ライフサイエンスコーパス: PTM

1 PTM catalyzing enzymes have become significant drug targ

2 PTM-centric network analyses combine PhosphoSitePlus, iP

3 PTMs are well documented to influence protein activity,

4 PTMs can control the function of transcription factors a

5 PTMs involve the covalent attachment of functional group

6 imultaneous analysis by mass cytometry of 28 PTMs in >1 million single cells derived from small intes

7 resolution quantitative proteomics map of 95 PTMs on multiple isoforms of Tau isolated from postmorte

8 d is well suited to reveal the presence of a PTM and its impact in the molecular environment.

9 mited amounts of purified EVs, low-abundance PTM proteins, and interference from proteins and metabol

10 achieve sensitive analyses of low-abundance PTMs in EVs isolated from 1 mL of plasma.

11 information in terms of mutations affecting PTMs, secondary structure features and per-residue solve

12 Although PTM MAIT cells generally resemble the phenotype and tran

13 red using size-exclusion chromatography, and PTM levels were calculated using peptide mapping.

14 file, computational structural features and PTM sites' data.

15 oviding important insight into mutations and PTM sites interaction mechanisms.

16 atform for simultaneous global proteomic and PTM analysis of biospecimens.

17 n analytical tool to measure degradation and PTMs in-line with therapeutic production.

18 Although some effectors and PTMs have clear pro- or antiviral functions, PTMs genera

19 However, assessing protein folding and PTMs is difficult because routine polyacrylamide gel ele

20 ical protein-small-molecule interactions and PTMs in native biological environments.

21 ear envelope, and specifically to levels and PTMs of Sad1/UNC-84 (SUN) domain-containing protein 2 (S

22 gamma-CH(2)) linkage of natural residues and PTMs, whereas in situ potentiation of pyridylsulfonyl de

23 for mapping both the amino acid sequence and PTMs; one of these techniques is matrix-assisted laser d

24 By comparing the structures and PTMs of tau filaments from CBD and Alzheimer's disease,

25 r to perform a function, which is defined as PTM cross-talk.

26 bril with and without the disease-associated PTM, L-isoaspartate, at position 23 (L-isoAsp23).

27 By comparing with background PTM pairs from the same protein pairs, we found that int

28 se a challenge for this targeted MS/MS-based PTM quantitation.

29 ic approaches to unveil interactions between PTMs and associated reader protein complexes of Plasmodi

30 ture-based model in which cross-talk between PTMs influences tau filament structure, contributing to

31 rs have higher sequence co-evolution at both PTM residue and motif levels.

32 Distinct residues of Cyt c are modified by PTMs, primarily phosphorylations, in a highly tissue-spe

33 as important molecules that are targeted by PTMs during infections of mammalian cells by bacterial p

34 We examine the role of Cyt c PTMs, including phosphorylation, acetylation, methylatio

35 Integrating single-cell PTM analysis with thiol-reactive organoid barcoding in s

36 tone code, this complex pattern of chaperone PTMs is now known as the "chaperone code." In this revie

37 e derived precursors into the characteristic PTM and PTN scaffolds.

38 n proteomic methods that better characterize PTMs.

39 at 100 Da, it is one of the larger chemical PTMs) and in its ability to modify the net charge of the

40 meric proteoforms arising from combinatorial PTMs, alternative splicing, and genetic variation in HCM

41 e ubiquitination in DNA methylation control, PTM crosstalk, nucleosome structure, and phase separatio

42 One critical PTM is acetylation/deacetylation, which is being investi

43 w design principles for rationally designing PTM systems for a variety of behaviour, (3) a basis and

44 n a comprehensive manner, including detailed PTM annotation on the 3D structure and biological inform

45 igestion-RPLC/MS) was developed to determine PTM levels including oxidation, deamidation, and succini

46 roteoforms, including isomers with different PTM positions.

47 evidence highlighting the role of different PTMs in this process.

48 ad-scale assays to monitor several different PTMs with a single detection platform.

