ライフサイエンスコーパス: deamidation

1 n as a result of stress (e.g., oxidation and deamidation).

2 consistent with predictions (pI 7.0 for one deamidation).

3 ll as other stimuli can increase the rate of deamidation.

4 s in overestimation of the original level of deamidation.

5 ead-based approaches may increase artificial deamidation.

6 investigating the structural consequences of deamidation.

7 th this to determine the extent of glutamine deamidation.

8 ound to increase linearly with the extent of deamidation.

9 of the rate-limiting elementary step of Asn deamidation.

10 vels of covalent damage, including glutamine deamidation.

11 was used could detect only a single site of deamidation.

12 odifications: methylation, demethylation and deamidation.

13 , LNW, SNL, NNF, DNA, GNS, and FNR showed no deamidation.

14 MAb) has several "hot spots" for spontaneous deamidation.

15 imensional structure of the antibody reduced deamidation.

16 essive decreases and changes consistent with deamidation.

17 MTN1 and MTN2 as putative targets of HopAF1 deamidation.

18 ese residues are potential targets of HopAF1 deamidation.

19 activation through amidotransferase-mediated deamidation.

20 id (Asp) isomerization, and asparagine (Asn) deamidation.

21 nate mononucleotide suggests a mechanism for deamidation.

22 We find that deamidation accelerates amyloid formation and the deamid

23 e these asparagines with aspartate (to mimic deamidation) according to their predicted deamidation ra

24 the molecular mechanism by which Nedd8 Gln40 deamidation affects CRL functions remains unclear.

25 ntial processes, provide the 0 K barrier for deamidation after accounting for unimolecular decay rate

26 In summary, the data suggested that the deamidation alone showed greater effect on chaperone act

27 e of the study was to compare the effects of deamidation alone, truncation alone, or both truncation

28 Deamidation altered amine reactivity, circular dichroism

29 either aspartyl isomerization or asparaginyl deamidation alters protein structure and potentially bio

30 underwent both methylation and demethylation/deamidation, although detection of the latter modificati

31 DNA damage and consequently represses Bcl-xL deamidation and apoptosis, thus giving rise to inappropr

32 Unlike Met oxidation, Asn deamidation and Asp isomerization mostly had very limite

33 spartyl/isoaspartyl products produced by Asn deamidation and Asp isomerization.

34 Asparagine deamidation and aspartate isomerization were identified

35 biochemical inhibition of PFAS impair RIG-I deamidation and concomitant activation.

36 dation resulted from three different events, deamidation and isomerization at asparagine 317 (Asn317)

37 n of the acidic variants can be explained by deamidation and isomerization, suggesting that additiona

38 phosphorylation and feedback control through deamidation and methylation of sensory receptors.

39 artificial modifications such as asparagine deamidation and N-terminal glutamine cyclization on prot

40 Subtle differences of modifications such as deamidation and oxidation between the innovator and bios

41 ergo chemical changes such as lactosylation, deamidation and protein cross-linking during processing

42 Lactosylation, deamidation and protein cross-linking were observed on 2

43 Charge species due to deamidation and sialylation were separated by CZE.

44 we incorporated the role of CheB in receptor deamidation and the slow fluctuations in receptor methyl

45 The inherent deamidation and those introduced by sample preparation c

46 maintenance of chaperone activity following deamidation and/or deletion of the N-terminal domain or

47 ned higher degrees of damage (carbonylation, deamidation) and far less IE.

48 mini and assayed methylation, demethylation, deamidation, and ability to mediate chemotaxis.

49 soform 1 (NHE-1), intracellular pH, Bcl-x(L) deamidation, and apoptosis.

50 mposition data, lack of evidence for peptide deamidation, and association of alpha1(I) collagen seque

51 The levels of oxidation, deamidation, and mutation of individual amino acids were

52 Including acetylation, phosphorylation, deamidation, and oxidized forms, a total of 8106 modifie

53 The effects of deamidation are investigated for five different amide-co

54 s study, methionine oxidation and asparagine deamidation are the only two modifications identified in

55 try (MS/MS) was established to calculate the deamidation artifacts.

