ライフサイエンスコーパス: solvent-accessible

1 inding to NF-kappaB, but AR 1 remains highly solvent accessible.

2 (AdoMet), only C15 and C431 of human CBS are solvent accessible.

3 MTS) sulfhydryl labeling agents, and is thus solvent accessible.

4 en the core and the cap domain and is freely solvent accessible.

5 proteolyzed and the conserved arginines are solvent accessible.

6 tic domain (199-203 and 310-317) became more solvent accessible.

7 ices are the only conserved regions that are solvent accessible.

8 e hinge region, which is highly flexible and solvent accessible.

9 ce fully encapsulated catalytic machinery is solvent accessible.

10 protein while residues in the V3 base remain solvent accessible.

11 s, whereas that on the small subunit remains solvent-accessible.

12 y, and is lined by many residues known to be solvent-accessible.

13 In the context of the open and fully solvent-accessible active site for the homologous peptid

14 2 linker allows for the formation of a deep, solvent-accessible, active-site pocket, which may allow

15 nking the adduct were impaired, and multiple solvent-accessible adduct conformations were observed.

16 at the newly created N terminus becomes more solvent-accessible after cleavage.

17 ts suggest that TMS7 of hPepT1 is relatively solvent-accessible along most of its length but that the

18 The exchange rates of the static solvent-accessible amide hydrogens of Pyrococcus furiosu

19 ding studies with LexA mutants, in which the solvent accessible amino acid residues in the putative D

20 The reactive and solvent-accessible amino acid side chains function as st

21 Side chains at X sites are more solvent accessible and considerably more mobile than res

22 rp723 and Trp775 were found to be relatively solvent accessible and inaccessible, respectively, while

23 The active site is solvent accessible and located in a cleft between the tw

24 The phosphorylation site in the CTR is solvent accessible and located in a negatively charged p

25 e mouse nicotinic acetylcholine receptor are solvent-accessible and are in a position to contribute t

26 that the metal binding site is likely to be solvent-accessible and contiguous with a large binding c

27 r the headgroups, making the headgroups more solvent-accessible and increasing surface hydrophilicity

28 esidues in their aminoterminal tails, on the solvent-accessible and lateral surfaces of the nucleosom

29 The outcome shows that CaM becomes less solvent-accessible and more compact upon Ca(2+)-binding,

30 rimarily the cytosolic half of TM4 is highly solvent-accessible and plays an important role in ASBT f

31 However, its hydrophobic core becomes solvent-accessible and some of its beta-strands lose the

32 This hydrogen is solvent-accessible, and exchanges slowly with H2O on the

33 2+)-free rat beta-PV, perhaps due to greater solvent-accessible apolar surface in the native form.

34 The magnitude of the buried solvent accessible area corresponding to the protein-pro

35 nds in the ternary complex: this reduces the solvent accessible area of the ligand and provides a fav

36 high-quality correlations with the change in solvent accessible area upon complexation.

37 We conclude that solvent accessible area, based on modelled mutant struct

38 umber of structural characteristics (such as solvent accessible area, distribution of (Phi, Psi) angl

39 r the Zn(2+) binding site and reached into a solvent accessible area.

40 he simulation results also indicate that the solvent-accessible area, traditionally used to measure s

41 This provides solvent accessible areas for proteins that are much clos

42 s, hydrogen bonding energies, and amino acid solvent-accessible areas.

43 the 5'-untranslated region (5'-UTR) remains solvent-accessible at high eIF4G concentrations.

44 uired for direct activation, is likely to be solvent-accessible at the extracellular domain vestibule

45 which contain significantly larger and more solvent accessible binding sites than DhlA.

46 ylated lysines 115 and 122 in histone H3 are solvent accessible, but in biochemical assays they appea

47 inal residues, Y101C and Y106C, were readily solvent-accessible, but upon incubation with alpha-facto

48 nchored ubiquitin in protein aggregates with solvent-accessible C termini.

49 enzyme-enzyme cross-linking by blocking the solvent-accessible carboxyl groups of horseradish peroxi

50 olar solvents such as toluene, the number of solvent accessible carboxylic acids decreases.

