ライフサイエンスコーパス: groove

1 ck substrate access to the substrate-binding groove.

2 ed by the binding of the glycan to a protein groove.

3 on and subsequent binding at the amphipathic groove.

4 the wing interacted with the adjacent minor groove.

5 n of lipid molecules that penetrate into the groove.

6 , with the alpha helices occupying the major groove.

7 erminants within its electropositive binding groove.

8 inds an essential region of the BCL6 lateral groove.

9 de of the well described polyproline-binding groove.

10 singularity is a hydrophobic antigen-binding groove.

11 dary binding site occupies the other binding groove.

12 linked hydrophobic substituents in the major groove.

13 zing four hydrophobic pockets in its binding groove.

14 pid headgroup-interaction sites flanking the groove.

15 ter-mediated interactions with the DNA major groove.

16 and perturbs FLI1 bound nearby in the major groove.

17 tryptophan residue obscuring the recognition groove.

18 cognition helix region relative to its major groove.

19 n interactions within a stable, open binding groove.

20 g in bilayer thinning across the hydrophilic groove.

21 occurs toward either the major or the minor groove.

22 n to protrude through one end of the binding groove.

23 a high tendency of bending toward the minor groove.

24 preferentially on an exposed major or minor groove.

25 m a dimer interface presenting a DNA-binding groove.

26 conformations with respect to the DNA major groove.

27 iously, including kinking into the DNA major groove.

28 the enzyme active site to be a deep surface groove.

29 of ~1.5 kcal/mol for sliding along the minor groove.

30 hat is due to alkylation of DNA in the minor groove.

31 or by binding in a zigzag fashion inside the groove.

32 x that binds the central portion of the CRM1 groove.

33 n the other uridines, thus filling the major groove.

34 two isoforms share an identical NLS-binding groove.

35 molecule, focused around the peptide-binding groove.

36 the linker lying in the TTD peptide-binding groove.

37 a beta sheet 'wing' into the adjacent minor groove.

38 fferent extents of the invariant NES-binding groove.

39 l of fluid lying within adjacent nanograting grooves.

40 ng" lysines and arginines into the DNA minor grooves.

41 substrates with 460 nm and 1.15 microm high grooves.

42 partite active site, combining a hydrophilic groove, a hydrophobic lipid-binding pocket and a tunnel

43 ation (R62W) that has produced an open-ended groove accommodating particularly long peptides.

44 terstrand cross-links (ICLs) and bulky minor groove adducts normally recognized by Fanconi anemia and

45 ein) and binding modes (intercalation, minor groove, allosteric switch).

46 with both the canonical hydrophobic binding groove (alpha2-5) and alpha6 at the rear of BAK, with in

47 rincipally, TgAMA4 lacks both a deep surface groove and a key surface loop that have been established

48 nded ligand binding potential of the antigen groove and a substantially different conformation compar

49 ense the structural changes of the DNA minor groove and can be considered a "minor groove sensor." Pr

50 at HLA-F contains a distinct peptide-binding groove and can present a diverse array of peptides.

51 logy, DNAphi, for predicting EP in the minor groove and confirmed the direct role of EP in protein-DN

52 duplex exhibits a significantly wider major groove and greater average values of stagger, slide, ris

53 ed proteins bind to hIRE1alpha LD's MHC-like groove and induce allosteric changes that lead to its ol

54 A structure suggest that MTM binds the minor groove and perturbs FLI1 bound nearby in the major groov

55 3-MeA protrudes into the DNA minor groove and strongly blocks synthesis by replicative DNA

56 satellite Phobos is criss-crossed by linear grooves and crater chains whose origin is unexplained.

57 the correlation between scores for radicular grooves and root canal morphology was analyzed.

58 Subsequently, the evolution of deep anterior grooves and their coupling to venom secretory tissue pro

59 pacious active site (especially in the major groove) and tolerance of DNA lesions.