56 used for the determination of the extent of deamidation as a measure of the amount of amide nitrogen

57 hionine loss with the relative amount of the deamidation, as well as the level of deamidation with gl

58 he strongly denaturing media that were used; deamidation at Asn67 could enhance that at Asn71, and th

59 Although deamidation at asparagine and glutamine has been found i

60 When simulating deamidation at both residues, there was a further decrea

61 These results suggest that deamidation at critical sites destabilizes betaB2 and ma

62 f different extents of oxidation at M207 and deamidation at N184, which could influence the clot lysi

63 Deamidation at the identified four sites was slow for th

64 method is needed to determine the extent of deamidation at the whole protein level.

65 heavy chain, is of particular interest since deamidation at this site greatly decreases the binding a

66 oxidation-induced structural changes foster deamidation at this site.

67 previously shown that human Bcl-xL undergoes deamidation at two asparaginyl residues and that DNA-dam

68 to mimic the effects of previously reported deamidations at Q162 in the C-terminal domain and at Q70

69 tion, the oxidized Fc displayed an increased deamidation (at pH 7.4) rate at the Asn 67 and Asn 96 si

70 d the eye and can be mobilized by hydrolysis/deamidation back to Ret-NH2.

71 l of human Bcl-xL is constantly modulated by deamidation because deamidation, like phosphorylation in

72 nusually large number of modifications, with deamidation being a major factor.

73 Heat treatment resulted in significant deamidation but almost no oxidation, which is consistent

74 elation between age of samples and levels of deamidation, but highlighting the effect of local enviro

75 peptides from ingested cereals, after their deamidation by TG2, induce T-lymphocyte activation accom

76 rpose of this study was to determine whether deamidation can alter clearance of crystallins by the UP

77 amidation is catalogued, and the impact that deamidation can have on peptide tandem mass spectra is d

78 Deamidation can influence the structure, stability, fold

79 ase Dcn1, our data are consistent with NEDD8 deamidation causing enhanced deneddylation of cullins by

80 des, often the autocatalytic nucleophiles in deamidation, correlated with the rate of degradation.

81 These data indicate that interface deamidation decreases the thermodynamic stability of Hga

82 of a possible 25 asparagine residues showed deamidation, demonstrating the effect of the primary ami

83 18)O, the formation of isoAsp and Asp by Asn deamidation during sample preparation results in a molec

84 e first time gamma/alpha-glutamyl isomers of deamidation, encountering a 1.7 gamma/alpha-glutamyl rat

85 Furthermore, gluten peptide deamidation extended the T-cell-receptor repertoire by r

86 The deamidation followed by subsequent methyl esterification

87 xin has a preferred enzymatic activity (i.e. deamidation for CNF1 and transglutamination for DNT) as

88 of post-translational modifications such as deamidation for this protein is challenging.

89 Uncoupling RIG-I deamidation from HSV-1 infection, by engineering deamida

90 Methodologies for estimating the degree of deamidation from peptide mass spectra are presented, the

91 The measured deamidation half-life for three different tryptic peptid

92 g this method, we were able to determine the deamidation half-life of amino acid residue Asn55 in viv

93 uence and biochemical data that suggest that deamidation has been conserved from the simplest extant

94 Protein deamidation has been considered a nonenzymatic process a

95 ovine ribonuclease A (13,689 Da), only Asn67 deamidation has been demonstrated previously, although o

96 Deamidation has been detected at the domain and monomer

97 asparagine (Asn), studies on glutamine (Gln) deamidation have been scarce, especially on the differen

98 ble residues but other modifications such as deamidation have been scarcely reported in the literatur

99 9) that are predicted to undergo significant deamidation (i.e., to >20%) on time scales comparable to

100 success in the site-specific quantitation of deamidation in a 14 kDa protein mixture, despite the min

101 to elucidate the biological implications of deamidation in aging and disease conditions.

102 ith a total of 277 and 282 sequences showing deamidation in both muscles, respectively.

103 To test this, we predicted sites of deamidation in cartilage oligomeric matrix protein (COMP

104 rk shows a method to determine the extent of deamidation in collagen using Fourier transform ion cycl

105 NGR deamidation in Cp was associated with gain of integrin-b

106 nt questions concerning the roles of protein deamidation in infection and immunity.