51 polar solvents such as water, the number of solvent accessible carboxylic acids in the polymers incr

52 e metal ion, located at the bottom of a wide solvent-accessible cavity in the C-terminal domain of th

53 The latter delineates a solvent-accessible cavity where substrates bind and cata

54 Here, we report the identification of a solvent-accessible cavity within the PrfA N-terminal dom

55 Libraries were constructed such that solvent-accessible CDR positions were randomized with a

56 an effort to alter the volume of an apparent solvent accessible channel at the interface or to alter

57 This allows the inhibitor to extend into the solvent-accessible channel farther away from the active

58 The existence of a large solvent-accessible channel in the dimer interface as wel

59 h are far apart and bisected by a wide open, solvent-accessible cleft.

60 ate binding due to increased exposure of the solvent-accessible cluster of non-polar groups.

61 himpanzee KIRs with HLA-C specificities form solvent-accessible clusters outside the KIR-HLA interfac

62 lagen chains, burying a total of 720 A(2) of solvent-accessible collagen surface.

63 S predicts sites that are significantly more solvent accessible compared to Williamson.

64 cleft in the protein surface and is uniquely solvent-accessible compared with other PQQ enzymes.

65 eases the lifetimes of the bases in an open, solvent-accessible conformation.

66 terface between the two domains, but Cys9 is solvent-accessible, consistent with its role in catalysi

67 at the lower limit for Cys and is common for solvent-accessible Cys thiols.

68 Unique solvent-accessible cysteine residues were introduced int

69 The solvent-accessible disulfide bond in the isolated SH2 do

70 Identification of solvent-accessible disulfides using published structural

71 In addition, computational analysis of solvent-accessible domains identified five key solvent p

72 of ROS leading to increased availability of solvent-accessible extracellular thiols.

73 urface formed from the three beta-sheets and solvent-accessible faces of the other three helices.

74 ive probable epitopes have been located on a solvent-accessible flexible region by computational anal

75 cleotide-binding pocket of Ypt1p in an open, solvent-accessible form.

76 It contains a solvent-accessible globular domain that interfaces with

77 l vibrational probe covalently attached to a solvent accessible His residue.

78 pKa values than His-19, indicating that the solvent-accessible His-27 facilitates proton conduction

79 lar hot spots for dehydration propensity, or solvent-accessible hydrogen bonds in soluble proteins, n

80 rly folding stage, barstar forms a partially solvent-accessible hydrophobic core consisting of severa

81 otein-bound form follows from an analysis of solvent-accessible hydrophobic patches on the surface of

82 ophila enzyme containing only ADP revealed a solvent-accessible hydrophobic pocket formed by residues

83 that the initiating domain of apoB contains solvent-accessible hydrophobic sequences, which, in the

84 nt of tertiary structure with a considerable solvent-accessible hydrophobic surface, but is not a cla

85 solic half of the TM3 helix were found to be solvent accessible (i.e., S128C, L143C-T149C).

86 n of the L299W mutant indicates that L299 is solvent accessible in the absence of Ca(2+)/CaM but beco

87 these regions of the RNA were observed to be solvent-accessible in previous footprinting studies unde

88 idues, with one out of five tryptophans more solvent-accessible in the ADAR2.RNA complex.

89 become more structurally dynamic and/or more solvent-accessible in the ADCs.

90 and chymotrypsin inhibitor 2 (CI2) that are solvent-accessible in the high-resolution X-ray structur

91 eous quenching agents whereas Trp-41 remains solvent-accessible in the presence of PS-containing vesi

92 the exception of M108 in ApoE4 which is more solvent-accessible in this isoform than in ApoE2 and Apo

93 lly those at the N-terminal region, were not solvent-accessible, including residues of the binding-co

94 The solvent-accessible inner surface area was found to be a

95 rs (DeltaH and DeltaS) are consistent with a solvent-accessible ISU-bound cluster, with desolvation a

96 are gated through binding of glutamate to a solvent-accessible ligand-binding domain.

97 ich makes the nucleotide-binding pocket more solvent accessible, likely also facilitates exchange.

98 ral domains on the extracellular side, three solvent-accessible low-density cavities, and a potential

99 de (TBHP), a bulky peroxide, to oxidise only solvent accessible Met residues or H2O2, the smallest pe

100 that appear primarily in the nonfunctional, solvent-accessible NNRTI binding pocket.

