ライフサイエンスコーパス: groove

1 served residues in a putative client-binding groove.

2 f the NES motifs bound to the CRM1's binding groove.

3 (i.e. 8-10-mers) to fit into the MHC class I groove.

4 eins utilizes a membrane-exposed hydrophilic groove.

5 mblase fold, with an open lipid transporting groove.

6 x alpha13 that form edges of the RNA binding groove.

7 6-4PP:AA nucleotide pairs towards the major groove.

8 group of DNA backbone, or 5caC in the major groove.

9 en-bond acceptor or donor group in the major groove.

10 BBP4 within the conserved histone H3-binding groove.

11 tif spans the entire length of the TAR major groove.

12 g of two protofibrils separated by a shallow groove.

13 volved in peptide editing toward the binding groove.

14 and a propensity to interact with the N RNA groove.

15 ion of a long helix binding in the DNA major groove.

16 binding domain associated with the DNA minor groove.

17 facilitate Xis-DNA contacts within the major groove.

18 ck substrate access to the substrate-binding groove.

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

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

21 cognition helix region relative to its major groove.

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

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

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

25 two isoforms share an identical NLS-binding groove.

26 molecule, focused around the peptide-binding groove.

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

28 divergent substrates utilizing a hydrophilic groove.

29 a-helix within Orc4 inserts into a DNA major groove.

30 ning angle, width and depth of the bicipital groove.

31 -DP allele-specific sequences of the binding groove.

32 ogues within the HLA-B*57:01 peptide binding groove.

33 one phosphates in the ribonucleotide-binding groove.

34 re often found at sites that bend into minor grooves.

35 r distances, higher than that of the grating grooves.

36 red orientation of lexitropsins in the minor grooves.

37 ening angle (60 vs 50(o), p=0.044) and wider grooves (11.9 vs 9.7mm, p=0.019).

38 t, respectively, with a thymine in the minor groove, a phosphate group of DNA backbone, or 5caC in th

39 triking features are its wide and deep major groove, a smaller inclination angle and all three strand

40 ucture shows that it contains a deep surface groove absent in the G3P-bound wild-type UgpB.

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

42 er in an X-shape to form two nonplanar minor-groove-aligned G.C.G.C tetrads.

43 a mysterious bone of platypus, and external grooves along the crura.

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

45 a loop within Orc2 inserts into a DNA minor groove and an alpha-helix within Orc4 inserts into a DNA

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

47 A lipid binding groove and clusters of conserved residues highlight pote

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

49 that bypasses abasic sites, as well as minor-groove and exocyclic guanine adducts.

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

51 phic morphologic evaluation of the bicipital groove and LHBT pathology.

52 sitions the 2-amino group of OG in the major groove and provides a means to indirectly select only th

53 d to the phosphate backbone of the DNA minor groove and showed a preference for DNA molecules bearing

54 of two isolated P.Z pairs enlarges the minor groove and slightly narrows the major groove at the site

55 (v)1.5 organizes as distinct clusters in the groove and T-tubules which density, distribution, and or

56 inds with fast kinetics to a surface-exposed groove and that interactions at the identified site are

57 ligands indicates a preference for the minor groove and weaker unspecific and more salt-dependent bin

58 by complementing "lock and key" hydrophobic grooves and inserts and electrostatic charges between th

59 through narrow channels and pipes, entering grooves and itinerating in a maze by adapting and recove

60 ally occur at DNA sites that bend into major grooves and SS (where S is G or C) dinucleotides are oft

61 ning electron microscopy, we observed that Z-grooves and t-tubule openings at the cell surface appear

62 d the alpha(2) domain of the peptide-binding groove, and depends on the formation of a conserved MHC-

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

64 t the lateral membrane, the lateral membrane groove, and T-tubules in cardiomyocytes from wild-type (

65 te, as well as formation of the nasolacrimal groove, and they furnish a powerful resource for those i

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

67 Several conformations of the groove are observed in TMEM16 protein structures, but ho

68 oying a regular array of semicylinder-shaped grooves around a nanoslit has been investigated based on

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

70 air shafts reveals deformities (longitudinal grooves) as well as plaque-like adhesions to the hair, l

71 diated by the structure of the RecA filament groove, associated by conformation changes propagated in

72 minor groove and slightly narrows the major groove at the site of this synthetic genetic information

73 defined by a characteristic peptide binding groove B pocket.

