entire protein domains.

31 ional imaged proteins when studying membrane protein domains.

32 sibly control binding between two engineered protein domains.

33 intra and intermolecular distance changes of protein domains.

34 extracting k-mer compositions and predicted protein domains.

35 that drive methylation-state recognition by protein domains.

36 ors include only query sequences with single protein domains.

37 naptotagmin-like mitochondrial-lipid binding protein) domain.

38 rular endothelium via its complement control protein domains 19 and 20, which also recognize heparan

39 and recombinant human FH complement control proteins domains 19 and 20 (FH19-20) binding to mouse gl

40 All mutations affect complement control protein domains 2 through 7, and thus are predicted to i

41 not only essential genes, but also essential protein domains, (4) generates both null and other infor

42 experiments have revealed the importance of protein domains 403-596 and 349-402 for synaptic suppres

43 ith deletion/mutation constructs reveal that protein domains 598-854 and 349-402 are both required fo

44 sh retrotranslocation of a misfolded luminal protein domain across a lipid bilayer, we have reconstit

45 , visualize and analyze mutation hotspots in protein domains across genes and tumor types.

46 Mining of protein domains across the genome, followed by phylogene

47 and displays those, along with the matching protein domains affected by the LSV, on UCSC Genome Brow

48 surface potential distributions within each protein domain against their relative contribution to bi

49 M (4.1, ezrin-, radixin-, and moesin-related protein) domain, also known as the talin head domain, an

50 Protein domain analysis enhances the statistical power t

51 ased homology search has been widely used in protein domain analysis in many different species.

52 ff supplements a comprehensive collection of protein domain and protein family models, which have bee

53 phosphorylation of the N-terminal thylakoid protein domains and changes in electrostatic forces indu

54 Hinge-bending regions demarcate protein domains and collectively control the domain move

55 esence or absence of clusters of orthologous protein domains and constructed a dendrogram based on th

56 cription strategies, and the conservation of protein domains and functions among the viruses.

57 ntified mutations were enriched in essential protein domains and genes identified by NIPPER were asso

58 or that has no homology to any characterized protein domains and is posttranscriptionally up-regulate

59 quitin transfer to be specific to particular protein domains and lysine residues.

60 ation and acetylation sites, suggesting that protein domains and post-translational modification site

61 isms described here are based on widely used protein domains and post-translational modifications; th

62 thod by predicting the folds of 34,330 human protein domains and showing that these predictions can y

63 ntrinsically disordered regions that connect protein domains and structural elements within domains a

64 The alignment between the boundaries of protein domains and the boundaries of exons could provid

65 ns that connect regions of nucleic acids and protein domains and through the assembly of biomolecular

66 we present MetaGeneHunt to identify specific protein domains and to normalize the hit-counts based on

67 ween the binding affinity of two interacting protein domains and transcriptional activation of a fluo

68 sis revealed common pathways, gene ontology, protein domains, and cell type-specific expression.

69 ation sites, signal peptides, trans-membrane protein domains, and phosphorylation sites.

70 ene expression and its regulation, proteins, protein domains, and protein-protein interactions.

71 e still not annotated lack orthologues, lack protein domains, and/ or are membrane proteins.

72 From an abstract, informational perspective, protein domains appear analogous to words in natural lan

73 ationships between homologous proteins, (ii) protein domain architecture and (iii) gene neighborhoods

74 tterns with respect to in-silico analyses of protein domain architectures that revealed a diverse arr

75 These protein domains are considered to function by targeting

76 Specific protein domains are enriched in DEEPEST calls, indicatin

77 Seven universal protein domains are preferentially included among the sp

78 Protein domains are subunits that can fold and function

79 Protein domain arrays and pull-down assays identified ac

80 pute the folding properties of various large protein domains as a function of nascent chain length.

81 In this study, we used natural protein domains as modular building blocks to develop en

82 ng affinities of dozens of human RNA binding protein domains as reported in the CISBP-RNA database we

83 rare variation collapsing on homology-based protein domains as the unit for collapsing, and the othe

84 Additionally, knockoff can be applied to protein domains as we show for another synaptic vesicle

85 Such rules exist for protein domains as well, because only a small fraction o

86 lla luciferase and monomeric red fluorescent protein domains, as well as a truncated form of herpes s

87 cotina gene repertoires, affecting all known protein domains, as well as symbiosis-related orphan gen

88 tifs associate with specific sites on folded protein domains at the level of individual amino acids.