101 ends correlate with the specific fraction of solvent-accessible nonpolar surface area present at diff

102 rs to oligomerize through coalescence of the solvent-accessible nonpolar surfaces.

103 oxylic acid recognition groups into either a solvent accessible or inaccessible orientation.

104 periments, backbone amide hydrogens that are solvent accessible or not involved in hydrogen bonding b

105 , Ile(267), and Ile(268)) form a contiguous, solvent-accessible patch on the surface of the protein l

106 highly protected PKA binding site and a more solvent-accessible PDZ binding motif, which may serve as

107 Because the solvent-accessible peptide area constitutes only a small

108 T cell recognition involves solvent-accessible peptide residues along with minor cha

109 lix 1 and 1' of the apposing monomers form a solvent-accessible pocket at the dimeric interface that

110 ions that affected avirulence localized to a solvent-accessible pocket in the protein structure.

111 lmS ribozyme binds its activator in an open, solvent-accessible pocket.

112 del of the Jak2 kinase domain and identified solvent accessible pockets on the surface of the structu

113 al location in the inactive enzyme to a more solvent accessible position in the active enzyme.

114 ical either abstracts a hydrogen atom from a solvent accessible position in the enzyme or obtains a p

115 inward-facing hydrophilic cavity or at other solvent-accessible positions in LacY react well with thi

116 d tryptophans are in a structured, partially solvent-accessible, positively charged environment.

117 troduced cysteines was employed to probe the solvent-accessible profile of highly conserved transmemb

118 ed photoswitchable ligands, however, require solvent-accessible protein labeling, face structural con

119 , a protein-protein interaction surface, the solvent-accessible protein surface, and the stability of

120 frequencies in interface patches versus the solvent-accessible protein surface, we define a propensi

121 ng conditions, whereas the region 95-105 was solvent-accessible regardless of the solvent conditions.

122 This position is presumably close to the solvent-accessible region of the target protein-inhibito

123 Mutation of Trp-247 at the solvent-accessible region significantly reduced the hydr

124 The secondary structure and solvent accessible regions of oncomiR-1 reveal that most

125 tly folded regions, flanked by disordered or solvent accessible regions.

126 dicated that the oxidation sites were all on solvent-accessible regions at the protein surface.

127 s is therefore a rapid approach to elucidate solvent-accessible regions of folded proteins.

128 This calculation quantifies burial of solvent-accessible regions.

129 phorylation site in this domain is Thr393, a solvent-accessible residue in a key hinge region of the

130 Here we show that covalent labeling of solvent accessible residues followed by their MS-based i

131 Molecular dynamics simulation revealed solvent accessible residues within the beta1 strand of t

132 Three non- conserved, potentially solvent-accessible residues at positions 762, 763 and 76

133 /mol), whereas the apparent contributions of solvent-accessible residues at the periphery are much le

134 aries and by randomly mutating four putative solvent-accessible residues in CDR1 to A, D, S, or Y.

135 the most reactive residues correspond to the solvent-accessible residues in the bacterial KcsA channe

136 t other Glut1 transmembrane domains in which solvent-accessible residues lie along a single face of t

137 e optimized procedure, native and introduced solvent-accessible residues on proteins were selectively

138 The functions of these solvent-accessible residues were assessed by determining

139 ing or disrupting protein interactions using solvent-accessible residues, and it can provide addition

140 er to create a more open structure with more solvent-accessible Rieske centers.

141 ies of thermolysin inhibitors addressing the solvent-accessible S2' pocket with different hydrophobic

142 folding introduces covalent modifications at solvent accessible side chains.

