ライフサイエンスコーパス: solvent accessibility

1 iality, tissue specificity, localization and solvent accessibility.

2 hereby yielding diagnostic information about solvent accessibility.

3 he open conformers is correlated with higher solvent accessibility.

4 e NTD in these species gains flexibility and solvent accessibility.

5 d and used to express the magnitude of their solvent accessibility.

6 yme-inhibitor thioester adduct stability and solvent accessibility.

7 in H-D exchange rates that reflect relative solvent accessibility.

8 ucture in a way that is strictly governed by solvent accessibility.

9 t the primary factor governing reactivity is solvent accessibility.

10 the center of the contact region with a low solvent accessibility.

11 Cys residues for mutation based on predicted solvent accessibility.

12 d an increase in the thiopurine-binding site solvent accessibility.

13 to enzymatic digestion, suggesting increased solvent accessibility.

14 n about protein structure, due to changes in solvent accessibility.

15 h are suitable for circular permutation than solvent accessibility.

16 n hydrophobic residues with a high degree of solvent accessibility.

17 rves as a quantitative measure of side-chain solvent accessibility.

18 similar affinities and associated changes in solvent accessibility.

19 -sheet content, and patterns of variation in solvent accessibility.

20 ng dependent on its intrinsic reactivity and solvent accessibility.

21 nsitive to protein conformational change and solvent accessibility.

22 over coordination geometry, reactivity, and solvent accessibility.

23 strongly, positively correlates with protein solvent accessibility.

24 xplain about half of the variance of protein solvent accessibility.

25 protein evolution such as residue packing or solvent accessibility.

26 mobility of tertiary structure elements and solvent accessibility.

27 area reveals the method successfully probes solvent accessibility.

28 mbering atoms and residues to calculation of solvent accessibility.

29 ng evidence for their physical proximity and solvent accessibility.

30 both the peptide's secondary structures and solvent accessibility.

31 patially resolved measurements of changes in solvent accessibility.

32 0, residues of the GH loop exhibit decreased solvent accessibilities.

33 analytical formula for the approximation of solvent accessibilities.

34 Fields) to predict secondary structure (SS), solvent accessibility (ACC) and disorder regions (DISO).

35 myeloperoxidase and ONOO(-), suggesting that solvent accessibility accounted in part for the reactivi

36 e find that LASER reactivity correlates with solvent accessibility across the entire ribosome, and th

37 Nearly all differences in solvent accessibility among subunits disappear after the

38 roups, are crucial for these properties, but solvent accessibility and a disulfide bond (present in o

39 cal electrophiles is therefore gated by both solvent accessibility and additional electrostatic facto

40 e of oxidation may not be dictated solely by solvent accessibility and amino acid identity.

41 graphy-mass spectrometry (DXMS) to probe the solvent accessibility and backbone flexibility of the C2

42 y structure, JPred also makes predictions of solvent accessibility and coiled-coil regions.

43 s of His122 and Tyr125 not only enhanced the solvent accessibility and conformational flexibility of

44 resulting RNA model rationalizes independent solvent accessibility and cryo-electron microscopy struc

45 restructured dimer interface with decreased solvent accessibility and dynamics.

46 Solvent accessibility and energy calculations of the map

47 apart from expected results such as reduced solvent accessibility and flexibility of the interface r

48 A and Mg2+, the H-helix showed a decrease in solvent accessibility and flexibility that was relaxed o

49 beling makes it only sensitive to changes in solvent accessibility and insensitive to changes in prot

50 ER2/neu antibody at three sites differing in solvent accessibility and local charge.

51 The solvent accessibility and local pKa of the adducted and

52 Furthermore, a detailed analysis correlating solvent accessibility and local structural contacts for

53 acid sequence profile, secondary structure, solvent accessibility and native disorder, which will al

54 ,3 family, but with variations in side-chain solvent accessibility and orientation.

55 its environment, which consists of predicted solvent accessibility and secondary structure of each am

56 d by JoY, which include secondary structure, solvent accessibility and sidechain hydrogen bonds, XSuL

57 photoreactivity of His is determined by both solvent accessibility and structural flexibility.