60 ening is highly confined to the underlying Z-groove, and especially to the first T-tubule opening, wh

61 ured for removing the ligands from the minor groove, and of ~1.5 kcal/mol for sliding along the minor

62 chronization, entrainment, the perception of groove, and other temporal factors that constitute a fir

63 Bachmann's bundle, the left atrioventricular groove, and the pulmonary vein area was performed during

64 ith the bases of the 7-bp motif in the major groove, and the wing interacted with the adjacent minor

65 The 500 mum thick wafer IREs with groove angles of 35 degrees are significantly more trans

66 By incorporating slot-groove antennas into the metal electrode, we show that L

67 Anomalous grooves are relatively young, and crosscut tidally predi

68 with periodic subwavelength staggered double groove arrays supported by a flexible dielectric substra

69 at corresponds to accessibility of the minor groove as DNA winds around the nucleosome--we develop a

70 into the minor groove, rather than the major groove as in a normal Watson-Crick base pair.

71 Finally, we use these grooves as self-labeled and ex situ markers to resolve s

72 tory Arp3 C-terminal tail from a hydrophobic groove at Arp3's barbed end to destabilize the inactive

73 eading of the base sequence in the DNA major groove at the binding site.

74 defined by a characteristic peptide binding groove B pocket.

75 Besides hydrogen bonding in the major groove (base readout), proteins recognize minor-groove g

76 By quantifying the energetics of DNA groove bending and rationalizing the origins of the anis

77 The anisotropy of B-DNA groove bending was quantified for eight DNA sequences by

78 a free energy offset between major and minor groove bending.

79 ong with a peptide-binding site located in a groove between the alphaB and betaB structural elements

80 -Rich Motif) ARM, which enters the TAR major groove between the bulge and the central loop.

81 These ligands bind in a groove between the integrin alpha and beta-subunits; the

82 formed DNA runs symmetrically across central groove between two ATPgammaS-bound Rad50 nucleotide-bind

83 Meanwhile, the grooves between nanohemispheres will provide the extra d

84 s are nucleated and grown selectively in the grooves between the microposts as the vapor pressure inc

85 High oscillatory shear index (OSI) in the grooves between trabeculae, compared to lower values on

86 et of primers and corresponding TaqMan Minor Groove Binder (MGB) probes were designed to target Agrob

87 nal changes of DNA upon binding of the minor groove binder netropsin.

88 s well as the Ebola Zaire Target 1 and major groove binder quantitative reverse-transcription polymer

89 beria (including Ebola Zaire Target 1, major groove binder real-time-polymerase chain reaction assays

90 chromosomes were labeled with the DNA minor groove binder, DAPI, followed by measurement and imaging

91 investigate the mechanism of how these minor-groove binders affect pol II transcription elongation.

92 we demonstrated that intercalators and minor groove binders affect the conformation of the DNA and RN

93 iption elongation by sequence-specific minor groove binders may present opportunities to target trans

94 , derived from existing classes of DNA minor groove binders, were designed, synthesized, and evaluate

95 r this purpose, specific primers and a minor groove binding (MGB) TaqMan probe were designed to ampli

96 are a family of sequence-selective DNA minor-groove binding agents that form a covalent aminal bond b

97 c, highly efficient, dynamic nature of minor groove binding agents.

98 teraction modes like intercalation and minor groove binding already have been identified, associated

99 We discuss briefly minor and major groove binding ligands, and then focus on intercalators,

100 eotides, peptide nucleic acids (PNAs), minor groove binding polyamides, and--more recently--engineere

101 to dsDNA via electrostatic and intercalative/groove binding, and this binding allows the DNA-mediated

102 d be assigned to bis-intercalation and minor groove binding, respectively, DRAQ5 exhibited both bindi

103 ctivator-like effectors (TALEs) as DNA major groove-binding probes in affinity enrichment.

104 n AT-sequence, we show that the ICD of minor-groove-bound 4',6-diamidino-2-phenylindole (DAPI) origin

105 tricopeptide-like motifs that form a concave groove, but their relative orientation differs by approx

106 tory transfer on substrates with terraces or grooves, but also gives rise to a successful result for

107 This groove cannot form with the bacterial ortholog.

108 complex binds to the mismatch from the minor groove, characteristic of metalloinsertion.

