ライフサイエンスコーパス: denaturant

1 physiological temperature in the absence of denaturant).

2 es with solvent quality (or concentration of denaturant).

3 of experimental conditions (pH, temperature, denaturants).

4 by shifting the distribution reversibly via denaturant.

5 nd stable at a high concentration of protein denaturant.

6 unfolded under force and the one unfolded by denaturant.

7 tein unfolding in the presence of a chemical denaturant.

8 nfolded polypeptide chains in the absence of denaturant.

9 efficiency and becomes broader at increasing denaturant.

10 y populated at equilibrium in the absence of denaturant.

11 ther extended due to the addition of another denaturant.

12 transition with the onset near 290 K without denaturant.

13 from those observed at equilibrium at higher denaturant.

14 ase of lambda(6-85) D14A does appear in mild denaturant.

15 chloride and renaturing them by removing the denaturant.

16 rienced by full-length chains diluted out of denaturant.

17 ves of the crystallins in the absence of the denaturant.

18 n with other chemicals, as the most suitable denaturant.

19 s versus dilution of full-length chains from denaturant.

20 is not a likely cause of urea's action as a denaturant.

21 o be largely unfolded even in the absence of denaturant.

22 DPs contract significantly in the absence of denaturant.

23 s expansion with increasing concentration of denaturant.

24 he SOD1 C terminus was uniquely sensitive to denaturant.

25 ins can fold on their own after removal from denaturant.

26 erature quenching and dilution from chemical denaturant.

27 ters depend linearly on the concentration of denaturant.

28 ven contraction of the unfolded state at low denaturant.

29 nlikely to expand further on the addition of denaturant.

30 n of polypeptide backbones in the absence of denaturants.

31 ieved through preferential interactions with denaturants.

32 queous solutions with high concentrations of denaturants.

33 binant PrP amyloids formed in the absence of denaturants.

34 protein stability by titration with chemical denaturants.

35 isting experimental approaches using harsher denaturants.

36 Wild-type htt was more resistant to denaturants.

37 oride (GdmCl) are frequently used as protein denaturants.

38 hange in A(230) in varying concentrations of denaturants.

39 h both proteins on unfolding in the chemical denaturants.

40 and is typically studied in the presence of denaturants.

41 ted in the absence of high concentrations of denaturants.

42 e activity, even in the absence of forces or denaturants.

43 ucture at room temperature in the absence of denaturants.

44 E and RG that is amplified in the absence of denaturants.

45 ts can act as powerful and versatile protein denaturants.

46 proteins and IDPs in the absence of chemical denaturants.

47 lly disordered protein ACTR in two different denaturants.

48 KCl), as well as in the presence of protein denaturants (4.0 M urea and guanidinium chloride).

49 F-A2 residues were cleaved in the absence of denaturant, 4M urea was required for the efficient cleav

50 nature of the transporter structure allowing denaturant access via the substrate binding pocket, as w

51 ntration, providing a sensitive probe of the denaturant action.

52 chains make significant contributions to the denaturant activity of GdmCl, whereas interactions with

53 that it is possible to detect a total of 10 denaturants/additives in extremely low concentrations wi

54 unfolded by high concentrations of chemical denaturants adopt expanded, largely structure-free ensem

55 e competing interplay between metal ions and denaturant agents provides a platform to extract informa

56 atment of pure protein with acid, chaotropic denaturants, alkylators, and detergents failed to unmask

57 cantly populated at pH 3.8 in the absence of denaturant, allowing the native state and the unfolded s

58 izing Hofmeister anion), and urea (a neutral denaturant) alter the folding free energy remains indist

59 ine how the kinetic behavior is perturbed by denaturant and carefully chosen mutations.

60 nd equilibrium constants on concentration of denaturant and found that they follow well-established l

61 4A-NTL9, populates the DSE in the absence of denaturant and is in slow exchange with the native state

62 lts compare variations in the landscape with denaturant and temperature to varphi value measurements

63 gated in bulk conditions under the effect of denaturant and temperature.