58 whereas HDX is sensitive to changes in both solvent accessibility and structural fluctuations.

59 receptor has tertiary structure that limits solvent accessibility and that its conformation changes

60 predicted secondary structure, the predicted solvent accessibility and the contact prediction scores

61 shown by large increases in probe dynamics, solvent accessibility and the elimination of all intersu

62 owed reasonable agreement between amino acid solvent accessibility and the resulting oxidation status

63 s demonstrate that adding predicted relative solvent accessibility and torsion angle information impr

64 new structural information such as predicted solvent accessibility and torsion angles into the profil

65 specific naive T cell frequency and peptide solvent accessibility and/or mobility for a subset of mo

66 The site with partial solvent-accessibility and neutral charge displayed both

67 g amino acid sequence, secondary structures, solvent accessibilities, and residue-residue contacts to

68 ly, (i) its immediate interactions, (ii) its solvent accessibility, and (iii) its conformational flex

69 sordered secondary structure, an increase in solvent accessibility, and a decrease in intrinsic stabi

70 on, the smaller the PF value, the higher the solvent accessibility, and a value of 1 indicates full e

71 d scores, predicted secondary structures and solvent accessibility, and amino acid properties.

72 S, approximately 66% Q3 accuracy for 3-state solvent accessibility, and approximately 0.89 area under

73 A correlation between antigenicity, solvent accessibility, and flexibility in proteins was d

74 ses a higher anionic surface charge density, solvent accessibility, and greater degree of local confo

75 nergy, strain energy, solvation free energy, solvent accessibility, and hydrophobic, polar, acid, and

76 or changes in the size, secondary structure, solvent accessibility, and intrinsic stability of the ol

77 tween the protein compactness, inferred from solvent accessibility, and mRNA structure, inferred from

78 r effect can be measured by contact order or solvent accessibility, and network analysis shows a spec

79 NMR studies of imino proton lifetime, solvent accessibility, and NOE connectivity suggest that

80 tity, tolerance to amino acid substitutions, solvent accessibility, and side-chain weighted contact n

81 end of the m- and n(B)-values, the degree of solvent accessibility, and the midpoint potential observ

82 which predictions of secondary structure and solvent accessibility are made.

83 ss spectrometry, we were able to monitor the solvent accessibilities around 13 cysteines distributed

84 also inhibits membrane fluidity and reduces solvent accessibility around the lipid headgroup region.

85 footprinting and mass spectrometry for their solvent accessibility as a function of Ca(2+) concentrat

86 recall of 55.4%, while not requiring residue solvent accessibility as an input.

87 Hydroxyl radicals are ideal probes of solvent accessibility as their size approximates a water

88 providing insight into chemical exchange and solvent accessibility at a site-resolved level.

89 tion, and used EPR to determine dynamics and solvent accessibility at each site.

90 in many laboratories, provides a measure of solvent accessibility at individual nucleotides.

91 direct and quantitative approach for probing solvent accessibility at the base pairing face of guanos

92 wed by LC/MS/MS, providing information about solvent accessibility at the peptide and even the amino-

93 A simple volume-based, rather than solvent accessibility-based, model is constructed for De

94 Comparing side-chain solvent accessibilities between these three states illum

95 exhibits secondary structure, dynamics, and solvent accessibility broadly like those of the monomeri

96 ic features of membrane proteins, as well as solvent accessibility, by utilizing the lactose permease

97 otection include all of the sites of reduced solvent accessibility calculated from two different crys

98 itution tables, evolutionary trace analysis, solvent accessibility calculations and 3D-structures wer

99 s of PAI-1 are underestimated by theoretical solvent accessibility calculations derived from crystall

100 lyses (helicity, disorder, and polarity) and solvent accessibility calculations were performed to ide

101 g, but tertiary structure parameters such as solvent accessibility can provide an additional layer of

102 comparably protected by DNA, consistent with solvent accessibility changes calculated from core domai

103 conformation by monitoring substrate-induced solvent accessibility changes of broadly distributed pos

104 yses on this novel substitution matrix (i.e. solvent accessibility charge volume (SCV) matrix) suppor

105 usly reported NMR data satisfied most of the solvent-accessibility constraints.

