ライフサイエンスコーパス: specific contact

1 zed by RT more by structure than by sequence-specific contacts.

2 ing residues in all other subunits make base-specific contacts.

3 hich are then stabilized by additional dimer-specific contacts.

4 interactions are predominantly through base-specific contacts.

5 prisingly, Pan2 does not form canonical base-specific contacts.

6 t there is a temporal order for formation of specific contacts.

7 of antisense oligomers blocking formation of specific contacts.

8 inding than mutations predicted to make base-specific contacts.

9 ons to bind to coactivators, with few if any specific contacts.

10 rion morphogenesis does not involve sequence-specific contacts.

11 t rely solely on the residues that make base-specific contacts.

12 ve, with a number of amino acids making base-specific contacts.

13 e receptor domains that make the actual base-specific contacts.

14 g of the common contacts more than G protein specific contacts.

15 at different positions to make similar base-specific contacts.

16 long variable arm of tRNA(Sec) with few base-specific contacts.

17 performs better on both conserved and family-specific contacts.

18 ix domain (WHD), but use remarkably few base-specific contacts.

19 mined in relationship to the nature of three specific contacts: a turn-hydrogen bond, a mainchain-to-

20 Both the HMG-I(Y) and HMG-1 proteins made specific contacts across the 4H DNA branch point, as wel

21 ver" in which surfaces cause specific or non-specific contact activated conformational changes in C3.

22 lizes the loop containing Met80 and, through specific contacts, affects the mobility of helix 3 and p

23 xposure of previously sensitized skin to the specific contact allergen.

24 e bases in the major groove and numerous non-specific contacts along the sugar-phosphate backbone.

25 apse directly on the ipsilateral M-cell, the specific contacts and anatomical distributions of these

26 Five amino acids make base-specific contacts and are expected to contribute signifi

27 Several arginine side chains make base-specific contacts, and an asparagine residue contacts a

28 s embraces Pum and RNA, contributes sequence-specific contacts, and increases Pum RNA-binding affinit

29 the difference between predictions based on specific contacts (approach introduced here) and those b

30 Specific contacts are found between charged lysine and a

31 and vitamin D3, and whether these substrate-specific contacts are important for CYP11A1 monooxygenat

32 timer, and it remains to be determined which specific contacts are in cis or trans with respect to th

33 Moreover, important sequence-specific contacts are made with bases that are not conse

34 emonstrate that potential phosphate and base-specific contacts as well as ribose moieties protected u

35 t pronounced regional differences in the age-specific contacts at home were noticeable, with more int

36 The individual homologous subunits form specific contacts at interfaces with neighboring subunit

37 interfere with the ability to establish base-specific contacts at resolution hotspots.

38 y electrostatics at long range and guided by specific contacts at short range, particularly involving

39 , while the selectivity comes from G protein specific contacts at the periphery of the interface.

40 Rev-RNA recognition relies on sequence-specific contacts at the well-characterized IIB site and

41 uperspreading and permits assigning risks to specific contact behavior.

42 tructurally rigid binding site with numerous specific contacts bestows specificity on HH26 whereas th

43 sed on psoralen photochemistry to identify a specific contact between a fragment of Tat protein (resi

44 is is the first identification of a sequence-specific contact between P protein and pre-tRNA that con

45 act approach we have obtained evidence for a specific contact between RhaR D276 and sigma70 R599.

46 arrangement of the AAA(+) rings, suggesting specific contact between the heads.

47 High-resolution micro-C maps reveal specific contact between transcription initiation sites

48 Formation of a specific contact between two residues of a polypeptide c

49 The structure shows specific contacts between a single copy of the internal

50 l structure of a modified PUF domain reveals specific contacts between an arginine side chain and the

51 een the pair of ARG boxes facilitate the non-specific contacts between ArgR subunits and the residual

52 showed that this activation does not require specific contacts between C and the carboxyl-terminal re

53 onent of the basement membrane that mediates specific contacts between cellular surfaces and their en

54 h specific protein-base interactions and non-specific contacts between charged side-chains and the ph

55 organization within the TAD and formation of specific contacts between enhancers and promoters.

56 us completing a survey of the major sequence-specific contacts between GlnRS and tRNAGln.