109 ine-1-carboximidamide, that binds to the TTD groove, competes with linker binding, and promotes open

110 resolution structures revealed a hydrophobic groove complementary to the GalNAc and, to a minor exten

111 HLA-C*06:02 possesses a deep peptide-binding groove comprising two electronegative B- and E-pockets t

112 Our model establishes the groove-crest modulation of tissue thickness as a morphom

113 a confined flow, or how surface topography (grooves, crevices, pores) influence QS-mediated communic

114 The fraction of cations in the minor groove decreases for the larger Sr(2+) ions and becomes

115 of BAK beyond the BH3 domain and hydrophobic groove did not inhibit multimerization and mitochondrial

116 integral membrane Bax proteins form a BH3-in-groove dimer interface on the MOM surface similar to tha

117 Therefore, the BH3-in-groove dimerization on the MOM nucleates the assembly of

118 Oligomerization was initiated by BH3-in-groove dimerization, without which neither the other dim

119 kbone conformation; sugar repuckering, major-groove directed kinking ( approximately 9 degrees ); and

120 results show how RNA Pol II copes with minor-groove DNA alkylation and establishes a mechanism for dr

121 eptide that displays highly selective, major groove DNA binding, (2) a reversible, metal-dependent DN

122 The promiscuity inherent to minor groove DNA recognition rationalizes the observation that

123 water molecules confined in the narrow minor groove exhibit very slow dynamics.

124 The lipid-binding groove exhibits flexibility and spans both monomers, ado

125 helix must bend in such a way that its major groove expands to conform to the dsRBD's binding surface

126 er of HLA-C alleles sharing a common binding groove F pocket with HLA-C*04:01.

127 The patches form grooves for specific lipid headgroup recognition or flat

128 feration might explain cartilage bending and groove formation at the macro-scale.

129 The fluorescent dye moves in the hydrophobic groove formed after folding of the peptide in the presen

130 n its canonical binding site consisting of a groove formed between switch II and helix alpha3.

131 te distinct from the ATP-binding pocket in a groove formed between two neighboring subunits.

132 al structure that projects into a deep, wide groove formed by the RNA.

133 Structural plasticity in the groove generates promiscuity allowing accommodation of h

134 i-methylation induced non-local backbone and groove geometries that were not conserved in the fully m

135 ove (base readout), proteins recognize minor-groove geometry using positively charged amino acids (sh

136 The roots with radicular grooves (grade 3 or 4) were defined as Tome's anomalous

137 used over a cylindrical "finger" part with a groove having a width corresponding to the braille dot s

138 We propose that previously described BH3-in-groove homodimers (BGH) are juxtaposed via the 'alpha3/a

139 iption factor proteins bind in the DNA major groove; however, we are interested in an approach using

140 structural properties, while differences in groove hydration play a large role for non-A-tracts.

141 is thought to originate from differences in groove hydration.

142 H-bonding, stacking interactions, and minor groove hydrations to some extent at the modified site, a

143 l side of Site 2 PXXP, which might contact a groove identified under the RT loop of the SH3 domain.

144 teraction between the tail and a hydrophobic groove in Arp3 blocks movement of Arp2 and Arp3 into an

145 THP binds near a predicted collagen-binding groove in D1, but a more extensive interaction with D2 i

146 t reveals that the LRS lies in a hydrophobic groove in the autoinhibited MTD.

147 other residues combine to form a GAG-binding groove in the CCL3 oligomer.

148 conserved epitope encompassing a hydrophobic groove in the fusion domain and a large portion of the f

149 s can also bind by either bulging out of the groove in the middle of the peptide or by binding in a z

150 identified a shallow pocket adjacent to the groove in the N-terminal region of NHR trimer as a new d

151 identified a shallow pocket adjacent to the groove in the NHR trimer and added a short artificial pe

152 internal ligand binding site; 2) a striking groove in the surface of the proteins as a putative bind

153 The membrane-distal one possesses a long groove instead of a small, well-defined pocket.

154 r interactions were more labile than the BH3:groove interaction within dimers, suggesting there is no

155 and compact core of Tat, while the TAR major groove interacts with the extended Tat ARM.

156 er agents that form DNA adducts in the minor groove interfere with DNA replication and transcription

157 drugs interact with the HLA peptide binding groove is important in the immunopathogenesis of T-cell

158 f processive PMEs, and the substrate-binding groove is negatively not positively charged.