107 Here, we review studies on protein deamidation in innate immune signaling and present sever

108 Despite technological advances, detection of deamidation in large proteins remains a challenge and th

109 trometry techniques we identified asparagine deamidation in light chain complementarity determining r

110 motif in a structural loop, this is prone to deamidation in one of the antibodies but not the other.

111 The sites and levels of Asn deamidation in proteins are often determined by LC-MS an

112 or "aging." Recent studies implicate protein deamidation in regulating signal transduction in fundame

113 uctural models of amylin fibers reveals that deamidation in the N-terminal beta-sheet region may be t

114 t a full molecular description of asparagine deamidation in the Na(+)(Asn) complex by studying its co

115 This work has been focused on the impact of deamidation in those peptides generated in 12-months dry

116 ht mass spectrometry (MALDI-TOF-MS) to study deamidation in wool textiles, we identified eight peptid

117 metry (nanoLC-ESI-MS/MS) data indicated that deamidation in wool's alpha-keratin was influenced by pr

118 lecules may be partially due to a process of deamidation independent of glycosylation.

119 RhoA deamidation induces caspase-1 inflammasome activation, w

120 Asparagine deamidation is a decisive event in chemotherapy-induced

121 Deamidation is a major degradation pathway for all natur

122 Thus, deamidation is a post-translational modification that cr

123 in why the same enzyme that catalyzes gluten deamidation is also an autoantigen, something that is ha

124 that adjacent residues exert on the rate of deamidation is catalogued, and the impact that deamidati

125 Protein deamidation is emerging as a post-translational modifica

126 wn tandem mass spectrometry shows that Asn67 deamidation is extensive before Asn71 and Asn94 react; t

127 half deamidated before Asn34 reacts, and its deamidation is extensive before that at Gln74 is initiat

128 It appears that deamidation is not influenced by the type of muscle but

129 Deamidation is the irreversible substitution of an amide

130 Deamidation is very difficult to detect with standard me

131 Deamidation is, nonetheless, chemically equivalent to As

132 formed by tissue transglutaminase-catalyzed deamidation, is an important anchor residue as it partic

133 acid (Asp) isomerization or asparagine (Asn) deamidation, isoaspartic acid (isoAsp, isoD, or beta-Asp

134 digestions and used to monitor site-specific deamidation, isomerization, and other chemical modificat

135 Deamidation-isomerization to iso-Asp317, but not deamida

136 Moreover, we found that deamidation kinetics between in vivo samples and samples

137 was confirmed upon mutation to stabilize the deamidation lability via a generally applicable orthogon

138 Deamidation leads to disruption of the N-terminal beta-s

139 Therefore, it is necessary to monitor the deamidation levels [during storage] and after in vivo ad

140 ol samples buried for up to 8 years in which deamidation levels were relatively low under short-term

141 constantly modulated by deamidation because deamidation, like phosphorylation in other proteins, act

142 Thus deamidation, like phosphorylation, introduces a negative

143 oAsp) sites in peptides and proteins via the deamidation-linked isomerization of asparaginyl-Xaa bond

144 Despite the importance of deamidation, little is known about the elementary reacti

145 Deamidation may change the structure and function of a p

146 lar interest is the investigation of in vivo deamidation mechanisms of protein drug candidates.

147 viral deamidase and extends the paradigm of deamidation-mediated suppression of innate immunity by m

148 The deamidation-methyl esterification products are greatly e

149 Similarly, the deamidation mutants lowered the kinetic barrier to unfol

150 Thermal stabilities of the deamidation mutants were also reduced at pH 7.0.

151 Compared with wild type, the deamidation mutants were destabilized at pH 7.0.

152 m unfolding transitions of wild type and the deamidation mutants were indistinguishable.