57 dues and negative charges, but the result of specific contacts between gp120 and a well defined sulfa

58 The data indicate that specific contacts between gp59 molecules and the A-domai

59 reconstructions that allowed us to visualize specific contacts between HAs from neighboring trimers a

60 uced by Sos is mediated by a small number of specific contacts between highly conserved residues on b

61 ome models of carboxysome function depend on specific contacts between individual RuBisCOs and the sh

62 transcription factor TFIID complex requires specific contacts between its Taf14 and Taf2 subunits, h

63 on as protein interaction modules, mediating specific contacts between members of functional complexe

64 A network of DNA- and histone-specific contacts between NSD2 or NSD3 and the nucleosom

65 evidence highlighting the importance of base-specific contacts between ppGpp and specific cytosine re

66 As these signatures enable proteins to form specific contacts between protein residues and bp, their

67 yond simple A/B compartment types to predict specific contacts between regulatory elements using poly

68 across the domain interface may depend upon specific contacts between residues of the 280's loop and

69 ognition of the P1 promoter does not require specific contacts between RNA polymerase and its poor -3

70 tegrin beta3 cytoplasmic domain and identify specific contacts between talin and the integrin tail re

71 the paromomycin-ribosome complex, we observe specific contacts between the apical tip of H69 and the

72 Specific contacts between the carbonyl groups from the T

73 The two structures together suggest that specific contacts between the chaperone and Cse4, rather

74 The ETV/PEA3*Med25 ensembles are directed by specific contacts between the disordered activator and t

75 by solution-state NMR spectroscopy revealed specific contacts between the Fn N terminus and two of t

76 richia coli RNase P are enhanced by sequence-specific contacts between the fourth pre-tRNA nucleotide

77 activation is limited by the availability of specific contacts between the G protein and the third in

78 ound conformations of G proteins reveals how specific contacts between the gamma-phosphate of GTP and

79 s simultaneously with H1s without disturbing specific contacts between the H1 globular domain and nuc

80 al surfaces and proteins very likely involve specific contacts between the lattice and the protein si

81 Specific contacts between the PKG Ibeta AI sequence and

82 M.EcoKI despite the removal of non-sequence-specific contacts between the protein and the DNA phosph

83 h binding and bending with little regard for specific contacts between the protein and the DNA.

84 bioinformatic analyses suggest that sequence-specific contacts between the protein subunit and the le

85 We determined the specific contacts between the ribosomal proteins and 16S

86 ein-surface interaction likely involves very specific contacts between the surface atoms and the key

87 ent of peptide-MHC class II ligands involves specific contacts between the TCR and residues on both t

88 HC "anchor point." Strikingly, there are few specific contacts between the TCR CDR3 loops and the MBP

89 e resulting structure revealed how eukaryote-specific contacts between the two proteins remodel the i

90 but a generalizable strategy for engineering specific contacts between these particles is an outstand

91 hermore, this conformational change requires specific contacts between transposase and the flanking T

92 periments designed to test the importance of specific contacts between VP1 and the carbohydrate moiet

93 However, binding to GRCGNC requires base-specific contact by two Mad proteins, and here we provid

94 tion, DNA bases that are subject to sequence-specific contacts by regulatory proteins.

95 seems to arise from a larger number of base-specific contacts contributing to affinity than for Fis.

96 del for the Michaelis complex to examine the specific contacts critical for substrate binding and cat

97 ithin an occluded pocket in OR51E2 and makes specific contacts critical to receptor activation.

98 ns, and we introduce a method to combine age-specific contact data to geographical movement data.

99 Allele-specific contact decay profiles obtained by single-cell

100 tutions at positions in which there are base-specific contacts decrease the level of repression.

101 From this work, we identified a specific contact-dependent growth inhibition (CDI) syste

102 us G.C flanking base pairs, rather than base-specific contacts, determines HMG1domA protein selectivi

103 However, the specific contacts differ substantially between the two c

104 While ZF2 does not make sequence-specific contacts, each finger of ZF3-7 contacts three b

105 zes features extracted from PSSM and residue specific contact-energy to help train a stacking based m

106 ropionate) cross-linking was used to measure specific contacts for both H5 and GH5 free in solution a

107 Specific contacts form at the loci experimentally inferr

108 physiological functions via a combination of specific contact formation with generation of complexes

109 is achieved through the formation of highly specific contacts formed by charged residues as demonstr

110 s high-affinity sites, there are no sequence-specific contacts formed with the protein.