106 with predicted secondary structure, relative solvent accessibility, contact map and beta-strand pairi

107 We present an approach for incorporating solvent accessibility data from electron paramagnetic re

108 d glob models can be further refined against solvent accessibility data, if available, and then conve

109 y the hydroxyl radical reactions, amino acid solvent-accessibility data for native and denatured C14S

110 uclear magnetic resonance (NMR) data and the solvent-accessibility data obtained in this study.

111 luorescence measurements, in addition to the solvent-accessibility data presented here, was generated

112 predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disu

113 A28 regulators to the 20S proteasomes modify solvent accessibility due to conformational changes of t

114 2 and residues 126-132, undergo decreases in solvent accessibility due to steric contacts with PPACK

115 the interface are crucial factors affecting solvent accessibility during the reaction pathway; compu

116 , whereas the N-terminus retains most of its solvent-accessibility during aggregation, and the hydrop

117 The solvent accessibility expressed by the PF values agreed

118 secondary structure features and per-residue solvent accessibility features of PTM sites, domain cont

119 of properties including secondary structure, solvent accessibility, flexibility, conservation, quater

120 Complex formation decreased solvent accessibility for both actin-bound probes, but i

121 onitor both local nucleotide flexibility and solvent accessibility for nearly all nucleotides in the

122 After addition of MalF-P2, an increased solvent accessibility for residues in the vicinity of th

123 ith conformational changes playing a role in solvent accessibility for these mutants.

124 from predictions of secondary structure and solvent accessibility, from the region between two resid

125 ns, including secondary structures, relative solvent accessibilities, functional motifs and polymorph

126 ORS) and predictions of secondary structure, solvent accessibility, globular regions, transmembrane h

127 ture and predictions of secondary structure, solvent accessibility, globular regions, transmembrane h

128 one-dependent conformational change limiting solvent accessibility had occurred.

129 Residues exhibiting higher levels of solvent accessibility have been shown to contact TCR, bu

130 orphology has implications in topics such as solvent accessibilities in proteins, vibrational energy

131 ringent conformational constraints, reducing solvent accessibility in almost all histone regions by >

132 ield a near-perfect measure (r >or= 0.82) of solvent accessibility in an RNA with a complex tertiary

133 ase cleavage produced significant changes in solvent accessibility in the AID and upper lobe of the c

134 the fVIII C2 domain, are consistent with the solvent accessibility in the context of the entire fVIII

135 sidue, Cys327, out of three, has an enhanced solvent accessibility in the inward-facing (relative to

136 allosteric inhibition, as shown by increased solvent accessibility in the upper and lower lobes, incl

137 Amide H/D exchange experiments indicate that solvent accessibility increases across the entire LRP1 c

138 icted to be a large contributor, because the solvent accessibility increases only slightly in mutant

139 obic pockets and positions with intermediate solvent accessibility, indicating that hydrophobic inter

140 sidues from profile, secondary structure and solvent accessibility information.

141 evel to the tryptophan oxidation, where high solvent accessibility is a prerequisite for heavy chain

142 Their solvent accessibility is analyzed through a dedicated bi

143 modified at side chains with medium to high solvent accessibility is compatible with such a view.

144 ing protein secondary structure and relative solvent accessibility is important for the study of prot

145 res of various protein sites regarding their solvent accessibility is revealed, where high-PF regions

146 Finally, local solvent accessibility is shown to be a primary determina

147 Here we describe a new NMR method, SALMON (solvent accessibility, ligand binding, and mapping of li

148 s to decrease the stability (DeltaG) and the solvent accessibility (m-value) of the N if I transition

149 ns at 25 and 100 degrees C, Tanford-Kirkwood solvent accessibility Monte Carlo electrostatic calculat

150 mpact carbohydrate conformation with greater solvent accessibility observed for smaller phospholipid

151 ated conformational changes could change the solvent accessibilities of affected residues, as reflect

152 consisted of PSI-blast sequence profiles and solvent accessibilities of each surface residue and 14 o

153 Under native conditions, the solvent accessibilities of most 2-AP-labeled RNA substra

154 Solvent accessibilities of the active-site-bound spin pr

155 The solvent accessibilities of the lysine residues were alte

156 The solvent accessibilities of the probe sites, as measured

157 ue pairs, pairwise distance and the relative solvent accessibilities of the residues.

