ライフサイエンスコーパス: solvent accessibility

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

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

3 t the primary factor governing reactivity is solvent accessibility.

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

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

6 to enzymatic digestion, suggesting increased solvent accessibility.

7 h are suitable for circular permutation than solvent accessibility.

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

9 strongly, positively correlates with protein solvent accessibility.

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

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

12 protein evolution such as residue packing or solvent accessibility.

13 similar affinities and associated changes in solvent accessibility.

14 ng dependent on its intrinsic reactivity and solvent accessibility.

15 sidues 138-145, showed no regular pattern in solvent accessibility.

16 , and substrate binding causes a decrease in solvent accessibility.

17 mobility of tertiary structure elements and solvent accessibility.

18 area reveals the method successfully probes solvent accessibility.

19 mbering atoms and residues to calculation of solvent accessibility.

20 ng evidence for their physical proximity and solvent accessibility.

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

22 patially resolved measurements of changes in solvent accessibility.

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

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

25 nsitive to protein conformational change and solvent accessibility.

26 yme-inhibitor thioester adduct stability and solvent accessibility.

27 0, residues of the GH loop exhibit decreased solvent accessibilities.

28 analytical formula for the approximation of solvent accessibilities.

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

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

31 oxyl radical cleavage was used to define the solvent accessibility along the backbone of a ribozyme d

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

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

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

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

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

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

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

39 veral types on the basis of their length and solvent accessibility and counts were made for the repla

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

41 restructured dimer interface with decreased solvent accessibility and dynamics.

42 Solvent accessibility and energy calculations of the map

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

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

45 The solvent accessibility and local pKa of the adducted and

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

47 o demonstrate the feasibility of determining solvent accessibility and membrane immersion depth of ea

48 y heterogeneous; each residue has its unique solvent accessibility and motional environment.

49 ,3 family, but with variations in side-chain solvent accessibility and orientation.

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

51 pe labeling and (19)F NMR to investigate the solvent accessibility and side-chain dynamics of aromati

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

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

54 ed fluorescence quenching to investigate the solvent accessibility and surface charge of the soluble

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

56 of the TPQ ring possess different degrees of solvent accessibility and that the rates of C5 [double b

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

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

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

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

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

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

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

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

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

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

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

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

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

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

71 be defined in terms of secondary structure, solvent accessibility, and hydrogen bonding status.

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

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

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

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

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

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

78 hreshold (hits) are removed if residues have solvent accessibilities appreciably lower than those obs

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

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

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

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

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

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

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

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

87 e used to construct a high-resolution map of solvent accessibility at individual reactive sites.

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

89 us, phosphorylation causes subtle changes in solvent accessibility at the interdomain interface of Ch

90 methods to distinguish H/2H exchange due to solvent accessibility at the interface from H/2H exchang

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

92 The kinetics of solvent accessibility at the protein-protein interface b

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

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

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

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

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

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

99 allel to the different conditions, since its solvent accessibility changed only in the presence of si

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

101 Solvent accessibility changes in this transiently phosph

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

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

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

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

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

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

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

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

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

111 2 and residues 126-132, undergo decreases in solvent accessibility due to steric contacts with PPACK

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

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

114 X-ray crystallographic and solvent accessibility experiments suggest that these sol

115 The solvent accessibility expressed by the PF values agreed

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

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

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

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

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

121 to wild-type, indicating that the change in solvent accessibility for unfolding was similar.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

137 ANSmal emission properties and its solvent accessibility indicate that Cys-24 is in an aque

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

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

140 In the native state, the order of solvent accessibility is as follows: W118 > W60 > W104.

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

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

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

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

145 the structure is determined according to its solvent accessibility, its position relative to the seco

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

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

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

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

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

151 The solvent accessibilities of individual tryptophan residue

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

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

154 The solvent accessibilities of the lysine residues were alte

155 The solvent accessibilities of the probe sites, as measured

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

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

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

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

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

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

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

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

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

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

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

167 hat RNA binding creates heterogeneity in the solvent accessibility of ADAR2 tryptophan residues, with

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

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

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

171 25-HC changes the position, orientation, and solvent accessibility of cholesterol, shifting it into t

172 gand binding results in clear attenuation of solvent accessibility of Cys at position 326 and a margi

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

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

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

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

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

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

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

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

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

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

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

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

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

190 does not significantly alter the packing and solvent accessibility of other regions of the molten glo

191 The solvent accessibility of R696 is likely mediated by the

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

211 to the active site of the caspase eliminates solvent accessibility of the catalytic dyad.

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

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

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

215 The solvent accessibility of the Cu(II) in PcoC may allow fo

216 The solvent accessibility of the Cys residues is also determ

217 (3.50) and Asp-542(6.30) and the increase in solvent accessibility of the cytosolic extensions of hel

218 The similar excited-state lifetime and solvent accessibility of the fluorophore N-1-pyrenyl-mal

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

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

221 The solvent accessibility of the indole side chains was foun

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

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

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

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

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

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

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

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

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

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

232 The solvent accessibility of the residue was shown to direct

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

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

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

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

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

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

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

240 Solvent accessibility of the Tyr ring was studied using

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

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

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

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

245 The solvent accessibility of thrombin in its substrate-free

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

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

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

249 Remarkably, the solvent accessibility of W118 in the alpha-LA molten glo

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

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

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

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

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

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

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

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

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

259 Multiple solvent accessibility probes can be applied simultaneous

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

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

262 Solvent accessibility reagents, such as dimethyl sulfate

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

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

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

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

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

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

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

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

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

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

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

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

275 tion and residual dipolar couplings, and the solvent accessibility studies.

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

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

278 st accurate predictions are obtained using a solvent-accessibility term, the C(beta) density, and a s

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

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

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

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

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

284 esponding changes are observed in either the solvent accessibility to molecular oxygen or the maximal

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

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

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

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

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

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

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

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

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

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

295 Solvent accessibility was assessed based on the relaxati

296 (residues 147-349) showed that the increased solvent accessibility was less than would have occurred

297 Sequence-dependent solvent accessibility was measured as a change in power

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

299 No changes in solvent accessibility were seen in the regulatory domain

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