ライフサイエンスコーパス: native structure

1 at we can produce PG in vitro that resembles native structure.

2 methods that predict their similarity to the native structure.

3 structural role for certain hydroxyls in the native structure.

4 store these activities and thus functionally native structure.

5 ltiple, competing folding routes to a unique native structure.

6 bly of MRP1 into a fully transport competent native structure.

7 good approximation, to faithfully report on native structure.

8 thout the helix, and have rmsds close to the native structure.

9 rence of 2.60 A with the actual distances to native structure.

10 btilis RNase P RNA is more extended than its native structure.

11 mainly by the ability to sample close to the native structure.

12 measures exposure of cysteines buried in the native structure.

13 native-like secondary structure but also non-native structure.

14 specific ion interactions in specifying the native structure.

15 oncentrations below those needed to fold the native structure.

16 f all globular proteins, regardless of their native structure.

17 ding and unfolding, as well as the protein's native structure.

18 es not interfere with rapid formation of the native structure.

19 f amino acid sequences that fold to the same native structure.

20 conformation likely reflects the integrin's native structure.

21 models was superimposable within 4 A on the native structure.

22 ese data make it trivial to discriminate the native structure.

23 iological activity, it appears to retain its native structure.

24 n a given ensemble, which are closest to the native structure.

25 eral positions, retaining varying amounts of native structure.

26 ial can drive protein models closer to their native structure.

27 f which is only 6.35 A above the iron in the native structure.

28 energy attractor basin that pulls toward the native structure.

29 thways that lead directly and rapidly to the native structure.

30 A root mean-square deviations away from the native structure.

31 e interactions must be disrupted to form the native structure.

32 the existence of two dynamic states for the native structure.

33 might be able to drive proteins toward their native structure.

34 g intermediate can be as well defined as the native structure.

35 to take advantage of the fluctuations in the native structure.

36 cular mechanics force fields to maintain the native structure.

37 ation causes the protein to refold to a near-native structure.

38 etween the folding intermediate and the full native structure.

39 and may require retention of some aspects of native structure.

40 d secondary structural elements yielding the native structure.

41 of the intermediate structures to the final native structure.

42 ar-native decoy protein structure toward the native structure.

43 a protein's amino acid sequence dictates its native structure.

44 complex with C96 or colicin E3 restored the native structure.

45 ompact monomer with little similarity to the native structure.

46 to shear flow while maintaining its overall native structure.

47 nits, which are determined directly from the native structure.

48 the individual domains largely retain their native structure.

49 or misfolded polypeptides can fold to their native structure.

50 formation of spheroidal intermediates with a native structure.

51 de a molecule with fewer disturbances to the native structure.

52 n the conformational space determined by the native structure.

53 ational rearrangements during folding to the native structure.

54 sequence and spatially well separated in the native structure.

55 g holocytochrome c for proper folding to its native structure.

56 oldon-foldon interactions that construct the native structure.

57 t chain length at which they fold into their native structures.

58 edly fold to their experimentally determined native structures.

59 such as tau protein, that lack fully ordered native structures.

60 different classes of P RNA and have distinct native structures.

61 for which there is little prior knowledge of native structures.

62 present, where the covariances disfavor non-native structures.

63 in unfolded polypeptides but hidden in most native structures.

64 tures obtained by reversing the sequences of native structures.

65 etically conserved elements form stable, non-native structures.

66 somewhat surprising feature, a knot in their native structures.

67 d of non-Watson-Crick base pairs seen in the native structures.

68 an be predicted using the contact map of the native structures.

69 soluble trimeric Env immunogens that assume native structures.

70 replicate the glycosylation pattern on these native structures.

71 structure and derive a criterion to identify native structures.

72 various chain lengths, and widely differing native structures.

73 of nucleic acids and proteins into correct, native structures.

74 an amino acid sequence dictates a protein's native structure?