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

75 helix (TM)-III and TM-IV and a lipid-exposed groove between the intracellular segments of these helic

76 -strand-like conformation and inserts into a groove between the kinase domain of one TBK1 subunit and

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

78 ligands, namely, a representative DNA minor-groove binder (netropsin) and ligands binding DNA base-p

79 -specific PCR with a blocking reagent (minor groove binder [MGB] oligonucleotide blocker) to suppress

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

81 FRET-based reporters armed with a DNA minor groove binder, which monitor DNA-bound NE and CG activit

82 mic and binding characteristics of DNA minor groove binders (MGBs) is important for the rational desi

83 ing therapies including those based on minor groove binders (MGBs), such as the diamidines, which hav

84 shijimicin A in competition with known minor groove binders, UV spectroscopic studies, and electropho

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

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

87 iled analyses reveal sequence-enhanced major groove binding (SEGB) of point-charged alkali ions as th

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

89 bations to the AR cistrome caused by a minor groove binding molecule that is designed to target a seq

90 cular dynamics simulations showed that minor groove binding perturbed the conformational dynamics and

91 ges result in a switch from intercalation to groove-binding DNA interaction and concomitant reduction

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

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

94 onding between a native cysteine pair at the groove (C55) and C-terminal alpha9 helix (C175) of BFL-1

95 positions in a continuous positively charged groove compatible with viral genome binding.

96 n and expression of a "crown buccal vertical groove complex", all of which are uncommon in modern hum

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

98 ar dynamics simulations showed that the open-groove conformation is necessary for scramblase activity

99 3/TM4 interaction patch that braces the open-groove conformation, which should be changed by an L302A

100 in conjunction with different HLA-DP binding groove conformations.

101 creased ~380-fold when Asn279-mediated minor groove contact to dGTP was abolished.

102 which was stabilized by Gln38-mediated minor groove contacts to oxoA:dGTP.

103 t Phactr1 binding remodels PP1's hydrophobic groove, creating a new composite surface adjacent to the

104 Alterations in this groove decrease the ability of BMF and HRK to bind BAK,

105 resence of dome structures, a corrugated and grooved detachment fault, and subdetachment deformation

106 rved residues in the putative client-binding groove did not alter the UCS domain secondary structure

107 otif, with most contacts formed in the minor groove, differs from previously observed protein-DNA rea

108 to the high risk for fatal atrioventricular groove disruption and significant paravalvular leak.

109 uggest that Phe31 of ELA may bind to a tight groove distinct from that of Phe13 of Ape13, while the P

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

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

112 XA9/DNA interaction through binding as minor groove DNA ligands on the HOXA9 cognate sequence.

113 ns with the phosphate backbone and the major-groove edge of guanine and (ii) simultaneous cation-pai

114 pairs as long blocks and highlight the minor-groove edges.

115 ntry now include 13 shape features and minor groove electrostatic potential for standard DNA and four

116 which promotes mitochondrial translocation, groove exposure for BH3 interaction and inhibition of mi

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

118 articularly at positions where the DNA minor groove faces away from the histone octamer.

119 h of two spatial textures formed by parallel grooves feels rougher) while continuously measuring the

120 ageneses confirm that a triplex deep binding groove for CATCs is a hotspot that holds promise for ant

121 aximized by optimizing the dimensions of the grooves for potential use in applications involving neur

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

123 pport a model in which SurA binds uOMPs in a groove formed between the core and P1 domains.

124 K involves a previously unrecognized binding groove formed by BAK alpha4, alpha6, and alpha7 helices.

125 whereas altering residues in the hydrophobic groove formed by the two extracellular loops abrogates c

126 hanism of a conformational transition of the groove from membrane-exposed to occluded from the membra

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

128 ructures that surround the substrate-binding groove, generating a negative surface potential, are dif

129 ntext-dependent effect of methylation on DNA groove geometry can affect DNA binding by homeodomain pr

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

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

132 The presence of nanoscale grooves greatly enhances the outgrowth of neurites from

133 ginines could bind simultaneously with major-groove guanines.

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

135 le in the PLC, stabilizing the MHC-I binding groove in a conformation reminiscent of antigen-loaded M

136 the radiographic evaluation of the bicipital groove in predicting long head of biceps tendon (LHBT) p

137 The tau-binding groove in the ACD also binds short hydrophobic regions w

138 are mediated predominantly by a DNA-binding groove in the Cenp-L-Cenp-N subcomplex.

139 eveal that the Drs2p C-terminus lines a long groove in the cytosolic regulatory region to inhibit the

140 se activation map to a previously identified groove in the EnvC LytM domain that is here found to be

141 amolecular interactions with the DNA binding groove in the free factor, which, we propose, inhibits i

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

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

144 e out of plane stress at the boundary of the grooves in the reaction layer could inhibit the propagat

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

146 ated mutagenesis is greatly induced by minor groove interactions.

147 :dGTP misincorporation was promoted by minor groove interactions.

