ライフサイエンスコーパス: substate

1 ities, with numerous conformational isomers (substates).

2 econdary elements and adopt 1 conformational substate.

3 dence of a transient intermediate structural substate.

4 es C to attain a more dynamic conformational substate.

5 of intracellular viral DNA as the packaging substate.

6 with experiments for the largest conducting substate.

7 the only possible pathway involves the first substate.

8 icient to precisely fit the data within each substate.

9 structure of the RNA portion of the helicase substate.

10 ) that favors residency in a low-conductance substate.

11 ture for SERCA in the E2 (Ca-free) enzymatic substate.

12 ime at +/-40 mV, and absence of a long-lived substate.

13 emporal dynamics specific to each identified substate.

14 d lead to remodeling of their conformational substates.

15 through an enormous number of conformational substates.

16 >10 s) exhibit fluctuations between numerous substates.

17 ion bands corresponding to the A(1) and A(3) substates.

18 neous pathways connecting diffuse mesoscopic substates.

19 more excursions to functionally incompetent substates.

20 and mainly occupy a small number of helical substates.

21 transitions between different conformational substates.

22 K state, and, most importantly, 4 discrete L substates.

23 hing between the SSEA3 positive and negative substates.

24 ional knowledge of accessible conformational substates.

25 in states are not unique but consist of many substates.

26 hich allow the dangling base to sample these substates.

27 o well defined conductance states, and other substates.

28 roteins can exist in multiple conformational substates.

29 mpounds II exist as two major conformational substates.

30 ment or by thermally sampling conformational substates.

31 multiple TST-bound P450(eryF) conformational substates.

32 factor exchange occurs through these excited substates.

33 which are assignable to different taxonomic substates.

34 and the structure of trapped conformational substates.

35 at "trap" them in nonstandard conformational substates.

36 allows visualization of distinct sleep/wake substates.

37 predominantly exhibit transitions to various substates.

38 howing increased transitioning to long-lived substates.

39 ct on the amplitudes of the neomycin-induced substates.

40 nformational interconversions from BI to BII substates.

41 open state, then a series of transitions to substates.

42 and calculated dephasing dynamics for these substates.

43 ural assignments for the MbCO conformational substates.

44 activity exhibiting full, 3/4, 1/2, and 1/4 substates.

45 on the redistributions of the conformational substates.

46 fects the distribution of the conformational substates.

47 ignal of Mo reveals that it has at least two substates.

48 ution were differentially modulated by sleep substates.

49 nergy barriers between native conformational substates.

50 inhomogeneous distribution of conformational substates.

51 ited voltage-dependent closure with multiple substates.

52 y crystal structures exist as conformational substates.

53 late between several distinct conformational substates.

54 selves precisely in transient conformational substates.

55 h protein state is split into conformational substates.

56 onformations for the E1 (Ca-bound) enzymatic substates.

57 's experimentally established conformational substates.

58 suggesting a complex landscape of states and substates.

59 pends on the exchange between conformational substates.

60 sequential molecular steps or conformational substates.

61 can assume a large number of conformational substates.

62 three distinguishable, time-resolvable open substates.

63 es provide insight into the structure of the substates.

64 s spectra were decomposed into the taxonomic substates A(0), A(1), and A(3), previously introduced in

65 For the A3 substate, a significantly lower peak enthalpy was obtain

66 ecombination in the individual taxonomic (A) substates, A0, A1, and A3.

67 ltage-dependent transitions to a predominant substate (about 2 nanosiemens).

68 rared lines by about 2 cm(-1), so that the A substates actually appear in pairs, such as A(0) and A(0

69 suggests greater sampling of conformational substates, affecting the full length of helix B and beta

70 Thus, there are several conformational substates along the reaction coordinate with different t

71 crystallographic evidence for conformational substates along the trajectory towards the catalytically

72 t modes: 1) a fast block consisting of brief substate and closed events with a mean duration of appro

73 xperimental identification of conformational substates and characterization of conformational equilib

74 l clustering to learn energetically coherent substates and dynamic modes of motion from a 0.5 mus ubi

75 ase and occurrence of various conformational substates and its impact on studies of context effects.

76 are known to open easily and transiently to substates and stop cell growth.

77 t oxyhemes exist in two major conformational substates and that this is true for both alphaO(2) and b

78 reveal the rates of interconversion between substates and the corresponding relative populations.

