ライフサイエンスコーパス: folding rate

1 tural rearrangements that control the global folding rate.

2 ntly more stable, showing a 100 times faster folding rate.

3 folding rates at the temperature of maximum folding rate.

4 in the turn or loop region mostly affect the folding rate.

5 itions under which frustration increases the folding rate.

6 pared it with the corresponding experimental folding rate.

7 to quantify the influence of knotting on its folding rate.

8 of peptide backbone, thereby increasing the folding rate.

9 p leading to significant enhancements in the folding rate.

10 ation results in a 5-fold retardation of the folding rate.

11 ically decreased stability but increased the folding rate.

12 ive position, thereby decreasing the overall folding rate.

13 pendent experimental method to determine the folding rate.

14 es primarily with unfolding rate rather than folding rate.

15 d a web of nonnative states slow the average folding rate.

16 environment influences protein stability and folding rate.

17 of the mechanism by which urea enhances RNA folding rates.

18 e them from kinetic traps and increase their folding rates.

19 otein in the cis cavity, produces effects on folding rates.

20 t sequences with longer loops display slower folding rates.

21 apparent equilibrium constants and relative folding rates.

22 erived from known structures correlates with folding rates.

23 f native state contact orders for predicting folding rates.

24 uffer unfolding are similar, as are in vitro folding rates.

25 Macroscopically, this results in faster folding rates.

26 ry different temperature dependencies of the folding rates.

27 teins gives rise to their topology-dependent folding rates.

28 ir complex topologies and intrinsically slow folding rates.

29 and obtained coefficients that predict their folding rates.

30 ter describe the role of topology in protein-folding rates.

31 o be the most important determinant of their folding rates.

32 n misfolded conformations, and non-Arrhenius folding rates.

33 gnificant correlation with the logarithms of folding rates.

34 walls induces a very strong reduction of the folding rates.

35 s that cover a wide range of stabilities and folding rates.

36 Indeed, both the raw TIP3P folding rate (4.5 +/- 2.5 micros) and the diffusion-cons

37 Although the folding rate accelerates as the viscosity declines, it t

38 d the relationship between RNA structure and folding rates accounting for hierarchical structural for

39 itive correlation between hydrophobicity and folding rate across all of the residues we have characte

40 The resulting (un)folding rates agree well with experiments.

41 d TZ1 and TZ2 properties well; the estimated folding rates agreed with the experimentally determined

42 The folding rate also appeared to be influenced by differenc

43 Moreover, we find that the logarithm of the folding rates also scale as R(-gamma(c)), with deviation

44 llent agreement with experimentally measured folding rates, although pathways sampled in these simula

45 play an important role in dictating relative folding rates among topologically equivalent proteins.

46 erent members, with a 5000-fold variation in folding rate and 3000-fold variation in unfolding rate s

47 tution indicate a strong correlation between folding rate and charge state.

48 export competence is related to the protein folding rate and could be exploited for the isolation of

49 a linear relationship between the log of the folding rate and DeltaG* (H2O) .

50 tein plays a primary role in determining the folding rate and mechanism of relatively small single-do

51 sidues 509-511 and only minor differences in folding rate and stability.

52 mate is based on the correlation between the folding rate and the number of predicted long-range cont

53 To increase the folding rate and to gain insight into the folding proces

54 for the role of unfolded chain diffusion on folding rates and barrier heights are discussed.

55 e toward the folded state by both increasing folding rates and decreasing unfolding rates.

56 ic core but that are predicted to affect the folding rates and dynamics dramatically.

57 To determine the extent to which protein folding rates and free energy landscapes have been shape

58 the concentration dependence of the observed folding rates and intermolecular FRET measurements.

59 test of such models, provide predictions of folding rates and mechanisms for a comprehensive set of

60 The prediction of protein folding rates and mechanisms is currently of great inter

61 predict the effects of mutations on protein folding rates and mechanisms would greatly facilitate fo

62 explanation for the experimentally measured folding rates and mechanisms, in terms of the intrinsic

63 es agreed with the experimentally determined folding rates and native conformations were the global p

64 logy plays a key role in determining protein-folding rates and pathways.

65 imulation, to study protein kinetics through folding rates and population kinetics from approximate f

66 Upon tethering, we find that folding rates and stability are impacted differently by

67 ure, there is no simple relationship between folding rates and stability for the archael histones.