143 ble globular domain that interfaces with the solvent accessible side of the large subunit that is lin

144 the T jump lead to oxidative modification of solvent-accessible side chains whose "protection" change

145 ith the exception of methionine, have highly solvent-accessible side chains, but the rate of oxidatio

146 (.OH) introduces oxidative modifications at solvent-accessible side chains, while buried sites are p

147 The highly solvent-accessible site rapidly lost conjugated thiol-re

148 taining radicals that undergo reactions with solvent accessible sites of macromolecules inducing stab

149 nformers were defined by surface mapping the solvent-accessible sites for strategic secondary structu

150 ntly been demonstrated to oxidatively modify solvent-accessible sites of proteins inside live cells (

151 or identifying such proteins that (i) have a solvent accessible structural motif necessary for DNA-bi

152 ever, significant average differences of the solvent accessible surface and crystallographic displace

153 Simple models based on buried solvent accessible surface and one-dimensional potential

154 The solvent accessible surface and T(2) relaxation of Tg inc

155 s to accurately measure the absolute average solvent accessible surface area (<SASA>) of amino acid s

156 characterized by several measures including solvent accessible surface area (ASA), residue depth (RD

157 by the user, ANCHOR calculates the change in solvent accessible surface area (DeltaSASA) upon binding

158 Solvent accessible surface area (SASA) calculations on a

159 olecular dynamics simulation to quantify the solvent accessible surface area (SASA) of beta1 strand r

160 binding kinetics, binding interactions, the solvent accessible surface area (SASA) of the ligands, a

161 The solvent accessible surface area (SASA) of the polypeptid

162 of motifs such as sequence conservation and solvent accessible surface area are also displayed in th

163 of motifs such as conservation strength and solvent accessible surface area at each position are vis

164 in the presence of either MoaD subunit, the solvent accessible surface area buried upon formation of

165 ent accessible surface area/generalized Born solvent accessible surface area calculations led to the

166 Solvent accessible surface area calculations suggest tha

167 r the complex are correlated with calculated solvent accessible surface area changes and indicate hyd

168 es shows that only those hydrogen atoms with solvent accessible surface area exposure > or = 8.0 A(2)

169 urea m-values, which report on the change in solvent accessible surface area for unfolding, to probe

170 plot) is identical to the fraction of buried solvent accessible surface area in the structures of the

171 Approximately 25% of the solvent accessible surface area of each subunit is invol

172 The prediction method is based on solvent accessible surface area of residues in the isola

173 tagenesis of 97 residues covering 53% of the solvent accessible surface area of the enzyme identifies

174 The solvent accessible surface area of the K1-K10 structure

175 of the extent of oxidative modification with solvent accessible surface area reveals the method succe

176 ns orient the peptides so as to minimize the solvent accessible surface area, and the dimer structure

177 he DOCK score, empirical scoring, and buried solvent accessible surface area.

178 minant of triplex binding free energy is the solvent accessible surface area.

179 teractions, as well as conserved interfacial solvent accessible surface area.

180 face than a random surface patch of the same solvent accessible surface area.

181 ondary structure, backbone torsion angle and solvent accessible surface area.

182 ith the molecular mechanic-Poisson-Boltzmann solvent accessible surface area/generalized Born solvent

183 present a new method for the calculation of solvent accessible surface areas at the atomic and resid

184 ressed by the PF values agreed well with the solvent accessible surface areas obtained from the X-ray

185 ucture-based energy function parametrized to solvent accessible surface areas.

186 For the mutants where a solvent accessible surface cysteine residue is substitut

187 A solvent accessible surface is generated for a target fol

188 ng the molecular mechanics Poisson-Boltzmann solvent accessible surface method.

189 des the area and volume of pocket or void by solvent accessible surface model (Richards' surface) and

190 uster of hydrophobic residues located on the solvent accessible surface of choline oxidase.

191 become a powerful technique for mapping the solvent accessible surface of proteins and examining pro

192 e that do not interact with IIA(Glc) but the solvent accessible surface of which decreases when it bi

193 ry large, burying approximately 5400 A(2) of solvent accessible surface per monomer.

194 ion of polar and hydrophobic residues on its solvent accessible surface, such a constraint should pro

195 hboring subunit burying approximately 921 A2 solvent accessible surface.

196 nce despite a relatively small 675 A2 buried solvent accessible surface.

197 n domains II and III of EpsL burying 1700 A2 solvent accessible surface.

198 an apolar region comprising almost half its solvent accessible surface.

