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

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

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

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

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

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

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

10 attached trimers, ~20 per particle, retained native-like antigenicity, judged by reactivity with NAbs

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

12 s of CF, CheA, and CheW bound to vesicles in native-like arrays reveals that the CF is well-ordered o

13 7 degrees C, respectively) and predominantly native-like, as determined by negative-stain electron mi

14 has allowed for gas-phase analysis of their native-like assemblies, including rapid evaluation of st

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

16 We show that (1) tandem-TIMS/MS retains native-like avidin tetramers with deeply buried solvent

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

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

19 r and oligomers have a significant degree of native-like beta-sheet structures (35-38%), but with mor

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

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

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

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

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

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

26 egies developed that can easily recapitulate native-like cell and biofactor gradients in 3D materials

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

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

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

30 ss, the mechanism by which PRC2 engages with native-like chromatin remains incompletely understood.

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

32 All three could be overexpressed and had native-like circular dichroism spectra and 1D-NMR spectr

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

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

35 ge to characterize these fluctuations, under native like conditions.

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

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

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

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

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

41 ng the energetics of membrane proteins under native-like conditions.

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

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

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

45 in binding partner Tat, is able to restore a native-like conformation by preferentially binding and s

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

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

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

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

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

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

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

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

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

55 Most nascent CRM ions retain native-like conformations.

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

57 eveals that deep-learning predicts coherent, native-like contact patterns compared to co-evolutionary

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

77 ibody, complexed with a CD4-bound open HIV-1 native-like Env trimer.

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

79 Native-like Env trimers can induce autologous NAb respon

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

81 he incorporation of exclusively well-folded, native-like Env trimers into NPs that self-assemble in v

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

83 We describe a new recombinant native-like envelope glycoprotein (Env) SOSIP trimer, te

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

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

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

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

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

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

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

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

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

93 od spots and thin tissue sections, by use of native-like extraction/ionization solvents.

94 spect to most mutations but can display more native-like features for some highly destabilizing mutat

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

96 s designed in the new membrane model exhibit native-like features including interfacial aromatic side

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

98 secretase within supported biomembranes with native-like fluidity.

99 tly produce the large scale of proteins with native-like fold and hence can act as an efficient vacci

100 that the Shaker-VSD in LPPG micelles is in a native-like fold and is likely to provide valuable insig

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

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

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

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

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

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

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

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

109 demonstrate that such a kinetic trap retains native-like functional activity, as shown by the preserv

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

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

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

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

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

115 The development of native-like HIV-1 envelope (Env) trimer antigens has ena

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

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

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

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

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

121 Using native-like incubation and electrospray conditions toget

122 xamine the effect of E2 mutations under more native-like infection conditions, a neomycin-selectable

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

147 e, zinc, nor ethoxzolamide) simply by use of native-like LESA solvents.

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

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

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

151 two-fold symmetry is more pronounced in the native-like lipid environment of the nanodiscs.

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

153 ia monocytogenes strain EGD-e while bound to native-like lipid membranes.

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

155 Informative native-like mass spectra were collected for each charge

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

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

158 cagon receptor (GCGR) ECD in the presence of native-like membrane bilayers.

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

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

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

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

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

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

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

166 R can discriminate between poorly folded and native-like models by using decay traces that cannot be

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

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

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

170 Bioengineering of native-like multiscale building blocks provides refined

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

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

173 Soluble recombinant native-like (NL) envelope glycoprotein (Env) trimers of

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

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

176 ective for future structural studies of some native-like nucleosomes that play critical roles in chro

177 ble to the structural determination of other native-like nucleosomes with distinct DNA sequences.

178 res and review the few structural studies on native-like nucleosomes.

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

180 spin-echo spectroscopy in different states: native-like, partially folded (molten globule) and compl

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

198 Current databases for native-like proteins and protein complexes provide CCS v

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

200 ion procedure (for TWIMS) yields (TW)CCS for native-like proteins which are largely similar to those

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

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

203 Native-like recombinant Env trimers of the SOSIP design

204 Here, we studied the immunogenicity of native-like recombinant envelope glycoprotein (Env) trim

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

206 s and protein complexes were analyzed from a native-like sample droplet to investigate the technique.

207 able for this purpose, enabling analysis of "native-like" samples that mimic physiological conditions

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

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

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

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

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

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

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

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

216 In HIV-1 vaccine research, native-like, soluble envelope glycoprotein SOSIP trimers

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

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

219 oscopy structure of Ab1485 in complex with a native-like SOSIP Env trimer showed conserved contacts w

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

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

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

223 tal of 78 animals immunized with recombinant native-like (SOSIP) Env trimers.

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

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

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

227 While the internal dynamics of the native-like state can be understood using normal mode an

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

229 ted proximal N-glycans while maintaining the native-like state of the cleavage-independent NFL trimer

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

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

232 nt exists in a major native state, two minor native-like states, and two locally unfolded states in a

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

250 lding/restructuring, helping to preserve the native-like structure.

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

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

253 elices, one from each domain, that display a native-like structure.

254 MS) have allowed proteins to be preserved in native-like structures and support applications in the i

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 oduction of artificial proteins by mimicking native-like structures has shown to be a promising appro

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

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

260 ing noncovalent interactions and maintaining native-like structures.

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

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

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

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

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

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

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

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

269 he massive conformational space and generate native-like topology.

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

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

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

273 12 gp140UNC-Fd-His proteins but very rare in native-like trimer populations.

274 The resulting engineered native-like trimer variants were both more reactive with

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

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

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

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

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

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

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

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

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

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

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

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

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

288 Native-like trimers mimicking virion-associated spikes p

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

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

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

292 subtype B AMC009 SOSIP protein formed stable native-like trimers that displayed multiple bNAb epitope

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