75 Among 278 native structures, 239 and 249 native structures were re

76 7 causes the greatest destabilization of the native structure (6.9 kcal/mol), which is consistent wit

77 In the native structure, a crystal contact results in one of th

78 unique class of proteins that have no stable native structure, a feature that allows them to adopt a

79 es leading energetically downhill toward the native structure, a principle that is captured in funnel

80 g mechanism by computational analysis of the native structure alone will help toward the ultimate goa

81 structures within 1-3 A C(alpha) rmsd of the native structure), also known as the protein structure r

82 S3 binding site in L-ficolin, whereas in the native structure an acetate ion has been placed in the S

83 The native structure and a complex with diisopropyl fluoroph

84 ingle-strand DNA binding protein (SSB) whose native structure and binding properties may be drastical

85 These materials retain the native structure and catalytic ability of the hydrolytic

86 studies provide the first insights into the native structure and catalytic mechanism of FBT family c

87 rge-depleted S6 variant not only retains its native structure and cooperative folding transition, but

88 y binds nascent alpha globin to maintain its native structure and facilitate its incorporation into h

89 t that in addition to predicting the correct native structure and folding time constant, molecular dy

90 variety of proteins in such a way that their native structure and function are maintained.

91 orescent labeling often results in a loss of native structure and function, and single cysteine label

92 en very important for preserving a protein's native structure and function.

93 ever, the correspondence between a protein's native structure and its structure in the mass spectrome

94 nting these targets, possibly altering their native structure and leading to misleading or incorrect

95 and classification of ribosomes revealed the native structure and organization of the cytoplasmic tra

96 ta to direct Rosetta trajectories toward the native structure and produces more accurate models than

97 interplay between thermodynamic bias toward native structure and residual conformational disorder ma

98 ure solvent-free myoglobin liquids with near-native structure and reversible dioxygen binding ability

99 vailable information suggests that quantized native structure and stepwise folding coevolved in ancie

100 rplay between the effects of symmetry in the native structure and the effects of asymmetry from speci

101 rmined by the free energy gap separating the native structure and the N() state, a finding that can b

102 , namely, the thermodynamic determination of native structure and the sufficiency of thermodynamic st

103 ses cycles of ATP hydrolysis to denature any native structure and to translocate the unfolded polypep

104 d from solutions in which the molecules have native structures and activities.

105 ls in terms of both its ability to recognize native structures and consistency in achieving high Z-sc

106 folding mechanism for proteins with diverse native structures and establishes general principles for

107 San1's target substrates have lost their native structures and expose hydrophobicity.

108 gh extensive experimental tests both for the native structures and for the folding thermodynamics.

109 Salts are often necessary to maintain the native structures and functions of many proteins and pro

110 The native structures and functions of those proteins can of

111 itu, which does not reflect accurately their native structures and functions.

112 observation contrasts with predictions that native structure, and in particular intermolecular beta-

113 enerating protein-RNA complexes close to the native structure, and outperforms free docking, successf

114 ngle dominant route in which elements of the native structure appear in an order highly correlated wi

115 oteins that contain a distinct knot in their native structure are impressive examples of biological s

116 rge-scale conformational rearrangement, both native structures are dynamically and reversibly adopted

117 ytic activities and selectivities, but their native structures are optimized for very specific bioche

118 Two degenerate native structures are stabilized by an energy barrier of

119 Our results indicate that two degenerate native structures are stabilized by subtle balance betwe

120 , higher energy conformations similar to the native structures are still sampled frequently but not a

121 o the minor groove and that the modified and native structures are virtually identical.

122 f all globular proteins, regardless of their native structure, are directed at least in part by poten

123 nsic flexibility of proteins by treating the native structure as a rigid molecule.

124 ith native similarity and the scoring of the native structure as the lowest in energy.

125 can result in covalent linkages found in the native structure as well as those that are not, so-calle

126 s containing 278 targets, and recognized 226 native structures as best from the decoys, whereas DFIRE

127 acromolecule defines its folded, active (or 'native') structure as a global energy minimum in the fol

128 some, can lead to lifelong population of the native structure, as opposed to aggregation.

129 t high concentrations without altering their native structure associated with specific biological fun

130 te a funnel-shaped energy landscape with the native structure at the global minimum.