89 stingly we revealed that a hyperglucosylated protein domain, based on the cell-surface adhesin HMW1A,

90 the accuracy of predicting pairs of related protein domains beyond simpler correlation-based approac

91 interdependent functional roles of specific protein domains, beyond our current functional annotatio

92 size that about 14% of currently known human protein domains bind proteins.

93 spCN, a CFH-binding Streptococcus pneumoniae protein domain, binds CFH tightly and increases accessib

94 oped a new algorithm, FUpred, which predicts protein domain boundaries utilizing contact maps created

95 filtered fusions, visualize breakpoints and protein domains by transcript, and plot recurrent fusion

96 the recovery of phylogenetically-informative protein domains can be up to 55%.

97 in-based nanoparticles that display multiple protein domains can exhibit enhanced functional properti

98 s, which can display a variety of functional protein domains (cargo) at defined positions around its

99 s occur within rather than between conserved protein domains, challenging the view that their primary

100 aracterization of two interacting disordered protein domains, CID and NCBD.

101 g sequence clustering, network analysis, and protein domain classification.

102 00 000 domain structures and over 53 million protein domains classified into 2737 homologous superfam

103 t for gene fusions that preserve protein and protein domain coding potential.

104 Interacting proteins and protein domains coevolve on multiple scales, from their

105 41 in vivo interactomes and determined their protein domain composition, correlation to gene expressi

106 NHR4 domains can be replaced by heterologous protein domains conferring tetramerization and repressor

107 d evolution, we document changes in gene and protein domain content and provide temporal and phylogen

108 ttern, sequence conservation, transcription, protein domain content, and gene network properties.

109 We mapped the protein domains crucial for the Nxf2/Panx complex format

110 neages in the Evolutionary Classification of Protein Domains database.

111 ession profiles, GeneRIF, pathway databases, protein domain databases and other organism-specific res

112 nge spectroscopy on two autonomously folding protein domains derived from the ribosomal protein, L9.

113 y Aq1 of peptides from the repetitive gluten protein domains during baking.

114 Evolutionary Classification Of protein Domains (ECOD) comprehensively classifies protei

115 ated into our Evolutionary Classification of protein Domains (ECOD) database.

116 ,016 domains [Evolutionary Classification of Protein Domains (ECOD) database] or 20,398 chains [Prote

117 e, namely the Evolutionary Classification of Protein Domains (ECOD) that led to the creation of 825 n

118 this variation intolerance is driven by the protein domains encoding the epigenetic function, sugges

119 spliced exons that preferentially alter key protein domains-especially in cytoskeletal proteins-and

120 s arthropods and examples of gene family and protein domain evolution coincident with the appearance

121 CCRs highlight protein domain families under high constraint and sugges

122 chical classifications of widely distributed protein domain families, and to record conserved sites a

123 hat this highly duplicated and underexamined protein domain family plays an important role in inherit

124 te that macrodomains, an ancient and diverse protein domain family, are key players in the recognitio

125 ith the location of evolutionarily conserved protein domain footprints, and functional sites inferred

126 y constructing hybrid Ccm systems containing protein domains from both E. coli and S. oneidensis MR-1

127 ranslation-elongation rates, can switch some protein domains from folding post-translationally to fol

128 RUNX1/ETO through modular recomposition with protein domains from RUNX1, ETO, BCR and N-CoR without a

129 We show related protein domains from Salmonella enterica and Escherichia

130 cilitate de novo identification of essential protein domains from such screens, we propose ProTiler,

131 ple events by systematically dissecting LKB1 protein domain function in combination with live cell im

132 ng-sgRNA design permit in situ evaluation of protein domain function.

133 ven larger than previously thought, and that protein domain gains and losses are prevalent.

134 y, regions of individual mRNAs that code for protein domains generally have higher reactivity to DMS

135 opensity of an interaction between a pair of protein domains, given their structural classification o

136 hitlists), enhanced reference lists, and new protein domain graphics.

137 3-dimensional model of FGFR1 to assess which protein domains harbored the highest number of pathogeni

138 These electrophiles are reacted with a protein domain harboring three solvent-exposed cysteine

139 but recognition of specific motifs within a protein domain have never been reported.