79 for the A0 substate, intermediate for the A1 substate, and slowest for A3.

80 of the relative abundance of each state and substate, and the ensemble average free energy of the tr

81 ifts, comparison to a crystal structure of a substate, and through designed ensemble redistribution v

82 etween the closed state and a low-conducting substate, and validates both the use of the integral cur

83 tifying single channel conductance of 11 pS, substates, and an approximately 3:1 Na(+)/K(+) permeabil

84 ically switch between metastable conductance substates, and display characteristic macromolecule-indu

85 mational substates of the protein, and a new substate appearing upon membrane binding could be uncove

86 e C2'-endo conformation the first and second substates are able to persist for different time spans,

87 and possible transitional pathways among the substates are also examined using the conformational sta

88 vibrational echo line shapes for both of the substates are analyzed using the center line slope (CLS)

89 s a subset of the ensemble in which multiple substates are apparently retained.

90 the possibility of long-lived conformational substates are discussed.

91 In this work, these substates are investigated as a possible source of the d

92 ve energy barriers separating conformational substates are not significantly influenced by pressure.

93 e Doze/Wake probabilities and the sleep/wake substates are tied to specific biological processes.

94 n, corresponding to different conformational substates, are reported here with reference to the confo

95 directly revealing the presence of multiple substates as distinguishable components in the EPR spect

96 modification decreased the number of channel substates as the diameter of the current carrier increas

97 d distributions of long-range conformational substates (as probed by time-resolved fluorescence reson

98 However, identifying a cell's substate at all time points within a cell lineage tree i

99 gions of htADH are in a rigid conformational substate at reduced temperatures with limited cooperativ

100 tch of the energetically most favorable open substate at the lowest examined temperature of 4 degrees

101 not caused by freezing-in of conformational substates at low temperature.

102 By analyzing these substates at millisecond resolution, we derive a detaile

103 se from an ensemble of frozen conformational substates at the cryogenic temperatures.

104 This concerns both the ratio of the B-DNA substates B(I) and B(II) associated with the backbone di

105 In the presence of batrachotoxin, substates became evident and the single-channel conducta

106 , a mammalian decoding complex visualized in substates before and after codon recognition reveals str

107 sly been shown to induce a voltage-dependent substate block in the cardiac isoform of the ryanodine r

108 ue to the presence of protein conformational substates but rather is an inherent property of the solv

109 erum albumin, do not close the H+-conducting substate, but it closes spontaneously when respiration b

110 not only inverts the equilibrium between the substates, but also causes large, parallel reductions in

111 y has provided insight into SERCA structural substates, but it is not known how well these static sna

112 Moreover, an additional, weakly populated substate, called A(x), was identified.

113 Most of these substates can be associated with a molecular configurati

114 terconversion between protein conformational substates can occur on very fast time scales.

115 lude that rivalry and fusion are multistable substates capable of direct competition, rather than sep

116 The exchange between substates changes the frequency of the CO, which is dete

117 ensembles of interconverting conformational substates channel the enzyme through its catalytic cycle

118 g is accomplished by pulling the vinylallene substate closer to the metal and, as a result, the trans

119 lytic cycle intermediate that can react with substates, compound Q, is unaffected.

120 nnel with two or more wt subunits showed one substate conductance at approximately 40% of the full co

121 The channel showed a substate conductance of about 8 pS.

122 Substate conductance was not seen during low pHi.

123 nfigurations showed the same pH sensitivity, substate conductance, and long-time closure.

124 its an ensemble of conformations within each substate corresponding to its functions.

125 The substate current level was unaffected by most of the mut

126 hains, while the relative populations of the substates depend greatly on glycols and IHP.

127 us different conformations or conformational substates, described by an energy landscape, is now acce

128 he ensemble level, underlying conformational substates differ significantly.

129 10-20 ms), often involving several transient substates distinct from gammasub.

130 cL has conductance, pressure dependence, and substate distribution similar to those of the recombinan

131 tein environments in the context of distinct substate distributions, with concomitant changes to the

132 itated by explicitly sampling conformational substates during design and specifically stabilizing pro

133 is technology allows us to identify cortical substates during quiet and active wakefulness, and trans

134 a brain state as an ensemble of "metastable substates," each with a probabilistic stability and occu

135 ional knowledge of accessible conformational substates, ensemble-simulation-based protocols have been

136 All of the mutants induced discrete substate events at the single-channel level.

137 ermini in functional variants for all tested substates fall within the same four distinct loop/lid re

138 nce Raman data for reduced H175G/Im show two substates for heme-coordinated Im differing in the stren

139 There can be identified two structural substates for proton passage.

140 We detected four discrete structural substates for SERCA expressed in cardiac muscle cells.

141 s shows that there are at least two distinct substates for the native adrenergic membrane receptor.

