Abstract：
:Plant secretory (Class III) peroxidases are redox enzymes that rely on N-glycosylation for full enzyme activity and stability. Peroxidases from palm tree leaves comprise the most stable and active plant peroxidases characterized to date. Herein, site-specific glycosylation and microheterogeneity of windmill palm tree (Trachycarpus fortunei) peroxidase are reported. The workflow developed in this study includes novel tools, written in R, to aid plant glycan identification, pGlycoFilter, for annotation of glycopeptide fragmentation spectra, gPSMvalidator, and for relative quantitation of glycoforms, glycoRQ. Mass spectrometry analysis provided a detailed glycosylation profile at the 13 sites of N-linked glycosylation on windmill palm tree peroxidase. Glycan microheterogeneity was observed at each site. Site Asn211 was the most heterogeneous and contained 30 different glycans. Relative quantitation revealed 90% of each glycosylation site was occupied by three or fewer glycans, and two of the 13 sites were partially unoccupied. Although complex and hybrid glycans were identified, the majority of glycans were paucimannosidic, characteristic of plant vacuolar glycoproteins. Further studies pertaining to the glycan structure-activity relationships in plant peroxidases can benefit from the work outlined here.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Baker MR,Tabb DL,Ching T,Zimmerman LJ,Sakharov IY,Li QXdoi
10.1021/acs.jproteome.6b00205subject
Has Abstractpub_date
2016-06-03 00:00:00pages
2026-38issue
6eissn
1535-3893issn
1535-3907journal_volume
15pub_type
杂志文章abstract：:We analyzed a unique rice (Oryza sativa L.) blast lesion mimic (blm) mutant for differentially expressed proteins in leaves of one- and two-week-old seedlings manifesting the lesion mimic phenotype. Gel-based one- and two-dimensional electrophoresis (1- and 2-DGE) was performed using leaves (blm and wild-type, WT) bef...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060092c
更新日期：2006-10-01 00:00:00
abstract：:In this paper, we present a new purification procedure that yields a new crystalline form of rubisco and has enabled us to completely remove this most abundant protein from tobacco leaf extract. The crystals formed within 48 h after refrigeration at 4 degrees C at pH 5.6. However, these crystals were not well-ordered ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr025548e
更新日期：2002-09-01 00:00:00
abstract：:Approximately 25% of eukaryotic proteins possessing homology to at least two transmembrane domains are predicted to be embedded in biological membranes. Nevertheless, this group of proteins is not usually well represented in proteome-wide experiments due to their refractory nature. Here we present a quantitative mass ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200759m
更新日期：2012-02-03 00:00:00
abstract：:Protein or peptide sample losses could accompany all steps of the proteomic analysis workflow. We focused on suppression of sample adsorptive losses during sample storage in autosampler vials. We examined suppression capabilities of six different sample injection solutions and seven types of autosampler vial surfaces ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400183v
更新日期：2013-06-07 00:00:00
abstract：:The missing human proteome comprises predicted protein-coding genes with no credible protein level evidence detected so far and constitutes ~18% of the human protein coding genes (neXtProt release 19/9/2014). The missing proteins may be of pharmacological interest as many of these are membrane receptors, thus requirin...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00728
更新日期：2015-12-04 00:00:00
abstract：:Quorum sensing (QS) in Xanthomonas oryzae pv. oryzicola (Xoc), the causal agent of bacterial leaf streak, is mediated by the diffusible signal factor (DSF). DSF-mediating QS has been shown to control virulence and a set of virulence-related functions; however, the expression profiles and functions of extracellular pro...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4001543
更新日期：2013-07-05 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr025538d
更新日期：2002-11-01 00:00:00
abstract：:Roux-en-Y gastric bypass (RYGB) is one of the most effective treatments for long-term weight loss and diabetes remission; however, the mechanisms underlying these changes are not clearly understood. In this study, the serum metabolic profiles of 23 remission and 12 nonremission patients with type 2 diabetes mellitus (...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00022
更新日期：2016-04-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00778
更新日期：2021-01-01 00:00:00
abstract：:Aspergillus fumigatus is a ubiquitously distributed filamentous fungus that has emerged as one of the most serious life-threatening pathogens in immunocompromised patients. The mechanisms for its pathogenicity are poorly understood. Here, we analyzed the proteome of dormant A. fumigatus conidia as the fungal entity ha...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr9010684
更新日期：2010-07-02 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr1000994
更新日期：2010-08-06 00:00:00
abstract：:We assessed proteomic patterns in breast cancer using MALDI MS and laser capture microdissected cells. Protein and peptide expression in invasive mammary carcinoma versus normal mammary epithelium and estrogen-receptor positive versus estrogen-receptor negative tumors were compared. Biomarker candidates were identifie...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr7008109
更新日期：2008-04-01 00:00:00
abstract：:In this work, we developed a general perturbation theory and machine learning method for data mining of proteomes to discover new B-cell epitopes useful for vaccine design. The method predicts the epitope activity εq(cqj) of one query peptide (q-peptide) under a set of experimental query conditions (cqj). The method u...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00477
更新日期：2017-11-03 00:00:00
