ライフサイエンスコーパス: induced fit

1 ules by mechanisms that can be described as "induced fit".

2 receptor rearrangement upon ligand binding (induced fit).

3 not part of the NMR ensemble, or leading to induced fit.

4 mpty transporter, GltPh binds amino acids by induced fit.

5 obs) with [L] is not unequivocal evidence of induced fit.

6 terplay between conformational selection and induced fit.

7 g, the inherited mutation presumably hinders induced fit.

8 mechanism for the evolution of allostery and induced fit.

9 t of the substrates, indicating a process of induced fit.

10 ally shifts from conformational selection to induced fit.

11 cess of conformational selection rather than induced fit.

12 cture matching via conformational capture or induced fit.

13 , indicating that the differences are due to induced fit.

14 n require extensive RNA folding to create an induced fit.

15 s the mutation-driven destabilization of the induced fit.

16 o bind small molecules in grooves created by induced fit.

17 s and indicating that sugar binding involves induced fit.

18 eveloped as the PreTS state assembles during induced-fit.

19 e with greater reliance on slower motions or induced-fit.

20 mplexity in mt tRNAs by sequence-independent induced-fit adaption to the cognate mitochondrial aminoa

21 nformational change into a closed state with induced-fit adjustments of the active site, and inhibiti

22 cket, while streptavidin undergoes transient induced fits, all varying with loading rate.

23 based design efforts due to a high degree of induced fit and a mobile flexible loop encompassing the

24 in the translation field: the importance of induced fit and conformational changes for progression t

25 m, which often results from a combination of induced fit and conformational selection.

26 The induced fit and conformational selection/population shif

27 The widespread importance of induced fit and order-disorder transition in RNA recogni

28 The induced fit and population shift models, which differ by

29 These results are discussed in terms of induced fit and pre-existing equilibrium theories of lig

30 amyloidogenic intermediate, we envisage that induced fit and self-assembly represent complementary mo

31 rs LFA-1 activation through a combination of induced fit and tension-based mechanisms.

32 he limiting cases involved; the first is the induced fit and the second is the conformational selecti

33 A minimum action path computed for the induced-fit and catalytic conformation changes shows tha

34 interplay between two classical mechanisms: induced-fit and conformational selection.

35 r importance of stacking interactions during induced-fit and of specific hydrogen bonds during confor

36 echanisms such as multiple ligand occupancy, induced-fit, and conformational-selection.

37 ared with reference antagonists is due to an induced fit around Trp(755), resulting in a decreased st

38 ction pathway at low ligand concentration to induced fit at high ligand concentration.

39 es diagnostic of conformational selection or induced fit based on whether it decreases or increases,

40 An "induced fit" became apparent for the side chain conforma

41 ex, and biochemical experiments confirm this induced-fit behavior of the enzyme.

42 Our results revealed a novel mechanism of an induced fit between anesthetic molecule and its protein

43 ucture, later steps correspond to regions of induced fit between the proteins and the rRNA.

44 A (tRNA) transferring correct amino acid is "induced fit" between the ribosome and tRNA.

45 mplex formation involves both pre-formed and induced fit binding interactions.

46 Induced fit binding is recurrent in protein-protein and

47 r recognition of this internal loop involves induced fit binding, which could confer several advantag

48 ies of antibacterial agents showing a novel, induced-fit binding mode.

49 Our results showed that the induced-fit binding of these probes led to the preferred

50 r protein-binding aptamers because of their "induced fit" binding mechanism.

51 ng access; (iv) galactoside binding involves induced fit, causing transition to an occluded intermedi

52 ng from microseconds to years, often involve induced-fit, challenging computational or kinetic analys

53 ically disordered protein regions as well as induced-fit changes in the structured regions are both i

54 The pocket displays induced fit characteristics in the presence of the two i

55 Induced-fit complexation is reliant on the structural pl

56 Both employ the "induced fit" concept with flexibility in side chains and

57 he requirements necessary for binding to the induced-fit conformation.