49 Third, different PTMs on the same protein or on different proteins in the

50 phy to fractionate proteoforms with distinct PTM sets, differential or field asymmetric waveform IMS

51 (MS) but, since raising antibodies for each PTM in a study can be prohibitive, lots of potential is

52 -1 antibodies with the potential to engineer PTMs.

53 Finally, PTMs form a multidimensional regulatory system that prov

54 Using a fluid PTM, as Nujol or high-viscosity silicone oil, results in

55 re developments of computational methods for PTM site prediction, expedite the discovery of new malon

56 ergy transfer (TR-FRET) detection method for PTMs of cysteine residues using a single-peptide approac

57 Fourth, PTMs take part in the repair of stress-induced damage (e

58 nalysis is often carried out separately from PTM analysis.

59 PTMs have clear pro- or antiviral functions, PTMs generally play regulatory roles to tune protein fun

60 us quantitation of quality attributes (e.g., PTMs) for multiple samples in a single LC-MS run.

61 Age, type and severity of glaucoma, PTM, or total energy delivery had no association with pr

62 ns with polyanionic cofactors, and highlight PTMs as a major force driving the prion disease phenotyp

63 s are associated with the activating histone PTM H3K4me3.

64 position of the classical inhibitory histone PTM H3K9me3 on HBV-DNA in around half of the patient bio

65 ssociated with enrichment for cccDNA histone PTMs related to repressed transcription.

66 In this review, we discuss novel histone PTMs identified within the past 10 years, with an extend

67 hermore, we consider how these novel histone PTMs might fit within the framework of a so-called 'hist

68 Identification and quantification of histone PTMs has become routine in mass spectrometry (MS) but, s

69 , our work shows that the profile of histone PTMs in chronic infection is more nuanced than previousl

70 specimens to investigate the role of histone PTMs in chronically HBV-infected patients.

71 vely less is known about the role of histone PTMs in the cellular adaptive response to stress.

72 Over the past decade alone, several histone PTMs have been discovered, including acylation, lipidati

73 precipitation of presumed off-target histone PTMs after inhibitor treatment, a trend predicted by the

74 In this review, we discuss how PTMs, including phosphorylation, S-acylation, and ubiqui

75 We particularly highlight how PTMs control the phase separation and aggregation behavi

76 Thus, our findings provide insight into how PTMs and pH regulate PKM2 and offer a broader understand

77 These studies provide insight into how PTMs impact PrP interactions with polyanionic cofactors,

78 oncepts common to all viruses, reviewing how PTMs facilitate and thwart each step of the replication

79 regate in neurodegenerative disease, yet how PTMs impact the aggregate conformation and disease progr

80 Identifying PTMs in large-scale datasets is a problem with distinct

81 has demonstrated competitive performance in PTM site predictions by other researchers.

82 s from naive and SIV- or simian HIV-infected PTM.

83 ions, and the challenge ahead of integrating PTMs into an understanding of protein function in plants

84 protocol takes 2 d, including EV isolation, PTM/peptide enrichment, mass spectrometry analysis, and

85 op- or middle-down level to preserve the key PTM connectivity, which condensed-phase separations fail

86 predicted PTM sites in the context of known PTM annotations and protein 3D structures through homolo

87 Database searching of isotopically labelled PTMs can be problematic and we frequently find that only

88 ss shift (difference between heavy and light PTM) between two MS/MS spectra.

89 analysis revealed that a wild-type CFTR-like PTM pattern and function was restored in DeltaF508 CFTR

90 We have utilized a natural lipidation PTM (hedgehog-mediated cholesterol modification of prote

91 a number of computational methods for lysine PTM identification have been developed.

92 of 49 state-of-the-art approaches for lysine PTM prediction.

93 We generated a pigtail macaque (PTM)-specific MR1 tetramer and characterized MAIT cells

94 PTMs' extremely important roles, many major PTMs have been studied, while the functional and mechani

95 nal and mechanical characterization of major PTMs is well documented in several databases.

96 Many PTM sites from the same (intra) or different (inter) pro

97 Although many PTM-Abetas were shown to accelerate the fibrillation pro

98 nal modifications (PTMs), enabling us to map PTMs directly onto the structures.