148 synthetic molecules targeting an alpha-helix/groove interface essential for RED-SMU1 complex assembly

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

150 umenally-sealed, lipid-exposed intramembrane groove large enough to accommodate a single substrate TM

151 ages BHD2 to bend/untwist DNA from the minor groove, leading to unstacking and extrusion of the 6-4PP

152 terium prausnitzii binds to FMN on a surface groove located 30 angstrom away from the active site.

153 methionine or homocysteine chain lies in the groove making a single hydrogen bond, and there is no di

154 Untwisting/bending from the minor groove may be a common way to interrogate DNA in NER.

155 In vivo, these groove mutations were found to significantly alter the s

156 2'-deoxyguanosine (O (6)-alkyl-dG) and minor-groove N (2)-alkyl-dG lesions in human cells, where the

157 a-helices at the outer edges, and basic side grooves near the dimer interface.

158 ences, we characterized the unique hook-into-groove NEC interaction at various levels.

159 of these two polymerases in bypassing major-groove O (6)-alkyl-2'-deoxyguanosine (O (6)-alkyl-dG) an

160 ol nu and Pol theta promote TLS across major-groove O (6)-alkyl-dG lesions.

161 lated at Ser(16) or Thr(17) with the binding groove of 14-3-3, resulting in varied binding affinities

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

163 and harnessed a unique cysteine (C55) in the groove of anti-apoptotic BFL-1 to selectively neutralize

164 e preventing HMGA2 from binding to the minor groove of AT-rich DNA sequences.

165 loop that is inserted deep into the binding groove of CD1d where it makes intimate nonpolar contacts

166 h Na(v)1.5 being specifically reduced at the groove of DeltaSIV and increased in T-tubules of mdx car

167 scovered that selectively binds to the minor groove of DNA and is actively used as a scaffold for dev

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

169 s are small molecules that bind to the minor groove of DNA as antiparallel dimers in a specific orien

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

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

172 : 5LIT) shows that the drug covers the minor groove of DNA, displaces bound water and interacts with

173 rogen bonding and intercalation in the minor groove of DNA, involving hydrophobic interactions.

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

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

176 cate that shishijimicin A binds to the minor groove of double-stranded DNA and that its beta-carbolin

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

178 s locate under/adjoining the peptide-binding groove of DRB1, suggesting a plausible functional mechan

179 addition, the mutations located in the large groove of EBV gH/gL (R(152)A and G(49)C) also have decre

180 The drug binds within the peptide binding groove of HLA-B*57:01 altering peptides displayed on the

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

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

183 feathers is not homologous with the ventral groove of modern rachises.

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

185 consecutively bind into the open ATP-binding groove of the beta-subunit, which thereafter becomes tig

186 acid residues, mostly in the peptide-binding groove of the class II HLA molecules.

187 g a protein loop that intercalates the minor groove of the DNA (termed the intercalating loop).

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

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

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

191 Genetic variation in the peptide-binding groove of the highly polymorphic HLA class I molecules h

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

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

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

195 GSSV peptide specifically binds to the major groove of the TIP1 protein surface.

196 hUHRF1, the linker is anchored in a surface groove of the TTD domain, resulting in creation of a cou

197 The major groove of this helix provides the binding site for L-glu

198 binding domains that interact with the major groove of W-box DNA.

199 transiently folds back into the hydrophilic groove of YidC located in the inner leaflet of the membr

200 binding cleft shared by inter-bladed binding grooves of beta-propeller.

201 erminal domains dock into the adjacent major grooves of DNA to specifically recognize the 5'-TTGTACAN

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

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

204 the central channel, transversal loops, and grooves of the Oxytricha nova's telomeres' G-quadruplex

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

206 we show that a conserved, negatively charged groove on B56 mediates dynamic binding.

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

208 to its core beta-helical structure create a groove on one side of the protein for interaction with g

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

210 release of the disordered NTR from a binding groove on the ACD enhances chaperone activity toward tau

211 is weakly associated with a shallow anionic groove on the DspB protein surface with recognition driv

212 he results support a model in which multiple grooves on the ACD interact with specific NTR regions, c

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

214 and cBL measurements, individually adjusted grooves on the reference stent were prepared for each pe

215 ains two >80 degrees kinks towards the minor groove, only 3 bp apart.

216 an extended loop going through the DNA minor groove, or the N-terminal portion of a long helix bindin

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

218 stinal stromal tumours, Crohn's disease, and groove pancreatitis are discussed.

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

220 tion had significantly poorer performance on grooved pegboard (P < .001) and fingertapping nondominan

221 or Trails-1 (CTT1)], and two motor function [Grooved Pegboard-dominant (GP-DH) and non-dominant (GP-N

222 Consistently, restriction of MHC-I groove plasticity through the introduction of a disulfid

223 t expression strategy based on NEC-hook::NEC-groove protein fusion constructs.