140 le specific heterodimerization between small protein domains have a wide scope of applications, from

141 le and the dynamic nature of small lipid and protein domains have made characterization of such organ

142 variants in IFIH1 and TYK2 disrupt conserved protein domains, highlighting potential mechanisms throu

143 topes near the hinge region between envelope protein domain I (EDI) and EDII.

144 gnition determinants of these bNAbs are in E protein domain I, distinct from the only known class of

145 In contrast, antibodies against E protein domain I/II (EDI/II) were cross-reactive and, al

146 ons, we studied recall responses to envelope protein domain III (DIII).

147 s constructed to display ten dengue envelope protein domain III (ED3)-targeting aptamers into a two-d

148 have previously reported that ZIKV envelope protein domain III (EDIII) is a subunit vaccine candidat

149 vaccine components, a dengue virus Envelope protein Domain III (EDIII) subunit antigen and two adjuv

150 ied an epitope on Zika virus (ZIKV) envelope protein domain III (EDIII) that is buried in the full-le

151 The dengue envelop protein domain III (EDIII), which is capable of elicitin

152 ore antigen (HBcAg) that displays the ZIKV E protein domain III (zDIII), and shown that it can be pro

153 and inferred-germline Ab binding to envelope protein domain III of ZIKV and other flaviviruses.

154 3-23/VK1-5 neutralizing Abs to ZIKV envelope protein domain III, and identify interacting residues th

155 116 recognizes the lateral ridge of envelope protein domain III, with one critical residue varying be

156 2 zinc finger (C2H2-ZF) is the most numerous protein domain in many metazoans, but is not as frequent

157 )investigate the precise distribution of any protein domain in short-reads metagenomes.

158 and discuss the evolution of copper-only SOD protein domains in animals and fungi.

159 test and improve the mechanical integrity of protein domains in general.

160 has been extensively investigated in several protein domains in isolation.

161 y to quickly and precisely identify discrete protein domains in sequenced metagenomes processed with

162 is still unknown how the association between protein domains in supramodules, consitituting so-called

163 tations that disrupt either of the conserved protein domains in TBC1D24 are implicated in neuronal de

164 consisting of 1426 proteins and tested on 84 protein domains in the CASP12 dataset, our single networ

165 Using multiple sequence alignments of protein domains in the human genome, we extend the princ

166 erfamilies, doubling the number of predicted protein domains in the previous version.

167 h a similar operational 'grammar' and shared protein domains in the sensing and limiting of infection

168 hat alters the native linear-chain topology; protein domains in which the chemical composition of the

169 ironment to achieve an efficient ligation of protein domains independently from their structure or so

170 with the disordered propensity plots, known protein domain information, and the predicted secondary

171 elated network specificity, we also analyzed protein domain interactions and gene expression patterns

172 Protein domain interactions with short linear peptides,

173 l and functional information encapsulated by protein domains into the analysis of somatic variants in

174 ng and neutralizing a structurally conserved protein domain involved in pathogen iron acquisition.

175 t groups each with a distinct arrangement of protein domains involved in import.

176 like other coactivators, PGC-1alpha contains protein domains involved in RNA regulation such as serin

177 ting new gene (RING) finger-associated (SRA) protein domain is conserved across bacteria and eukaryot

178 not occur unless the entire sequence of the protein domain is translocated.

179 on suggests that flexibility between the two protein domains is important to allow the protein subuni

180 osteric networks to the presence of adjacent protein domains is likely a common property of supertert

181 ed DMS reactivity of RNA regions that encode protein domain junctions or intrinsically disordered reg

182 cessible As and Cs, than regions that encode protein domain junctions.

183 , and present detailed results for two short protein domains (Kunitz and WW), one long chaperone prot

184 hnique to overcome these limitations termed "Protein Domain mapping using Yeast 2 Hybrid-Next Generat

185 In contrast, the cellular protein domain MARCKS and the PS sensor Evectin2 show pr

186 suitable for clinical applications, as each protein domain may contribute to unwanted effects, such

187 Protein domains mediate drug-protein interactions and th

188 switching in signal transduction, we built a protein domain microarray that harbors PDZ domains and 1

189 mutations across entire gene families using protein domain models.

190 f translation and cotranslational folding of protein domains monitored in real time by Forster resona

191 flexible structures that are facilitated by protein-domain motions in alpha- and beta-catenin.

192 ated VioA structure indicated involvement of protein domain movement during enzyme catalysis.