199 linear relation is recovered if fractions of solvent-accessible surface are used as the measure of co

200 A simple proxy for this, the relative solvent-accessible surface area (Arel), therefore shows

201 HY values of rare gases are proportional to solvent-accessible surface area (ASA), whereas the HY va

202 to surface side chains that bury the largest solvent-accessible surface area after forming the comple

203 h by crystal structure-based calculations of solvent-accessible surface area and by hydrogen-deuteriu

204 Based on these discoveries, the amino acid solvent-accessible surface area and dihedral angles were

205 dimer in solution that maximizes the buried solvent-accessible surface area and intermolecular conta

206 ces of the conventional MM/Poisson-Boltzmann solvent-accessible surface area and MM/generalized Born

207 ults in variations of helical parameters and solvent-accessible surface area around the major and min

208 e found to correlate with the alterations in solvent-accessible surface area calculated from availabl

209 peptide oxidation levels with the values of solvent-accessible surface area calculated from molecula

210 Solvent-accessible surface area calculations determined

211 essible surface area and MM/generalized Born solvent-accessible surface area calculations.

212 face area, and there is no notable change in solvent-accessible surface area during the formation of

213 tes for cases where a sizeable difference in solvent-accessible surface area exists between the state

214 he hydrophilic and hydrophobic components of solvent-accessible surface area for several ideal confor

215 force field along with the generalized Born/solvent-accessible surface area implicit solvent model,

216 at capacity indicate a large decrease of the solvent-accessible surface area in SelB, amounting to 43

217 in the lattice which both buried significant solvent-accessible surface area in their interface and c

218 ame peptide/MHC bury very similar amounts of solvent-accessible surface area in their transition stat

219 dilute protein systems; however, the popular solvent-accessible surface area model was shown to be in

220 , we address this issue by supplementing the solvent-accessible surface area model with additional vo

221 ld coupled with an implicit solvent model (a solvent-accessible surface area model).

222 d could not be accounted for by conventional solvent-accessible surface area models.

223 pitope (19 nonconsecutive amino acids with a solvent-accessible surface area of >2,000 A2) of an HIV-

224 result is consistent with a net reduction of solvent-accessible surface area of 2370 +/- 550 A.

225 radical cleavage patterns to interrogate the solvent-accessible surface area of DNA.

226 ttern is a measure of the local variation in solvent-accessible surface area of duplex DNA, and thus

227 Molecular modeling was used to calculate the solvent-accessible surface area of FITC and FMP bound to

228 The solvent-accessible surface area of proteins is important

229 Over 1200 A(2) of the solvent-accessible surface area of the complex are invol

230 ution of cholesteryl oleate molecules to the solvent-accessible surface area of the entire ms-HDL par

231 ity or by a term that is proportional to the solvent-accessible surface area of the peptide.

232 The solvent-accessible surface area of the Tg nucleotide inc

233 and truncated inhibitors correlated with the solvent-accessible surface area of their N-terminal regi

234 an approaching protein partner, and (iii) a solvent-accessible surface area term that is used to des

235 s to solvation energy, and calculates scaled solvent-accessible surface area to account for hydrophob

236 computational alanine scanning and change in solvent-accessible surface area values for every interfa

237 uctures, revealing a positive correlation of solvent-accessible surface area with quenching but not a

238 three-dimensional structure are buried (<50% solvent-accessible surface area) in the native state.

239 ding to approximately 1000A(2) of additional solvent-accessible surface area, and the N termini of th

240 on of sizes of hydrophobic patches and total solvent-accessible surface area, and the prediction of s

241 of chemical denaturation rely on changes in solvent-accessible surface area, and there is no notable

242 es such as radius of gyration, rms distance, solvent-accessible surface area, contact order, and pote

243 bility and structure-based identification of solvent-accessible surface area, the latter does not dis

244 a factor relating molecular surface area to solvent-accessible surface area, we obtain 24 cal/mol A(

245 s somewhat smaller than the more traditional solvent-accessible surface area, which is the area trans

246 requently, it is assumed to be linear in the solvent-accessible surface area, with a positive surface

247 uum model, and the hydrophobic effect with a solvent-accessible surface area-dependent term.

248 32-0.59 kJ/mol per 100 A(2) of newly exposed solvent-accessible surface area.

249 a protruding hydrophobic stalk with a large solvent-accessible surface area.

250 ithout altering its structural properties or solvent-accessible surface area.