64 the pH range from 6.0 to 8.0 using chemical denaturants and a variety of spectroscopic probes.

65 he engineered covalent linkage was stable to denaturants and exhibited ligand binding and auto-oxidat

66 asing protein stability toward both chemical denaturants and heat.

67 exposure to elevated temperature or chemical denaturants and is kinetically trapped at room temperatu

68 The effect of denaturants and osmolytes on protein structure and activ

69 h as ionic strength, pH, and the presence of denaturants and osmolytes.

70 ere provides proof of concept for the use of denaturants and other solutes as probes of amount and co

71 Interactions between denaturants and proteins are commonly used to probe the

72 I is considerably more resistant to chemical denaturants and reducing agents than nepenthesin I, and

73 Urea is a commonly used protein denaturant, and it is of great interest to determine its

74 s (e.g., temperature, pH, salts, detergents, denaturants, and excipients), post-translational modific

75 oride, one of the most commonly used protein denaturants, and tetrapropylammonium chloride can specif

76 hermal denaturation, sensitivity to chemical denaturants, and the solubility of pairs of repeats, the

77 Here we present the cryo-EM structure of a denaturant- and protease-resistant fibril formed in vitr

78 Quenching rates measured in the absence of denaturant are four times larger than those in 6 M guani

79 case electrophoresis-compatible alternative denaturants are required.

80 Chemical denaturants are the most commonly used agents for unfold

81 ta of seven mAbs, where GuHCl was a suitable denaturant, are modeled using PARAFAC2.

82 L9 (CTL9) can be populated in the absence of denaturant at low pH.

83 mproved by using a mixture of detergents and denaturants at high concentrations along with large amou

84 death and when cell lysates were exposed to denaturants before BNP.

85 pport a mechanism of urea unfolding in which denaturant binds to distinct sites in the I-domain.

86 loids are resistant to conventional chemical denaturants, but they dissolve in formic acid (FA) at hi

87 avor of obligate polypeptide collapse at low denaturant cannot be considered conclusive yet.

88 se results imply that the effect of chemical denaturants cannot be interpreted solely as a disruption

89 ubation of PKCgamma without heat or chemical denaturants, causes amyloid-like fibril formation of thi

90 periment, we find that over a large range of denaturant concentration (>3 M) the m-value is a constan

91 lding phase diagrams of SH3 as a function of denaturant concentration ([C]), mechanical force (f), an

92 sis of the rate data as a function of pH and denaturant concentration allowed calculation of the kine

93 ntricate details of folding as a function of denaturant concentration can be predicted by using a nov

94 Ultimately, the denaturant concentration dependence of the oxidation rea

95 nfolded states contract significantly as the denaturant concentration falls from high ( approximately

96 ansion of the unfolded state with increasing denaturant concentration irrespective of the protein, de

97 of globular proteins should decrease as the denaturant concentration is reduced from a high to a low

98 andom coil to more compact dimensions as the denaturant concentration is reduced.

99 27) protein and single-chain monellin as the denaturant concentration is varied.

100 nsition of HP35 reported by FRET occurs at a denaturant concentration lower than that measured by cir

101 difference in the unfolding free energy at a denaturant concentration midway between the two unfoldin

102 trend of increasing hydrodynamic radius with denaturant concentration obtained by 2f-FCS and DLS.

103 ) variants allowed analysis of the effect of denaturant concentration on the compaction and breadth o

104 tion time is determined as a function of the denaturant concentration using either electrospray or ma

105 ics of folding as a function of pressure and denaturant concentration with exquisite site-specific re

106 Logarithms of rate constants versus denaturant concentration yielded plots (chevrons) that a

107 te, DeltaG(ND)([C]), changes linearly as the denaturant concentration, [C], is varied.