68 disulfide bridges: large variability in both folding rates and stability of intermediates, multi-stat

69 sms by comparing the effects of mutations on folding rates and stability, but determining varphi-valu

70 of polyglutamine guest inserts, the kinetic folding rates and structural perturbation of these CI2 i

71 can be used to extract population kinetics, folding rates and the formation of particular substructu

72 Plotting the folding rates and the reduced contact order from ten dif

73 or diffusive barrier crossing, including the folding rates and the transition time for crossing the b

74 tic interactions have a pronounced effect on folding rates and thermodynamic stability.

75 protein conformational dynamics, but protein folding rates and transition times have not been calcula

76 an drastically change the protein stability, folding rate, and cooperativity.

77 his stability increase greatly increases the folding rate, and suggests that the transition state ens

78 uorescence and CD experiments yield the same folding rate, and the chevron plots have the characteris

79 m expressed in terms of transcription speed, folding rates, and metabolite binding rates predicts dif

80 The diverse folding rates appear to reflect large differences in the

81 The folding rate approaches the diffusion-limited value and

82 m the data agrees well with the experimental folding rate (approximately 640/s).

83 The equilibrium stability and the folding rate are found to be strongly dependent upon the

84 Further, these predicted folding rates are correlated strongly with contact order

85 The folding rates are faster for designed variants compared

86 In the presence of a crowding agent, folding rates are faster in the two-state regime, and at

87 The observed folding rates are found to be proportional to the number

88 Much lower folding rates are predicted when the folding is initiate

89 uch proteins frequently are hindered because folding rates are too fast to measure using conventional

90 We show that observed folding rates are well predicted by a Kramers model with

91 Errors in the folding rates arising from instrument artifacts were onl

92 The folding rate at 300 K is (0.7 micros)(-1) with little or

93 Remarkably, the calculated folding rate at [C] = 0 is only 16-fold larger than the

94 o-Hyp)(4) region significantly decreases the folding rate at low but not high concentrations, consist

95 e sequences used exhibit a 600-fold range of folding rates at the temperature of maximum folding rate

96 on found between experimental and calculated folding rates based on free energy barrier heights using

97 compact denatured polypeptide can limit the folding rate, but the limiting time scale is very fast.

98 e same region of a beta-strand decreased the folding rate by 20- and 50-fold, respectively, suggestin

99 inhibitor 2 (CI2), accelerates the protein's folding rate by a factor of 36 relative to that of the w

100 anine residue with alanine will increase the folding rate by removing a transient non-native interact

101 ng Asp46 with Ala leads to a decrease in the folding rate by roughly 9 times.

102 ntramolecular interactions influence protein folding rates by altering dynamics and not activation fr

103 t rather adopts an active role, accelerating folding rates by decreasing the roughness of the energy

104 hain models of natural proteins with diverse folding rates by extensive comparisons between the distr

105 majority (55%) of these substitutions affect folding rates by less than a factor of 2, and that only

106 than a factor of 2, and that only 9% affect folding rates by more than a factor of 8.

107 a protein and provide insights into how its folding rate can be modified during evolution by mutatio

108 erstand the molecular basis of the decreased folding rate, changes in the unfolded as well as the fol

109 ment between simulation and experimental CI2 folding rates, CI2 structural perturbation, and polyglut

110 me in the unfolded state (the inverse of the folding rate coefficient).

111 the unfolded protein is extremely large, the folding rate coefficient, k(f), is much smaller than k(a

112 Whereas the folding rate coefficients differ by a factor of 10,000,

113 onds within the turn region elicits a slower folding rate, consistent with the hypothesis that these

114 , the corresponding estimated values for the folding rate constant are larger by two to three orders

115 Rs, a second exponential phase with a slower folding rate constant is observed.

116 The 1.9-fold increase in folding rate constant observed for this change at the ch

117 pient downhill folder having an extrapolated folding rate constant of 2 x 10(5) s(-1) and a stability

118 ve similar unfolding rate constants, but the folding rate constant of gcUUCGgc is 4.1-fold faster at

119 erature dependence of the natural log of the folding rate constant suggests that folding occurs via a

120 ease is largely correlated with an increased folding rate constant, and with a smaller but significan

121 The folding rate constants approached limiting values with i

122 te state is significantly populated, and the folding rate constants are relatively slow compared to t

123 cal peptides and from demonstration that the folding rate constants for coiled coils, as obtained by

124 The extrapolated folding rate constants in water at 298 K were 210,000 s(

125 With increasing calcium, the folding rate constants increase while unfolding rate con

126 mula fits well the experimentally determined folding rate constants of the 24 proteins, with single v

127 Experiments have shown that the folding rate constants of two dozen structurally unrelat

128 erted together into R16 or R17, increase the folding rate constants, reduce landscape roughness, and

129 families, stability is also a determinant of folding rate constants.

