ライフサイエンスコーパス: amide proton

1 ine's unique feature, the lack of a backbone amide proton.

2 bonds between the phosphate group and nearby amide protons.

3 tate analogue complex exchanges 126 of these amide protons.

4 calculation of z-coordinates for individual amide protons.

5 chnique to enhance signals from exchangeable amide protons.

6 are selectively promoted for the majority of amide protons.

7 ection factors were obtained for 52 backbone amide protons.

8 en bond restraints from 24 slowly exchanging amide protons.

9 nnectivities, exhibits fast exchange for all amide protons.

10 couplings, and patterns of slowly exchanging amide protons.

11 egions of slow-, medium- and fast-exchanging amide protons.

12 NMR exchange rates of more than 157 assigned amide protons.

13 Thermal coefficients of backbone amide protons, 2D-NMR spectra, and molecular modeling re

14 e data also provided evidence for an unusual amide proton-amide nitrogen hydrogen bond within the eth

15 osylated is exposed to solvent, and both the amide proton and carbonyl oxygen of the peptide backbone

16 te for cTnI(33-80) was determined by mapping amide proton and nitrogen chemical shift changes, induce

17 to make accurate assignments of the protein amide proton and nitrogen chemical shifts.

18 atic interactions involving the intraresidue amide proton and the C3-OMe, which helped in the stabili

19 The second group includes backbone amide protons and a few aliphatic and aromatic protons i

20 capabilities, but the other face is missing amide protons and its ability to hydrogen bond is severe

21 ation between the temperature coefficient of amide protons and the strength of hydrogen bonding in sm

22 d S26, exhibit readily exchangeable backbone amide protons and therefore may be located on a turn or

23 fication of transient hydrogen bonds between amide protons and titrating carboxylate groups.

24 In particular, the amide nitrogen, amide proton, and carbonyl carbon chemical shifts are hi

25 correlations between two alpha carbons, two amide protons, and two nitrogen nuclei.

26 ction between an aromatic ring and a glycine amide proton appears to be retained in the longer peptid

27 periments show that only 43% of the backbone amide protons are exchangeable with solvent.

28 by the native structure: the most protected amide protons are located in regions of hydrogen bonding

29 strate-binding site (residues 148-152) whose amide protons are poorly protected from solvent.

30 roximately 12 of the 39 Abeta(1-40) backbone amide protons are protected from exchange in the protofi

31 ative transition of (15)N chemical shifts of amide protons as a function of urea concentrations befor

32 cal shift dispersion of the native rLIN-12.1 amide protons, as seen for the Ca2+-binding LDL-A module

33 cross-peaks of relatively rapidly exchanging amide protons at early time points.

34 Second, by measuring the PREs of the amide protons at increasing hGH concentrations and a con

35 ration ( approximately 10-20mM) and owns two amide protons (at 2.1 and 2.8ppm down field from water)

36 aspartic acid modified chelates produced an amide proton-based PARACEST signal.

37 of iopamidol but containing a single set of amide protons, both in vitro and in vivo.

38 Protection of amide protons by formation of hydrogen-bonded helical st

39 In free subtilisin, amide protons can be categorized according to exchange r

40 The locations of these amide protons can be used to map the sites of structural

41 A computational methodology for backbone amide proton chemical shift (delta(H)) predictions based

42 , the existence of a correlation between the amide proton chemical shift and temperature coefficient.

43 s predominantly native-like according to the amide proton chemical shifts and their temperature depen

44 nary results suggest that amide nitrogen and amide proton chemical shifts in a selectively labeled sa

45 isotropic and anisotropic components of the amide proton chemical shifts were used as benchmarks to

46 that interact with Mg2+ exhibit pH-sensitive amide proton chemical shifts which appear to be coupled

47 NMR studies reveal that cations and valine amide protons compete for the carbonyl oxygen atoms, con

48 Although amide proton concentrations are in the millimolar range,

49 ; apparent thermodynamic parameters for each amide proton considered.

50 40 showed a clear dispersion of the nitrogen-amide proton correlation cross-peaks indicative of a pur

51 distance between the spin label and 30 to 60 amide protons could be calculated for each spin-labeled

52 nt a method for site-resolved measurement of amide proton CSAs in fully protonated solids under magic

53 gnificant molecular dynamics contribution to amide proton deprotection.

54 For the backbone amide proton detected "out-and-back" experiments, data c

55 Novel backbone amide proton-deuterium exchange CP-MAS NMR experiments o

56 Local stability is obtained from amide proton-deuterium exchange data, using model peptid

57 H-bonds was quantified by the half-lives of amide proton-deuterium exchange reactions, which show th

58 mass spectrometry (MS) was used to determine amide proton/deuteron (H/D) exchange rates.

