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 tein unfolding in the presence of a chemical denaturant.

5 efficiency and becomes broader at increasing denaturant.

6 y populated at equilibrium in the absence of denaturant.

7 ther extended due to the addition of another denaturant.

8 transition with the onset near 290 K without denaturant.

9 from those observed at equilibrium at higher denaturant.

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

11 chloride and renaturing them by removing the denaturant.

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

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

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

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

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

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

18 s expansion with increasing concentration of denaturant.

19 to 25 degrees C at pD 6.6 in the absence of denaturant.

20 erature quenching and dilution from chemical denaturant.

21 olding process is a function of the employed denaturant.

22 ected around Trp53 at high concentrations of denaturant.

23 ven contraction of the unfolded state at low denaturant.

24 nlikely to expand further on the addition of denaturant.

25 by shifting the distribution reversibly via denaturant.

26 nd stable at a high concentration of protein denaturant.

27 unfolded under force and the one unfolded by denaturant.

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

29 protein stability by titration with chemical denaturants.

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

31 isting experimental approaches using harsher denaturants.

32 Wild-type htt was more resistant to denaturants.

33 ts can act as powerful and versatile protein denaturants.

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

35 proteins and IDPs in the absence of chemical denaturants.

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

37 h both proteins on unfolding in the chemical denaturants.

38 and is typically studied in the presence of denaturants.

39 ted in the absence of high concentrations of denaturants.

40 ucture at room temperature in the absence of denaturants.

41 lly disordered protein ACTR in two different denaturants.

42 n of polypeptide backbones in the absence of denaturants.

43 ieved through preferential interactions with denaturants.

44 queous solutions with high concentrations of denaturants.

45 binant PrP amyloids formed in the absence of denaturants.

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

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

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

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

50 ons, a phenomenon that correlates with their denaturant activities.

51 Gdm2SO4 was found to retain considerable denaturant activity against alanine-based alpha-helical

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

53 ractions with the peptides that underlie its denaturant activity.

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

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

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

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

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

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 e major free energy barrier, together with a denaturant- and reaction coordinate-dependent diffusion

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

79 rates of unfolding at low concentrations of denaturant are very low, consistent with the slow establ

80 case electrophoresis-compatible alternative denaturants are required.

81 Chemical denaturants are the most commonly used agents for unfold

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 A possible role of denaturant binding in inducing the pretransition changes

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

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

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

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

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

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

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

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

104 As the denaturant concentration was lowered, the mean FRET effi

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 he observed first-order rate constant versus denaturant concentration, "chevron plots," displayed the

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

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

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

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

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

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

114 l log of the observed relaxation rate versus denaturant concentration, so-called chevron plots, exhib

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

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

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

118 and solution conditions, especially salt and denaturant concentration.

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

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

121 milar and even exhibit similar dependence on denaturant concentration.

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

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

124 ensemble of protein configurations for each denaturant concentration.

125 protein chain indeed swells with increasing denaturant concentration.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

144 ng the overall unfolding transition to lower denaturant concentrations.

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

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

147 deviation from linearity even at the lowest denaturant concentrations.

148 esidual secondary structures persist at high denaturant concentrations.

149 .e., rearranges more slowly) with decreasing denaturant concentrations.

150 equilibrium intermediate at low to moderate denaturant concentrations.

151 deviation from linearity was observed at low denaturant concentrations.

152 y extrapolation of measurements made at high denaturant concentrations.

153 protein at different solvent viscosities and denaturant concentrations.

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

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

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

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

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

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

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

161 kinetics; however, nonlinear effects in the denaturant dependence of the unfolding data demonstrate

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

163 -1 receptor antagonist (IL-1ra) are strongly denaturant-dependent as evidenced by high-resolution two

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

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

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

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

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

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

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

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

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

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

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

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

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

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

178 ze wild-type capsids, UL25 null capsids, and denaturant-extracted capsids, we conclude that (1) the C

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

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

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

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

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

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

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

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

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

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

189 termediate observed at low concentrations of denaturant has no protection from hydrogen-deuterium exc

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

191 This increased with denaturant in a noncooperative fashion to approximately

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

193 e that was observed in low concentrations of denaturant in earlier studies.

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

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

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

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

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

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

200 roism, and NMR were used to characterize the denaturant-induced unfolding equilibrium of ferrocytochr

201 Denaturant-induced unfolding of helical membrane protein

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

203 In order to clarify the mechanism of denaturant-induced unfolding of proteins we have calcula

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

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

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

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

208 Ising-like theoretical model shows that this denaturant-invariant relaxation rate can be explained by

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

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

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

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

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

214 The rate of unfolding in the absence of denaturant, k(u)(H(2)O), is surprisingly very slow ( app

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

246 Denaturants, reducing agents, acidic buffers, and therma

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

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

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

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

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

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

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

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

255 6), Denaturants should melt out fibrils.

256 etry of alpha(1)-AT at low concentrations of denaturant shows no heat capacity peak during thermal de

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 d tuna cytochromes c after photoreduction in denaturant suggested that the non-native His18-Fe-His33

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

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

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

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

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

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

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

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

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

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

274 idues 144-153) occurs by hydrogen bonding of denaturants to charged side chains and backbone carbonyl

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

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

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

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

279 el according to which the most commonly used denaturants unfold proteins by altering electrostatic in

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

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

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

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

284 on to promoting unfolded protein states, the denaturants urea and guanidinium (Gdm(+)) accumulate at

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

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

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

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

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

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

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

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

293 A decrease in Rg with decreasing denaturant was also observed in all-atom molecular dynam

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

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

296 dinium (Gdm+) chloride is a powerful protein denaturant, whereas the sulfate dianion (SO42-) is a str

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