251 ury 627 A2 that accounts for 7% of the total solvent-accessible surface area.

252 ude the change in total Coulombic energy and solvent-accessible surface area.

253 ng trajectories, the contour length, and the solvent-accessible surface area.

254 ffinities based on simple parametrization of solvent-accessible surface area.

255 either fluorine content or changes in apolar solvent-accessible surface area.

256 similarly, correlates with changes in apolar solvent-accessible surface area.

257 lates well with calculated changes in apolar solvent-accessible surface area.

258 n increased antibody paratope net charge and solvent-accessible surface area; and (iv) public heavy-c

259 se in the major groove, and to calculate the solvent-accessible surface areas in each groove separate

260 s of candidate complexes based on changes in solvent-accessible surface areas upon binding support th

261 he desolvation-characterizing changes in the solvent-accessible surface areas, correlated with experi

262 he calculated electrostatic potential on the solvent-accessible surface as well as iso-electrostatic

263 same coefficient defined with respect to the solvent-accessible surface decreases with decreasing sol

264 t forms a tetrameric interface is exposed as solvent-accessible surface in dimeric orthologs.

265 The electrostatic potential on the solvent-accessible surface is primarily negative with th

266 g primarily in a localized region on the 40S solvent-accessible surface near the messenger RNA entry

267 tions identified four potential sites on the solvent-accessible surface of the ERalpha ligand-binding

268 proposed catalytic residues, located on the solvent-accessible surface of the parallel beta-helix an

269 ; the ion is contained completely within the solvent-accessible surface of the RNA.

270 a with the comparable difference maps of the solvent-accessible surface of the rRNA calculated for th

271 ) RNA footprinting to explore changes in the solvent-accessible surface of the rRNA with single-nucle

272 ain Tail arrhythmia mutations cluster on the solvent-accessible surface of the subunit interface at a

273 s have hydrophobic residues clustered on the solvent-accessible surface of their beta-sheets although

274 o characterize the changes in heat capacity, solvent-accessible surface, and hydration that accompany

275 ch the active site geometry, the hydrophobic solvent-accessible surface, channel gating dynamics, wat

276 By calculating the solvent-accessible surface, we observed that the exposed

277 aying the chaperone recognition motif on its solvent-accessible surface.

278 ferent folds, hydrogen bonding patterns, and solvent accessible surfaces.

279 nvenient and sensitive technique for mapping solvent-accessible surfaces of proteins and examining th

280 e majority of such sites are situated on the solvent-accessible surfaces of putative pheromones and t

281 in combination with mass spectrometry to map solvent-accessible surfaces of the iron-bound and iron-f

282 ontributions from charged, polar, and apolar solvent-accessible surfaces.

283 events should be interpreted with caution in solvent-accessible systems.

284 g of longer peptides that bulge out into the solvent-accessible, T cell contact area.

285 type, probably because it is larger and more solvent accessible than Ala9 in alpha-ImI.

286 PSII, a PSII preparation expected to be more solvent accessible than intact PSII.

287 KMnO4 footprinting detects solvent-accessible thymine bases in RP(o), but not in I(

288 ss toward the expression of proteins bearing solvent accessible tryptophan residues as reactive handl

289 d into two domains with the active site in a solvent accessible tunnel at the domain interface.

290 rminal dimerization domain contains a unique solvent accessible tunnel connected to an amphipathic ca

291 These simulations revealed the presence of solvent-accessible tunnels through the major groove of l

292 l aqueous reagent that specifically modifies solvent-accessible tyrosine residues to o-nitrotyrosine,

293 re solvent exposed, while Trp723 became less solvent accessible under these conditions, indicating si

294 rea buried in the Ca(2+)-bound state becomes solvent accessible upon Ca(2+) removal.

295 t in the beta-subdomain, which appears to be solvent-accessible via a narrow passageway between the a

296 The solvent-accessible volume within a monomer has a vestibu

297 l forms that experience a large reduction in solvent-accessible volume.

298 These findings map solvent-accessible volumes along the tunnel and provide

299 n the C-terminus of 3-OST-1 that become more solvent accessible when 3-OST-1 binds to HS.

300 reas 99% of the residues are predicted to be solvent-accessible with 42% in alpha-helix and 57% in co