59 fitting to the NMR structures relates to the amide proton deviating from its idealized, in-peptide-pl

60 that the chemical environment of many of the amide protons differed and thus that the three-dimension

61 The availability of both amide proton dipolar shifts and unpaired electron to ami

62 ical shifts, residual dipolar couplings, and amide proton distances into the Rosetta protein structur

63 oton dipolar shifts and unpaired electron to amide proton distances permitted the direct calculation

64 rmitted the measurement of unpaired electron-amide proton distances using paramagnetic relaxation enh

65 lings, dipolar shifts, and unpaired electron-amide proton distances.

66 Amide proton exchange and (15)N relaxation rate data pro

67 g the temperature dependence of NMR-detected amide proton exchange and used these data to extract the

68 The kinetics of amide proton exchange are also enhanced by a factor betw

69 Considering the event of amide proton exchange as an energetically quantifiable s

70 oton chemical shift, paramagnetic shift, and amide proton exchange data to obtain atomic level struct

71 alar coupling, secondary chemical shift, and amide proton exchange data were used to characterize the

72 ts obtained from NOE, coupling constant, and amide proton exchange data.

73 Amide proton exchange experiments indicate that the two

74 Quenched amide proton exchange experiments revealed a greater str

75 Amide proton exchange experiments suggest a stable hydro

76 he H-D exchange methodology and assessed the amide proton exchange in substrate-free and cholesterol-

77 mary RNA sites (aa 56-63) was protected from amide proton exchange in the presence of poly(C), as was

78 stallographic observations and evidence from amide proton exchange kinetics are consistent with local

79 ncreased by a factor of at least 37 based on amide proton exchange measurements.

80 taining 1% water was studied by using CD and amide proton exchange monitored by two-dimensional 1H NM

81 Measurement of amide proton exchange protection during the first severa

82 rements of the time course of acquisition of amide proton exchange protection of human dihydrofolate

83 ed forms; this hypothesis is consistent with amide proton exchange rate data.

84 in 3D (15)N- and (13)C-edited spectra, fast amide proton exchange rates (all greater than 1 s(-1)),

85 Differences in NOE patterns and amide proton exchange rates are also observed in the B-C

86 ddition, however, we have measured the rapid amide proton exchange rates for the DNA binding region o

87 orrelation spectroscopy was used to quantify amide proton exchange rates of the uniformly (15)N-label

88 Amide proton exchange rates showed that the region of th

89 ar to that obtained from a detailed study of amide proton exchange rates, but differs markedly from t

90 ce, also reveals ligand selective changes in amide proton exchange rates.

91 ta, including residual dipolar couplings and amide proton exchange rates.

92 nfolded forms previously characterised using amide proton exchange studies is discussed.

93 e mobility of the protein is evident by fast amide proton exchange throughout the chain.

94 the cellular interior and used NMR-detected amide proton exchange to quantify the free energy of unf

95 NMR-detected amide proton exchange was then used to quantify the stab

96 NMR-detected amide proton exchange was used to investigate the stabil

97 Protection factors for amide proton exchange were quantitatively measured in an

98 lear Overhauser enhancements and accelerated amide proton exchange.

99 ublished redox-dependent dynamics studied by amide proton exchange.

100 0) fibrils show that about half the backbone amide protons exchange during the first 25 h, while the

101 Whereas amide-proton exchange in the A1-A8 segment remained rapi

102 al shifts and rapid (15)N-detected (1)H-(2)H amide-proton exchange were observed in one of the three

103 However, a large fraction of amide protons exchanged in less than 20 min, indicating

104 The exchange rate of the amide proton for the reactive threonine correlated well

105 Intact sIGPS strongly protects at least 54 amide protons from hydrogen-deuterium exchange in the in

106 The data suggest that deviations of the Gly amide protons from their standard positions arise from h

107 ent accessibility is determined for backbone amide protons from various segments of wild-type Yersini

108 Amide proton H/D exchange experiments showed that 60-80%

109 The protein was shown to be resistant to amide proton H/D exchange, providing evidence that most

110 ogen/deuterium exchange rates for individual amide protons have been measured for the carbon monoxide

111 most compact protein with nearly 50% of the amide protons having long exchange lifetimes, but CsE-v5

112 Protein-amide proton hydrogen-deuterium exchange (HDX) is used t

113 For the current project, amide proton hydrogen-deuterium exchange coupled with MA

114 We used amide proton hydrogen/deuterium (HD) exchange detected b

115 nformation changes upon ligand binding using amide proton hydrogen/deuterium exchange and mass spectr

116 six exchangeable protons for CEST which are amide protons in [Fe(L1)](2+) or amino protons in [Fe(L2

117 Analysis reveals that amide protons in beta-strands 7, 8, 9 and 10 have, on av

118 The H-(2)H exchange kinetics of the core amide protons in cyt c, which in the native protein unde

119 lectron on the unique nitroxide and 30 to 60 amide protons in each protein could be approximated.