193 The DynDom database of protein domain movements comprises sequences annotated t

194 The major sperm protein domain (MSPd) has an extracellular signaling fun

195 ins (VAPs) contain an N-terminal major sperm protein domain (MSPd) that is associated with amyotrophi

196 Protein domains native to the carboxysome core were used

197 Several RdRP-linked protein domains not previously detected in any RNA virus

198 are known to interact via the FK506-binding protein domain of AIPL1, the contribution of the tetratr

199 polyketide chain from the final acyl carrier protein domain of the synthase to a separate carrier pro

200 We find that the force-transmitting protein domains of filamin and titin are kinetically duc

201 dered regions (IDRs) are often fast-evolving protein domains of low sequence complexity that can driv

202 Even though many protein domains of Rep have been characterized, little i

203 By exchanging signal sequence and protein domains of similar size between PhoA and OmpA, w

204 mbly are covalently tethered to acyl carrier protein domains of the synthase.

205 Can simulations decipher the role of protein domains of unknown function in large macromolecu

206 Intrinsically disordered protein domains often have multiple binding partners.

207 ple, we study the influence of a cytoplasmic protein domain on the clustering behaviour.

208 s a pioneer protein with no previously known protein domain or motif.

209 w translation, allowing time for the nascent protein domain or ordered region of the protein to fold,

210 m understanding interactions at the level of proteins, domains, or atoms.

211 teins (SCOP) database is a classification of protein domains organised according to their evolutionar

212 s, phylogenetic analysis revealed that their protein domain organization is more complex in multicell

213 The analysis of the core protein domain organization revealed that all chondroiti

214 the structural basis for "dominance" by one protein domain over the other and provide insights into

215 In contrast, structured protein domains pack more closely and have to break exte

216 austively explore the binding specificity of protein domain-peptide interactions.

217 Protein domain prediction is one of the most powerful ap

218 rase motif defines an evolutionarily ancient protein domain present in several enzymes that hydrolyze

219 valuates proposed/potential contacts between protein domains, presents a complete catalog of both str

220 nown RNA-binding motifs, we detected several protein domains previously unknown to function in RNA re

221 Low-complexity protein domains promote the formation of various biomole

222 n sequences, genes, gene products, proteins, protein domains, protein families, enzymes and macromole

223 to create a highly detailed map of editosome protein domain proximities, leading to identification of

224 Some interactions between IDRs and folded protein domains rely on short linear motifs (SLiMs).

225 inactivation of Rheb, but functions of other protein domains remain elusive.

226 We map the protein domains required for pathway activation in membr

227 By defining protein domains responsible for targeting FMN2, we show

228 cluster blocks PIP(2) binding, this mutated protein domain retains the ability to bind physiological

229 p a chemical kinetic model that calculates a protein domain's co-translational folding curve during s

230 orthology data, Human Disease Model Reports, protein domain search and visualization, concise gene su

231 ing of the overall abundance of proteins, or protein domains, sharing a specific functional annotatio

232 medical knowledge (such as the hierarchical protein domain similarity or gene-gene interactions).

233 Biological annotations such as protein domains, single nucleotide variations, etc.

234 nt (LEA) proteins containing seed maturation protein domains (SMP; PF04927) have been linked to stora

235 P. patens resemble Arabidopsis PIFs in their protein domain structure, molecular properties, and phys

236 ge events congruent with the enzyme's mosaic protein domain structure.

237 se provides a hierarchical classification of protein domain structures including a sub-classification

238 copy number of sequences encoding an Olduvai protein domain subtype (CON1) shows a linear association

239 Furthermore, RNAs and low-complexity protein domains such as RNA-binding proteins also accumu

240 PCR regulator of G-proteins to a small plant protein domain, such that light uncages the G-protein ac

241 equences that correspond to the C-termini of protein domains, suggesting ribosome protection at these

242 identifies phosphorylation hotspots for 162 protein domains suggestive of an ancient role for the co

243 arge IAP expansion, with new combinations of protein domains, suggestive of evolutionarily novel aphi

244 yme function within 379 structurally defined protein domain superfamilies, linking the changes observ

245 Structural matches covered 429 known protein domain superfamilies, with the most highly repre

246 carbohydrate-binding module family 1 (CBM1) protein domain suppressed GH12 protein-induced cell deat

247 Several viral proteins domain swap to increase their structural comple

248 Protein domain-swap experiments identify a region includ

249 in which a small molecule is used to trigger protein domain swapping and subsequent activation of bio

250 mple two-dimensional coarse-grained model of protein domain swapping in the cytoplasm.