158 Differences in the solvent accessibilities of the seven quasi-equivalent ca

159 numbers, types of coordinating residues, and solvent accessibilities of these sites are providing ins

160 The solvent accessibilities of Tyr-213 and Tyr-216 suggested

161 The data on solvent accessibilities of various amino acids within th

162 mains in the kinase-off state by probing the solvent accessibility of 129 cysteine substitutions.

163 the enzyme-aminoglycoside complex increases solvent accessibility of a number of amides and is respo

164 cessible area, traditionally used to measure solvent accessibility of a protein site, of the sulfur a

165 n the presence of CTFs was comparable to the solvent accessibility of Abeta(1-40) oligomers formed in

166 , only CTFs but not Abeta(21-30) reduced the solvent accessibility of Abeta(1-42) in region D1-R5.

167 The reduced solvent accessibility of Abeta(1-42) in the presence of

168 ords an in situ, real-time monitoring of the solvent accessibility of Abeta1-42 at various stages of

169 ing (HRF) provide rich information about the solvent accessibility of amino acid side chains of a pro

170 ure changes in protein structure via altered solvent accessibility of amino acid side chains.

171 eveloped accurate methods for predicting the solvent accessibility of amino acids from a protein sequ

172 25-HC changes the position, orientation, and solvent accessibility of cholesterol, shifting it into t

173 ication can also be used to easily probe the solvent accessibility of cysteine residues, which provid

174 is altered by H3K4me3, we mapped changes in solvent accessibility of cysteine thiols by differential

175 challenged with an alkylating agent to probe solvent accessibility of different residues in the fibri

176 nsive reagents to study local changes in the solvent accessibility of DNA, RNA and proteins associate

177 For relative solvent accessibility of exposed residues, we observed h

178 inge element, as evidenced by the diminished solvent accessibility of FMal relative to the native str

179 become a powerful approach for measuring the solvent accessibility of folded protein structures.

180 escence quenching experiments to observe the solvent accessibility of helix B at pH 6.0 and 7.4.

181 of several residues, resulting in decreased solvent accessibility of hemes and the withdrawal of a p

182 We report a method for expressing the solvent accessibility of histidine imidazole groups in p

183 ished triple resonance NMR experiments: high solvent accessibility of IDPs promotes water exchange, w

184 To quantitatively describe the solvent accessibility of imidazole groups in proteins, i

185 spectrometry has been used to determine the solvent accessibility of individual residues in monomeri

186 s in secondary structure states and relative solvent accessibility of individual residues in proteins

187 ied group pKas is computationally intensive, solvent accessibility of ionizable groups is displayed,

188 Agonists do not affect solvent accessibility of loop F, whereas certain antagon

189 lly, in addition to providing information on solvent accessibility of lysine sites, dead end iqPIR cr

190 a reproducibility and inflates the perceived solvent accessibility of Met-containing peptides.

191 We measured the peptide level solvent accessibility of multiple Abeta(1-40) aggregated

192 nge (HDX) mass spectrometry to determine the solvent accessibility of mVP40 residues in the absence a

193 ass spectrometry, we measure the decrease in solvent accessibility of one of beta2m's Trp residues, w

194 is associated with a significant increase in solvent accessibility of one of the disulphide bonds (li

195 The solvent accessibility of R696 is likely mediated by the

196 eactive of chemical oxidants; it reports the solvent accessibility of reactive sites on macromolecule

197 hereas acetylation disclosed the decrease in solvent accessibility of regions containing Lys 447 and

198 anine nucleotides resulted in changes in the solvent accessibility of regions of each protein that le

199 with the three other P450 2B enzymes and the solvent accessibility of residues in the ligand-free cry

200 he other three His residues, and changes the solvent accessibility of residues near His31 and near th

201 We established that mutation type, solvent accessibility of residues, and the predicted eff

202 H/(2)H exchange mass spectrometry to compare solvent accessibility of RIIbeta and the C subunit in th

203 ct is properly marked by the increase in the solvent accessibility of selected amino acids at the cyt