142 ed during the formation of the late M (M(N)) substate formed by three-dimensional crystals of the D96

143 cteriorhodopsin crystals, confirm that the M-substate formed represents a structure that occurs early

144 s were identical within error for the two CO substate frequencies, T1delta(B1) = 335 +/- 115 ps and T

145 The concept of conformational substates has been described; however, the challenge is

146 sample catalytically relevant conformational substates has been invoked to model kinetic and spectros

147 Only a limited number of substates have been identified for Brk, and the link of

148 of dynamic interconversion between distinct substates; however, the regulatory circuits specifying t

149 in ends and exist in multiple conformational substates, i.e., they move on multiple-minima free-energ

150 cally enhance the sampling of conformational substates in duplex DNA during molecular dynamics (MD) s

151 n solution reveals additional conformational substates in equilibrium exchange with a WT-like populat

152 balance between active and inactive receptor substates in favor of the active state, agonist-induced

153 attribute to the presence of conformational substates in oxy-P450cam.

154 s an important mechanism to create taxonomic substates in proteins.

155 It is likely that the A and B conformational substates in the alphaO(2) and betaO(2) subunits differ

156 vation of partially annealed, conformational substates in the annealing mechanism.

157 s in the population of nucleic acid backbone substates in the case of 7,8-dihydro-8oxo-guanosine comp

158 er of hierarchically arranged conformational substates in the crystalline environment and may sample

159 erentially sampled particular conformational substates in the denatured state, pairwise Calpha root-m

160 ers the populations and exchange kinetics of substates in the MHC conformational ensemble.

161 he protein to access only its conformational substates in the neighborhood of the preburn state, any

162 rogressive depletion of distinct microscopic substates in the order of their increasing activation ba

163 ing the presence of two major conformational substates in the oxy-ferrous precursor.

164 s, reflecting the presence of conformational substates in the oxyferrous precursor.

165 In nanodiscs, the ensemble of substates in the photoactivated receptor spontaneously d

166 c coordinates for multiple, weakly populated substates in the protein conformational ensemble.

167 f) is controlled by the number of accessible substates in the unfolded protein and the solvent.

168 Because the number of conformational substates in the unfolded protein is extremely large, th

169 ressibility (Deltabeta(T)) of conformational substates in two-component equilibria from the pressure

170 sence of ligand binding suggest that the new substates induced by the cavity-creating mutations repre

171 tion and access, but direct evidence of such substate interconversion has thus far remained elusive.

172 ation step at the heme is fastest for the A0 substate, intermediate for the A1 substate, and slowest

173 Conformational substates involved in the process and a key residue D171

174 Population of this new substate is accompanied by structural reorientations of

175 The H+-conducting substate is apparently regulated by the redox status of

176 al of the native state and of each denatured substate is calculated as a function of the concentratio

177 l exchange and characterizing conformational substates is essential for elucidating mechanisms of fun

178 The large number of conformational substates is essential; proteins cannot function without

179 When the free energy difference between substates is estimated from the EPR spectra, the crystal

180 , an ensemble of pH-dependent conformational substates is observed, even at pH 6.0 where the MIIbH(+)

181 s the visual response--rather an ensemble of substates is present, due to the entropy gain produced b

182 the distribution of a protein's equilibrium substates is sensitive to small pH differences.

183 pe for which the existence of conformational substates is well established.

184 h energy barrier found between the two major substates leads to transitions that are slow on the time

185 he infrared absorption from the A(1) or A(3) substate lines to A(0).