58 domain and compound 1 reveals a significant induced fit conformational change of the G loop and orde

59 An induced fit conformational change upon binding of the P1

60 Both the induced fit conformational changes of the compound and t

61 reexisting conformational equilibrium and an induced-fit conformational change are discussed.

62 ing questions about the putative large-scale induced-fit conformational change of HPPK and the functi

63 intersubunit pocket in the 20S undergoes an induced-fit conformational change on binding of the HbYX

64 We conclude that the ACB domain facilitates induced-fit conformational changes and confers high-affi

65 zation; and (4) combined conformer selection/induced fit (CS/IF) model.

66 de preferentially diverts binding through an induced-fit disease pathway enabling high-affinity GPIba

67 ow that the "conformational selection versus induced fit" distinction on which this debate is based i

68 ed that combining aMD simulations with Glide induced fit docking (IFD) provided much-improved enrichm

69 Induced fit docking computational simulations performed

70 A theoretical analysis based on induced fit docking explains many of the observed effect

71 nalysis, intrinsic fluorescence studies, and induced fit docking simulations provided a mechanistic u

72 ransporters, we combined molecular modeling, induced fit docking, genetic, and biochemical approaches

73 Here we employ an induced fit docking/molecular dynamics protocol to ident

74 idues adopted different conformations in the induced-fit docking poses compared with the experimental

75 Docking the inhibitors with an induced-fit docking protocol suggested that the inhibito

76 This induced fit dramatically alters the electrostatics of th

77 that there is still an important role for an induced fit during ligand binding to cryptic sites and s

78 ule complexes, structural changes due to the induced-fit effect play an equally important role.

79 nsemble docking is used to take into account induced fit effects on the receptor conformation, and pr

80 urther validates the additional benefit from induced-fit effects.

81 lis MDD that describe sequential steps in an induced fit enzymatic reaction.

82 h a complementary conformation selection and induced-fit enzymatic loop-gated conformational change m

83 nd lost toward Src, primarily by shifting an induced-fit equilibrium that is also disrupted in the cl

84 te aromatic substrates, in a lock and key or induced fit fashion, by a conjunction of pai-pai, C-H...

85 atched for C70 which was tightly bound in an induced-fit fashion.

86 heir relative amplitudes, we attribute to an induced-fit "fly casting" type of model in which transie

87 eased occupancy for bound GDP, suggesting an induced-fit folding of the donor-binding subsite.

88 Our data reveal the importance of induced fit for substrate selection in EAATs and illustr

89 Although the concept of induced fit has been widely adopted for describing the s

90 nd recognition, conformational selection and induced fit, have dominated our interpretation of ligand

91 el" to other paramyxoviruses and propose an "induced fit" hypothesis for F-HN/H/G interactions as con

92 s 5 to other paramyxoviruses and propose an "induced fit" hypothesis for F-HN/H/G interactions as con

93 ver whether conformational selection (CS) or induced fit (IF) is the governing mechanism for protein-

94 and concentrations to being predominantly an induced fit (IF) mechanism at high ligand concentrations

95 sing a novel ensemble docking algorithm; (3) induced fit (IF) model, using energy-gradient-based back

96 mmonly discussed macroscopic mechanisms: (i) induced fit, (ii) population shift, and (iii) entropy dr

97 lements of both conformational selection and induced fit in a manner that blends features of popular

98 udies have demonstrated the dominant role of induced fit in enzyme specificity of HIV reverse transcr

99 Knowing the extent of induced fit in enzymes is important for our understandin

100 esidue linker within the protein facilitates induced fit in protein-RNA recognition.

101 ynamics offer an alternative explanation for induced fit in RNA-protein complexes.

102 tners and provide detailed information about induced fit in structured regions.

103 on with EPR distance measurements to analyze induced fit in the binding of endonuclease I to a DNA fo

104 NA aptamer:thrombin complexes reveals an RNA-induced fit in the latter.

105 n of the mutant insulin) presumably reflects induced fit in the native mechanism of hormone-receptor

106 This pocket is formed by an induced fit in which one of the tryptophan residues invo

107 n 20% across this series, which exemplifies 'induced fit' in a model host-guest system.

