ライフサイエンスコーパス: native-like

1 set of benchmark proteins that appear to be native-like.

2 a partially folded state with neither domain native-like.

3 MR, indicating that they are well packed and native-like.

4 ergy structures are not necessarily the most native-like.

5 rmediate with the N-td unfolded and the C-td native-like.

6 with the rest of the alpha-domain remaining native-like.

7 o 33 231 ms, the collision cross sections of native-like, 7+ cytochrome c ions increase monotonically

8 d analogues of Gtalpha(340-350) demonstrated native-like activity in their ability to bind and stabil

9 not be able to support potentially important native-like activity of the apoprotein.

10 TS2 is highly native-like (alpha(TS2)=0.93) and represents a late entr

11 substitution by Ala leads to an unstable but native-like analog of low activity.

12 Under these conditions, a folded, native-like and a disordered state exist in slow exchang

13 Apart from the native state, native-like and molten-globule states have been identifi

14 Transient long-range contacts, both native-like and non-native-like, have previously been sh

15 , the average charge states observed for all native-like anions were less than those for the correspo

16 The trimers maintained native-like antigenicity and structure, activated PGT121

17 , there are also many structures that have a native-like appearance.

18 7 degrees C, respectively) and predominantly native-like, as determined by negative-stain electron mi

19 Here, we present a native-like assay geometry to test the rupture force of

20 many transmembrane domains that appear to be native-like; at the same time, there are others that app

21 imaging shows that the purified, nonclipped, native-like B41 SOSIP.664 trimers contain two subpopulat

22 The native-like BChl-a dimer has Q(y) absorption at 820 nm a

23 uniformly (15)N-labeled Pf1 coat protein in native-like bilayers.

24 onsists of two predicted helices and retains native-like binding affinity for the transcriptional act

25 A large-scale benchmark test shows that the native-like binding is highly likely in the structural e

26 ow that RECON is able to efficiently recover native-like, biologically relevant sequences in this div

27 lopment of tissue engineering scaffolds with native-like biology and microarchitectures is a prerequi

28 The effects of charge state on structures of native-like cations of serum albumin, streptavidin, avid

29 microgel environments that where composed of native-like cellular microarchitectures resembling vascu

30 s facilitated the detection of endogenous or native-like cellular systems that are possibly more phys

31 d also shows the potential for verifying the native-like character for numerous other membrane protei

32 thers that appear to have less than complete native-like character.

33 ractions along the nucleosome chain generate native-like chromosome features and recapitulate chromos

34 lected precursors do not distinguish between native-like, collapsed, and expanded forms of a protein

35 onsistent with the H4b linker being a key to native-like collective motion in the protein.

36 th examine folding under highly stabilizing, native-like conditions and probe the pretransition state

37 ribosomal protein L9 can be populated under native-like conditions by taking advantage of a destabil

38 rating that the unfolded state of CTL9 under native-like conditions is more structured.

39 Under native-like conditions MscL, MscS as well as MscK distri

40 jor differences when comparing MsbA in these native-like conditions with double electron-electron res

41 er of the GdnHCl denatured state ensemble to native-like conditions.

42 try of non-engineered cytochromes P450 under native-like conditions.

43 Mutations that give native-like conductance at low pH as well as minimal lea

44 The modified beta-lactoglobulin showed a native like conformation, besides a moderate loosening o

45 d whether there is any association between a native-like conformation and the presence of only the ca

46 izing antibodies 35O22 and 9H+109L reveals a native-like conformation and the successful incorporatio

47 , though only the latter appeared to be in a native-like conformation capable of binding strychnine,

48 yclization constrained the peptide in a loop native-like conformation to better mimic the anti-parall

49 el and that the aggregated protein retains a native-like conformation, with no evidence for large-sca

50 ar protein able to aggregate in vitro from a native-like conformational ensemble without the need for

51 Strands B, C, and E appear to maintain native-like conformations in the partially unfolded, amy

52 elationship and thus, enables us to generate native-like conformations more easily.