251 ad, uncharacterized cyclic nucleotide sensor protein domain that activates cell defense systems.

252 e CAP domain may serve as a stable, secreted protein domain that can accommodate multiple ligand-bind

253 We describe the emergence of a protein domain that confers the capability of interactin

254 ethod to map peptide binding sites on folded protein domains that allows consideration of their dynam

255 n domains are densely O-glycosylated modular protein domains that are found in a wide variety of cell

256 on A02 is rich in genes encoding TIR-NBS-LRR protein domains that are involved in plant defenses.

257 module from the NuRD complex contains three protein domains that control the recruitment of chromati

258 To tune REST activity, we selected two protein domains that impair REST-DNA binding or recruitm

259 matin remodelling proteins possess conserved protein domains that interact with nucleosomal features.

260 In contrast to self-association, PBX1 protein domains that mediate interactions with HOX DNA-b

261 We also identified 64 plant-associated protein domains that potentially mimic plant domains; so

262 We propose that drTRPM7 has two protein domains that regulate inhibition by intracellula

263 n summary, our results identify distinct BET protein domains that regulate protein turnover and biolo

264 lcium elevations - depends on an overlapping protein domain (the MID-domain), but is separate from it

265 netically conserved but previously unstudied protein domain, the DMA domain.

266 The crystal structure of a shared protein domain, the GPCR Autoproteolysis INducing (GAIN)

267 increased the size shift by fusing a compact protein domain, the Propionibacterium shermanii transcar

268 Five small protein domains, the CC-domains, at the N terminus of th

269 ncorporated into a solvent-exposed loop of a protein domain; the protein exhibited micromolar binding

270 ons via mechanisms utilizing properly folded protein domains, thereby facilitating elevated local con

271 have the signature characteristics of viable protein domains: They are spatially separated but indivi

272 teins ubiquitin and lysozyme, as well as the protein domains third IgG-binding domain of protein G an

273 protein networks by means of alterations in protein domains, thus providing insight into deep mechan

274 g of a fluorine-labeled Src homology 3 (SH3) protein domain to four proline-rich peptides.

275 Fusion of a small protein domain to the N terminus greatly facilitates dir

276 ergy transfer from a cytoplasmic fluorescent protein domain to the retinal chromophore bound within R

277 , which uses the modular structure of repeat protein domains to amplify signals of selection from pop

278 Genetically fusing protein domains to Cas9 has yielded several transformati

279 llustrate how evolution used a common set of protein domains to create a diversity of corepressors, a

280 dynamics on the scales ranging from isolated protein domains to live cells, from nanoseconds to hours

281 Transient, regulated binding of globular protein domains to Short Linear Motifs (SLiMs) in disord

282 Docking of protein domains to unbound double-stranded nucleic acids

283 te species trees, gene trees and subgene or (protein) domain trees using a probabilistic birth-death

284 ich may comprise an intrinsically disordered protein domain unique to mycobacteria.

285 hreshold of 90% amino acid similarity in the protein domains used to demarcate Coronaviridae.

286 annoFuse annotates protein domains using the PFAM database, assesses recipr

287 1 protein that lacks the nucleosome assembly protein domain was retained in the Golgi of fibroblasts

288 An analysis of the exon/intron structure and protein domains was conducted to suggest their functiona

289 Using a dataset of 863 protein domains, we assessed the physico-chemical intera

290 ssion, and purification of the corresponding protein domains, we confirmed methylation for 11 of them

291 ortex that exhibit exon variation across two protein domains, we found a 3-fold higher abundance of a

292 Protein complex membership and specific protein domains were found to be strong predictors of de

293 The binding pocket lies between the two protein domains, whereas all known D7s bind ligands eith

294 udy many factors that interact with unfolded protein domains, which underlie many important biologica

295 under slow interconversion; and drkN SH3, a protein domain whose folded and unfolded forms interchan

296 ancient and highly evolutionarily conserved protein domain widely distributed throughout all kingdom

297 The concomitant folding of a nascent protein domain with its synthesis can generate mechanica

298 metics can be divided into three categories: protein domains with side-chain functionality that alter

299 nisms of individual multidomain proteins and protein domains within these megasynthases.

300 Protein domains without the usual distribution of amino