108 ion dominates unfolded-state dynamics at low denaturant concentration, and the results are in remarka

109 found an increase in radius of gyration with denaturant concentration, but most small-angle X-ray sca

110 at polypeptide chains expand with increasing denaturant concentration, but several studies using smal

111 expansion of unfolded chains with increasing denaturant concentration, providing a sensitive probe of

112 omains showed intermediate resistance to the denaturant concentration, similar to the overall unfoldi

113 ular dichroism spectroscopy as a function of denaturant concentration, thus arguing against a classic

114 ET efficiencies and SAXS intensities at each denaturant concentration, we show that the simulation tr

115 hat unfolding free energy is not linear with denaturant concentration.

116 e-like (higher molar volume) with increasing denaturant concentration.

117 and solution conditions, especially salt and denaturant concentration.

118 folding and unfolding data as a function of denaturant concentration.

119 uorescence emission spectra as a function of denaturant concentration.

120 iting a log-linear relationship on the final denaturant concentration.

121 e studied by experiment over a wide range of denaturant concentration.

122 ate are plastic and change with mutation and denaturant concentration.

123 ensemble of protein configurations for each denaturant concentration.

124 protein chain indeed swells with increasing denaturant concentration.

125 xperimental uncertainty of a few percent) of denaturant concentration.

126 folded molecules was comparable only at high denaturant concentrations and deviated under less denatu

127 ded chains, and approaches zero both at high denaturant concentrations and in intrinsically disordere

128 ty of proteins is typically measured at high denaturant concentrations and then extrapolated back to

129 etermined melting temperatures and unfolding denaturant concentrations for WT DHFR and 42 mutants.

130 tured even in the presence of unusually high denaturant concentrations involving a combination of 10

131 the soft folding structures at intermediate denaturant concentrations is so slow that it is not obse

132 than their respective C-terminal domains at denaturant concentrations predicted to disrupt the domai

133 lysis of the results from the two methods at denaturant concentrations varying from 1.5-6.0 M guanidi

134 e faster in the two-state regime, and at low denaturant concentrations, a kinetic intermediate is fav

135 hosphoglycerate kinase (PGK) with decreasing denaturant concentrations, a mechanism known as coil-glo

136 l proteins converge to 0.62 +/- 0.03 at high denaturant concentrations, as expected for a polymer in

137 nances disappeared gradually starting at low denaturant concentrations, indicating noncooperative cha

138 least for single-domain proteins at non-zero denaturant concentrations, such compaction may be rare.

139 to disrupt the domain interface, but at low denaturant concentrations, the relative kinetic stabilit

140 g to global unfolding, is observed at higher denaturant concentrations, with DeltaG(0) value of 65 +/

141 e partially folded monomers populated at low denaturant concentrations-yielded essentially identical

142 y extrapolation of measurements made at high denaturant concentrations.

143 protein at different solvent viscosities and denaturant concentrations.

144 s zones of sieving polymer, electrolyte, and denaturant concentrations.

145 of the N-td, shifted to significantly lower denaturant concentrations.

146 ng the overall unfolding transition to lower denaturant concentrations.

147 verage end-to-end distance (collapse) at low denaturant concentrations.

148 x different sites and ZnP through a range of denaturant concentrations.

149 deviation from linearity even at the lowest denaturant concentrations.

150 esidual secondary structures persist at high denaturant concentrations.

151 rly as expanded in water as they are in high denaturant concentrations.

152 Mixed denaturant conditions consisting of 3% SDS and 8 M urea,

153 ntrations and then extrapolated back to zero denaturant conditions to obtain unfolding free energies

154 The magnitude of the temperature-denaturant cross-interaction parameter is larger for NTL

155 of mutants due to thermal (DeltaDeltaG) and denaturant (DeltaDeltaG(H2O)) denaturations, as well as

156 In the protocol, the chemical denaturant dependence of the rate at which globally prot

157 protein-ligand complexes using the chemical denaturant dependence of the slow H/D exchange reaction

158 on spectroscopy (2f-FCS) to characterize the denaturant dependence of the unfolded state of the spect

159 pyrroline-3-methyl)methanesulfonate] and the denaturant dependences of the relaxation properties of t

160 -1 receptor antagonist (IL-1ra) are strongly denaturant-dependent as evidenced by high-resolution two