153 litates detection of PTMs such as oxidation, deamidation, N-terminal pyroglutamic acid formation, and

154 dentify the gamma/alpha-glutamyl products of deamidation, none of these methods allows the characteri

155 Dissociative deamidation occurs along the N-C(alpha) bond, resulting

156 At low pH, the calculations show that deamidation occurs by direct acid-catalyzed hydrolysis t

157 Asparagine deamidation occurs spontaneously in proteins during agin

158 n to activate several signaling pathways via deamidation of a conserved glutamine residue in the alph

159 onstitutively activates small Rho GTPases by deamidation of a conserved glutamine residue, and HlyA1

160 activate small GTPases of the Rho family by deamidation of a glutamine, which is crucial for GTP hyd

161 rm, we successfully quantified the levels of deamidation of a humanized monoclonal antibody in cynomo

162 ion of a mAb, (ii) quantifying the extent of deamidation of a mAb, (iii) providing charge variant inf

163 ect of storage and formulation conditions on deamidation of a protein drug candidate.

164 e with the host cell cycle by catalyzing the deamidation of a specific glutamine residue (Gln40) in N

165 These 1,014-amino-acid toxins catalyze the deamidation of a specific glutamine residue in RhoA, Rac

166 employed reaction conditions facilitate the deamidation of amide-containing residues.

167 here a LC/MS/MS method used to evaluate the deamidation of an antibody after in vivo administration.

168 generated a transgenic mouse model mimicking deamidation of Asn at position 101.

169 We show that deamidation of Asn to Asp is dependent on glycosylation

170 Carbohydrate removal results in deamidation of Asn(371) to aspartic acid.

171 curs spontaneously in proteins during aging; deamidation of Asn-Gly-Arg (NGR) sites can lead to the f

172 The deamidation of asparagine (Asn) residues is the most com

173 Deamidation of asparagine and glutamine is the most comm

174 sed in ammonia as well as constant rates for deamidation of asparagine in collagen.

175 soAsp, isoD, or beta-Asp), generated via the deamidation of asparagine or isomerization of aspartic a

176 Deamidation of asparagine residues of biological pharmac

177 lts from this study suggest that spontaneous deamidation of asparagine residues predicted to occur du

178 ere investigated, with five derived from the deamidation of asparagine that were confirmed to contrib

179 The deamidation of asparagine--an analytically elusive, sub-

180 Nonenzymatic deamidation of asparaginyl residues can occur spontaneou

181 of proteins and peptides is the spontaneous deamidation of asparaginyl residues via a succinimide in

182 investigated the effect of oxidation on the deamidation of both NGR motifs and, consequently, on the

183 d for age assessment, it has been shown that deamidation of collagen is remarkably increased in old b

184 Deamidation of crystallins is associated with protein pr

185 T-induced mTORC1 activation proceeds via the deamidation of Galpha(q/11), which leads to the activati

186 Deamidation of glutamine (Gln) residues is a spontaneous

187 Deamidation of glutamine (Q) and asparagine (N) has been

188 The deamidation of glutamine (Q) to glutamic acid (E) result

189 cein-HPHQ(10)RR, and mass accuracy rules out deamidation of glutamine to glutamic acid as an explanat

190 BPSL1549 promotes deamidation of glutamine-339 of the translation initiati

191 The spontaneous nonenzymatic deamidation of glutaminyl and asparaginyl residues of pe

192 In addition, the enzyme is responsible for deamidation of gluten peptides, which are subsequently t

193 taminase 2 (TG2) catalyzes transamidation or deamidation of its substrates and is ordinarily maintain

194 ficient homologues (pseudoenzymes) to induce deamidation of key signaling components and evade host i

195 heD plays an important role in chemotaxis by deamidation of methyl-accepting chemotaxis protein recep

196 Deamidation of N-terminal Gln by Nt(Q)-amidase, an N-ter

197 Deamidation of N-terminal Gln by the Ntaq1 Nt(Q)-amidase

198 ate that is targeted for degradation through deamidation of N-terminal Gln.

199 ing residues and steric hindrance preventing deamidation of N.

200 n chaperone activity in homomers occurred on deamidation of N123 residue, but it was substantially re

201 Specifically, the study investigated whether deamidation of one or two sites in alphaA-crystallin (i.

202 al methods are available to characterize the deamidation of peptides and proteins.

203 e immunogenic to adults with celiac disease; deamidation of peptides increased these responses.