159 mulations show that bending toward the major groove is preferred for non-A-tracts while the A-tract h

160 Water in the minor groove is, thus, orchestrated by the arrangement of AT g

161 y of the TMEM16 proteins localize around the groove, it was suggested that the ion and lipid pathways

162 ribble PDZ domain sequences in their binding grooves, it is common for these domains to show overlapp

163 This groove likely provides a pathway for lipid translocation

164 Rimmed grooves, lineations and elongate craters around Mare Imb

165 determined by either a 60 nL internal sample groove machined in a high-pressure valve rotor or by a 1

166 phasize the critical nature of the DNA minor groove microstructure for sequence-specific recognition

167 trium (N=105, 48%) and left atrioventricular groove (N=67, 31%), followed by Bachmann's bundle (N=27,

168 B-helix, accompanied movement of the peptide groove obscuring tryptophan residue, and consequent open

169 omomycin A3) binds specifically to the minor groove of (CCG)n repeats in duplex DNA, with unique fluo

170 tion of a phosphopeptide into an amphipathic groove of 14-3-3.

171 pitch and radius complementary to the major groove of B-DNA.

172 a helical conformation upon binding the BH3-groove of Bcl-xL, although lacking the h1-subregion inte

173 ng and loading of lipid antigens inside this groove of CD1 molecules require localization to endosoma

174 the final version of the antigen inside the groove of CD1.

175 nd show that it binds in the antigen-binding groove of CD1d in a manner compatible with its presentat

176 ghtly with its C-terminus to the hydrophobic groove of crenactin.

177 mechanism involving contacts with the minor groove of DNA and oligomerization.

178 lass cannot be accommodated within the minor groove of DNA due to a change in the shape of the molecu

179 -imidazole polyamides that bind to the minor groove of DNA in a sequence-specific manner without caus

180 ng side chains designed to bind in the minor groove of DNA while spanning a wide range of base streng

181 idazole (Py-Im) polyamides bind to the minor groove of DNA with programmable sequence specificity and

182 : 5LIT) shows that the drug covers the minor groove of DNA, displaces bound water and interacts with

183 teins make important contacts with the minor groove of DNA.

184 NA than Ndt80 and may bind only at the major groove of DNA.

185 vatives, which preferentially bind the minor groove of double-stranded DNA, inhibit vaccinia virus in

186 usual base-specific recognition in the minor groove of dsRNA are conserved between NF90 and ADAR2.

187 ce recognition properties of the hydrophobic groove of DYNLT1 known to accommodate dynein intermediat

188 uilibrium at the edge of the peptide-binding groove of HLA-DPB1 could account for most of the associa

189 d at position 71, within the peptide-binding groove of HLA-DRB1 (P = 2 x 10(-4) ).

190 domains, blocking access to the DNA-binding groove of its RecJ-like fold, and a helical insertion in

191 binds with high affinity to the BH3-binding groove of MCL1.

192 TAPBPR remodels the peptide-binding groove of MHC I, resulting in the release of low-affinit

193 cognizes a single G*C base pair in the minor groove of mixed base pair sequences of the type AAAGTTT.

194 permine is sequestered deep within the major groove of mixed-sequence RNA.

195 en the EC and TM domains, near the interlobe groove of NCT, emerges as an allo-targeting site that wo

196 The groove of such MH1Like, as well as iTRA chains used by m

197 quence make triple interactions in the major groove of the (GAUC)2.

198 ey binding site of CFTR (pS768) occupies one groove of the 14-3-3 dimer, and a weaker, secondary bind

199 erase active site by aligning with the major groove of the adducted DNA within the ternary complex of

200 the IIB1 class and interacts with the minor groove of the catalytic domain V.

201 NA-bound Rb(+) ions penetrate into the minor groove of the DNA and half adsorb on the DNA backbone.

202 rosine residues, which insert into the minor groove of the DNA duplex.

203 dies show that fdG is tolerated at the minor groove of the DNA to a better extent compared with other

204 he protein can bind both the major and minor groove of the DNA, but uses different features to locate

205 due is entirely solvent-exposed in the major groove of the DNA.