53 ons is immense; existing methods to identify native-like conformations mostly resort to random sampli

54 The results reveal the existence of two native-like conformations of Cyt that present significan

55 eutral pH, where the proteins have native or native-like conformations prior to ESI droplet formation

56 rmation sampling algorithm that can generate native-like conformations quickly.

57 ins can access aggregation-prone states from native-like conformations without the need to cross the

58 Most nascent CRM ions retain native-like conformations.

59 ecular dynamics which generally samples more native-like conformations.

60 nsistent with both forms adopting equivalent native-like conformations.

61 the ensemble of secondary structures toward native-like conformations.

62 enatured state provides further evidence for native-like contact formation in the denatured state.

63 radii, RMSDs from native state, fraction of native-like contacts are accessible from iFoldRNA.

64 rustration, leading to enhanced formation of native-like contacts in the transition-state ensembles (

65 es of folding, ACBP dynamics are governed by native-like contacts on a minimally frustrated energy la

66 atients (G202R and S227P) were analysed in a native-like context in recombinant fibulin-5 fragments.

67 regation with an unstructured strand A and a native-like core.

68 merase Pin1 in Xenopus laevis oocytes and in native-like crowded oocyte extract by in-cell NMR spectr

69 As appropriately purified, native-like CZA97.012 SOSIP.664 trimers induce autologou

70 older, generates a much higher percentage of native-like decoys than FARNA and BARNACLE, although we

71 s as a source sufficient to form globules of native-like dimensions.

72 ation of the sequence database resulted in a native-like dimeric TIM with near-diffusion-controlled k

73 conditions can cause beta2m to organize into native-like dimers prior to forming amyloid fibrils.

74 We initially demonstrate that the use of native-like distance maps is able to reproduce 3D struct

75 ng T-PioDock, a framework for detection of a native-like docked complex 3D structure.

76 ructures of metalated proteins do not retain native-like elements.

77 wo major conformational states: 1), a stable native-like ensemble of structures characterized by an e

78 G505 SOSIP.664 trimers are more homogeneous, native-like entities that contain predominantly the nati

79 ntribute additional diversity to the pool of native-like Env immunogens as key components of strategi

80 w subtype B trimer adds to the repertoire of native-like Env proteins that are suitable for immunogen

81 The availability of a native-like Env trimer and a bNAb from the same elite ne

82 C195, that can be added as Fabs to a soluble native-like Env trimer to stabilize it in a CD4-bound co

83 he interactions between a panel of bNAbs and native-like Env trimers (SOSIP.664 trimers).

84 Native-like Env trimers can induce autologous NAb respon

85 In contrast, native-like Env trimers fail to activate B cells express

86 p41 was an effective method for removing non-native-like Env.

87 Soluble, recombinant native-like envelope glycoprotein (Env) trimers of vario

88 , we tested the first generation of soluble, native-like envelope trimer immunogens in a conventional

89 e studies of isolated membrane proteins in a native like environment using neutron reflectometry (NR)

90 the conformational flexibility of Bfrs in a native-like environment and the way in which the protein

91 that the interaction interface observed in a native-like environment differs markedly from that infer

92 ed that individual receptor molecules in the native-like environment of phospholipid nanodiscs underg

93 native H helix) becomes locked into a fully native-like environment within 6 ms, suggesting that thi

94 process to produce highly soluble samples in native-like environments and to study lipid-dependent ef

95 rs that dictate cellular behavior in complex native-like environments.

96 ultiphoton-excited 3D printing to generate a native-like extracellular matrix scaffold with submicron

97 validation allowed the identification of non-native-like features in several membrane proteins and al

98 ovide many opportunities for introducing non-native-like features into membrane protein structures.

99 where neural networks are used to learn the native-like features of protein structures using a set o

100 secretase within supported biomembranes with native-like fluidity.