108 rmational selection mechanism (as opposed to induced fit) in a supramolecular system.

109 te that GSTA4-4 undergoes no enantiospecific induced fit; instead, the active site residue Arg15 is i

110 ombin and by triggering a Lys(114)-dependent induced fit interaction with activated antithrombin that

111 uggesting that RNA binding occurs through an induced-fit interaction.

112 Induced fit is a predominant phenomenon in protein-ligan

113 y related family thought to have evolved as "induced fit" ligand-binding macromolecules.

114 hat interacts with the activation loop in an induced-fit manner.

115 se peptides in the canonical fashion, and an induced fit mechanism allows for the accommodation of a

116 nd the possible role for domain motion in an induced fit mechanism are discussed.

117 es distant from the DNA interface suggest an induced fit mechanism for binding in the 'hot spot' for

118 Consistent with these data, an induced fit mechanism for nucleotide specificity is prop

119 The ensemble obtained suggests an induced fit mechanism for recognition of target RNA by t

120 t from that described earlier, suggesting an induced fit mechanism for sst(1) binding of these novel,

121 g DNA replication, DNA polymerases follow an induced fit mechanism in order to rapidly distinguish be

122 the enzyme-catalyzed reaction and support an induced fit mechanism in which a wide cavity is establis

123 ase activity of PSTK may be activated via an induced fit mechanism in which binding of tRNA(Sec) spec

124 By using single-molecule methods, the induced fit mechanism is shown to position favorably the

125 hibitors were interpreted as evidence for an induced fit mechanism of association, the presence of a

126 ible junction of three helices, occurs by an induced fit mechanism that involves reorganization of th

127 s for this specificity, highlighting a novel induced fit mechanism that is likely to be conserved wit

128 the flexible binding of proteins such as the induced fit mechanism where the ligand is postulated to

129 ar binding to the permease is involved in an induced fit mechanism, and the transport process require

130 ligands for FKBP51 were reported based on an induced fit mechanism, but they are too large for a furt

131 Our data are consistent with an induced fit mechanism, in agreement with previous simula

132 hed, the association must proceed through an induced fit mechanism.

133 nucleotide binding site of T7 helicase by an induced fit mechanism.

134 f alternative anchoring modes rather than an induced fit mechanism.

135 ligand in this novel series we confirmed the induced fit mechanism.

136 ns upon carbohydrate binding in line with an induced fit mechanism; on the other hand, GGBP shows ext

137 ally, to determine whether pol lambda has an induced-fit mechanism and open-to-closed transition befo

138 osed transition before the chemical step and induced-fit mechanism exist in DNA polymerase mu (pol mu

139 y a factor of ten at room temperature) by an induced-fit mechanism first formulated by Koshland.

140 This includes an induced-fit mechanism for cytochrome c binding to regula

141 tions, we previously provided support for an induced-fit mechanism for pol X in the presence of the c

142 ansferase substrate analogues that reveal an induced-fit mechanism in which substrates and active-sit

143 structural analyses led to dissection of the induced-fit mechanism into ligand-induced and temperatur

144 This induced-fit mechanism is likely a major contributor resp

145 The results support a substrate induced-fit mechanism of beta-PGM catalysis, which allow

146 w rate of this loop closure implies that the induced-fit mechanism of heme uptake in HasAp is not bas

147 Although an induced-fit mechanism of nonstop mRNA surveillance media

148 tead, promoter recognition is achieved by an induced-fit mechanism of transcription factor-dependent

149 Such an induced-fit mechanism serves three purposes: 1) assures

150 novel apo-CSN crystal structure indicate an induced-fit mechanism that drives CSN activation by nedd

151 second analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrat

152 ms shows that the XP2 groove is formed by an induced-fit mechanism that involves movements of the W27

153 rt the notion that sugar binding involves an induced-fit mechanism that is inhibited by IIA(Glc) bind