206 reverse Hoogsteen interactions in the major groove of the duplex, and we show physical evidence (i.e

207 e reveals that the glycan fills up a surface groove of the EGF with multiple contacts with the protei

208 Furthermore, a binding site in a groove of the extracellular domain was proposed but not

209 The hydrophobic groove of the human immunodeficiency virus type 1 (HIV-1

210 h the shallow hydrophobic pocket outside the groove of the NHR trimer, resulting in enhanced inhibiti

211 hey bind to a structurally conserved surface groove of the protein, and some of them inhibited pKM101

212 ese inhibitors bind within the ssDNA-binding groove of the RAD52 oligomeric ring.

213 is extending beyond its hydrophobic binding groove of the SRP M domain towards the translocon.

214 cellular proteins insert within the binding groove of this PDZ domain and determine the subcellular

215 an extended conformation spanning the minor grooves of helices 89 and 91 of the 23S rRNA and interac

216 A-binding-domains (DBD) of R insert in major grooves of O pre-TS, forming most Coulombic interactions

217 ll viral particles, with the major and minor grooves of RNA helices clearly visible.

218 Several strategies focusing on the binding grooves of the NHR trimer have been adopted to increase

219 Ridges and grooves of the template are 10 microm width and depth ra

220 CDC73-NTD contains an extended hydrophobic groove on its surface that may be important for its func

221 ed RAM binds to a positively charged surface groove on RNMT, distal to the active site.

222 to a unique and highly conserved hydrophobic groove on SNX5.

223 of the membrane by traversing a hydrophilic groove on the membrane-spanning surface of the protein.

224 the electropositive character of a 20 A-wide groove on the surface of Prp24.

225 lpha, which binds to the coactivator-binding groove on tRXRalpha and dissociates from tRXRalpha upon

226 bit HIV fusion by binding to the hydrophobic grooves on the N-terminal heptad repeat (NHR) trimer and

227 e their association to the canonical binding groove or to the secondary site within the DYNLT1 surfac

228 external sample loop, although other sample grooves or loops could be selected.

229 acid tail with two CRD palmitoleoyl-binding grooves oriented end to end, suggesting that the Wnt pal

230 signal sequence forms a helix that sits in a groove outside the lateral gate, while the following pol

231 was also printed using collagen coated micro-grooved Parylene C.

232 l test 0.29, -1.2 to 1.8), manual dexterity (Grooved Pegboard Test 4.2, -1.3 to 9.7), and attention o

233 sterrieth Complex Figure Test, and Lafayette Grooved Pegboard Test).

234 state this tunnel can be transformed into a groove prone for RNA binding by large rearrangements of

235 ich the 5-methyl group points into the minor groove, rather than the major groove as in a normal Wats

236 exploring different occupancy states of the groove reenacted these different CD1c conformations and

237 Changes include groove relaxation, modifications of key binding pockets,

238 tive modes of interactions between the minor groove residues.

239 tic center and a conserved substrate-binding groove, respectively.

240 ges that clench the ssDNA within the binding groove, revealing the architecture and mechanism of ssDN

241 minor groove and can be considered a "minor groove sensor." Prolonged interference of transcription

242 cies are significantly reduced for flat- and groove-shape binding sites, suggesting that adjustments

243 es lead to rodlike ligands that bind well to groove-shaped binding sites.

244 lt target classes that have large, flat, and groove-shaped binding sites.

245 their indole nitrogen atoms lie on the major groove side, and thus their pendant methyl groups are on

246 is recognized in duplex form, from the minor groove side, by three structural features in the Cascade

247 their pendant methyl groups are on the minor groove side.

248 adenine (3-dMeA), which blocks the DNA minor groove similarly to 3-MeA.

249 ccelerate the hydration dynamics in confined groove sites.

250 located at the bottom of the peptide-binding groove, spanning from the P1 to P4 pockets, renders the

251 RNA kinks by an association of the two minor grooves, stabilized by the formation of a number of key

252 s, such as for cells on cyclically stretched grooved substrates, the effects of these stimuli can be

253 on of cells cultured on cyclically stretched grooved substrates.