111 unbiasedly ranked according to their allele-specific contact frequencies, a set of allele-specific T

112 aged by the proximal domain, with proper and specific contacts from Phe194 and Gln201 (Q motif) to th

113 protein-DNA interaction, involving sequence-specific contacts from the wing to the minor groove.

114 stitution at the only residue making an oxoG-specific contact (G42A mutation) introduced torsional st

115 ny cases, residues not expected to make base-specific contacts had effects on specificity.

116 gh electronic conductance, its dependence on specific contacts has important technological implicatio

117 identical half-sites through extensive base-specific contacts; however, RXR binds exclusively to the

118 sisting of a loop structure which makes base-specific contacts (HR1) and a helix which primarily cont

119 ic natural killer (NK) cells mediate antigen-specific contact hypersensitivity (CHS) in mice deficien

120 r immunological memory in the form of hapten-specific contact hypersensitivity independent of T and B

121 was required for efficient priming of hapten-specific contact hypersensitivity responses, but was dis

122 uggesting that the enzyme does not make base-specific contacts important for binding or catalysis in

123 ved to interact with SpyCatcher, pointing to specific contacts important for rapid split protein reco

124 The predicted requirement for base-specific contacts in exon 1 for cleavage by I-BasI was c

125 act areas and predicts correctly orientation-specific contacts in NMR data.

126 e, GAM highlights a role for gene-expression-specific contacts in organizing the genome in mammalian

127 The F alpha-helix, which provides all base-specific contacts in the CRP-DNA complex, became hyperse

128 a2 mutant lacking side chains that make base-specific contacts in the major groove is able to discrim

129 mers, with each protein monomer making base- specific contacts in the major groove.

130 cognition and allows us to assign additional specific contacts, in particular those involving the (al

131 endent on secondary structure and on residue-specific contact information.

132 d cross-linking measurements have identified specific contact interactions between the cytosolic and

133 These additional, T3Rbeta-2-specific contacts interfere with the subsequent associat

134 der plays in these transitions, identify the specific contacts involved, and describe how these inter

135 results suggest that a F3.36(201)/W6.48(357)-specific contact is an important constraint for the CB(1

136 The DNA-binding domains form few base-specific contacts leading to a binding preference that r

137 more likely than controls to report using a specific contact lens solution, ReNu with MoistureLoc (6

138 mutant (DU1090/pDU1212) were bound to rabbit-specific contact lenses, treated with spermidine (50 mM)

139 This approach enabled us to dissect specific contacts made by different monomers within the

140 ndings, we propose a model in which sequence-specific contacts made by PI-SceI contribute to its loca

141 sitions, in which there are no apparent base-specific contacts made by the protein in the alpha2-DNA

142 majority of DNA interactions are mediated by specific contacts made by the third alpha helix and the

143 nds is a function of both shared and complex-specific contacts made with each epitope.

144 ctive site suggests that, in addition to the specific contacts maintained between Tnp and its recogni

145 ed to the duplex by a similar set of nonbase specific contacts, malleable protein-DNA interactions en

146 The proposed ASHIC methods impute allele-specific contact maps from diploid Hi-C data and simulta

147 can use phased genotype data to build allele-specific contact maps.

148 cterise mixing patterns and generate setting-specific contact matrices according to age and urban/rur

149 ase parameters, as well as age- and location-specific contact matrices to represent contacts.

150 es are based on sparse and inaccurate allele-specific contact matrices, which might lead to incorrect

151 anemone STING recognizes through nucleobase-specific contacts not observed in human STING.

