ライフサイエンスコーパス: protein domain

1 le protein in the Astral-40 database (11 154 protein domains).

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

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

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

5 dramatically affect the later unfolding of a protein domain.

6 additional aggregation-prone segments into a protein domain.

7 F-actin and represents a novel actin-binding protein domain.

8 leavage activities that are dominated by one protein domain.

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

10 ional imaged proteins when studying membrane protein domains.

11 power strokes are sufficient to unfold some protein domains.

12 R) immune receptors carry fusions with other protein domains.

13 their constituent structural and functional protein domains.

14 previously been limited mainly to very small protein domains.

15 ical of small, intrinsically rapidly folding protein domains.

16 as9 mutagenesis to exons encoding functional protein domains.

17 ally separable activities requiring distinct protein domains.

18 embers with phosphatidylethanolamine-binding protein domains.

19 that serve as binding interfaces for modular protein domains.

20 ssibly due to a deterioration of hydrophobic protein domains.

21 closer sequence-based relationships between protein domains.

22 ing with profound structural effects on LRP5 protein domains.

23 the retroviral protease into its constituent protein domains.

24 unction, such as DNA binding site motifs and protein domains.

25 in patients were found in likely functional protein domains.

26 sphorylated inositol head groups to specific protein domains.

27 inases that phosphorylate residues in folded protein domains.

28 depict the overall shape and organization of protein domains.

29 rained amino acid covariation for 40 diverse protein domains.

30 to each other and similar in size to intact protein domains.

31 the level of single evolutionary families of protein domains.

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

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

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

35 classifications for over 100 000 additional protein domains.

36 tutive exons and exons that encode conserved protein domains.

37 rvature-generating activity present in other protein domains.

38 e presence and coordination between multiple protein domains.

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

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

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

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

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

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

45 ed on two different intrinsically disordered protein domains, a binding domain from activator of thyr

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

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

48 Small molecule bioactivities mapped to protein domains add important precision to approaches th

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

50 Thus, GIL is the second protein domain, after PilZ, dedicated to c-di-GMP-bindin

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

52 ibosomal exit tunnel and physically separate protein domains, allowing them to fold in a cotranslatio

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

54 Protein domain analysis enhances the statistical power t

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

56 Protein domain analysis in Steinernema revealed a striki

57 lity or complete reference genomes, existing protein domain analysis pipelines are applied to short r

58 we showed that Carabin Ras-GTPase-activating protein domain and calcineurin-interacting domain were b

59 first task of this study was to analyse the protein domain and domain architecture content of the 13

60 otif that increases the acidity of an ORF11p protein domain and postulate that this has either arisen

61 etween proteins and nucleic acids using only protein domain and probe sequences as inputs.

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

63 6.6%) for species, 9.0% (max 28.7%) for Pfam protein domains and 9.4% (max 22.9%) for PANTHER gene fa

64 karyotes, contains bacterial uvrB/C and YccV protein domains and a unique N-terminal domain.

65 riation details, maps, expression, homologs, protein domains and external databases) is available via

66 in proteins that more often contain multiple protein domains and function as scaffolds for protein co

67 Methyl-binding protein domains and improved antibodies with broad speci

68 protein functional regions (PFRs), including protein domains and intrinsically disordered regions.

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

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

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

72 of the first models predicted for 78 CASP11 protein domains and second according to the total scores

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

74 unknown, despite the description of numerous protein domains and the recent focus on its potential ro

75 e conformational heterogeneity of disordered protein domains and their complexes, we performed single

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

77 ssense variants are located within annotated protein domains and whether they form clusters, using a

78 cing events, and to integrate them with both protein-domains and microRNA binding annotations.

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

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

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

82 omplexes, the functional properties of their protein domains, and variation between complexes.

83 The dcGO is a comprehensive resource for protein domain annotations using a panel of ontologies i

84 nity with the ease to analyse ontologies and protein domain annotations, particularly those in the dc

85 hs showing the relationships between related protein domain architectures, analyses of ligand binding

86 Protein domains are commonly used to assess the function

87 These protein domains are considered to function by targeting

88 A variety of catalytic and noncatalytic protein domains are deployed by select microorganisms to

89 Protein domains are generally thought to correspond to u

90 s, we received accurate results that suggest protein domains are more basic units for the essentialit

91 Pfam protein domains are often thought of as evolutionarily i

92 del of allosteric gating, according to which protein domains are quasi-independent: they can move ind

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

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

95 microcompartment (in reference to the shell protein domain)] assemble to form a polyhedral barrier t

96 GluRS and GlnRS further acquired additional protein domains assisting function in cis (the GlnRS N-t

97 ternative first exons, which encode distinct protein domains at the N-terminus of the protein also kn

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

99 ification of acceptor sites in cysteine-rich protein domains before disulfide bond formation.