161 ommonly used FRET dye pair, however, produce denaturant-dependent changes in transfer efficiency simi

162 are well predicted by a Kramers model with a denaturant-dependent diffusion coefficient and speculate

163 ons, we spatially and temporally resolve the denaturant-dependent nonspecific collapse of the unfolde

164 Furthermore, T(m) and T(max) denaturant-dependent shifts and noncoincidence of meltin

165 ecular transfer model that combines measured denaturant-dependent transfer free energies for the pept

166 is approximately 3 A on guanidinium chloride denaturant dilution from 7.5 to 1 M, thereby suggesting

167 these caveats, we have utilized the chemical denaturant dimethyl sulfoxide which, in conjunction with

168 rent article features novel use of formamide denaturant during bisulfite conversion of a suitably con

169 is impediment, we tested organic solvents as denaturants during on-line pepsin digestion of soluble b

170 onine residues as a function of the chemical denaturant (e.g., guanidine hydrochloride or urea) conce

171 r work lays the foundation for incorporating denaturant effects in a physically transparent manner ei

172 ts is that Ca(2+) loss effectively acts as a denaturant, enabling cooperative dimerization and robust

173 s such as addition of high concentrations of denaturant, encapsulation into reverse micelles, the for

174 ound in the unfolded state in the absence of denaturants except near the site of chaperone binding, d

175 Solutes (osmolytes, denaturants) exert often large effects on these self-ass

176 il formation kinetics and resistance against denaturants, fibrils formed by full-length PABPN1 had co

177 nal studies, which hypothesize that chemical denaturants first interact directly with the protein sur

178 d) increase in quenching rates on removal of denaturant for a hydrophilic control peptide containing

179 Urea has often been found to be a poor denaturant for transmembrane helical structures.

180 is one of the most commonly employed protein denaturants for protease digestion in proteomic studies.

181 We tested the possibility that these denaturants form hydrogen bonds with peptide groups by m

182 he ExsY array is stable to heat and chemical denaturants, forming a robust layer that would contribut

183 denaturing proteins, urea (and perhaps other denaturants) forms stronger attractive dispersion intera

184 he protein collapse, the relatively stronger denaturant GdmCl displays a higher tendency to be absorb

185 were investigated at different heights using denaturant gradient gel electrophoresis (DGGE) fingerpri

186 re used, as well as solutions containing the denaturants guanidinium hydrochloride and urea.

187 ing for many small single-domain proteins by denaturants has led to speculation that protein sequence

188 Urea as a protein denaturant improves hydration of the interior of the SWN

189 ing of this protein after dilution of a high denaturant in an ultrarapid microfluidic mixer at temper

190 in the presence of maximum concentrations of denaturants in the order TFA > GuHCl > urea > SDS + urea

191 External forces in vivo or denaturants in vitro trigger the unfolding of this domai

192 nce that dye-free PEG is well-described as a denaturant-independent random coil, this similarity rais

193 of the stability determined at zero and high denaturant indicates that any residual denatured state s

194 Here we report denaturant-induced and temperature-dependent folding stu

195 apparent cooperative unfolding detected with denaturant-induced and thermal-induced unfolding experim

196 nd swelling transitions and counteraction of denaturant-induced protein unfolding.

197 obtain a comprehensive structural picture of denaturant-induced unfolded state expansion, and to iden

198 Denaturant-induced unfolding of helical membrane protein

199 n with a dry core, have been observed during denaturant-induced unfolding of many proteins.

200 The thermal and denaturant-induced unfolding of single-domain proteins i

201 Here, we present a study following denaturant-induced unfolding transitions of yeast phosph

202 urally similar and theirstrong resistance to denaturant-inducedunfolding is comparable.

203 It is found that the denaturants inhibit the onset of dewetting, so that it o

204 Urea being a denaturant interacts more with these regions of alpha-sy

205 the absence of chaperones, on dilution from denaturant into buffer.

206 ve the native state if diluted directly from denaturant into solution.