152 the conserved Lys-532 residue, the only base-specific contact observed previously in the human topois

153 used a photocross-linking method to identify specific contact of CCAAT-binding factor (CBF) subunits

154 The winged-helix fold forms base-specific contacts of alpha-helix H3 with the major groov

155 x, which is known to confer most of the base-specific contacts of HDs with DNA, was almost identical

156 (RNAP) recognizes promoters through sequence-specific contacts of its promoter-specificity components

157 with docking calculations have defined many specific contacts of the complex between the AT-rich int

158 n the Rv1057 intergenic region and generates specific contacts on the same side of the DNA helix.

159 complex, suggesting that CBF makes sequence-specific contacts only in the CCAAT motif region.

160 eased CYT-18 binding, reflecting either base specific contacts or indirect readout of RNA structure b

161 ing a limit on the extent of selection for a specific contact pattern.

162 ailed contact network study to show that age-specific contact patterns alone can explain shifts in pr

163 oduce a flexible model that can estimate age-specific contact patterns at the subnational level by co

164 estimated the proclivity of age-and-location-specific contact patterns for the countries, using Marko

165 ousehold structure, social settings, and age-specific contact patterns.

166 hree dimensions into a rich variety of locus-specific contact patterns.

167 n Ste2p and alpha-factor, thereby defining a specific contact point between the bound ligand and its

168 city in the location of the third helix, DNA specific contact points (such as amino acids 4 and 29),

169 structure models with A3G and A3F by mapping specific contact points between both proteins.

170 he yHac1 and the YY1 binding sites uncovered specific contact points for an activator protein predict

171 form SMN-SMN disulfide crosslinks, defining specific contact points in oligomeric SMN.

172 entrance are critical for binding, although specific contact points vary between the two.

173 perativity contribution to determine residue-specific contact probabilities in the denatured state an

174 Without this specific contact, productive unwinding of plasmid ori ga

175 Together with age-specific contact rates in Finland, contemporary forces o

176 This is the first determination of a specific contact region between a Class IV GPCR and its

177 The specific contact resistance at high gate voltages for go

178 For the special case of constant ohmic specific contact resistivity along the contact length, o

179 ly overlapped parallel contacts with varying specific contact resistivity along the contact length.

180 bind in the ATP binding pocket and make S6K1-specific contacts, resulting in changes to the p-loop, a

181 Our results identify a specific, contact-rich pentameric arrangement of HBV cap

182 s the rate-limiting step in producing female-specific contact sex pheromone (CSP) that stimulates mal

183 Mutations affecting specific contact sites (L165V, L172V) or charge separati

184 Specific contact sites in STAT3 responsible for interact

185 yeast underlies the plasma membrane (PM) at specific contact sites to enable a direct transfer of in

186 These results indicate that specific contact sites, thermodynamics, and kinetics all

187 The contact width frequencies define tissue-specific contact spectra, and knockdown of adhesion fact

188 sed on crystal structures of either SLA (SLA-specific contacts, Ssc) or HLA supertype alleles (HLA co

189 olution, respectively, and revealed BRDT-BD2 specific contacts that explain the high affinity and sel

190 quinolone scaffolds do not take advantage of specific contacts that might be made with the enzyme.

191 effect derives from the organization of the specific contacts that SerRS makes with the neighboring

192 ay crystallography and NMR studies uncovered specific contacts that underlie the potency and selectiv

193 Thus, rather than loss of specific contacts, the free energy cost of distorting DN

194 e evidence that zinc finger 5 makes sequence-specific contact through the major groove of both nuclei

195 shed through electrostatic effects, although specific contacts through gamma-ionizable residue side c

196 ons to the flanking residues including a CpG specific contact to an A at the +1 flanking site.

197 obility, but also the stereochemistry of the specific contact to O6.

198 served L13 residue in the U1-C protein makes specific contact to stabilize the U1 snRNA/5' splice sit

199 virus Tat protein makes a critical sequence-specific contact to TAR RNA.

200 tein backbone, while the second makes a base-specific contact to the DNA sense strand.