204 supporting its use as a rapid measure of the solvent accessibility of specific residues, and in some

205 In site-directed spin labeling, the relative solvent accessibility of spin-labeled side chains is tak

206 ity, their largest effect is in altering the solvent accessibility of the active site by expanding th

207 he enzyme toward the state(s) with decreased solvent accessibility of the active site so that the flu

208 For example, the solvent accessibility of the alphaB-loop-alphaC region i

209 n be used to accurately estimate the average solvent accessibility of the amino acid side chain in th

210 ransition states and that the high degree of solvent accessibility of the AP active site also contrib

211 initiation of unfolding is due to increased solvent accessibility of the backbone atoms near the sma

212 e protein conformation but also decrease the solvent accessibility of the backbone atoms, thereby sta

213 There is no difference in the solvent accessibility of the bound FlAsH irrespective of

214 e structure of the Ig-fold and increases the solvent accessibility of the C-terminus.

215 the active site of the caspase to eliminate solvent accessibility of the catalytic residues.

216 reased the amide hydrogen/deuterium exchange solvent accessibility of the contact region between the

217 both N( *) and IE have retained native-like solvent accessibility of the core, suggesting that they

218 The solvent accessibility of the Cys residues is also determ

219 (3.50) and Asp-542(6.30) and the increase in solvent accessibility of the cytosolic extensions of hel

220 This transition largely attenuates the solvent accessibility of the heme pocket and causes an u

221 properties of the TnC(F29W) mutants and the solvent accessibility of the hydrophobic amino acids in

222 The solvent accessibility of the indole side chains was foun

223 mical modification of 3-OST-1 to measure the solvent accessibility of the lysine residues.

224 nd it provides a measure of residue-resolved solvent accessibility of the native protein.

225 markably well correlated with the fractional solvent accessibility of the native side chains at the c

226 here the U5-tract is located, increasing the solvent accessibility of the neighboring bases while mai

227 opt a unique conformation that decreases the solvent accessibility of the peptide backbone.

228 We observe increased solvent accessibility of the platinated DNA strand, whic

229 he luminescence observed is dependent on the solvent accessibility of the pyrazine nitrogen atoms, an

230 n X-ray crystal structures, we find that the solvent accessibility of the reactive atom in the side c

231 the residues' chemical reactivities and the solvent accessibility of the reactive carbons and sulfur

232 de chains occurs at rates in accord with the solvent accessibility of the residue so that the extent

233 The solvent accessibility of the residue was shown to direct

234 erties of the interactions between residues, solvent accessibility of the residues and their secondar

235 Hydroxyl radical footprinting can probe the solvent accessibility of the ribose moiety of the indivi

236 technique that monitors the local changes in solvent accessibility of the RNA backbone on millisecond

237 H) analyses that report local changes in the solvent accessibility of the RNA backbone.

238 size/rigidity as well as the composition and solvent accessibility of the selectivity filter.

239 rget peptides are governed by changes in the solvent accessibility of the side-chain probe residues.

240 ere we determined the membrane partition and solvent accessibility of the TMD in bicelles that mimic

241 Solvent accessibility of the Tyr ring was studied using

242 amino-acid, the electrostatic properties and solvent accessibility of the whole active site in LaCADS

243 g with mass spectroscopy (XFMS) to track the solvent accessibility of these and other side chains.

244 e residues in proteins in order to probe the solvent accessibility of these residues as a function of

245 ified by a fluorescent probe, revealing more solvent accessibility of this position than would be pre

246 hortening of the Ca(2+) switch helix changes solvent accessibility of Thr-171 and Leu-174 that affect

247 The solvent accessibility of thrombin in its substrate-free

248 H(2)O(2) enhanced the solvent accessibility of Trp residues in PMCA, whereas a

249 rotein structure suggests a key role for the solvent accessibility of Tyr168 in promoting molecular i

250 or maintenance of this structure and reduces solvent accessibility of U36.

251 These include a high average solvent-accessibility of residues within the recognition

252 ation (e.g. reports on individual nucleotide solvent accessibility offered by hydroxyl radical (()OH)

253 and subsequent elucidation of the effect of solvent accessibility on the sites of oxidation.