131 ch of these proteins folding into its stable native structure before the full-length protein is relea

132 red in six different mutants that retain the native structure but align differently relative to the s

133 ans depend not only on the energetics of the native structure but also on competing folds; in particu

134 ded conformation (M) that includes extensive native structure but is proposed to differ in topology f

135 An RNA molecule may fold to a near-native structure but not be able to continue to the corr

136 , in isolation, IL-12alpha fails to form its native structure but, instead, misfolds, forming incorre

137 ied (or indeed triggered) by the loss of the native structure, but a clear understanding of the compl

138 This includes not only proteins' native structures, but also all their respective functio

139 After unfolding the native structure by changing every phi and psi angle by

140 rix (ECM) that closely resembles that of the native structure by locally depositing basement membrane

141 is its ability to go beyond the the (known) native structures by accounting for the full free energy

142 the slight anomalous scattering from generic native structures by combining data measured from multip

143 esults suggest that models within 4 A of the native structure can be achieved for complex membrane pr

144 s, whereas the holoprotein loses heme before native structure can be attained.

145 given set of structure decoys and a putative native structure can be projected onto a theoretical fun

146 ting to the native complex, showing that non-native structures can offer a low free-energy path to pr

147 duct of fructose 1-phosphate cleavage, and a native structure containing copurified ligands, modeled

148 While native structures containing an MS3 core are often unava

149 Near-native structures could also be selected for heme-bindin

150 However, the accuracy of the native structure derivation of ncRNAs is still not satis

151 roved understanding of bacterial behavior in native, structured environments.

152 bridge deleted can still fold into its near-native structure even in its noncyclic form, confirming

153 t almost all polypeptides can either adopt a native structure (folded or intrinsically disordered) or

154 entification of the structure closest to the native structure for a blind prediction.

155 ucture, providing a rare example of such non-native structure formation in a folding pathway.

156 secondary structure and observed sequential native structure formation.

157 duced letter code are capable of determining native structure from a large decoy set for a majority o

158 ong all methods tested in discriminating the native structure from a set of decoys for all decoy data

159 that ROTAS has improved ability to recognize native structure from decoy models compared to other pot

160 ccurate scoring function differentiating the native structure from decoys.

161 ization problems, growing and assembling the native structure from peptide fragments, local structure

162 interactions requires the selection of near-native structures from a set of docked poses based on th

163 oo computationally expensive to predict most native structures from amino acid sequences.

164 on that can accurately discriminate the near-native structures from decoy complexes and at the same t

165 od is unable to identify the native and near-native structures from the sequence.

166 entropy is necessary for discriminating the native structures from their misassembled counterparts.

167 e protein misfolding and restore proteins to native structure, function, and localization could mitig

168 ed (II,II) cofactors, which deviate from the native structures functional in O2 activation, explainin

169 tion of an Ising-like theoretical model that native structure grows in only a few regions of the amin

170 uccessful when a model has a TM-score to the native structure >/= 0.4, when F(wt >/= 3)(cov) > 1.0 an

171 The fraction of proteins for which the native structure had lowest energy increased from 0.22 t

172 imulations are often chosen according to the native structure, implying that they are not truly "tran

173 amyloid in vivo, we investigated the role of native structure in modulating its conformational dynami

174 ith theory is indicative of the retention of native structure in the gas phase, which in turn, qualif

175 ues in the CE loop, which probably forms non-native structure in the intermediate that must be resolv

176 Some denatured proteins fold to their native structures in only microseconds, on average, impl

177 Newly synthesized proteins must form their native structures in the crowded environment of the cell

178 es with crystal structures, we achieved near-native structures in the top 20 models for two out of fo

179 on the transient formation of native and non-native structures in this acid-denatured state of ACBP,

180 cies that elongated the fibrils, returned to native structured insulin.

181 rate-limiting step in the conversion from a native structure into a pathological amyloidogenic fold.

182 thod can deliver protein molecules with near native structure into both hydrophilic and hydrophobic a

183 ges are critical for snapping the frustrated native structure into place.

184 the transition from an amorphous to ordered native structure involves complex energy landscapes, and

185 Minimization from the native structure is a weak test of potential energy func

186 tional pathway in which neither function nor native structure is completely lost.

187 Acquisition of native structure is generally considered to be the most

188 der, the network of sequences that share its native structure is identified.

189 ity of a protein structural model before its native structure is known.