154 AT utilises an induced-fit mechanism to bind with high affinity to a pe

155 sequently refined by a temperature-sensitive induced-fit mechanism to retain the canonical peptide re

156 d, the data are best explained by a modified induced-fit mechanism where cognate and non-cognate comp

157 o revealed that Y24 and E27 mediate a unique induced-fit mechanism whereby E27 specifically recognize

158 Ligand binding occurs via an induced-fit mechanism, i.e., the ligand binds to the ope

159 SICSTP opposite dNaM proceeds via a mutually induced-fit mechanism, where the presence of the triphos

160 ospecific binding reaction occurs through an induced-fit mechanism, wherein the ligand promotes a pri

161 the antigen loop is accommodated through an induced-fit mechanism.

162 rect nucleotide for incorporation through an induced-fit mechanism.

163 uN1/GluN2B amino terminal domain dimer by an induced-fit mechanism.

164 rucial coil-to-helix transition employing an induced-fit mechanism.

165 onstant, suggesting that binding follows the induced-fit mechanism.

166 t with conformational selection than with an induced-fit mechanism.

167 the SAM-bound (OFF) conformation through an induced-fit mechanism.

168 " down the SAM-bound conformation through an induced-fit mechanism.

169 ures and are inconsistent with a traditional induced-fit mechanism.

170 ndicating that the binding is mediated by an induced-fit mechanism.

171 ty of peptide release is achieved through an induced-fit mechanism.

172 show that HP2 opening with Na(+) follows an induced-fit mechanism.

173 -100) upon binding cognate DNA as part of an induced-fit mechanism.

174 igands promote pseudoknot docking through an induced-fit mechanism.

175 onformational changes in the protein via the induced-fit mechanism?

176 The 2 limiting cases are the "induced fit" mechanism (binding first) or "conformationa

177 The utilization of an "induced fit" mechanism by PolB1 exo- was supported by th

178 Our results point to a "limited change/induced fit" mechanism in which the clamp first opens, f

179 monitor DNA synthesis fidelity, through an "induced-fit" mechanism.

180 ein provide evidence that Dpo4 utilizes the 'induced-fit' mechanism to select a correct nucleotide at

181 at Sulfolobus solfataricus Dpo4 utilizes an 'induced-fit' mechanism to select correct incoming nucleo

182 MMP-1 appears to blend selected fit with induced fit mechanisms to catalyse collagen unwinding pr

183 ization of conformational changes that drive induced-fit mechanisms and their quantitative importance

184 as remote conformational switches to govern induced-fit mechanisms that ensure accuracy in codon rec

185 combination of conformational selection and induced-fit mechanisms that may promote hemin release fr

186 Computational docking studies using an induced fit methodology successfully reproduced the majo

187 of the protein-ligand complex, using a novel induced fit methodology.

188 e encounter complex that is intrinsic to the induced fit model and not required by the conformational

189 These results support a mutually induced fit model in which RNA-dependent conformational

190 An induced fit model is proposed that depends on the DNA co

191 This induced fit model provides mechanistic insights into the

192 g and peptidyltransfer, possibly through the induced fit model.

193 the L7Ae protein is added, corroborating the induced-fit model for L7Ae-box C/D RNA interactions.

194 osing rate increased, strongly supporting an induced-fit model for nucleotide recognition.

195 n the basis of these findings, we propose an induced-fit model in which prestructured substrates are

196 ce of actin, providing strong support for an induced-fit model of actin binding.

197 en together, the results support a substrate induced-fit model of catalysis in which betaG1P binding

198 rmation in the absence of ligand, whilst the induced-fit model predicts that the ligand-bound conform

199 anism for antibiotic binding, rather than an induced-fit model where the bases only flip in the prese

200 ween the ligand and G-quadruplex follows the induced-fit model.

201 d by either a conformational-selection or an induced-fit model.

202 These data support an "induced-fit" model for prolactin receptor binding where

203 Such an activation may be understood by the "induced-fit" model, which states that ligand-induced con

204 With both conformational selection and induced fit models considered, we extend ANM to include

205 hich fall under conformational selection and induced fit models, and which mirror classical SN1 and S

206 tly proposed hybrid conformational selection/induced-fit models.

