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 ment or by thermally sampling conformational substates.

15 and mainly occupy a small number of helical substates.

16 transitions between different conformational substates.

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

18 hing between the SSEA3 positive and negative substates.

19 ional knowledge of accessible conformational substates.

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

21 hich allow the dangling base to sample these substates.

22 o well defined conductance states, and other substates.

23 roteins can exist in multiple conformational substates.

24 ution were differentially modulated by sleep substates.

25 mpounds II exist as two major conformational substates.

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

27 factor exchange occurs through these excited substates.

28 which are assignable to different taxonomic substates.

29 and the structure of trapped conformational substates.

30 at "trap" them in nonstandard conformational substates.

31 predominantly exhibit transitions to various substates.

32 y crystal structures exist as conformational substates.

33 howing increased transitioning to long-lived substates.

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

35 nformational interconversions from BI to BII substates.

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

37 and calculated dephasing dynamics for these substates.

38 ural assignments for the MbCO conformational substates.

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

40 on the redistributions of the conformational substates.

41 fects the distribution of the conformational substates.

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

43 nergy barriers between native conformational substates.

44 inhomogeneous distribution of conformational substates.

45 ited voltage-dependent closure with multiple substates.

46 ging yields the same kinetics in all three A substates.

47 the solvent, and interconversion among the A substates.

48 late between several distinct conformational substates.

49 racteristic time of fluctuations among the A substates.

50 converting, structured, local conformational substates.

51 selves precisely in transient conformational substates.

52 h protein state is split into conformational substates.

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

54 's experimentally established conformational substates.

55 suggesting a complex landscape of states and substates.

56 pends on the exchange between conformational substates.

57 sequential molecular steps or conformational substates.

58 can assume a large number of conformational substates.

59 three distinguishable, time-resolvable open substates.

60 es provide insight into the structure of the substates.

61 through an enormous number of conformational substates.

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

63 neous pathways connecting diffuse mesoscopic substates.

64 more excursions to functionally incompetent substates.

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

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

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

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

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

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

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

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

73 Two classes of substates (alpha/beta) can be distinguished from their d

74 sence of bound substrate (L-arginine) or the substate analogue Nomega-nitro-L-arginine methyl ester (

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

76 Soret, contain contributions of all three A substates and can, therefore, be only approximately mode

77 xperimental identification of conformational substates and characterization of conformational equilib

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

97 ere is a thermal averaging of conformational substates around two reaction center configurations.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

124 Substate conductance was not seen during low pHi.

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

126 Within an A substate, correlations of S and H are recovered qualitat

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

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

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

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

131 he ensemble level, underlying conformational substates differ significantly.

132 10-20 ms), often involving several transient substates distinct from gammasub.

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

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

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 els from a fully open state, gammaopen, to a substate, gammasub, about one-third of the conductance o

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

173 The temperature dependencies of the A substate interconversion processes are fitted with a non

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

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

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

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

178 bstates is observed, and rebinding in each A substate is nonexponential in time and described by a di

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

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

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

182 heme pocket, no interconversion among the A substates is observed, and rebinding in each A substate

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

236 inhomogeneous distribution of conformational substates responsible for KHB.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

284 nformations of MbCO, the so-called A1 and A3 substates, whose activation barriers have been independe

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 d states near room temperature, we find that substates within these two subpopulations interconvert m

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