130 In contrast, the folding-rate constants are almost identical for the thre

131 -folding field is whether unfolding rates or folding rates correlate to the stability of a protein.

132 The accelerated folding rates could result from helix stabilization with

133 Under most conditions, the observed folding rate decreases with increasing counterion concen

134 Protein (un)folding rates depend on the free-energy barrier separati

135 folding can either speed up or slow down the folding rate depending on the amount of native and nonna

136 her accelerated or retarded compared to bulk folding rates, depending on the temperature of the simul

137 We find that the logarithm of the folding rate depends linearly on the entropic change ass

138 eely jointed chain models illustrate how the folding rate depends on the entropic and enthalpic energ

139 The folding rate determined for these cyclic peptides is acc

140 lusion of beta-turn mimics alters beta-sheet folding rates, enabling us to classify beta-turn mimics

141 In addition the 5-6-fold folding rate enhancement varied only slightly with pH, 7

142 In all cases examined, the folding rate enhancement with the aromatic thiol was 5-

143 These substrate proteins experience folding rate enhancements without undergoing multiple ro

144 The folding rates extracted using a simple kinetic model are

145 bility, and that the experimentally measured folding rates fall within this narrow triangle built wit

146 e slow diffusion that markedly decreases the folding rate for a designed alpha-helical protein.

147 results showing, if anything, a slowdown in folding rate for encapsulated Rhodanese.

148 had a nonnative free-energy minimum, and the folding rate for OPLS(aa) TZ3 was sensitive to the initi

149 is well-correlated with the logarithm of the folding rate for these small, well-characterized molecul

150 ness holds over a surprisingly wide range of folding rates for our designed sequences.

151 den triangle" limiting the possible range of folding rates for single-domain globular proteins of var

152 t with experimentally derived structures and folding rates for specific systems, leaving them positio

153 The folding rates for telomeric RNA and DNA G-quadruplexes a

154 thermodynamic and kinetic quantities such as folding rates, free energies, folding enthalpies, heat c

155 s can be jointly analyzed to compute unknown folding rates from detailed balance.

156 Here, we estimate two-state folding rates from predictions of internal residue-resid

157 dary structure prediction methods to predict folding rates from sequence alone.

158 dary structure had been exploited to predict folding rates from sequence.

159 ally, Kramers theory was used to predict the folding rates from the landscape profile, recovering the

160 t of many experimental studies, but its slow folding rate has made it difficult to observe and charac

161 tabilization of I(2)* correlated with slower folding rates, implying that NNS is not a kinetic trap b

162 ightly steeper temperature dependence of the folding rate in some cells that can be rationalized in t

163 The folding rate in the absence of denaturant is 260 s(-)(1)

164 We find that enhancement of the folding rate in the second, rate-limiting step is correl

165 between experimental observed and predicted folding rates in jackknife cross validation.

166 to contribute to the viscosity dependence of folding rates in larger proteins.

167 trapolating GuHCl-based chevrons to estimate folding rates in the absence of denaturant and in interp

168 The folding rates in the absence of denaturant were found to

169 thiol was initially determined and then the folding rates in the presence of each thiol were measure

170 The trends in folding rates in the presence/absence of gatekeepers obs

171 The folding rate increases due to reduced-dimension pathways

172 5.0 to 6.40 kcal mol(-1) at pH 8.0 while the folding rate increases from 0.60 to 18.7 s(-1).

173 Analysis of the urea dependence of the folding rates indicates that mutations modulate the unfo

174 /B/G/H helix core substantially decrease the folding rate, indicating that docking and folding of the

175 The folding rate is 640 s(-1) and the value of deltaG degree

176 The net folding rate is a product of the equilibrium constant of

177 as the sole factor to determine the hairpin-folding rate is an oversimplification.

178 At a higher force (f = 11 pN), the folding rate is controlled by the formation of the bulge

179 What controls the folding rate is hotly debated.

180 The folding rate is not retarded by populating an intermedia

181 ions), the influence of these factors on the folding rate is poorly understood.

182 the mutations and fluorophore locations, the folding rate is similar for various protease constructs.

183 rotein folds in a two-state fashion, and the folding rate is slow.

184 in protein stability and indicates that the folding rate is unchanged.