204 we show that Dop is not only involved in the deamidation of Pup, but also needed to maintain wild-typ

205 an emergency situation; however, spontaneous deamidation of purified vaccine antigens has the potenti

206 In order to explore whether spontaneous deamidation of recombinant protective antigen (rPA)--the

207 first time that, like mild oxidative stress, deamidation of some proteins makes them preferred substr

208 nly known biologically relevant function was deamidation of the anticancer drug bleomycin.

209 ed for quantitatively monitoring the in vivo deamidation of the biopharmaceutical monoclonal antibody

210 ted ELISA method for trastuzumab showed that deamidation of the drug at the CDR leads to a loss of re

211 oxidation of the same methionine residue and deamidation of the same asparagine in the corresponding

212 used as a method to predict the liability to deamidation of therapeutic antibodies in vivo.

213 Deamidation of therapeutic antibodies may result in decr

214 ein via the carboxyl-terminal glutamine with deamidation of this residue.

215 Deamidation of trastuzumab was observed in plasma both i

216 relies on methylation and demethylation (or deamidation) of specific modification sites of the chemo

217 used to perform an in-depth study of protein deamidation on a global proteome scale.

218 no structural studies of the consequences of deamidation on amyloid fibers, in large part because of

219 Predominance of deamidation on glutamine rather than asparagine in the a

220 investigated, and the biophysical effects of deamidation on SOD1 are unknown.

221 To test the effects of interface deamidation on stability and folding, single and double

222 To determine the effects of deamidation on structural and functional properties of a

223 ne, truncation alone, or both truncation and deamidation on structural and functional properties of h

224 Here we examine the effects of deamidation on the kinetics of amyloid formation by amyl

225 ains of isoAsp or Asp; in contrast, inherent deamidation only results in a molecular weight increase

226 fication arising from spontaneous asparagine deamidation or aspartate isomerization.

227 ll as faint modifications such as asparagine deamidation or aspartic acid isomerization.

228 es and signals efficiently in the absence of deamidation or methylation, methylation changes, methyla

229 in digestion method, little protocol-induced deamidation or N-terminal glutamine cyclization product

230 Undesired side reactions, such as deamidation or peptide hydrolysis, occur only at a very

231 pupylated proteins results in preferred Pup deamidation over protein depupylation by this enzyme.

232 e post-translational modifications including deamidation, oxidation, glycosylation variants, and frag

233 BCR-ABL and mutant JAK2 inhibit the Bcl-x(L) deamidation pathway and the apoptotic response to DNA da

234 ssing JAK2V617F compromises the NHE-1/Bcl-xL deamidation pathway by repressing NHE-1 upregulation in

235 r abnormalities of the proapoptotic Bcl-x(L) deamidation pathway in primary cells from patients with

236 The Bcl-x(L) deamidation pathway was inhibited in myeloid cells, but

237 domain or C-terminal extension and also with deamidation plus above N- or C-terminal deletions.

238 At neutral to basic pH, deamidation proceeds by the initial formation of a tetra

239 Although differentiation of the isomeric Asn deamidation products (Asp and isoAsp) at the peptide lev

240 efficiency with a minimal (<1%) formation of deamidation products during digestion.

241 ltaneously separate Gln and asparagine (Asn) deamidation products even for those peptides showing mul

242 rge) overestimation of the concentrations of deamidation products in the original plasma sample.

243 be used to generate diagnostic ions for the deamidation products of Asn: aspartic acid (Asp) and iso

244 1.7 gamma/alpha-glutamyl ratio for most Gln deamidation products.

245 ially on the differentiation of its isomeric deamidation products: alpha- and gamma-glutamic acid (Gl

246 ing site-directed mutagenesis to replace six deamidation-prone asparagine residues, at positions 408,

247 Here, the linkage between deamidation propensity and structural dynamics is invest

248 Due to its much slower deamidation rate compared to that of asparagine (Asn), s

249 ic deamidation) according to their predicted deamidation rate, yielding: N26D, N26D/N131D, and N26D/N

250 both located on the C(H)2 domain, while the deamidation rates of the other residues were not affecte

251 te analogous to that proposed for asparagine deamidation reactions potentially can contribute, and in

252 Our findings strongly suggest that deamidation-regulated Bcl-xL degradation is an important

253 Deamidation rendered RIG-I unable to sense viral dsRNA,

254 lational modifications such as oxidation and deamidation, residual leader sequence, and proteolytic c

255 es in proteins and peptides and help develop deamidation-resistant biological therapeutics.