99 rt a MC package Particle Transport in Media (PTM) to demonstrate the implementation of coupled photon

100 py with several pressure transmitting media (PTM).

101 ma, pigmentation of the trabecular meshwork (PTM), total energy delivered, and baseline intraocular p

102 Indeed, from the large variety of model PTM containing amino acids and peptides which have been

103 *))-mediated posttranslational modification (PTM) of cysteine thiols (SNO), modulates the activity of

104 tion of this posttranslational modification (PTM) or mimics thereof into evasins may provide a strate

105 ess-induced, posttranslational modification (PTM) protein S-nitrosylation on viral proteins to determ

106 n-containing posttranslational modification (PTM) reader that recognizes acetylated H4.

107 is a common posttranslational modification (PTM) throughout the human proteome that plays important

108 fundamental posttranslational modification (PTM).

109 s reversible post-transitional modification (PTM) involves the attachment of a fatty acyl chain, usua

110 nt and common post-translation modification (PTM) that occurs on lysine residues.

111 ealing with post-translational modification (PTM) analysis like reversible cysteine oxidation are eva

112 ed how CTCF post-translational modification (PTM) could contribute to function.

113 an abundant post-translational modification (PTM) in prokaryotes, regulates various microbial metabol

114 is the only post translational modification (PTM) of the eight possible methylation states of Lys and

115 pe-specific post-translational modification (PTM) signaling networks in organoids are absent.

116 for protein post-translational modification (PTM) site prediction and visualization.

117 for protein post-translational modification (PTM) site prediction provide a useful approach for study

118 e, and some post-translational modification (PTM) sites appear to be associated with both enhanced se

119 (O-GlcNAc) post-translational modification (PTM) sites in proteins by mass spectrometry (MS) remains

120 soforms and post-translational modification (PTM) stoichiometry in Alzheimer's disease (AD), we gener

121 Post-translational modification (PTM) such as phosphorylation did not prevent the generat

122 tability in post-translational modification (PTM) systems.

123 reversible post-translational modification (PTM) which regulates the function of several non-histone

124 me-mediated post-translational modification (PTM), is important for mRNA processing and transport and

125 discovered post-translational modification (PTM), lysine malonylation (Kmal) regulates a myriad of c

126 but crucial post-translational modification (PTM), namely O-sulfated tyrosine in the heavy chain comp

127 rmation and post-translational modification (PTM).

128 s a form of Post-Translational Modification (PTM): addition of a ubiquitin to the chain is catalyzed

129 and histone posttranslational modifications (PTM) are central to the biology of several cancers.

130 bNAbs with posttranslational modifications (PTM).

131 etworks of post-translational modifications (PTM) are ubiquitous in cell signalling.

132 one of the post-translational modifications (PTM) where sugar molecules and residues in protein seque

133 lization of posttranslational modifications (PTMs) affecting single amino acids and peptides.

134 Posttranslational modifications (PTMs) and alternative splicing regulate the function of

135 of histone posttranslational modifications (PTMs) and chromatin-associated factors across genomes.

136 Posttranslational modifications (PTMs) are common among proteins that aggregate in neurod

137 Posttranslational modifications (PTMs) are important physiological means to regulate the

138 roteins and posttranslational modifications (PTMs) in bovine seminal plasma.

139 be through posttranslational modifications (PTMs) of axonal microtubules.

140 subject to posttranslational modifications (PTMs) that regulate cellular functions such that PTM dys

141 orated with posttranslational modifications (PTMs), enabling us to map PTMs directly onto the structu

142 to tubulin posttranslational modifications (PTMs).

143 ted posttranslational protein modifications (PTMs) in mitochondrial metabolic regulation.

144 ne tails post-transcriptional modifications (PTMs) by micro-chromatin immunoprecipitation.

145 Post-translational modifications (PTMs) afford both the virus and the host means to readil

146 l-specific post-translational modifications (PTMs) and cooperative cofactors.

147 to detect Post-Translational Modifications (PTMs) and degradation seen in mAbs.