201 that GR binds directly to TREs via sequence-specific contacts to a GR-binding sequence (GBS) half-si

202 plex, and that the co-activator makes stereo-specific contacts to both the POU protein and the major

203 the transcription start site, makes sequence-specific contacts to region 1.2 of the sigma subunit of

204 Both TADs I and IV were also shown to make specific contacts to the C-terminal segment of TFIIB.

205 N4 binds as a dimer, with one monomer making specific contacts to the consensus half-site and the oth

206 hese data indicate that TFIID makes sequence-specific contacts to the DCE and that TFIID binding is n

207 In addition, SimR makes a number of sequence-specific contacts to the major groove via its helix-turn

208 While the protein makes numerous specific contacts to the non-consensus nucleotides in th

209 mechanism by the Vd3 TCR chain that mediated specific contacts to the side of the MR1 antigen-binding

210 llite Tobacco Necrosis Virus-1 make sequence-specific contacts to the viral CPs helping to nucleate f

211 y of DNA binding, despite an absence of base-specific contacts to this region.

212 late M77 of Adx alpha helix-3 as a substrate-specific contact towards CYP11A1.

213 e RRE sequence than Rev by forming more base-specific contacts, using water to mediate peptide-RNA co

214 Specifically, new fetal stage-specific contacts were uncovered between a region separa

215 d with helix H3 contributing to all the base specific contacts, while the N-terminus, wing 1, and the

216 This is the first example of HU making a specific contact with another protein.

217 n, the spacer region does not appear to make specific contact with C.

218 indicate that the brown gene is silenced by specific contact with centromeric heterochromatin.

219 hat only one subunit of a pi35.0 dimer makes specific contact with DNA.

220 a conserved region that is required for base-specific contact with DNA.

221 e beta-hairpin amino acids that mediate base-specific contact with GTCT.

222 Arg254 and Glu189 join to form a specific contact with one of the phenolic hydroxyls of t

223 oregulation at the operator site by making a specific contact with ParA.

224 imilarly, ParA acts in partition by making a specific contact with ParB bound at parS.

225 hich overlaps the promoter, where it makes a specific contact with the C-terminal domain of the alpha

226 n may indicate that the LCR need only make a specific contact with the proximal gene promoter to acti

227 We combined PROFcon predictions for protein-specific contacts with a generic pairwise potential to p

228 report that B. subtilis NusG makes sequence-specific contacts with a T-rich sequence in the non-temp

229 catalytic site of one molecule is blocked by specific contacts with a wedge from the other.

230 In this transition, ArkA makes specific contacts with AbpSH3 and buries more hydrophobi

231 ng mode is augmented by unexpected chemotype-specific contacts with amino acid residues Asn352 and Gl

232 cond and fifth positions of the G tract make specific contacts with amino acids in the RNase H domain

233 lix motif lies deep in the major groove with specific contacts with bases in both strands in the core

234 hates, steer side chains that end up forming specific contacts with bases into bound-like conformatio

235 1, we found that Arg202 and Arg206 both make specific contacts with bp -65 and -67 in rhaI1, and that

236 n the ribosomal intersubunit space and forms specific contacts with components of the ribosomal A, P,

237 All sequence-specific contacts with core promoter elements are mediat

238 alyses illustrated that CXCL12 monomers made specific contacts with CXCR4 that were lost following di

239 onserved thymine bases while Gln43 makes non-specific contacts with different types of bases in diffe

240 Adr1-F1F2 in which finger 2 makes three base-specific contacts with DNA had a higher affinity for DNA

241 ctured protein domain, which then makes base-specific contacts with DNA.

242 t the non-duplex sequences may form sequence-specific contacts with duplex portions of the ribozyme,

243 on of receptor Ig domain 2 (D2) to introduce specific contacts with FGF10.

244 SS (FRU) transcription factor, but form male-specific contacts with FRU-expressing neurons; calcium i

245 ecule in the DNA minor groove, and potential specific contacts with functional groups in the floor an

246 on of the posterior lateral line establishes specific contacts with hair cells of the same hair-bundl

247 s to open apo-TRiC through polyvalent domain-specific contacts with its chamber's equatorial and apic

248 does not require E protein to make sequence-specific contacts with M protein.

249 The ability of RNAs to form specific contacts with other macromolecules provides an

250 d the splice junction but U1-C makes no base-specific contacts with pre-mRNA.

251 at substrates bind predominantly through non-specific contacts with protein hydrophobic residues.