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

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

102 Deformation of protein domains by application of stress, previously doc

103 cells that do not or do contain invaginated protein domains called caveolae.

104 In general, protein domains can be considered the structural buildin

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

106 Protein domains can fold into stable tertiary structures

107 tional module are replaced with heterologous protein domains, can serve as a general platform for gen

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

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

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

111 00 000 domain structures and over 53 million protein domains classified into 2737 homologous superfam

112 ate vision-signaling cascade but composed of protein domain components arranged as a novel gene fusio

113 41 in vivo interactomes and determined their protein domain composition, correlation to gene expressi

114 recorded on the level of single proteins and protein domains, comprising in excess of 1.5 billion pai

115 Searches for similar structures in the SCOP protein domain database yield only weak matches with dif

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

117 al keratinocytes to express individual IQGAP protein domains designed to compete with endogenous IQGA

118 Protein domains display a range of structural diversity,

119 gent sequence homology, we identified a MYRF protein domain distantly related to bacteriophage tailsp

120 The results establish protein domain distortion as a bona fide mechanism for m

121 cript Quantification (Net-RSTQ) to integrate protein domain-domain interaction network with short rea

122 ms for quantification, we propose to explore protein domain-domain interactions as prior knowledge fo

123 A novel highly conserved protein domain, DUF162 [Pfam: PF02589], can be mapped to

124 In neuronal NOS (nNOS), protein domain dynamics and calmodulin binding are impli

125 owever, little is known about what role each protein domain (e.g., A, B, and C) of E2 plays on these

126 at bind and cleave the target through linked protein domains (e.g. TALENs and zinc-finger nucleases).

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

128 ,016 domains [Evolutionary Classification of Protein Domains (ECOD) database] or 20,398 chains [Prote

129 These engineered protein domains enable rapid, reversible and dose-depend

130 s, one member of which carries an additional protein domain, enable perception of pathogen effectors

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

132 We identify the protein domains essential for VAP formation in PVAP trun

133 fall within the 10 most abundant allergenic protein domain families (EF-hand, Tropomyosin, CAP, Prof

134 re we compared the usage and distribution of protein domain families in the free-living proteomes of

135 g matches to hidden Markov models describing protein domain families.

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

137 hat all mutations have structural effects on protein-domain folding.

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

139 ding finer-grained classifications of common protein domains, for which a wealth of functional and st

140 nomy of BMC loci, based on their constituent protein domains, foregrounds the functional diversity of

141 interaction (SpyTag/SpyCatcher), based on a protein domain from Streptococcus pyogenes, that locks i

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

143 ce that maps small molecule bioactivities to protein domains from the Pfam-A collection of protein fa

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

145 amino acid substitution matrix in inferring protein domain function.

146 teracting site and Ras/Rab GTPase-activating protein domain, functions as an endogenous inhibitor of

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

148 s, gene homologs and association of InterPro protein domains, GO terms and Kyoto Encyclopedia of Gene

149 3-dimensional model of FGFR1 to assess which protein domains harbored the highest number of pathogeni

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

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

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

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

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

155 MAbs, most of which recognized a region in E protein domain I/II containing the fusion loop.

156 greater percentage of antibodies targeting E protein domain I/II than domain III.

157 Overall, one-third of the protein domains identified in mitochondrial proteins are

158 We applied this method to the envelope protein domain III (ED3) of two medically important flav

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

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

161 These studies shed new light on the protein domains important for intracellular and extracel

162 2 zinc finger (C2H2-ZF) is the most numerous protein domain in many metazoans, but is not as frequent

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

164 investigated the occurrence of mitochondrial protein domains in bacteria and eukaryotes.

165 o measure the structure of these hydrophilic protein domains in detergent-solubilized LHCII.

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

167 The PAM2 motif and R3H protein domains in NFX1-123, which were important for in

168 analysis of the occurrence and abundance of protein domains in proteomes has recently showed that th

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

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

171 show that EndoS is composed of five distinct protein domains, including glycosidase, leucine-rich rep

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

173 , we report computational studies of the SH3 protein domain interacting with various single-walled ca

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

175 The protein was designed based on protein domain interactions in the carboxysome core.

176 rogeneous data from multiple sources such as protein domain, interactome, functional annotation, geno

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

178 t structures in the phylogenomic analysis of protein domains introduced many mechanistic step types t

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

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

181 activity in vitro, and each distinct Gyc76C protein domain is crucial for regulating Gyc76C activity

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

183 The functional role of the different CCBE1 protein domains is completely unknown.

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

185 ECOD (Evolutionary Classification of protein Domains) is distinct from other structural class

186 ing the substructures of synthetic drugs and protein domains, is important in fragment-based drug dis

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

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

189 correlated mutations and cancer types at the protein domain level.