185 es that the topology-dependence of two-state folding rates is a direct consequence of the extraordina

186 racy of total contact distance in predicting folding rates is essentially unchanged if "short"-ranged

187 ethanol cosolvent allows us to determine the folding rate (kf approximately 0.3 (micros)(-1)) and the

188 en able to predict the temperature-dependent folding rate, kinetic intermediates, and folding pathway

189 r the observation of "chevron behavior" (log folding rate linear in denaturant concentration) typical

190 phobicity of a side-chain and the log of the folding rate, ln(k(f)).

191 ar relationship between stability (logK) and folding rates (logk(f)) over the range of pH 5-9 for all

192 Moreover, starting structures with folding rates most similar to experiment show some nativ

193 Accordingly, the folding rate must be slower than the product of the frac

194 agree with the extrapolated barrier-limited folding rate observed near the melting transition.

195 Little change in folding rates occurred for the Ala/Gly pair mutations at

196 free energy barrier and results in a maximum folding rate of (2.0 +/- 0.3 micros)(-1), which is appro

197 The known folding rate of 20 s-1 at 1.5 M guanidinium chloride in

198 The folding rate of 26.4 mus(-1) (at 80 degrees C), extracte

199 We measure the stability and folding rate of a mutant of the enzyme phosphoglycerate

200 e studied the effect of Gly mutations on the folding rate of barnase to investigate the secondary str

201 -Pro bonds are crucial for the stability and folding rate of collagen, the most abundant protein in m

202 l limiting law, both the stability and (log) folding rate of FynSH3 increase nearly perfectly linearl

203 to "zipper up," while having an extrapolated folding rate of k(f) = 2 x 10(5) s(-1).

204 We interpret the acceleration of the folding rate of MrH3a in 8% HFIP as a direct consequence

205 While GroELS increases the folding rate of PepQ by over 15-fold, we demonstrate tha

206 the effect of crowding on the stability and folding rate of protein tertiary structures, very little

207 At pH 6.0, the aromatic thiols increased the folding rate of RNase A by a factor of 10-23 over that o

208 vestigated for their ability to increase the folding rate of scrambled RNase A.

209 y binds to its client, the more it slows the folding rate of the bound client.

210 The folding rate of the CLN025 beta-hairpin is unchanged wit

211 0)PC liposomes resulted in a decrease in the folding rate of the fast pathway.

212 of the 5' end to G303 in J8/7 decreased the folding rate of the P4-P6 domain.

213 ding leads to an appreciable decrease in the folding rate of the shortest beta-hairpin peptide, indic

214 ore a target for engineering to increase the folding rate of the subdomain from approximately 0.5 mic

215 Folding rate of this class of proteins is positively cor

216 mical basis for the previously observed slow folding rate of this mutant, compared to its analogue (d

217 Our results suggest that the folding rate of two-state proteins is a function of thei

218 the basis of our simulations we estimate the folding rate of villin to be approximately 5micros.

219 These results contrast with folding rates of 2-0.2 s(-1) previously observed for for

220 eters, we obtain a good correlation with the folding rates of 24 two-state folding proteins.

221 ing, two-state proteins and confirm that the folding rates of a diverse set of Go 27-mers are poorly

222 igated the effects of point mutations on the folding rates of a small single domain protein.

223 lts suggest that the differences in regional folding rates of AKe are not derived from the specific d

224 The folding rates of all the other constructs were lower tha

225 To examine this division, folding rates of circularly permutated isomers are compa

226 By comparing folding rates of consensus ankyrin repeat proteins (CARP

227 imited by rates of protein synthesis, by the folding rates of its slowest proteins, and--for large ce

228 trast, SurA showed no effect on the observed folding rates of PagP, consistent with the view that the

229 We also assayed folding rates of PGK-FRET in spatial proximity to and fa

230 This model gives estimates of folding rates of proteomes, leading to a median folding

231 The oxidative folding rates of RNase B are between 1.7 and 1.3 times f

232 The relative folding rates of simple, single-domain proteins, protein

233 Folding rates of small single-domain proteins that fold

234 In contrast, the relative folding rates of small, Go-potential lattice polymers, w

235 rotected in the bulk and (b) by accelerating folding rates of the protein.

236 The folding rates of the redesigned proteins are greater tha

237 The folding rates of the slow kinetics phase calculated over

238 ed by results from an Eyring analysis of the folding rates of the two proteins.

239 lation between sigma and either the relative folding rates of these proteins or the presence or absen

240 Folding rates of two-state folding proteins correlate we

241 The folding rates of two-state single-domain proteins are ge

242 with the 9 order of magnitude dependence of folding rates on protein size for a set of 93 proteins,

243 rimentally identified from the dependence of folding rates on solvent viscosity.