190 refolded pepsin and how the formation of the native structure is mediated.

191 ntacts, the web application runs even when a native structure is not available, visualizing the conta

192 te state under physiological conditions, the native structure is not maintained and is likely to requ

193 cell, but how each polynucleotide finds its native structure is not understood.

194 The number of near-native structures is used to estimate the probability of

195 he protein rapidly loses its low-temperature native structure; it then unfolds before refolding to a

196 rsion angle are opposite with respect to the native structure, led to the complete disruption of the

197 native for all 20 and correctly chooses the native structures (<4 A) for 15 of them, including ubiqu

198 This deformation of the native structure means that these methods are not genera

199 Furthermore, FimH with native structure mediates weak binding at low shear stre

200 A switch between competing native structures might be triggered by external factors

201 3, which lies on the opposite surface in the native structure, near the P3-P8 domain, has no effect.

202 folding reaction must involve aspects of non-native structure not detected by the Go model simulation

203 ly unfolded states from which folding to the native structure occurs.

204 We explore the possibility for the native structure of a protein being inherently multiconf

205 (c) Can we predict the native structure of a protein from its amino acid sequen

206 By assuming that the native structure of a protein is known and representing

207 the same foldon interactions that encode the native structure of any given protein also naturally enc

208 Here, we analysed the native structure of BBL as a function of pH, temperature

209 The native structure of FHA2 is predominantly helical and na

210 The native structure of helix IV and loop D antagonizes bind

211 ncapsulation has significantly preserved the native structure of HRP and therefore its enzymatic acti

212 Despite their importance, the native structure of human cilia is unknown, and structur

213 are of prime importance for maintaining the native structure of IgG.

214 e apply electron cryotomography to image the native structure of intact dividing cells and show that

215 Our findings will allow studying native structure of many other membrane proteins.

216 Comparative information on the near-native structure of microorganisms is an important and n

217 gs thus emphasize that subtle changes in the native structure of peptide hormone(s) could alter its c

218 ion of this site is followed by formation of native structure of Phe-2 and Phe-17, then by Phe-47, an

219 s is that they generally do not preserve the native structure of proteins as observed by x-ray crysta

220 he protein-nanoparticles interaction and the native structure of proteins using SERRS spectroscopy.

221 ng at residue approximately 169) that in the native structure of PrP monomer corresponds to alpha-hel

222 rientation of these segments observed in the native structure of SDF.

223 Results revealed that the native structure of SELfd is more folded than that of eb

224 The native structure of the Azoarcus group I ribozyme is sta

225 y and subtomogram averaging to determine the native structure of the COPI coat within vitrified Chlam

226 A native structure of the cytochrome b(6)f complex with im

227 ed poses cluster in a narrow vicinity of the native structure of the dimer, then one can assume that

228 alty imposed on folding of one domain by the native structure of the other.

229 n the primary sequence, without changing the native structure of the RNA.

230 s a test, we apply MELD + CPI to predict the native structures of 20 small proteins.

231 tions of the observed ions revealed that the native structures of detergent solubilized MPs were not

232 average of 2.2 A from the Protein Data Bank native structures of eight of nine proteins that we test

233 s from HPLC-DAD analysis clearly showed that native structures of phenolic compounds were simplified

234 ift information to characterize not only the native structures of proteins but also their conformatio

235 likely similarity between the predicted and native structures of proteins have become essential for

236 Organic solvents may induce non-native structures of proteins that mimic folding interme

237 ults provide important clues to the study of native structures of proteins.

238 ating water-soluble analogues with preserved native structures offer an attractive alternative.

239 wn that 2DX4 possesses two nearly degenerate native structures: one is a helix structure with the oth

240 ial (>2.5 kJ mol(-1)) destabilisation of the native structure or even prevents efficient folding to t

241 However, PC does not support native structure or function for several reconstituted t

242 for GPCR loops that interact, either in the native structure or in low-energy false-positive structu

243 Sup35, p53), independent of their sequence, native structure, or function could self-assemble into h

244 om in-frame translation that fail to achieve native structure owing to inevitable imperfections in tr

245 we apply the ZA search mechanism to protein native structure prediction by using the AMBER96 force f

246 RACER achieves accurate native structure prediction for a number of RNAs (averag

247 e to their successful use in de novo protein native structure prediction.