101 tance constraints that are consistent with a native-like fold for the +2 charge state in the gas phas

102 clear Overhauser effects demonstrates that a native-like fold is maintained in solution.

103 f fragments may prevent them from building a native-like fold.

104 partially due to the difficulty in obtaining native-like folded proteins in vitro.

105 , optimizing sample conditions to retain the native-like folding and function of membrane proteins fo

106 he cell surface was not affected, indicating native-like folding of the receptor.

107 stepwise pathway, determined by cooperative native-like foldon units and the way that the foldons fi

108 cooperativity determines the central role of native-like foldon units.

109 at the ability of reverse sequences to adopt native-like folds is strongly influenced by protein size

110 searches for and interactively incorporates native-like fragments from proven protein structures.

111 g need for validation tools that distinguish native-like from non-native-like structures.

112 of guidelines is proposed for distinguishing native-like from nonnative-like membrane protein structu

113 combinant cell surface trimers, to reproduce native-like glycosylation was then assessed.

114 ong-range contacts, both native-like and non-native-like, have previously been shown to be present in

115 , our results have demonstrated directly the native-like heteromeric interaction among the isolated I

116 experiences Hammond behavior, becoming more native-like (higher molar volume) with increasing denatu

117 Native-like HIV-1 Env immunogens representing distinct c

118 ion to the pool of other recently identified native-like HIV-1 Env trimers suitable for use as antige

119 d antimicrobial piscidin 1 (p1) oriented in "native-like" hydrated lipid bilayers.

120 splaying cis-trans proline isomerisation and native-like hydrogen bonding.

121 ure (in the mutant G23A/G25A) and to promote native-like hydrophobic packing interactions with helix

122 They also have a native-like (i.e., abundant) oligomannose glycan composi

123 In contrast, native-like immunogens failed to activate VRC01-class pr

124 /IR and stabilizing the activation loop in a native-like inactive conformation.

125 Using native-like incubation and electrospray conditions toget

126 Proinsulin contains a native-like insulin moiety (A- and B-domains); the tethe

127 ts monomeric form, (i) proinsulin contains a native-like insulin moiety and (ii) the C-domain footpri

128 n the transition state leading to N(2), more native-like interactions are developed and nonnative int

129 o apoflavodoxin's native state revealed that native-like interactions in most of the beta-strands mus

130 lices in H24L/H119F also favors formation of native-like interactions in the GH turn and between the

131 Thus, while native-like interactions may contribute to the formation

132 both sites III and IV appeared necessary for native-like interactions with PEP-19, the data also indi

133 hat stabilization of the B helix facilitates native-like interactions with the C-terminal region of h

134 of secondary structure elements, often with native-like interactions.

135 acid-level dynamics biased toward selecting native-like interactions.

136 onally design protein-protein complexes with native-like interface composition and interaction densit

137 e termed "sequential stabilization" based on native-like interfoldon interactions orders the pathway.

138 dence presented here shows that the trapped, native-like intermediate has structural heterogeneity in

139 This renders a native-like intermediate that oxidizes in a slow uncatal

140 form cooperatively in the transition from a native-like intermediate to the native state.

141 these residues show chemical shifts when the native-like intermediate {N(iso)} responsible for GFP's

142 the loosening of tertiary interactions in a native-like intermediate, N( *).

143 stepping through a reproducible sequence of native-like intermediates in an ordered pathway.

144 t of proteins known to fold through distinct native-like intermediates in distinct pathways.

145 e the fast folding event as well as identify native-like intermediates on energy landscapes enroute t

146 fold through a classical pathway sequence of native-like intermediates rather than through a vast num

147 al structure in the unfolded state of PYP is native-like, involving native-like protein-chromophore i

148 rted directly from experimental data for the native-like ion of a protein complex.

149 results are consistent with the retention of native-like ion structures throughout these experiments.