148 itoring of post-translational modifications (PTMs) are key analytical requirements during the develop

149 ication of post-translational modifications (PTMs) are key elements in protein structural analysis.

150 Post-translational modifications (PTMs) are key events in signal transduction since they a

151 Post-translational modifications (PTMs) are one of the most important regulatory mechanism

152 Histone post-translational modifications (PTMs) contribute to chromatin accessibility due to their

153 Peptidyl post-translational modifications (PTMs) could influence the final quality of processed mea

154 how these post-translational modifications (PTMs) disrupt the oligomeric state of PKM2.

155 avage, two post-translational modifications (PTMs) essential for RG fiber maintenance and the switch

156 Post-translational modifications (PTMs) greatly expand the structures and functions of pro

157 of histone post-translational modifications (PTMs) have been associated with transcriptional activati

158 Histone post-translational modifications (PTMs) have emerged as exciting mechanisms of biological

159 itoring of post-translational modifications (PTMs) in therapeutic monoclonal antibodies (mAbs) is ess

160 ulation by post-translational modifications (PTMs) is not binary, making methods to quantify the modi

161 , the main post-translational modifications (PTMs) of etanercept were assessed, and a global overview

162 ss induced post-translational modifications (PTMs) of Hb and red blood cell (RBC) membrane proteins o

163 mimic key post-translational modifications (PTMs) of proteins and can be used to understand the role

164 acterizing post-translational modifications (PTMs) of therapeutic monoclonal antibodies (mAbs).

165 t array of post-translational modifications (PTMs) on Hsp70 family proteins that include phosphorylat

166 Lysine post-translational modifications (PTMs) play a crucial role in regulating diverse function

167 Post-translational modifications (PTMs) play very important roles in various cell signalin

168 sequential post-translational modifications (PTMs) regulate SPRTN chromatin accessibility to repair D

169 ts such as post-translational modifications (PTMs) represent a powerful class of tools for interrogat

170 of protein post-translational modifications (PTMs) such as phosphorylation and glycosylation can be a

171 numbers of post-translational modifications (PTMs) that are being identified, developing effective me

172 a range of post-translational modifications (PTMs) that are implicated as triggers of disease patholo

173 ystems use post-translational modifications (PTMs) to control the structure, location, and function o

174 he correct post-translational modifications (PTMs) to exhibit appropriate biological activity.

175 bjected to post-translational modifications (PTMs) which control its activity.

176 y multiple post-translational modifications (PTMs), and we observe both known and new sites of modifi

177 ensity and post-translational modifications (PTMs), elevated NOX2 expression, altered Ca(2+) release

178 al protein post-translational modifications (PTMs), it has historically been biased towards just a fe

179 including post-translational modifications (PTMs), protein-protein interaction, or by the global env

180 impact of post-translational modifications (PTMs), stoichiometry, and conformational changes induced

181 influence post-translational modifications (PTMs), which play central roles in the activation of tra

182 oteins and post-translational modifications (PTMs).

183 overned by post-translational modifications (PTMs).

184 nd protein post-translational modifications (PTMs).

185 or protein post-translational modifications (PTMs).

186 to detect post-translational modifications (PTMs).

187 forms, and post-translational modifications (PTMs).

188 body (mAb) post-translational modifications (PTMs).

189 of histone post-translational modifications (PTMs).

190 tes (e.g., post-translational modifications [PTMs]) of monoclonal antibodies (mAbs) during drug devel

191 tides and N-glycopeptides, enabling multiple PTM analyses of the same clinical samples.

192 ng prediction and visualization for multiple PTMs simultaneously for users to analyze potential PTM c

193 Here, we uncover O-glycosylation as a novel PTM present on mouse OCN and occurring on a single serin

194 iochemical networks, the general behavior of PTM cycles subject to synthesis and degradation has not

195 he information processing characteristics of PTM systems are a focal point of broad interest.

196 he stability of fibrils, the contribution of PTM-Abetas to structural polymorphisms and their patholo

197 er-residue solvent accessibility features of PTM sites, domain context, predicted natively disordered

198 lls during HIV infection; and 2) the lack of PTM MAIT cell enrichment at the gut mucosa may prevent d

199 occur on PTMs and in the close proximity of PTM sites with functional impact.