186 The more stable of the two apo substates may not be the one observed in the complex wit

187 active state may occur through promotion of substates mediated by an allosteric switch mechanism tha

188 ace protein is represented as an ensemble of substates modeled by random coils having the same contou

189 e test the reliability and robustness of the substate number determination by investigating the appli

190 s (<1 ms) between the fully open state and a substate of approximately 75 pS and slow transitions (>5

191 rmational switching between two well defined substates of a myoglobin mutant is observed on the appro

192 We recently reported distinct conformational substates of Ca(2+)-CaM-DA and apoCaM-DA, with peaks in

193 es values for the Fe-C-N angles in the three substates of ca. 123 degrees (C3) and 133 degrees (C2),

194 ransfer measurements revealed conformational substates of CaM, and single-molecule polarization modul

195 However, three and four substates of conductance were seen in the tetrameric wt-

196 multiple nearly isoenergetic conformational substates of enzymes with similar but distinct catalytic

197 to characterize higher energy conformational substates of Escherichia coli dihydrofolate reductase.

198 ave failed to sample transitions between the substates of fasciculin and calmodulin, GNEIMO simulatio

199 which determining the diverse conformational substates of IDPs in their free states, in encounter com

200 The A(1) and A(3) conformational substates of MbCO are found to have different dephasing

201 e spectroscopic A(1) and A(3) conformational substates of MbCO, respectively, based on the agreement

202 Transitions between conformational substates of membrane proteins can be driven by torsiona

203 s of the 13C hyperfine tensors for the three substates of the 2Fe-SOR within a simple heuristic model

204 SPRNT reveals two mechanical substates of the ATP hydrolysis cycle of the superfamily

205 e presence of previously unseen intermediate substates of the bacterial ribosome during the first pha

206 spectrometry to dissect five conformational substates of the complex, including one in which the VPS

207 ns to promote transitions of the most common substates of the DNA backbone.

208 ts in the modification of the conformational substates of the enzyme.

209 ion) affects only a subset of conformational substates of the Fe-M80 interface, probed by the 695 nm

210 Here conformational substates of the GPCR rhodopsin are investigated in mice

211 ling to structurally unravel interconverting substates of the human proline isomerase, cyclophilin A

212 quilibria between spectroscopically resolved substates of the lipidated signaling protein N-Ras.

213 ibrium protein dynamics for the two distinct substates of the Mb double mutant are investigated by us

214 f transitions between various conformational substates of the native basin of globular proteins.

215 ced DS-substrate complex reveal two distinct substates of the parent.

216 that the number of accessible conformational substates of the protein increases upon 2',5'-ADP bindin

217 nal dynamics and selection of conformational substates of the protein, and a new substate appearing u

218 A model with two substates of the reactant, P(+)Q(A)(-)Q(B), one protonat

219 ormational equilibrium between the two major substates of this protein.

220 artners by exchanging between conformational substates on a wide range of spatiotemporal scales.

221 , energy of, and barriers between functional substates on protein reaction coordinates.

222 of our study indicate that discrete basins (substates) on a potential energy landscape of the enzyme

223 Substate openings O(1)', O(2)', and O(3)', between the f

224 sign and specifically stabilizing productive substates over all unproductive conformations.

225 common A-, B- and Z-forms and their various substates, plus five secondary clusters for kinked or be

226 A significant change in the conformational substate population is observed for the D251N oxy-P450ca

227 Our data therefore suggests different substate populations for these proteins, which is most l

228 s and that the glycol-induced changes in the substate populations of the R-state HbO(2) tetramer are

229 ing one of the previously identified helical substates present in the prerecognition ensemble in a no

230 This result suggests that the substates probed by the 695 nm band differ with respect

231 omain interaction model for the mechanism of substate production by Kunitz inhibitors based on curren

232 Each substate reflects a local minimum on the free-energy lan

233 However, an apparent H+-conducting substate remains open under these conditions, as indicat

234 roperties of PC2 and whether the conductance substates represent monomeric contributions to the chann

235 inhomogeneous distribution of conformational substates responsible for KHB.

236 ductances (i.e. 43% of pA-modified s1 and s2 substates), revealing a proportional gating mechanism.

237 lying the large effect of the conformational substate reveals the importance of coupling between prot

238 of the mixture of L's showed that 3 of these substates revert to bR(568) and that only the 1 substate

239 were performed to explore the conformational substates sampled by the glycopeptides.