150 that the excess charges initially present on native-like ions have a modest, but sometimes statistica

151 The average effective density of the native-like ions is 0.6 g cm(-3), which is significantly

152 The apparent resolving powers of native-like ions measured using SLIM are as high as 42,

153 to determine the collision cross sections of native-like ions of proteins and protein complexes, whic

154 Here, we evaluate the stability of native-like ions using tandem IM experiments implemented

155 gies may all be adaptable to the analysis of native-like ions, which will enable future applications

156 Ion Manipulations (SLIM) for the analysis of native-like ions.

157 beling of both the SSP and GP2 subunits in a native-like Lassa virus (LASV) GPC trimer expressed in i

158 rmine the structures of membrane proteins in native-like lipid bilayer environments.

159 Unlike detergent micelles, nanodiscs are native-like lipid bilayers that are well-defined and pot

160 and magic-angle spinning NMR spectroscopy in native-like lipid bilayers with restrained molecular dyn

161 The results indicate that in a native-like lipid environment rhodopsin activation is no

162 Schiff base and allowed reconstitution into native-like lipid membranes.

163 protein topologies: knotting via threading a native-like loop in a preordered intermediate.

164 le human pluripotent stem cell lines exhibit native-like maturation changes in AMPAR composition such

165 the idea that proteins should be studied in native-like media to achieve a faithful description of t

166 stem using engineered zebrafish apo A-I is a native-like membrane mimetic system for G-protein-couple

167 les a small portion of a lipid bilayer) have native-like membrane properties.

168 ion and permits the observation of transient native-like membrane protein conformations that are othe

169 their lower charge, the average mobility of native-like membrane protein ions is approximately 30% l

170 his finding is significant since maintaining native-like membrane proteins enables ligand binding to

171 s of lectin interactions with glycolipids in native-like, membrane environments.

172 us to probe all four major gating states in native-like membranes by combining electrophysiological

173 cking software are still not able to produce native like models for every target.

174 tational approach has the potential to yield native-like models for the diverse universe of functiona

175 ormed spatial constraints to recover >98% of native-like models of CcdB from a decoy dataset.

176 d from cross-linking and native MS, we built native-like models of four heterocomplexes with known su

177 However, maintaining native-like MP conformations in the gas phase using dete

178 Bioengineering of native-like multiscale building blocks provides refined

179 g experiments, (R), reveal the presence of a native-like N() with a disordered solvent-exposed amino-

180 ered state has structural propensities for a native-like N-terminal beta-hairpin and alpha-helix and

181 of diverse soluble Env trimers that maintain native-like (NL) structure present technical challenges

182 Thus far, the most promising native-like (NL) structures have been obtained by engine

183 log reveals striking enhancement of multiple native-like nuclear Overhauser effects within the tether

184 e weak nucleators but permit Pin WW folding, native-like nucleators, and strong nucleators.

185 calibration methods underestimate Omega for native-like or unfolded membrane protein complexes, high

186 by the top 10 folding pathways reveals that native-like pairing between strands 1 and 2 only occurs

187 Curcumin binds to native-like PC micelles with approximately 1 binding sit

188 IL-8 secretion, respectively, compared with native-like PC.

189 The binding of curcumin to native-like phosphocaseins (PC) dispersed in simulated m

190 in, into virus-like particles that possess a native-like procapsid morphology.

191 molecules in the inclusion bodies lose their native-like properties and convert into beta-sheet-rich

192 The difference in oligomeric states and native-like properties for the two consensus variants is

193 some integral membrane proteins can maintain native-like properties in lipid-free detergent micelles

194 of subunits is required to reconstitute the native-like properties of L-type Ca(2+) currents, but th

195 Ion mobility separation of native-like protein and protein complex ions expands the

196 or the first time, SLIM was used to separate native-like protein and protein complex ions ranging in

197 denatured protein, native-like protein, and native-like protein complex ions are reported here, form

198 ike protein complexes calibrated using other native-like protein complexes are significantly less tha

199 wave collision cross sections determined for native-like protein complexes calibrated using other nat

200 clear correlation between the population of native-like protein conformations and the degree of dete

201 e the mechanism by which detergents preserve native-like protein conformations in a solvent free envi

202 ons provides a useful filter to discriminate native-like protein models from non-native models.