207 nsemble of unfolded states populated at high denaturant is distinct from those accessible at high tem

208 ling, we demonstrate that the sensitivity to denaturant is the surprising result of a two-state-like

209 hat the denatured state of ACBP at near-zero denaturant is unusually compact and enriched in long-ran

210 cular dynamics simulations when a mixture of denaturants is used.

211 lding, whether by elevated temperature or by denaturant, is the formation of thioflavin T staining ag

212 rmined that guanidine, the prevalent protein denaturant, is the long-lost ligand sensed by the ykkC c

213 Unfolding rates extrapolated to 0 M denaturant, k(unf)(H(2)O), are relatively independent of

214 We interpret denaturant kinetic m-values and activation heat capacity

215 ide bonds mediated by the reducing agent and denaturant, leading to an instant and quantitative reduc

216 s is challenged because the addition of some denaturants leads to aggregation.

217 hen stepwise dialysis to remove the chemical denaturant, leads to self-assembly of two distinct DNA-o

218 urface area upon unfolding was quantified by denaturant m values and heat capacity changes (DeltaC(p)

219 e energy--as functions of temperature T; the denaturant m values in guanidine and urea; the pH-temper

220 fraught with considerable uncertainty as the denaturants may have complex effects on the membrane or

221 Here, we use a combination of chemical denaturant, mechanical force and site-directed mutations

222 otein L are found to undergo collapse in the denaturant mixture.

223 ular simulations with a carefully calibrated denaturant model, we find that the protein chain indeed

224 The pretransition binds more denaturant molecules and is more sensitive to unfolding

225 This rearrangement of denaturants near the protein surface and crowded local e

226 f folding intermediates relative to chemical denaturants; NMR, which allows their observation; and co

227 free energies of unfolding in the absence of denaturant of 9.4 and 6.7 kcal/mol, respectively.

228 mics simulations to study the effect of both denaturants on the dewetting of water confined between n

229 controversy regarding the effect of chemical denaturants on the dimensions of unfolded and intrinsica

230 is a practical way to simulate the effect of denaturants on the folding of large proteins.

231 ke covalent aggregation in the presence of a denaturant or when alpha-synuclein is present in noncova

232 ic acids without the use of strong oxidizing denaturants or of subcellular compartments from C. elega

233 ly relevant starting state in the absence of denaturants or organic cosolvents.

234 which combines simulations in the absence of denaturants or osmolytes, and Tanford's transfer model t

235 ds, are dispersed by treatment with chemical denaturants or soluble competing proteins.

236 t concentration irrespective of the protein, denaturant, or experimental method used.

237 al parameters, such as temperature, chemical denaturant, or pH, are adjusted to induce folding.

238 at was resistant to dissociation by boiling, denaturants, or reducing agents and was not observed in

239 This model also treats effects of denaturants, osmolytes, and other physical stressors.

240 Enzyme is fairly stable toward chemical denaturants, pH and temperature.

241 states as solution conditions (temperature, denaturants, pH) are altered or when they are subjected

242 of CTPR3 at low concentrations of a chemical denaturant, preceding the all-or-none transition to the

243 than that of human IAPP in water but not in denaturant, providing experimental evidence for roughnes

244 the chain contracts by 15-30% over this same denaturant range.

245 The chemical denaturant reduces the unfolding enthalpy DeltaH(cal) an

246 Denaturants, reducing agents, acidic buffers, and therma

247 e ingredients of optimized concentrations of denaturant, reductant, and hydroxide ion.

248 red proteins (IDPs), adopt in the absence of denaturant remain controversial.

249 rea act on polystyrene as a protectant and a denaturant, respectively, while complying with Tanford-W

250 This change in the denaturant response means that the difference in the unf

251 degrees C in the presence of urea as a mild denaturant results in proteolysis of VWF.

252 The addition of high amounts of chemical denaturants, salts, viscosity enhancers or macro-molecul

253 ) in the presence and absence of the protein denaturant SDS was assessed.

254 and increased when lysates were treated with denaturants (SDS, 8 M urea, DTT, or trypsin) before BNP.