240 aphy can provide snapshots of conformational substates sampled during enzymatic reactions, while NMR

241 (1)H ENDOR spectroscopy of the cryogenerated substates shows that H-bonding interactions between His

242 Substate-specific mutant T18A P2X(2)-GFP receptors showe

243 In contrast, vibrations within substates stiffen with pressure, due to increased curvat

244 We characterize the substate structure of current blockades produced when si

245 The two conformational substate structures B(epsilon) and R(epsilon) observed i

246 nformational equilibrium between one protein substate that binds the effector and a second substate t

247 on of Ca2+ in a distinct membrane-associated substate that is not readily releasable by opened InsP3-

248 ubstate that binds the effector and a second substate that less strongly binds the effector.

249 and FiP35 WW domain detects multiple native substates that are consistent with experimental data.

250 ence that proteins sample the conformational substates that are important for function in the absence

251 description of the alternate conformational substates that are sampled through picosecond to nanosec

252 he interconversion of protein conformational substates that are slower and more global than the local

253 Within each state, substates that correspond to various electron localizati

254 ing site, where aprepitant occupies multiple substates that exchange with frequencies in the millisec

255 Ca(2+), leading to stabilization of certain substates that favor interactions with other target prot

256 In the first substate the imidazole Ne2 of His51 is adjacent to the n

257 For both first and second substates the fluctuation of the distances between the r

258 istant from the CO ligand, while in the A(3) substate, the N(epsilon)-H of His64 is oriented toward t

259 In the A(1) substate, the N(epsilon)-H proton and N(delta) of His64

260 constants of partially folded conformational substates; the rate constants differ for each residue an

261 And in the second substate, there are two possible proton passages: path 1

262 s thermal switching between force-generating substates through changes in the configurational space o

263 rotein is able to sample more conformational substates, thus becoming biologically functional.

264 the apparent conductance of the BPTI-induced substate to 0% (K15G), 10% (K15F), 30% (K15 wild-type),

265 lightly different but related conformational substates to occur.

266 At -20 mV, all substates together occupy approximately 30% of the open

267 -ray crystallographic data on conformational substates trapped at 120 K.

268 Fluctuations between conformational substates, typically in the mus-ms time range, are slow

269 identify a theta-dominated wakefulness (TDW) substate underlying motivated behaviors and typically pr

270 rts of biomolecules shift between functional substates using concerted motions.

271 e specific activity of caspase-12 with these substates was several orders of magnitude lower than cas

272 s and center distances of the conformational substates were detected with variation in solution condi

273 ions, while the peak shifts in the A0 and A1 substates were small.

274 We frequently observe substates where the ionic current is reduced by approxim

275 cs, and dynamics of accessible higher energy substates where the nicotinamide ring transiently occupi

276 lock the enzyme into a single conformational substate, whereas weak binding low affinity ligands bind

277 We identify a substate, which at the single cell level coexpresses plu

278 The dwell time of the substate, which is inversely related to the dissociation

279 ely dynamic, adopting diverse conformational substates, which enables them to modulate their interact

280 proteins is characterized by a hierarchy of substates, which give rise to conformational heterogenei

281 ts a strengthening of the Fe-M80 bond in all substates, which probably destabilizes the oxidized stat

282 ing on backbone sampling within Ramachandran substates, while a slower component (5-25 ns) reports on

283 morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes.

284 rently in equilibrium between conformational substates whose populations are modulated by activation.

285 ible to understand for which sequences these substates will arise, and what impact they will have on

286 and suggest that more-compact, less-hydrated substates will be favored in protein crystals.

287 states revert to bR(568) and that only the 1 substate with both the strongest counterion and a fully

288 lectively stabilizes a single conformational substate with largely helical CL3, as it is found in cry

289 termediates probably consist of ensembles of substates with a common core of native-like secondary st

290 ur within four broad tiers of conformational substates with average apparent Arrhenius activation ent

291 lled because Mb exists in distinct taxonomic substates with different catalytic properties and connec

292 which fluctuate into discrete conformational substates with different kinetic and thermodynamic param

293 unctionally productive state via a series of substates with incremental changes in conformation.

294 lity and exists as an ensemble of structural substates with undefined tertiary structure.

295 to be difficult, as judged by the multiple L substates, with weaker counterion interactions, that are

296 physically-relevant reaction coordinates and substates within MD simulations.

297 ites of both proteases sample conformational substates within milliseconds.

298 SPRNT revealed the presence of two distinct substates within the Hel308 ATP hydrolysis cycle, one [A

299 of the 80 degrees and 40 degrees rotational substates, without any prior information about such stat

300 proteins often fluctuate among various open substates, yet the nature of these transitions is not fu