abstract：:Herein, we report on the venom proteome of Vipera anatolica senliki, a recently discovered and hitherto unexplored subspecies of the critically endangered Anatolian meadow viper endemic to the Antalya Province of Turkey. Integrative venomics, including venom gland transcriptomics as well as complementary bottom-up and...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00869
更新日期：2020-04-03 00:00:00
abstract：:Plasma biomarkers of exposure to environmental contaminants play an important role in early detection of disease. The emerging field of proteomics presents an attractive opportunity for candidate biomarker discovery, as it simultaneously measures and analyzes a large number of proteins. This article presents a case st...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070491n
更新日期：2008-01-01 00:00:00
abstract：:The Biology/Disease-driven (B/D) working groups of the Human Proteome Project are alliances of research groups aimed at developing or improving proteomic tools to support specific biological or disease-related research areas. Here, we describe the activities and progress to date of the B/D working group focused on pro...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/acs.jproteome.8b00401
更新日期：2018-12-07 00:00:00
abstract：:As spectral library searching has received increasing attention for peptide identification, constructing good decoy spectra from the target spectra is the key to correctly estimating the false discovery rate in searching against the concatenated target-decoy spectral library. Several methods have been proposed to cons...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr301039b
更新日期：2013-05-03 00:00:00
abstract：:Advancements in studies on the evolutionary mechanisms underlying bacterial antibiotic resistance are unclear. This study aimed to investigate the evolutionary mechanism underlying bacterial antibiotic resistance using isobaric tags for relative and absolute quantitation-based quantitative proteomics along with functi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00410
更新日期：2019-11-01 00:00:00
abstract：:Cannabinoid 2 receptor (CB2R), a Class-A G-protein coupled receptor (GPCR), is a promising drug target under a wide array of pathological conditions. Rational drug design has been hindered due to our poor understanding of the structural features involved in ligand binding. Binding of a high-affinity biarylpyrazole inv...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00023
更新日期：2017-07-07 00:00:00
abstract：:Renal cell carcinoma (RCC) tissue is composed of a mixture of neoplastic and normal cells, which complicate proteome analysis. The aim of our study was to investigate whether it is feasible to establish primary cell cultures of RCC and of renal cortex maintaining the tissue phenotype along with a more homogeneous and ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050002o
更新日期：2005-09-01 00:00:00
abstract：:Monoassociation of germfree Interleukin 10 gene deficient (IL-10-/-) 129SvEv but not wild-type mice with Enterococcus faecalis induces severe chronic colitis. Bacterial strain-specific effects on the development of chronic intestinal inflammation are not understood. We investigated the molecular mechanisms of E. faeca...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800785m
更新日期：2009-03-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00383
更新日期：2017-01-06 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00141
更新日期：2018-07-06 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800332p
更新日期：2008-08-01 00:00:00
abstract：:An online nonenzymatic digestion method utilizing a microwave-heated flow cell and mild acid hydrolysis at aspartic acid (D) for rapid protein identification is described. This methodology, here termed microwave D-cleavage, was tested with proteins ranging in size from 5 kDa (insulin) to 67 kDa (bovine serum albumin) ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr700596e
更新日期：2008-03-01 00:00:00
abstract：:Hydrogen peroxide (H(2)O(2)) and nitric oxide ((•)NO) elicit numerous processes in plants. However, our knowledge of H(2)O(2) and (•)NO-responsive proteins is limited. The present study aimed to identify proteins whose accumulation levels were regulated by these signaling molecules in citrus leaves. To address this qu...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100782h
更新日期：2010-11-05 00:00:00
abstract：:The chromatophore membrane of the photosynthetic diazotroph Rhodospirillum rubrum is of vital importance for a number of central processes, including nitrogen fixation. Using a novel amphiphile, we have identified protein complexes present under different nitrogen availability conditions by the use of two-dimensional ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100838x
更新日期：2011-06-03 00:00:00
abstract：:Dehydroeffusol (DHE) is a phenanthrene isolated from the Chinese medicinal plant Juncus effusus. Biological evaluation of DHE reveals in vitro and in vivo anticancer effects. We performed a shotgun proteomic analysis using liquid chromatography-tandem mass spectrometry to investigate the changes in the protein profile...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00227
更新日期：2018-07-06 00:00:00
abstract：:Clinical trials have been conducted for the neuronal ceroid lipofuscinoses (NCLs), a group of neurodegenerative lysosomal diseases that primarily affect children. Whereas clinical rating systems will evaluate long-term efficacy, biomarkers to measure short-term response to treatment would be extremely valuable. To ide...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00460
更新日期：2017-10-06 00:00:00
abstract：:The localization of proteins at a tissue- or cell-type-specific level is tightly linked to the protein function. To better understand each protein's role in cellular systems, spatial information constitutes an important complement to quantitative data. The standard methods for determining the spatial distribution of p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00486
更新日期：2020-12-04 00:00:00