190 nctional units of a protein, we explored the protein domain-level landscape of cancer-type-specific s

191 e a new concept called domain atrophy, where protein domains lose a significant number of core struct

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

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

194 Protein domains mediate drug-protein interactions and th

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

196 larity searches against various databases of protein domain models.

197 mutations across entire gene families using protein domain models.

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

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

200 A popular method for classification of protein domain movements apportions them into two main t

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

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

203 Protein domains native to the carboxysome core were used

204 tablishing proper orientation and spacing of protein domains necessary for assembly and restriction.

205 the E359K mutation, which is in the protein-protein domain of FEN1, abolished the interaction of FEN

206 87C>T [p. Arg1163Trp]) in a highly conserved protein domain of ZSWIM6; this variant has not been seen

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

208 Taking as inputs a list of protein domains of interest, the package is able to easi

209 nfer the functional importance of individual protein domains of interest.

210 lection of chimeric MX proteins, to identify protein domains of MX2 that specify HIV-1 inhibition.

211 The accessory protein domains of the oxidative phosphorylation system

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

213 the nucleation, growth and stabilization of proteins domains on the size of the cell.

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

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

216 es, localization of the variants in distinct protein domains, or the trigger of or escape from nonsen

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

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

219 proach to efficiently secrete PTD-containing protein domains, overcoming previous limitations, and al

220 e Gold-standard benchmark dataset (3 207 270 protein domain pairs), GR-Align is several orders of mag

221 On the Proteus_300 set (44 850 protein domain pairs), GR-Align is several orders of mag

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

223 Protein domain prediction is one of the most powerful ap

224 For the important problem of protein domain prediction, a key step in characterizing

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

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

227 own to 1 A, enabling accurate measurement of protein domains projecting from the membrane layer.

228 g sequences, genes, gene products, proteins, protein domains, protein families, enzymes and macromole

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

230 structure capable of caging the acyl carrier protein domain proximal to each active site.

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

232 The ZIM protein domain recruits the co-repressors NINJA and TOPL

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

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

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

236 ysine present on a highly conserved acceptor protein domain, resulting in the amide-linked coenzyme.

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

238 s based on the type of mutation and affected protein domain(s).

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

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

241 due correlations for a set of representative protein domains, showing that (i) the most representativ

242 lso unusual in that they share no detectable protein domain signatures with known polysaccharide-bind

243 Gene3D is a database of protein domain structure annotations for protein sequenc

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

245 tabase provides annotations for over 235,000 protein domain structures and includes 25 million domain

246 st appearance of homologous superfamilies of protein domain structures from CATH.

247 models, we find that the eukaryote-specific protein domains substantially influence amino acid bindi

248 While cellular acidic phospholipid-binding proteins/domains, such as the PI(4,5)P2-specific pleckst

249 also reveals associations among thousands of protein domains, suggesting a basis for examining struct

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

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

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

253 Protein domain-swap experiments identify a region includ

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

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

256 A protein domain-swapping approach was utilized to demonst

257 n and genetic dissection into three parts: a protein domain termed SpyLigase, which now ligates two p

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

259 uster domain (SCD) constitutes a new type of protein domain that is not defined by sequence similarit

260 g rapamycin-binding domain and FK506-binding protein domains that are attached to cisternal adhesive

261 We identified HapX protein domains that are essential for HapX functions du

262 ES within CIITA and place it among the other protein domains that contribute to the posttranslational

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

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

265 neral strategy for the identification of the protein domains that mediate each of the identified turn

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

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

268 ch may allow comprehensive identification of protein domains that sustain cancer cells and are suitab

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

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

271 e novo mutation affect residues in different protein domains, the first cytoplasmic domain and the fi

272 gene essentiality from a new perspective of protein domains, the independent structural or functiona

273 anes are organized into functional lipid and protein domains, the most widely studied being membrane

274 nvestigate the folding of a small five-helix protein domain-the N-terminal domain of Escherichia coli

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

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

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

278 structural designs incorporate a photoactive protein domain to enable light-dependent conformational

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

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

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

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

283 Results on fusions of stable protein domains to N-terminus, C-terminus or both termin

284 er, the contribution of conserved, druggable protein domains to this anticancer phenotype is unknown.

285 ain atrophy is an extremely rare phenomenon, protein domains under certain circumstances can tolerate

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

287 veral webservers exist for identification of protein domains using similarity searches against variou

288 classify the three dimensional structures of protein domains, using a set of folds taken from the str

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

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 elated VSV serotypes and inserting unrelated protein domains, we shed light on requirements for domai

293 g a large manually curated benchmark of 1007 protein domains, we show that CE-Symm performs significa

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

295 The differential roles of protein domains were supported by their individual expre

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

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

298 der 9,710 SCOP (Structural Classification of Proteins) domains with up to 70% sequence identity and p

299 In this work a conserved protein domain within human Scml2 has been identified, a

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