254 th and bone, periosteal reaction, serpentine grooving surrounding teeth (considered a sign of inflamm

255 The interaction between the minor groove tetrads and the nearby C:C(+) base pairs affords

256 ated C:C(+) base pairs, flanked by two minor groove tetrads resulting from the association of G:C or

257 eta strand, creating an extended hydrophobic groove that binds the C-terminal donor strands of the in

258 l MHC-I fold and possessed a peptide-binding groove that exhibited features similar to those found in

259 nding through interaction with the DNA minor groove that flanks PU.1-binding motifs.

260 n the form of a bilayer-spanning hydrophilic groove that is directly exposed to the membrane.

261 ket and a positively charged peptide-binding groove that together promote preferential binding of CLI

262 h HOPS subunit, an SM protein, has conserved grooves that bind R- and Qa-SNARE domains.

263 ein forms a dimer containing two amphipathic grooves that can potentially bind these phosphorylated m

264 SecB uses long hydrophobic grooves that run around its disk-like shape to recognize

265 the local DNA shape: the width of the minor groove, the relative orientations of adjacent base pairs

266 In both peptide binding grooves, the mutation of B:22R to E in the peptide chang

267 he Arp3 nucleotide cleft and the hydrophobic groove, thereby promoting the short-pitch conformation.

268 s the motif residues toward its deep binding groove, therefore explaining the molecular requirements

269 rmediate filament rods into basic PRD domain grooves through electrosteric complementarity in a widel

270 cts with a cysteine near the peptide-binding groove to augment specificity.

271 ch using small molecules to target the minor groove to control expression by an allosteric mechanism.

272 with interaction at alpha6 promoting an open groove to receive a BH3-only protein.

273 steric block, relocating spermine from major grooves to interhelical regions, thereby increasing DNA-

274 Steric inaccessibility of the grooves to large CoHex ions leads to their binding at th

275 , which forms a compact structure with major groove U*A-U and novel C*G-A(+) base triples.

276 bstituting as a surrogate beta-strand in the groove vacated by the native strand.

277 According to ASUDAS, the scores of radicualr grooves were 56.74%, 16.85%, 12.36%, 10.11%, 3.37% and 0

278 nd canals, canal configuration and radicular grooves were investigated.

279 The radicular grooves were scored according to the Arizona State Unive

280 bic pocket that runs perpendicular to a long groove where the active site is located.

281 ich is flanked by two Cas3 domains forming a groove where the protospacer binds to Cas1-Cas2.

282 erogeneity is especially strong in the minor groove, where groove width fluctuations occur on the sam

283 ineage except at the C-terminal Bag6-binding groove, which evolved to accommodate Bag6, a unique meta

284 hat opens up to expose a central hydrophobic groove, which interacts with the N-terminal portion of t

285 enerally larger for bending toward the minor groove, which is thought to originate from differences i

286 core subdomain of SHR forms the BIRD binding groove, which specifically recognizes the zinc fingers o

287 helix to read the base sequence in the major groove while inserting a beta sheet 'wing' into the adja

288 The groove widening aids the approach of, and the jump to, a

289 adout involves the correlation between minor-groove width and electrostatic potential (EP).

290 tures, Propeller twist, Helical twist, Minor groove width and Roll.

291 cal effect directly, rather than using minor-groove width as an indirect measure for shape readout, w

292 especially strong in the minor groove, where groove width fluctuations occur on the same time scale a

293 and six inter-base pair parameters and minor groove width, is available in our R/Bioconductor package

294 (A) sequences associated with narrowed minor groove width.

295 act experiments, shock physics codes and the groove widths indicate that multiple fragments (up to 2%

296 of the correlation coefficient between major groove widths inferred from a shorter molecular dynamics

297 arameters, helix parameters, and major/minor groove widths to examine how the presence of multiple, c

298 orm C3' endo sugar puckers but widened major groove widths, giving the RNA an overall architecture th

299 lds dopant-dependent, massive and ordered 3D grooves with spacing down to 5 nm.

300 mations dependent on ligand occupancy of its groove, with CE and ASG stabilizing CD1c conformations t

301 ha2,3 sialic acid moieties bind tightly to a groove within the PECAM-1 homophilic interface in an ori