ライフサイエンスコーパス: native structure

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

2 n the conformational space determined by the native structure.

3 ational rearrangements during folding to the native structure.

4 g route, and promotes domain swapping to the native structure.

5 sequence and spatially well separated in the native structure.

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

7 oldon-foldon interactions that construct the native structure.

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

9 methods that predict their similarity to the native structure.

10 structural role for certain hydroxyls in the native structure.

11 store these activities and thus functionally native structure.

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

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

14 eating units that constitute the full-length native structure.

15 good approximation, to faithfully report on native structure.

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

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

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

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

20 measures exposure of cysteines buried in the native structure.

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

22 ce of a protein encodes the blueprint of its native structure.

23 specific ion interactions in specifying the native structure.

24 oncentrations below those needed to fold the native structure.

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

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

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

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

29 conformation likely reflects the integrin's native structure.

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

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

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

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

34 eral positions, retaining varying amounts of native structure.

35 cts and residues in the context of the whole native structure.

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

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

38 energy attractor basin that pulls toward the native structure.

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

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

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

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

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

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

45 between residues that are in contact in the native structure.

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

47 cular mechanics force fields to maintain the native structure.

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

49 ompact monomer with little similarity to the native structure.

50 mote protein expansion and therefore loss of native structure.

51 to shear flow while maintaining its overall native structure.

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

53 the individual domains largely retain their native structure.

54 or misfolded polypeptides can fold to their native structure.

55 formation of spheroidal intermediates with a native structure.

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

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 structure and derive a criterion to identify native structures.

69 soluble trimeric Env immunogens that assume native structures.

70 replicate the glycosylation pattern on these native structures.

71 various chain lengths, and widely differing native structures.

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

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

74 7 causes the greatest destabilization of the native structure (6.9 kcal/mol), which is consistent wit

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

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

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

78 allosteric regulatory element, preserves the native structure, activity, and subcellular localization

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

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

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

82 Due to the lack of knowledge on the MPER native structure and accessibility, different and exclus

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

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

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

86 demonstrate how we can preserve the protein native structure and control the protein orientation on

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

109 The native structures and functions of those proteins can of

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

127 omic-level similarity to their corresponding native structures, as demonstrated by the fact that 87.8

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

143 ng simulations that rely on knowledge of the native structure can provide critical, detailed informat

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

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

146 While native structures containing an MS3 core are often unava

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

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

149 o a well-packed, extensively hydrogen-bonded native structure differs fundamentally from the nonspeci

150 ns in the bilayer, DeltaDeltaG calculations, native structure discrimination, and native sequence rec

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

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

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

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

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

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

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

173 o which noncovalent protein complexes retain native structure in the gas phase is highly dependent on

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 olution of model proteins to investigate how native structure influences evolution of cotranslational

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

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

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

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

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

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 ing discrepancies between protein models and native structures is at the heart of development of prot

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

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

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

200 3, which lies on the opposite surface in the native structure, near the P3-P8 domain, has no effect.

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

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

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

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

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

206 allowed the conjugate to better maintain the native structure of albumin and its intrinsic properties

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

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

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

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

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

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

224 tutions cause local disorder and misfold the native structure of the isolated platelet GPIbalpha-adhe

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

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

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

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

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

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

231 r and submicrometer sized capillaries on the native structures of the protein complexes streptavidin,

232 Native structures of the S proteins in pre- and postfusi

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

234 d models that can predict the effects of the native structure on folding to all-atom-based methods th

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

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

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

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

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

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

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

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

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

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

245 nucleotide sequences that are paired in the native structure, presuming that unbound molecules would

246 In contrast to native structured proteins, amyloids do not follow a def

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

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

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

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

251 ergy model yield significant improvements in native structure recovery of protein-protein and protein

252 s complexity and highly branched nature, the native structure remains partially unresolved.

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

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

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

256 The native structure revealed an unusual conformation of the

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

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

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

260 The native structure scored better than any of the decoys in

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

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

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

264 ith similar or better proximity to the known native structure than several state-of-the-art decoy gen

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

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

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

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

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

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

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

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

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

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

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

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

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

278 ution, unfolded proteins typically find this native structure through a biased sampling of preferred

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

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

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

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

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

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

285 some, the G-domain transitions to its stable native structure via folding intermediates.

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