203 tein design shifts emphasis from reproducing native-like protein structure to function, it has become

204 set of denatured peptide, denatured protein, native-like protein, and native-like protein complex ion

205 P is incorporated into inclusion bodies as a native-like protein, still exhibiting small but signific

206 olded state of PYP is native-like, involving native-like protein-chromophore interactions.

207 quality control mechanism that ensures only native-like proteins are displayed, thus eliminating poo

208 Env is cleaved, trimeric, and it retains its native-like quaternary conformation exposing mostly broa

209 Thus, prefabrication of a native-like r-protein subcomplex drives efficient and ac

210 A largely untested prediction is that native-like residual structure facilitates the conformat

211 cates that the biHis site is absent or fully native-like, respectively, while a fractional psi implie

212 Although native-like S8-RNA interactions are present in the aptam

213 roughput identification of combinatorial and native-like scaffolds for tissue engineering of function

214 or a liquid delivery medium, and facilitated native-like scale-up tissues.

215 The I1 state has native-like secondary structure and shows strong anilino

216 al protein L9) not only contains significant native-like secondary structure but also non-native stru

217 Cell-based studies revealed native-like signaling properties with negligible mitogen

218 site-specifically (15)N-labeled G4 units in native-like single-stranded telomeric DNA revealed that

219 on calibration strategies employ unfolded or native-like soluble protein standards with masses and mo

220 ted factors that influence the production of native-like soluble, recombinant trimers based on the en

221 At present, the only reliable way to make native-like, soluble trimers in practical amounts is via

222 ndicate that both N( *) and IE have retained native-like solvent accessibility of the core, suggestin

223 Using native-like SOSIP trimers, we examine the effects on ant

224 In contrast, the gp120 subunits of the native-like SOSIP.664 trimer almost exclusively retained

225 nt in nonnative uncleaved gp140 proteins and native-like SOSIP.664 trimers based on the BG505 env gen

226 ructure that rearranges/isomerizes to a more native-like species.

227 Chemical proteasome inhibition restored native-like SRY expression and transcriptional activity

228 Fully native-like, stable trimers that display multiple bNAb e

229 rmediate shows that the hinge region is in a native-like state in spite of having the pentasaccharide

230 ized the initial steps of aggregation from a native-like state of the acylphosphatase from Sulfolobus

231 n formed non-native polymers starting from a native-like state under physiological conditions.

232 the context of the loosely folded isomerized native-like state {N(iso)} predicted in simulation.

233 beta containing proteins can form long-lived native-like states with small register shifts.

234 transition leads to multiple interconverting native-like states, in which both zinc atoms remain boun

235 el found in the cell, proteins fold to fewer native-like states.

236 l gas-phase collisional "clean-up" to retain native-like stoichiometries are discussed.

237 disordered A1 lacking the disulfide retains native-like structural dynamics.

238 y that sequentially incorporates cooperative native-like structural elements to build the native prot

239 egions and form an ordered intermediate with native-like structure at their interface.

240 nfiguration of subunits, suggesting that the native-like structure can be preserved under the harsh a

241 ther, these results suggest that elements of native-like structure can have long lifetimes at near-am

242 a sequential stabilization principle; prior native-like structure guides the formation of adjacent n

243 The compact state rearranges into a native-like structure immediately after the full domain

244 cted mutants, reveals a very high content of native-like structure in the transition state and indica

245 populates a conformational ensemble in which native-like structure is retained throughout the sequenc

246 The intermediate refolds to a native-like structure upon charge neutralization under m

247 register across the P5c hairpin, creating a native-like structure, and occurs at rates of more than

248 ion cross sections than calculated for their native-like structure, has been reported previously for

249 Peptide 1 adopts a clear secondary, native-like structure, including the typical cysteine-kn

250 from suitable isolates can adopt a compact, native-like structure, supporting its use as a vaccine c

251 assemblies in which the protein retains its native-like structure, which subsequently convert into a

252 equires N-glycosylation to acquire a stable, native-like structure.