207 inguish between conformational selection and induced-fit models.

208 r than the other way around-as with classic "induced fit" models.

209 izes its cognate peptide with a component of induced fit molecular recognition involving the adoption

210 Ternary structures showed that induced-fit molecular mimicry underpins TRAV27/TRBV19(+)

211 Surprisingly, we find that induced fit motions in most enzymes is very small (usual

212 s many routes to the lock and rate-dependent induced-fit motions for intermediates, which might be re

213 ed with 1-deoxygalactonojirimycin reveals an induced fit movement; there is a rupture of the electros

214 e enzyme is structure-selective, significant induced fit occurs in the interaction, with changes in t

215 olecular dynamics simulations to account for induced fit of a flexible loop crucial for inhibitor bin

216 ibility of the distal N-terminus, and for an induced fit of ATP at the binding site.

217 Mutually induced fit of stem I and the tRNA exploiting the intrin

218 ggest that a basis for this mechanism is the induced fit of the 30S subunit upon cognate aa-tRNA bind

219 ucture, molecular water at the interface and induced fit of the C(2)H(2) TFs.

220 Induced fit of the nicked DNA into a distorted conformat

221 cant and tRNA-bound 70S ribosomes suggest an induced fit of the ribosome structure in response to tRN

222 In particular, the induced fit of the target small-molecule to their antibo

223 ts suggest that conformational selection and induced fit of the U2AF(65) RRMs are complementary mecha

224 of multidrug efflux pumps is accompanied by induced fit of TolC driven mainly by accommodation of th

225 chanism would be reminiscent of the mutually induced fit of tRNA and protein employed by some aminoac

226 e mechanism (conformational selection and/or induced fit) of molecular recognition.

227 ws conformational flexibility, indicating an induced fit on binding to the portal.

228 vel mechanistic details associated with both induced-fit (Open-PreTS) and catalysis (PreTS-Product).

229 ction and population shift followed by minor induced-fit optimization is the key mechanism in biomole

230 y of the protease, suggesting that either an induced fit or a conformational selection mechanism shou

231 her these proteins bind their substrates via induced fit or conformational selection is not understoo

232 ins can bind target molecules through either induced fit or conformational selection pathways.

233 derable interest is whether the mechanism is induced fit or conformational selection.

234 and shifts to its mature form upon a ligand-induced fit or exists in multiple conformations in equil

235 bility: is the system better described by an induced fit or population shift mechanism?

236 oconazole to P450 3A4 was consistent with an induced-fit or a conformational-selection model, but the

237 panies receptor conformational changes, i.e."induced fit" or "conformational selection," mainly deter

238 e of the minor groove and sequence-dependent induced fits over adjacent major groove interfaces.

239 receptor-ligand adjustments, typical of the induced-fit paradigm.

240 ognition can be accounted for by the classic induced-fit paradigm.

241 allowing for structural transitions along an induced fit pathway.

242 were thought to bind to their target via an induced-fit pathway instead of conformational selection.

243 loop similar to P14, and the rate along the induced-fit pathway resembles that of an isolated tetral

244 y but after the rate-limiting step along the induced-fit pathway.

245 our-state kinetic model to 1) determine that induced-fit pathways dominate the binding flux over a la

246 find that both conformational selection and induced fit play a role in the binding mechanism, reconc

247 model in which conformational selection and induced fit play important roles in the recognition of s

248 The side chain of this series binds in an induced-fit pocket forming a cation-pi interaction with

249 e, affecting plasticity of the protein in an induced-fit pocket.

250 The theory of induced fit predicts that enzymes undergo conformational

251 he interpretation that IIA(Glc) inhibits the induced fit process and restricts the conformational dyn

252 After approximately 4 ns, a critical "induced fit" process was observed to last for approximat

253 high degree of flexibility related to guest-induced fit processes of the solvent molecules included

254 both flexibility of the dimer interface and induced-fit protein structure changes caused by sequence

255 mbin:PS2-aptamer complex reveals a localized induced-fit rearrangement of the PS2-containing nucleoti

256 5abc binding the core and then undergoing an induced-fit rearrangement.