252 the recognition helix predicted to make base-specific contacts with RE2 have relatively little effect

253 Furthermore, it was postulated that base-specific contacts with residues in the middle domain cou

254 his work, amino acids in RhaS that make base-specific contacts with rhaI were identified.

255 cleoprotein-stabilizing role involve nonbase-specific contacts with RNA upstream of the AU-rich motif

256 sitioning reveals that each TM segment makes specific contacts with Sec61alpha and is retained at a f

257 gineered DRM2 C397R mutation introduces base-specific contacts with the +2-flanking guanine, thereby

258 analog studies suggest that IntDOT may make specific contacts with the A residues in the major groov

259 the N-terminal domain include disruptions of specific contacts with the alpha1 helix, which were reve

260 mined at 1.82 angstrom and revealed BRDT-BD1-specific contacts with the alphaZ and alphaC helices tha

261 te that the observed stimulation arises from specific contacts with the beta5 strand (residues 239-24

262 irpin loop (the specificity loop) that makes specific contacts with the binding region of the promote

263 s with a flagellar basal body and MotA makes specific contacts with the C ring and/or the MS ring.

264 ytic site of the bisphosphatase and includes specific contacts with the C-terminal regulatory region

265 a that the substrate participates in subunit-specific contacts with the chaperonin.

266 n of CXCR4, including sulfotyrosine 21, make specific contacts with the chemokine ligand.

267 ng consensus in which the protein makes base specific contacts with the cognate DNA further improved

268 WhiA C-terminal domain (WhiA-CTD) makes base-specific contacts with the conserved WhiA GACAC motif.

269 ng an interaction with WhiA while making non-specific contacts with the DNA upstream of the -35 core

270 o orientate the arginine side chain to allow specific contacts with the DNA.

271 Selected peptides make specific contacts with the effector-binding region of Ga

272 n binds to the closed form of KcsA and makes specific contacts with the extracellular surface of the

273 d mutational investigations suggest that DNA-specific contacts with the four-finger tandem array of Z

274 s within individual finger domains make base-specific contacts with the major groove of DNA.

275 , GW5638 repositions residues in H12 through specific contacts with the N terminus of this helix.

276 ino acids in the connection domain that make specific contacts with the nucleic acid.

277 -pHis mAbs with the selectivity arising from specific contacts with the phosphate group and triazolyl

278 RNA polymerase (RNAP), which makes sequence-specific contacts with the promoter -10 and -35 elements

279 nto the major groove of the DNA to make base-specific contacts with the promoter region.

280 of 28 kb in primary placental nuclei to make specific contacts with the promoters of the two GH genes

281 A binding site does not form strong sequence specific contacts with the protein.

282 classical binding mode, the SH2 domain makes specific contacts with the pY residue and the three resi

283 does not require the continuous formation of specific contacts with the ribose-phosphate backbone as

284 However, a kink in H16 that makes specific contacts with the S4 N-terminal extension, as w

285 minor groove and a large network of non-base-specific contacts with the sugar phosphate backbone.

286 onstrate the importance of DNA structure and specific contacts with the viral DNA processing site for

287 cal for productive viral DNA binding through specific contacts with the virus DNA ends in the 3'-proc

288 Eight peptide residues make specific contacts with the X11 PTB domain, and they coll

289 Specific contacts with three WIP epitopes corresponded t

290 Transcription factor AP-1 is known to make specific contacts with thymine methyl groups of DNA in i

291 he ribosomal decoding site and may make base-specific contacts with tmRNA ligands.

292 suggested that TraR makes extensive sequence-specific contacts with tra box DNA.

293 nt groups of ORC subunits that make sequence-specific contacts with two distinct regions of the DNA.

294 e to promoter recognition by making sequence-specific contacts with upstream (UP) elements that are a

295 volves two minor grooves and has no sequence-specific contacts, with the exception of a single hydrog

296 n TM1 and TM2 were used to further elucidate specific contacts within a monomer subunit, enabling a m

297 are often composed of bound monomers forming specific contacts within the bilayer.

298 between kinase domain N-lobes, in which the specific contacts within the interface are coupled to th

299 We conclude that the sequence-specific contacts within the recognition sites contribut

300 hereas I-HmuI is known to make its only base-specific contacts within this exon region, structural mo