248 ing, it is concluded that the native and non-native structures present in the I(2) ensemble enable ef

249 d by the inability to quantify the residual (native) structure present in an unfolded protein or nucl

250 Despite its beneficial effects on the native structure, prior studies have shown that early fo

251 As a result the geometry of the native structure provides key constraints that shape pro

252 n-pathway and appears to have long-range non-native structure, providing a rare example of such non-n

253 decoys, which eliminates the possibility of native structure recognition by trivial potentials.

254 than other competing potentials not only in native structure recognition, but also in best model sel

255 which represent the absence and presence of native structure, respectively.

256 rogen bond of Ser195 OG to the latter in the native structure, resulting in an interaction that has n

257 ridges and hydrogen bonds not present in the native structure, resulting in slight differences in the

258 yme's catalytic activity but destabilize its native structure, resulting in the degradation of the mi

259 The native structure revealed an unusual conformation of the

260 ogy and shows some local deviations from the native structure, revealing that the structure of the fo

261 The perturbation in native structure (S-S cleavage) led to a significant inc

262 ative GPI anchors and included mimics of the native structure's three domains.

263 tive state in contrast with models having no native structure-seeking tendency.

264 Proteins fold into unique native structures stabilized by thousands of weak intera

265 For kinetically trapped native structures such as GFP, folding correctly the fir

266 portantly, conformational heterogeneity in a native structure that changes with conditions will lead

267 The results reveal a robust native structure that is not perturbed by the presence o

268 conditions, resulting in gradual melting of native structure that permits resolving folding mechanis

269 component of the I(2) ensemble contains non-native structure that rearranges/isomerizes to a more na

270 little known about the local transitions of native structures that possibly lead to such intermediat

271 ng conditions, wild-type myoc-OLF adopts non-native structures that readily fibrillize when incubated

272 the energy landscape in the vicinity of the native structure, the nonlinear manifold describing the

273 In the native structures, the calcium-binding site is similar t

274 o not form a large enough cluster around the native structure, then it is unlikely that the subunits

275 When viewed in the context of the native structure, these clusters have the signature char

276 apes that contain only contacts found in the native structure, this study introduces "chemical frustr

277 utilize information from databases of known native structures, this work opens up the possibility of

278 we identify and characterize two alternative native structures, three intermediate states, and numero

279 t one of the top five models agrees with the native structure to better than 4 A rmsd over the backbo

280 del used was a minimalist Go model using the native structure to determine attractive energies in the

281 removing the carboxyl-terminal helix in the native structure to produce a highly populated structura

282 Ribozymes must fold into compact, native structures to function properly in the cell.

283 ross-linking proteins while preserving their native structures to maintain their selective binding af

284 rtitioning between productive folding to the native structure versus aggregation.

285 ddition, revealing a stepwise buildup of the native structure via a single dominant pathway.

286 G pair compared to the unmodified C-G in the native structure was revealed.

287 onship between the folding mechanism and the native structure, we develop a unified approach for pred

288 procedure that minimizes degradation of the native structure, we extracted glucans from C. albicans

289 Among 278 native structures, 239 and 249 native structures were recognized by OPUS-DOSP without a

290 approach enhances the identification of near-native structures when applied to four docking methods,

291 ttractions play a lesser role in finding the native structure, whereas polar-polar attractions are mo

292 of an RNA molecule is not only linked to its native structure, which is usually taken to be the groun

293 This spectrum reveals a native structure whose beta-strands and turns within the

294 protein, gpW, that folds very rapidly into a native structure with an alpha/beta topology in which al

295 mprovement of >20% in C(alpha) rmsd from the native structure with GBSA, compared to just 7 proteins

296 odel captures the known stability of protein native structures with stable energy basins that are nea

297 residue chains that span the membrane in the native structure, with varying levels of heavy ((13)C=(1

298 ulting TASSER_2.0 models are closer to their native structures, with an average root mean-square devi

299 bel mutants were able to converge toward the native structure within 1-3 A root mean-square deviation

300 pportunity for an unbiased assessment of the native structure within genetic interaction networks and