256 idation from HSV-1 infection, by engineering deamidation-resistant RIG-I or introducing deamidase-def

257 uction; loss of RIG-I or inhibition of RIG-I deamidation results in elevated cytokine production.

258 Deamidation results in the replacement of asparginyl res

259 n: a stable signature peptide (FTISADTSK), a deamidation-sensitive signature peptide (IYPTNGYTR), its

260 values showed variable results based on the deamidation site.

261 ially the -1 and +1 amino acids flanking the deamidation site.

262 Peptides with deamidation sites at asparagine residues but lacking a t

263 In this study the effects of two potential deamidation sites at the monomer-monomer interface on di

264 as to determine the effects of two potential deamidation sites at the predicted interface of the beta

265 the 2 Da molecular weight difference at the deamidation sites can only be used to differentiate deam

266 Of the three deamidation sites identified in the aged beta(2)M, isoAs

267 great detail; however, the identification of deamidation sites in a given protein remains a challenge

268 Our findings should help predict deamidation sites in proteins and peptides and help deve

269 s study, we identified and characterized all deamidation sites in the conserved region of a recombina

270 e glutamine residues at the reported in vivo deamidation sites of Q180 in the C-terminal domain and a

271 IsoAsp formation at all three deamidation sites was successfully identified by this CA

272 By preparing the acid- and base-catalyzed deamidation standards in H2(18)O, isomer-specific mass t

273 Furthermore, two novel deamidation steps leading to nicotinic acid mononucleoti

274 intermediate reaction species for Na(+)(Asn) deamidation, structures that are further optimized at th

275 Here, a comprehensive top-down deamidation study is presented using the protein beta2-m

276 of at least 18 glycoforms, plus a variety of deamidation, succinimide, and oxidation products, repres

277 It thereby provides a link between gluten deamidation, T cell activation, and the production of TG

278 algorithm is used to determine the extent of deamidation that gives the best fit to the measured dist

279 b ions were used for the calculation of Asn deamidation that occurred prior to or during sample prep

280 However, deamidation that occurs during sample preparation steps

281 tion sites can only be used to differentiate deamidation that occurs prior to or during sample prepar

282 Asn(16) and Asn(45) underwent a nonenzymatic deamidation, the sequence Asn(45)-Gly(46) being deamidat

283 ll mass change of the eluting species (e.g., deamidation), this task can be completed using online to

284 idation-isomerization to iso-Asp317, but not deamidation to Asp317, resulted in altered retention tim

285 Gluten proteins can be modified by deamidation to enhance their solubility and technologica

286 Analysis of potential sites of deamidation together with structural models of amylin fi

287 w-cost, high-throughput method for assessing deamidation using matrix-assisted laser desorption/ioniz

288 nd showed little relationship to the site of deamidation using N157D and Q204E mutants.

289 Deamidation was confirmed for 28 peptides (90%).

290 For each chosen peptide, the extent of deamidation was determined by comparing the calculated t

291 Deamidation was enhanced after reduction, alkylation, an

292 In contrast, deamidation was higher in archeological textile fragment

293 Rapid in vitro deamidation was observed at higher pH, leading to a (lar

294 Variations in the levels of deamidation were observed between peptides and in modern

295 cific modifications (e.g., M-oxidation and N-deamidation) were identified and quantified.

296 d to HLA-DQ8cis and six to HLA-DQ8trans upon deamidation, whereas all other peptides bound equally to

297 LNG, and LNN were found to be more prone to deamidation, whereas the motifs GNT, TNY, YNP, WNS, SNF,

298 by TG2-reactive B cells directly to peptide deamidation, which is necessary for the activation of gl

299 patients, but not in control CSF, causes Cp deamidation with gain of integrin-binding function, sugg

300 of the deamidation, as well as the level of deamidation with glycan structure.