254 include buriedness (as measured by relative solvent accessibility), packing density (as measured by

255 y, intersubunit spin-spin proximity, and the solvent-accessibility parameters in the two states clear

256 tics, such as tertiary structure, fractional solvent accessibility, pK(a) of the conjugation site, su

257 s in hydrogen bonding, residue depth, and/or solvent accessibility predicted from the crystal structu

258 structure prediction accuracy of 82.0% while solvent accessibility prediction accuracy has been raise

259 A recently introduced method for solvent accessibility prediction trained on a set of sol

260 ools include secondary structure prediction, solvent accessibility prediction, disorder region predic

261 Multiple solvent accessibility probes can be applied simultaneous

262 hich involves the application of established solvent-accessibility probes and chemical crosslinkers w

263 s were defined as amino acid groups based on solvent-accessibility, radius, atomic depth, and interac

264 Solvent accessibility reagents, such as dimethyl sulfate

265 nucleocapsid protein p7 (NC) were probed by solvent-accessibility reagents and electrospray ionizati

266 This approach, "pseudoatom-driven solvent accessibility refinement", was validated by refo

267 s of these His residues were correlated with solvent accessibility-related parameters both by crystal

268 e devised a cost measure matrix based on the solvent accessibility, residue charge, and residue volum

269 ined information arising from local relative solvent accessibility (RSA) between two residues into th

270 evolutionary rate of sites and the relative solvent accessibility (RSA) of the corresponding residue

271 ter of mass (GCM) of the structure, relative solvent accessibility (RSA), and the use of relative ent

272 droxyl radical labeling, we probed real-time solvent accessibility (SA) changes at key OCP residues d

273 lementary to widely studied measures such as solvent accessibility (SA), residue depth (RD) and to th

274 The resulting changes in solvent accessibility show strong correlation with exper

275 dicted 1D structure (secondary structure and solvent accessibility) significantly improved over seque

276 The method successfully probed solvent accessibility similarily to in vitro FPOP, demon

277 A gradual reduction in solvent accessibility, spreading from the C-terminal reg

278 characterized as a paramagnetic reagent for solvent accessibility studies, and it is shown that abso

279 ine-scanning mutagenesis in conjunction with solvent-accessibility studies using the membrane-imperme

280 simulations, cross-linking, mutagenesis, and solvent accessibility suggested that membrane binding of

281 in CDR3 did not linearly correlate to higher solvent accessibility, suggesting that other factors inc

282 with theoretically derived pKa and relative solvent accessibility surface values.

283 d had greater overall, and SAM binding site, solvent accessibility than 108V COMT at 37 degrees C.

284 eractions, higher local stability, and lower solvent accessibility than segments 5-25 and 70-75, sugg

285 that the isolated subunit has overall higher solvent accessibility than the native dimer, with the ex

286 a molecular level, we determined changes in solvent accessibility that occur when an enzyme binds to

287 ver, H/DX demonstrated significantly greater solvent accessibility throughout most of the GSTA1-1 seq

288 kbone flexibility, hydrophobic interactions, solvent accessibility to polar groups and intrinsic back

289 compact si-face transition structure reduced solvent accessibility to the amide oxygen with a "closed

290 ker sequence plays a key role in controlling solvent accessibility to the FAD cofactor, as evidenced

291 pen or close the top of the beta-barrel, and solvent accessibility to the protein cavity favors diffu

292 ethanethiosulfonate reagents, denoting their solvent accessibility to the translocation pathway.

293 edictors of secondary structure and relative solvent accessibility together with their multi-class va

294 In this work, we integrate predicted solvent accessibility, torsion angles and evolutionary r

295 d aspects of structure (secondary structure, solvent accessibility, transmembrane helices (TMSEG) and

296 regions on IL-23 with reduced backbone amide solvent accessibility upon antibody binding were identif

297 cludes information on the conformational and solvent accessibility variation of the enzyme-bound cofa

298 Solvent accessibility was assessed based on the relaxati

299 that the alpha-factor-dependent decrease in solvent accessibility was not because of steric hindranc

300 f a ligand bound to a protein by mapping its solvent accessibility, which was used to unambiguously d