244 he alanine substitution has no effect on the folding rate or on the equilibrium constant.

245 misfolding is not determined by the relative folding rates or barrier heights for forming the domains

246 The nucleus increases PGK stability and folding rate over the cytoplasm and ER, even though the

247 In the example studied here, the analysis of folding rates, Phi-values, and folding pathways provides

248 The increased stability and high folding rate predicted by our simulations were subsequen

249 The posterior distribution of the folding rate predicted from the data agrees well with th

250 contact map prediction is useful for protein folding rate prediction, model selection and 3D structur

251 The model gives reliable folding rate predictions provided excluded volume terms

252 lding proteins to experimentally resolve the folding rate prefactor and investigate how much it varie

253 elix (helix I) unfolded, fold with identical folding rates, providing direct evidence for the conclus

254 gregation, or an active role in accelerating folding rates, remains a matter of debate.

255 d aggregation but did not alter the observed folding rates, resulting in a higher overall yield of ac

256 the protein by 1 kcal/mol and increases the folding rate sixfold, as measured by nanosecond laser T-

257 the effects of single-point mutations on the folding rate, stability, and transition-state structures

258 e of barnase do not significantly affect the folding rate, suggesting a lack of specific favorable in

259 y next to the beta-turn, does not change the folding rate, suggesting that most native interstrand H-

260 tion is completely reflected in an increased folding rate suggests that this region of the protein is

261 known correlation between contact order and folding rates, suggests that other proteins will have a

262 temperature at which it exhibits its fastest folding rate (T(m)<T(f)).

263 ins exhibit two-state folding kinetics, with folding rates that span more than six orders of magnitud

264 n thus does not appear to operate on protein folding rates, the majority of the designed proteins unf

265 gle, experimentally determined structure and folding rate, this does not ensure that a given simulati

266 is related to the ratio of the unfolding and folding rates, this increase completely accounts for the

267 r map-based kinetics techniques by comparing folding rates to known experimental results.

268 For confinement to positively impact folding rates under physiological conditions, it is henc

269 2.1 Single-domain chains: fast folding rates; unstable intermediates; two-state kinetic

270 presence of the salts markedly increased the folding rates (up to 5-fold).

271 transition state identified by the change in folding rate upon addition of metal ions.

272 protein exhibited a twofold acceleration in folding rates upon encapsulation.

273 The folding rate varies remarkably between different members

274 cillus subtilis RNase P RNA isomers, whereas folding rates vary by only 1.2-fold for circularly permu

275 Folding rates vary by tenfold for circularly permuted Ba

276 For a fixed pore size, the folding rates vary non-monotonically as lambda is varied

277 The ultrafast folding rate, very accurate X-ray structure, and small s

278 ding for all of the constructs; however, the folding rate was affected by their amino acid sequences

279 haracteristics of the native enzyme, but its folding rate was altered.

280 In contrast, a significant difference in folding rates was observed for the Ala/Gly pair mutation

281 hose substitutions that significantly affect folding rates, we find that accelerating substitutions a

282 Furthermore, under similar conditions folding rates were almost identical with either reduced

283 Both the opening and folding rates were found to vary with changing salt cond

284 Oxidative folding rates were further increased in the presence of

285 Two distinct folding rates were observed across a range of Mg(2+) con

286 Folding rates were observed to be either accelerated or

287 We found that the folding rates were relatively similar, approximately 0.1

288 We find a substantial acceleration of the folding rate when the connecting loop is made shorter (i

289 cs also provide a novel method for measuring folding rates when the exchange between folded and unfol

290 f a beta-hairpin primarily by increasing its folding rate, whereas a stronger hydrophobic cluster inc

291 f a beta-hairpin primarily by increasing its folding rate, whereas a stronger hydrophobic cluster inc

292 The increase in folding rate with chain length, as opposed to a decrease

293 ects of folding such as the variation of the folding rate with stability or solvent viscosity and the

294 roteins (CARPs), we find a clear increase in folding rates with increasing size and repeat number, al

295 p mutants show unusually strong increases in folding rates with marginal effects on stability.

296 ack disulfide bridges, and (ii) display slow folding rates with multi-state kinetics, to determine re

297 n path time is remarkably insensitive to the folding rate, with only a 2-fold difference for rate coe

298 by a 35-fold increase in tetraloop-receptor folding rate, with only a modest decrease in the corresp

299 ass, comprising all other residues, produces folding rates within a factor of two of the wild-type ra

300 o other hydrophobic residues often increases folding rates without significantly altering folding fre