255 ize of the transition states (estimated from denaturant sensitivity) remains unchanged.

256 6), Denaturants should melt out fibrils.

257 We investigated the effects of the chemical denaturants sodium dodecyl sulfate (SDS), urea, guanidin

258 red including differences in digestion time, denaturant, source of enzyme, sample cleanup, and denatu

259 tide backbones sample conformations that are denaturant-specific mixtures of coils and globules, with

260 Denaturants such as low pH buffers can be diffused throu

261 lutions with high concentrations of chemical denaturants such as urea and guanidinium chloride (GdmCl

262 vitro protein-folding studies using chemical denaturants such as urea are indispensible in elucidatin

263 mol(-1) to 23.4 +/- 1.5 kcal mol(-1) at zero denaturant, suggesting that the cofactor contributes 17.

264 s can be extracted from cells with low pH or denaturants, suggesting a loose association with the cel

265 ferent conditions, including the presence of denaturants, temperature, and pH.

266 sodium deoxycholate (SDC) as an advantageous denaturant that can be effectively removed following aci

267 ed by proteolysis and by treatment with mild denaturants that disrupted intramolecular interactions b

268 rmined can also be tuned, by adding chemical denaturants that shift the protein unfolding temperature

269 After decades of using urea as denaturant, the kinetic role of this molecule in the unf

270 Upon dilution from high denaturant, the unfolded state undergoes rapid contracti

271 sed to high concentrations of urea and GdmCl denaturants, the protein still exhibits two distinct FRE

272 s the protein more selectively than chemical denaturants, thereby facilitating the characterization o

273 iner surfaces, while urea serves as a strong denaturant to disrupt noncovalent complexes and release

274 undergo oxidative folding in the absence of denaturant to form N-VEGF(110) (N stands for native) or

275 (N stands for native) or in the presence of denaturant to generate five fractions of X-VEGF(110) iso

276 e of increasing concentrations of a chemical denaturant to oxidize proteins.

277 e because it cannot be broken down by gentle denaturants to form a "core" complex similar in size to

278 A screen of chemical denaturants to maximally unfold the mammalian membrane p

279 rotein model, melittin, in the presence of a denaturant, trifluoroethanol.

280 nant GST-theta activity was abolished by the denaturants triton X-100, Gua-HCl, Gua-thiocyanate, SDS

281 ucidation of the mechanism by which chemical denaturants unfold proteins is crucial; this study explo

282 Hydrogen/deuterium exchange and denaturant unfolding studies of this mutant protein (Opj

283 ding of a target protein using a gradient of denaturant urea to reveal the individual energetic contr

284 ench solution additives, we observe that the denaturant urea was beneficial, resulting in improved se

285 holo s3 is also stabilized against chemical denaturants urea and guanidine HCl.

286 s in two case studies using (i) a chaotropic denaturant (urea) and (ii) low-pH buffers used for monoc

287 an be accurately calculated as a function of denaturant (urea) concentration.

288 Here, we use effects of denaturants (urea, guanidinium chloride) and temperature

289 The denaturant, urea (0.6 M), blocked the osmolyte effects,

290 ding transition in the case of two different denaturants, urea and guanidine hydrochloride (GuHCl).

291 oxidase (CcO) was probed using two chemical denaturants, urea and guanidinium chloride (GdmCl).

292 eta-lactamase II in the presence of chemical denaturants using a variety of biochemical and biophysic

293 extensive molecular dynamics simulations in denaturant (using a range of force-fields), we derived r

294 uration are often facilitated by addition of denaturants, using destabilizing pHs or extremes of pres

295 the side-chains of almost all residues, with denaturant-water transfer free energies inferred from th

296 ly consistent results regarding expansion in denaturant when applied to the same proteins.

297 t understanding of the mechanism of chemical denaturants, which are widely employed to investigate pr

298 r simulations, driven by weak association of denaturant with the protein.

299 Interactions of the denaturants with the backbone are dominated by hydrogen

300 nomial extrapolation of all the data to zero denaturant yields a folding time of 220 (+100,-70) ns at