200 ated high sensitivity and reproducibility of PTM quantitation with levels as low as 1.0%.

201 xity of compartmentation in understanding of PTM function.

202 Finally, we consider the combined action of PTMs on the same proteins, their interactions, and the c

203 However, the analysis of PTMs in EVs has been complicated by limited amounts of p

204 the comprehensive and combinatorial array of PTMs that modulate Hsp90 chaperone function, a phenomeno

205 However, characterization of PTMs using a conventional peptide mapping procedure requ

206 By enabling broad characterization of PTMs, TagGraph informs as to how their functions and reg

207 specific focus on 3D structural contexts of PTMs sites and mutations that occur on PTMs and in the c

208 Here, we review the contributions of PTMs, such as phosphorylation, acetylation, SUMOylation,

209 We also review how disruptions of PTMs might be involved in aberrant phase transitions and

210 We consider the spatial distribution of PTMs, the subcellular distribution of modifying enzymes,

211 plex regulatory schemes where the effects of PTMs are time and context dependent as the virus and hos

212 r understanding of the regulatory effects of PTMs on zDHHC enzymes will provide new insight into the

213 enzymes and speculate on possible effects of PTMs that have emerged from larger screening studies.

214 verse organisms and allows identification of PTMs without the need for modification-specific enrichme

215 ield that have underscored the importance of PTMs in the functional regulation of these receptors.

216 unctionalization strategies allow mimicry of PTMs(3,4), as well as formation of unnatural protein var

217 to perform a fast and reliable monitoring of PTMs during the manufacturing process for both bioreacto

218 l-free approach for relative quantitation of PTMs requires a great amount of instrument time for LC-M

219 ee 3D structure database for a wide range of PTMs.

220 erstanding of the function and regulation of PTMs.

221 quence-structural-functional relationship of PTMs and providing important insight into mutations and

222 extent crucial to understanding the role of PTMs.

223 The processive addition and minimal set of PTMs associated with seeding activity was further define

224 re tool for discovering motifs among sets of PTMs that we make available as a web server and as downl

225 y IRMPD spectroscopy, specific signatures of PTMs such as phosphorylation or sulfonation can be deriv

226 n sequences, while the real 3D structures of PTMs have been largely ignored.

227 Therefore, studies of PTMs 3D structural signatures have been severely limited

228 l heterogeneity across subjects, a subset of PTMs display high occupancy and frequency for AD, sugges

229 ies (NCEs) from 35 to 90, different types of PTMs were quantified with percentages comparable to thos

230 ling proteins that undergo multiple types of PTMs.

231 entries pertaining to 37 different types of PTMs.

232 utation would generate downstream effects on PTM of critical proteins that lead to modification of sy

233 antitative proteomics data, with emphasis on PTM networks and integration with the LINCS library of c

234 indings suggest that many classic results on PTM cycles may not hold in vivo where protein turnover i

235 s we were able to separate proteins based on PTMs and degradation.

236 ts of PTMs sites and mutations that occur on PTMs and in the close proximity of PTM sites with functi

237 alysis of sequence coverage, charge state or PTMs.

238 ecluding determinations of folding states or PTMs.

239 the discovery of new malonylation and other PTM types and facilitate hypothesis-driven experimental

240 tional analysis of total proteomes and other PTMs of interest.

241 carboxylation and endoproteolysis, two other PTMs regulating this hormone.

242 HU treatment reversed these oxidative PTMs back to level observed in controls.

243 d proteomics to characterize these oxidative PTMs on a cross-sectional group of these patients (n = 4

244 lipid and protein oxidation, major peptidyl PTMs and the release of free amino acids (FAAs).

245 ee minutes to predict for 1000 sequences per PTM type.

246 a radical-carrying perchlorotriphenylmethyl (PTM) acceptor.

247 even in the presence of the more permissive PTM H3K36me2.

248 imultaneously for users to analyze potential PTM cross-talks directly.