120 Residue-specific exchange rates of 223 amide protons in free and prodomain-complexed subtilisin

121 revealed a greater structural protection of amide protons in glycerol than in water for a majority o

122 In particular, the slowly exchanging amide protons in HP-35 have protection factors that are

123 r Overhauser effects (NOEs) between backbone amide protons in successive acquisitions of 1H-15N HSQC-

124 Fast exchange has also been observed for all amide protons in the CE-loop and in turns, as expected f

125 Presaturation of the amide protons in the Cu2 complex at 37 degrees C leads t

126 We find that the hydrogen bonded amide protons in the DNA binding regions are stabilized

127 nch-flow process indicates that three of the amide protons in the E helix are in fact largely protect

128 determined for more than 85% of the backbone amide protons in the IgG binding domains of protein G, G

129 avior attributed to the fact that all of the amide protons in the ligand backbone cannot hydrogen bon

130 that contain the slowest exchanging backbone amide protons in the native protein.

131 The results reveal that the majority of the amide protons in the NTD of H3 are protected from exchan

132 suggest that the arginine finger of GAP and amide protons in the P-loop of Ras stabilize the negativ

133 he very fast hydrogen-deuterium exchange for amide protons in this helix.

134 Amide protons in two of these clusters, including residu

135 hydrogen bonding status of the exchangeable amide proton, indicating a significant molecular dynamic

136 magnetic relaxation enhancement (PRE) of the amide protons induced by the soluble paramagnetic relaxa

137 n, markedly restricts the exchange of loop C amide protons, influencing both the rates and degrees of

138 The CEST peak for the [Fe(L1)](2+) amide protons is at 69 ppm downfield of the bulk water r

139 Analysis of the effects of exchange-out of amide proton labels during the labeling pulse ( approxim

140 e was mapped by a novel method that compares amide proton line broadening by paramagnetic Gd-EDTA in

141 -deuterium exchange patterns of peptide bond amide protons monitored by mass spectrometry (MS), we ha

142 H/(2)H exchange of amide protons monitored by NMR on three proteins (p16, p

143 ne display the carbonyl oxygen (O7') and the amide proton (n + 1)H1' distances and N1'-H1'-(n - 1)O7'

144 er, an H-bond network is formed in which the amide proton NH is donated to the OH groups on carbons C

145 Native-state amide proton (NH) exchange in turkey ovomucoid third dom

146 Nuclear magnetic resonance amide proton/nitrogen chemical shift analysis of cardiac

147 round state in proteins can be obtained from amide proton NMR chemical shift temperature dependences

148 Line broadening and multiplicity of amide proton NMR peaks from hB are consistent with hB un

149 ain (13)C(beta), (1)H(beta) chemical shifts, amide proton NOEs, and (15)N R(2) relaxation rates were

150 is, backbone N-H residual dipolar couplings, amide proton NOEs, and R(2) relaxation rates all indicat

151 The backbone amide proton of Asn162 becomes protected from rapid exch

152 of the phosphorylated Thr205 residue to the amide proton of Gly207, and is further stabilized by the

153 o group can act as a H-bond acceptor for the amide proton of Gly219.

154 n the mutant A35T analog is observed for the amide proton of leucine-40.

155 interresidue hydrogen bond with the backbone amide proton of the following residue, (n + 1)H1'.

156 formation has been identified between the NH amide proton of the upper side chain (proton donor) and

157 D exchange revealed that a small fraction of amide protons of apocyt c, possibly associated with a st

158 e (1)H NMR chemical shifts of the side-chain amide protons of Asn34, a conserved, structurally releva

159 Hydrogen-deuterium exchange of 39 amide protons of Bacillus amyloliquefaciens ribonuclease

160 n from previous studies of 1H/2H-exchange of amide protons of barnase.

161 he rate-limiting step for exchange of buried amide protons of bound barnase is the unfolding of the f

162 The side chain amide protons of Gln are required for high-affinity inte

163 ntributed to the benzoyl C=O by the backbone amide protons of Gly114 and Phe64 and a possible dipolar

164 nd IgG-bound Z domains demonstrates that the amide protons of helices 1, 2 and 3 are protected from r

165 temperature-dependent shifts of the backbone amide protons of Leu 88, Ser 91, Cys 98, and Leu143 reve

166 roxide 4-hydroxy TEMPO were measured for the amide protons of perdeuterated rubredoxin from the hyper

167 change kinetics measured for the first three amide protons of the 3K peptide indicate that the NH of

168 fluctuation, the forward rate constants for amide protons of the antiparallel beta-sheet are signifi

169 x central base pairs, as well as for several amide protons of the backbone.

170 protection factors (1/K(op)) for individual amide protons of the bound smMLCKp domain span 5 orders

171 e results show that approximately 50% of the amide protons of the polypeptide backbone of Abeta(1-40)

172 the hydrogen exchange (HX) rates of a set of amide protons of the protein.