224 en the cytosolic vestibule and intramembrane groove provides a potential path for substrate egress fr

225 Typical channel geometries include grooves, rails, or beams and complex systems with multip

226 and the G-protein-binding site is a shallow groove rather than a cleft.

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

228 Minor groove recognition by DB1976, therefore, generates dynam

229 The structural basis of minor groove recognition of a DNA duplex containing synthetic

230 A structural hallmark of minor groove recognition of a P.Z pair by a polyamide is the r

231 molecular determinants that influence minor groove recognition of DNA containing synthetic genetic c

232 tter understand the factors that drive minor groove recognition.

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

234 ct combination of a new fold and hydrophobic grooves resembling preprotein-binding sites of the SecB

235 s faster than theta( ) due to pinning on the grooves resulting in an elongated drop shape.

236 Our analysis shows that positioning of the groove right at the exit of the slit is crucial for the

237 The Fis-structured minor groove shape that is optimized for Xis binding requires

238 Radiographic evaluation of the bicipital groove showed a mean medial opening angle of 53+/-15(o)

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

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

241 ta allows discerning details such as helical grooves, single-strand versus double-strand crossovers,

242 and dorsoventrally thin rachis, and a dorsal groove (sometimes pigmented) that we identify as the "me

243 d ribose zipper and jointly create a binding groove specific to the anticodon of its cognate tRNA.

244 shes that HRP3 PWWP is a new family of minor groove-specific DNA-binding proteins, which improves our

245 d in its nuclear export signal (NES)-binding groove, suggesting that binding of select NESs may be al

246 sed to study bacterial twitching on flat and groove surfaces under shear flow conditions.

247 s also indicate that when bacteria twitch on groove surfaces, they are likely to accumulate around th

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

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

250 rdination and generates a positively charged groove that binds substrates.

251 roscopy (cryo-EM) reveals a partially closed groove that could translocate ions, but not lipids.

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

253 show that recognition occurs via a conserved groove that is essential for MERS-CoV S-mediated attachm

254 rones includes a shallow, positively charged groove that poses a significant challenge for druggabili

255 amylose binding and suggest that the shallow groove that spans the active-site surface of AA13 PMOs f

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

257 llable microstructures feature undercuts and grooves that accommodate deformed surface microstructure

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

259 in an alpha-helix inserted in the DNA major groove (the recognition helix).

260 ng a horseshoe-shaped conformation in a deep groove, the glycan headgroup likely sits flat against th

261 In case of semicylinder-shaped grooves, the calculated intensity of the output beam was

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

263 groups sterically blocked the ligand-binding grooves, thereby strongly inhibiting the interaction wit

264 onetheless by their organellar cargo and the grooves they formed indenting MCs, which was consistent

265 s suppress cell death by deploying a surface groove to capture the critical BH3 alpha-helix of pro-ap

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

267 Fis binding both molds the minor groove to potentiate insertion of the Xis beta-hairpin w

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

269 aligned microfibers engraved with nanoscale grooves to promote neurite outgrowth and cell migration.

270 both near and distant to the peptide-binding groove, to selectively recognize discrete conformational

271 fairly conserved in CrmD and dominated by a groove under its 50s loop.

272 ally resulting in the formation of nanoscale grooves upon the removal of PVP.

273 accumulate around the downstream side of the groove walls.

274 iant (156Q) within the HLA-A peptide-binding groove was associated with greater odds of sepsis [OR 1.

275 A substrate-binding groove was formed between the EF domain and the conserve

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

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

278 tivate BAK through its canonical BH3 binding groove, whether the BH3-only proteins BMF, HRK or BIK ca

279 slit, we have successfully demonstrated that grooves which are embedded on the layer at the exit side

280 dges corrugated with an array of rectangular grooves which effectively confines the electromagnetic f

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

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

283 tion and compression of the atrioventricular groove, which worsened during stress and were related to

284 ate their preferred orientation in the minor grooves, which to date have not been investigated.

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

286 first flips out and is captured by a BHD2/3 groove, while the 3' adenine extrudes episodically, faci

287 leobase interaction sites in the RNA-binding groove, whose impact on assembly kinetics was measured u

288 Here, we constructed and applied Minor Groove Width (MGW) as a prioritization metric.

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

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

291 Using inferred knowledge about minor groove width readout, we design targeted protein mutatio

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

293 nce for DNA molecules bearing a narrow minor groove width.

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

295 se location has been shown to modulate minor groove widths in Fis-bound complexes to different DNA ta

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

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

298 This conformation leads to an open major groove with enough potential binding sites for peptide r

299 that tau binds both to a well-known binding groove within the structured alpha-crystallin domain (AC

300 ted in solvent accessible, consecutive major grooves without significant changes in nucleosome struct