249 s protein S-nitrosylated, we found this pp71 PTM diminishes its ability to undermine antiviral respon

250 users can interactively review the predicted PTM sites in the context of known PTM annotations and pr

251 ins a local database providing pre-processed PTM annotations from Uniport/Swiss-Prot for users to dow

252 We proposed a CapsNet for predicting protein PTM sites, including phosphorylation, N-linked glycosyla

253 y, comprehensive characterization of protein PTMs in EVs can be particularly valuable for early-stage

254 Many reported PTMs of Hsp90 alter chaperone function and consequently

255 eter and Koshland discovered that reversible PTM cycles function like on-off switches when the substr

256 Since they tend to be generally reversible, PTMs serve as regulators of signal transduction pathways

257 In particular, the rich PTM complement in histones controls the gene expression

258 t the amino acid level for the user-selected PTM types.

259 to describe the steady-states of a two-site PTM system as the solutions of two polynomial equations

260 s spectrometry for multiplexed site-specific PTM quantitation of monoclonal antibodies to overcome th

261 Cell-type-specific PTM analysis of colorectal cancer organoid cocultures re

262 While site-specific PTMs act very locally on the protein, specific protein i

263 e could correlate spectral peaks to specific PTMs.

264 proteins with a linear correlation suggests PTM cross-talk in the sarcomere and dysregulation of pro

265 nonradiative decay rates in the case of TAA-PTM radicals that have high CT energies are defined by t

266 p law dependence that is observed in the TAA-PTM radicals that have low CT energies.

267 airs, we found that inter-protein cross-talk PTM pairs have higher sequence co-evolution at both PTM

268 nockdown of enzymes upstream of their target PTM sites.

269 Although Tau PTM maps reveal heterogeneity across subjects, a subset

270 We previously established that PTM and PTN are produced by a single biosynthetic machin

271 ) that regulate cellular functions such that PTM dysregulation can lead to disease, including cancer.

272 Unsupervised analyses indicate that PTMs occur in an ordered manner, leading to Tau aggregat

273 The PTM quantitative performance of this approach demonstrat

274 d phosphopeptides and glycopeptides from the PTM enrichment.

275 However, the PTM mimetics exist as a mixture of tetramer and dimer, i

276 CT state with local excitations (LE) on the PTM moiety; also, these nonradiative rates deviate signi

277 s approach has been utilized to quantify the PTMs for forced degradation samples, comparability sampl

278 We find that the PTMs elicit major structural reorganization of the fruct

279 study the dynamics of microtubule and their PTM processes in living cells.

280 ures of polymorphic fibrils, including their PTMs, and neurodegenerative disease.

281 These PTMs were also confirmed using orthogonal immunoprecipit

282 We discuss how these PTMs regulate the phase behavior of prototypical RBPs an

283 can be used to understand the role of these PTMs in cellular processes.

284 asizing the physiological relevance of these PTMs in metabolism, development, and disease states.

285 However, the biological relevance of these PTMs is not fully understood because their regulation is

286 the functional importance of a few of these PTMs.

287 This PTM regulates various key biological and pathological pr

288 Thus, PTMs may exert conformational control over small GTPases

289 Due to PTMs' extremely important roles, many major PTMs have be

290 biological functions of the cellular tubulin PTM "code."

291 Tubulin PTMs are known to affect microtubule stability, dynamics

292 s no tool that can specifically mark tubulin PTMs in living cells, thus severely limiting our underst

293 Ubiquitin and ubiquitin-like (UBL) PTMs on histone proteins can function as signaling molec

294 s lost from MS datasets when uncharacterized PTMs are found to be significantly regulated.

295 terminal tyrosine of alpha-tubulin, a unique PTM site.

296 ages (LC and HC >97%), thus allowing various PTMs including oxidation, deamidation, and isomerization

297 oscopy of mass-selected ions holding various PTMs is an increasingly expanding field both in the vari

298 set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values.

299 d mapping between peptides and proteins with PTM sites; (ii) high resolution and interactive visualiz

300 compared to those using the peptides without PTM depletion.