173 een the glutathione carbonyl oxygens and the amide protons of thioredoxin residues Ile-75 and Ala-93

174 change in resonant frequencies of the indole amide protons of W9, W11, W13, and W15, with the most pr

175 te of approximately eight rapidly exchanging amide protons on actin.

176 Deuteration of amide protons on cyclic AMP-dependent protein kinase was

177 le at the same time increasing the number of amide protons protected from hydrogen exchange.

178 Amide proton protection factors were obtained from H-D a

179 eit not rigid, a result that is supported by amide proton protection factors, circular dichroism meas

180 The pattern and magnitude of amide proton protection indicate that the central parall

181 ide chain, and the resulting enhancements of amide proton relaxation were measured by NMR spectroscop

182 enhancement of both T1 and T2 relaxation for amide protons resolved in a 1H-15N correlation spectrum,

183 The transfer of amide proton resonance assignments from wild-type to the

184 In the A35T mutant this amide proton resonance is shifted upfield by 1.27 ppm re

185 1.27 ppm upfield shift of the corresponding amide proton resonance relative to the value observed fo

186 hanges in chemical shifts of several peptide amide proton resonances after addition of Ca2+ to con-G,

187 lins exchanged on average 25, 28, 30, and 38 amide protons, respectively.

188 uman and LysPro insulins exchanged 34 and 43 amide protons, respectively.

189 The slow solvent exchange of backbone amide protons revealed the helix from P403 to A416 was m

190 various local structure contributions to the amide proton shielding tensor that complements scarce ex

191 lculations to characterize the dependence of amide proton shielding to the local structure.

192 rea denaturation profiles for representative amide protons show that global unfolding is non-two-stat

193 nding interface was obtained from changes in amide proton signals of uniformly 15N-labeled Rom with i

194 The relaxation effects at the amide proton sites are found to be highly localized and

195 oked to explain solvent exchange at backbone amide proton sites that have an intermediate level of pr

196 A pattern of increased rates of amide proton solvent exchange in the alpha3 helix correl

197 nsverse 15N relaxation rates, as well as the amide proton solvent exchange rates.

198 Rapid exchange of 99% of the observable amide protons suggests that these fluctuations give high

199 condary chemical shifts, (1)H-(1)H NOEs, and amide proton temperature coefficients have been used to

200 hange rate constant for each solvent-exposed amide proton that is not hydrogen bonded to a backbone c

201 l domain is stable in solution, indicated by amide protons that are protected from solvent exchange.

202 d [Ni(L2)](2+) have CEST peaks attributed to amide protons that are shifted 72, 76, and 76 ppm from t

203 The amide protons that can be detected by APT provide a uniq

204 the E helix has a substantial complement of amide protons that show biphasic kinetics, i.e. are prot

205 lecule, followed by chemical exchange of the amide proton to bulk water.

206 l H(4)B transfers both an electron and a 3,4-amide proton to the heme during the first step of NO syn

207 shifts, extreme sensitivity of the backbone amide protons to solvent presaturation, and reduced hete

208 radiofrequency labeling from the reporter's amide protons to water protons, can be switched on and o

209 To show the potential of amide proton transfer (APT) contrast for detecting acute

210 Amide proton transfer (APT) imaging is a noninvasive mol

211 term chemotherapy with temozolomide (TMZ) by amide proton transfer (APT) imaging.

212 these lesions can be distinguished using the amide proton transfer (APT) magnetic resonance imaging (

213 In addition to significant changes in amide proton transfer and semisolid macromolecular magne

214 Amide proton transfer magnetic resonance imaging, a chem

215 proton exchange spectroscopy to measure the amide proton transfer rate.

216 al shift regions for the indole and backbone amide protons were 0.0106 +/- 0.0007 (n = 12) and 0.0105

217 Amide protons were allowed to exchange with deuterons in

218 Forty or so amide protons were found which do not undergo significan

219 pH-sensitive amide protons were identified and found to be associated

220 and the resulting enhancements of T2 for the amide protons were measured by NMR spectroscopy.

221 Clusters of solvent-shielded amide protons were observed in two alpha-helical segment

222 After the Gly amide protons were placed out of the C'-N-Calpha plane,

223 y FTIR revealed that only small fractions of amide protons were protected in R- or S-fibrils, an argu

224 een used to identify the most-protected core amide protons which exchange through global unfolding.

225 rotein proton, and (C) direct exchange of an amide proton with water.

226 dynamic as judged by the rate of exchange of amide protons with solvent.

227 ions and catalyzed exchange of deeply buried amide protons with solvent.

228 is at two different values of pH showed that amide protons within the beta-barrel structure exchange

229 hibits a low level of protection from HX for amide protons within this motif relative to Pa cyt c551.