253 ing a specific polarity for capturing a more native-like structure.

254 e structure guides the formation of adjacent native-like structure.

255 trimers from suitable isolates have compact, native-like structures and support their use as candidat

256 ment, there are good prospects for achieving native-like structures for these very important proteins

257 important previously in proteins that retain native-like structures in the gas phase.

258 nergy discriminate between the nonnative and native-like structures significantly better than the low

259 onformations, RNA molecules (<50 nt) fold to native-like structures within half an hour of simulation

260 d protein structure and numerous alternative native-like structures, are in common use for the evalua

261 alpy change drives the formation of compact, native-like structures, but requires Mg(2+) ions at all

262 environment is often necessary for achieving native-like structures.

263 tools that distinguish native-like from non-native-like structures.

264 t least nine unique species: three native or native-like structures; two that appear to be equilibriu

265 gomers with >20% modified backbones can form native-like tertiary folds with metal-binding environmen

266 These results underline the importance of native-like tertiary stabilizing interactions in folding

267 l four macromolecular complexes retain their native-like topologies at low energy.

268 t TM12, TM123, and TM127 adopt predominantly native-like topologies.

269 ensemble of structures exhibiting an overall native-like topology in which the N-terminal and C-termi

270 d simulations demonstrate a preference for a native-like topology.

271 g and a kinetic intermediate with some fully native-like traits.

272 GPC precursor can be produced as a discrete native-like trimer and that its proteolytic cleavage gen

273 uncleaved gp140-FL20-SOSIP protein increases native-like trimer formation to approximately 20 to 30%.

274 In animal models, the present generation of native-like trimer immunogens, exemplified by the BG505

275 12 gp140UNC-Fd-His proteins but very rare in native-like trimer populations.

276 FL20 construct is not sufficient to create a native-like trimer, but a small percentage of native-lik

277 that both V1V2 and gp120 can be presented in native-like trimeric conformations on nanoparticles.

278 tation likely requires the presentation of a native-like trimeric Env immunogen.

279 ther, we report on an HIV-1 B/C recombinant, native-like trimeric Env protein that is highly resistan

280 2.J41.SOSIP.664 Env could be stabilized in a native-like trimeric form by swapping a domain from BG50

281 envelope glycoprotein (Env) design generate native-like trimers and high-resolution clade A, B, and

282 In summary, native-like trimers are a now a platform for structure-

283 her with a simple, one-step method to purify native-like trimers by affinity chromatography with a tr

284 s are the designs of various constructs; how native-like trimers can be produced and purified; the pr

285 but many HIV-1 env genes do not yield fully native-like trimers efficiently.

286 However, first generation native-like trimers expose epitopes for non-neutralizing

287 linked (NFL) design allows the generation of native-like trimers from clinical isolates at high yield

288 The improved native-like trimers from diverse HIV isolates, and the d

289 Native-like trimers mimicking virion-associated spikes p

290 In rabbit immunizations with native-like trimers of the 327c isolate, improved trimer

291 Native-like trimers of the SOSIP design are being develo

292 Thus, native-like trimers represent a promising starting point

293 structure-guided design to develop improved native-like trimers that reduce exposure of non-nAb epit

294 ative-like trimer, but a small percentage of native-like trimers were produced when an I559P substitu

295 Here, we sought clade C native-like trimers with comparable properties.

296 g with a sequence of directional immunogens, native-like trimers with decreasing epitope modification

297 ased on the same env genes, very rarely form native-like trimers, a finding that is consistent with t

298 ubtype A BG505 Env, form homogeneous, stable native-like trimers.

299 gn and/or purification strategies that yield native-like trimers.

300 trimers are highly stable and they are fully native-like when visualized by negative-stain electron m