257 for specificity generation in which required induced-fit rearrangements are significantly modulated b

258 mechanism, and both are further mediated by induced-fit rearrangements, in which enzyme and tRNA und

259 ocess provides mechanistic insights into the induced fit recognition in this system and serves as an

260 Induced fit recognition may allow docking peptides to ac

261 turation introduced substitutions increasing induced-fit recognition and electropositivity, potential

262 how compact, prefolded RNAs that follow the induced-fit recognition mechanism adapt local structural

263 he dynamic structure of Nop10 facilitates an induced-fit recognition with the H/ACA Psi-synthase and

264 differs from other KARI enzymes in lacking "induced-fit", reflecting structural rigidity.

265 g methods have been developed to predict the induced fit reliably and, at the same time, to improve o

266 a mechanisms of conformational selection and induced fit, respectively.

267 itor, UDP-alpha-d-xylose, elicits a distinct induced-fit response; a buried loop translates approxima

268 enzyme subsequently displayed a substantial "induced fit" response to yield a conformation very simil

269 Thus, an induced fit results from conformational changes in both

270 and proteolysis experiments suggest that the induced fit results from the closure of helical hairpin

271 such a mode depends on binding, that in the induced fit scenario, there is an optimal stiffness k(a)

272 ing involves both conformation selection and induced fit steps.

273 ngth of tRNA(Glu), accessing A37 by using an induced-fit strategy that completely unfolds the tRNA an

274 nalysis of DB921 bound to AATT shows that an induced fit structural change in DB921 reduces the twist

275 Folding of the protein is accompanied by induced-fit structural changes in the DNA ligand.

276 stantial pK perturbations, mostly due to the induced-fit structural changes, in regions far from the

277 onal exchange in the peptide, supporting an "induced-fit" style TCR binding mechanism.

278 complexes of other DRE-TIM metallolyases and induced fit substrate docking studies conducted using th

279 describe, for example, a putative coenzyme-A-induced-fit substrate binding mechanism mediated by argi

280 rfect precision and that separate control of induced-fit substrate recognition sets up the catalytic

281 codon and the 30S subunit A site undergo an induced fit that results in stabilization of a conformat

282 ubstrate-triggered active site reshaping (an induced fit), the crystal structure explains the accumul

283 her change in electrostatics causes a second induced fit, the domain closure.

284 s punctata PEP that the mechanism is instead induced fit: the native enzyme exists in a conformationa

285 by its dual role in native self-assembly and induced fit, thus highlights the implicit role of misfol

286 led that the coactivator Trm112 undergoes an induced fit to accommodate its methyltransferase (MTase)

287 functions into discrete domains; the use of induced fit to enhance binding selectivity; the impositi

288 In this enzyme, two domains dock by induced fit to form a catalytic core that mediates a spe

289 nd that the interaction is formed via mutual induced-fit transitions that occur en route to the groun

290 ucleotide binding region of Cdc42 through an induced fit type of binding.

291 These findings suggest a mechanism of induced fit upon ligand binding by mammalian cellular re

292 in the N-terminal alpha-helix, suggesting an induced fit upon paxillin binding.

293 rt connecting segments (<3 residues) prevent induced fit upon receptor binding and so are essentially

294 Discussion concerning "induced fit" versus "conformational selection" has, howe

295 PS-mediated mechanism involving a series of induced-fit viral protein interactions with RNA.

296 edictions of the CFTR pore model, we applied induced-fit, virtual, ligand-docking techniques to ident

297 tep mechanism comprising initial binding and induced fit, were verified.

298 is stabilized by small-molecule binding) and induced fit (where a small molecule imposes a structure

299 lly, C5a and C5aR can be involved in "mutual-induced fit", where the interface between the molecules

300 onal fluctuations and enabling bidirectional induced fit within the bent complex.