Abstract：
:Research in the recent decade has demonstrated the usefulness of protein network knowledge in furthering the study of molecular evolution of proteins, understanding the robustness of cells to perturbation, and annotating new protein functions. In this study, we aimed to provide a general clustering approach to visualize the sequence-structure-function relationship of protein networks, and investigate possible causes for inconsistency in the protein classifications based on sequences, structures, and functions. Such visualization of protein networks could facilitate our understanding of the overall relationship among proteins and help researchers comprehend various protein databases. As a demonstration, we clustered 1437 enzymes by their sequences and structures using the minimum span clustering (MSC) method. The general structure of this protein network was delineated at two clustering resolutions, and the second level MSC clustering was found to be highly similar to existing enzyme classifications. The clustering of these enzymes based on sequence, structure, and function information is consistent with each other. For proteases, the Jaccard's similarity coefficient is 0.86 between sequence and function classifications, 0.82 between sequence and structure classifications, and 0.78 between structure and function classifications. From our clustering results, we discussed possible examples of divergent evolution and convergent evolution of enzymes. Our clustering approach provides a panoramic view of the sequence-structure-function network of proteins, helps visualize the relation between related proteins intuitively, and is useful in predicting the structure and function of newly determined protein sequences.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Mai TL,Hu GM,Chen CMdoi
10.1021/acs.jproteome.5b01031subject
Has Abstractpub_date
2016-07-01 00:00:00pages
2123-31issue
7eissn
1535-3893issn
1535-3907journal_volume
15pub_type
杂志文章abstract：:Protection against injurious external insults and loss of vital fluids is essential for life and is in all organisms, from bacteria to plants and humans, provided by some form of barrier. Members of the small proline-rich (SPRR) protein family are major components of the cornified cell envelope (CE), a structure respo...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300310b
更新日期：2012-06-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300006j
更新日期：2012-06-01 00:00:00
abstract：:A novel linear ion trap (LIT) mass spectrometer with dual matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) ionization sources has been built in the MALDI-LIT-ESI configuration. The design features two independent ion source/ion optical channels connected to opposite ends of a singl...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060514i
更新日期：2007-02-01 00:00:00
abstract：:Severe acute pancreatitis (SAP) is caused by complicated biological factors, and revealing its complex pathogenesis by single-target analysis is difficult. Systematic studies have developed slowly because extraction of degradable pancreatic proteins exposed to multiple proteases is challenging. We present integrated w...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00229
更新日期：2020-06-05 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101158p
更新日期：2011-01-07 00:00:00
abstract：:The development of systematic proteomic quantification techniques in systems biology research has enabled one to perform an in-depth analysis of cellular systems. We have developed a systematic proteomic approach that encompasses the spectrum from global to targeted analysis on a single platform. We have applied this ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00445
更新日期：2017-09-01 00:00:00
abstract：:Depletion of DNA replication initiation factors such as CDC7 kinase triggers the origin activation checkpoint in healthy cells and leads to a protective cell cycle arrest at the G1 phase of the mitotic cell division cycle. This protective mechanism is thought to be defective in cancer cells. To investigate how this ch...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr3010919
更新日期：2013-03-01 00:00:00
abstract：:In an attempt to find out the association of metabolic dysregulation with poor endometrial receptivity and pregnancy loss, serum metabonomic profiling of women with idiopathic recurrent spontaneous miscarriage (IRSM) is carried out and compared with fertile controls. (1)H nuclear magnetic resonance (NMR)-based metabon...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500379n
更新日期：2014-06-06 00:00:00
abstract：:A challenge in proteomics is that many observations are missing with the probability of missingness increasing as abundance decreases. Adjusting for this informative missingness is required to assess accurately which proteins are differentially abundant. We propose an empirical Bayesian random censoring threshold (EBR...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500171u
更新日期：2014-09-05 00:00:00
abstract：:The purpose of this discovery phase study was to identify candidate protein biomarkers for high-grade dysplastic cervical cells using mass spectrometry. Laser Capture Microdissection (LCM) was utilized to isolate high-grade dysplastic and normal cells from ThinPrep slides prepared from cervical cytological specimens. ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070319j
更新日期：2007-11-01 00:00:00
abstract：:Since 2012, missing proteins (MPs) investigation has been one of the critical missions of Chromosome-Centric Human Proteome Project (C-HPP) through various biochemical strategies. On the basis of our previous testis MPs study, faster scanning and higher resolution mass-spectrometry-based proteomics might be conducive ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00390
更新日期：2016-11-04 00:00:00
abstract：:Mass spectrometry is being used to identify protein biomarkers that can facilitate development of drug treatment. Mass spectrometry-based labeling proteomic experiments result in complex proteomic data that is hierarchical in nature often with small sample size studies. The generalized linear model (GLM) is the most p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b01050
更新日期：2017-09-01 00:00:00
abstract：:In this paper, we describe a method for analyzing large-volume protein samples using capillary electrophoresis in conjunction with laser-induced fluorescence detection (CE-LIF). To improve the stacking and separation efficiencies of proteins, we added either 0.01% sodium dodecyl sulfate (SDS) or 0.01% poly(ethylene ox...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050298y
更新日期：2006-02-01 00:00:00
abstract：:Cytological examination of cells from bronchoalveolar lavage (BAL) is commonly used for the diagnosis of lung cancer. Proteins released from lung cancer cells into BAL may serve as biomarkers for cancer detection. In this study, N-glycoproteins in eight cases of BAL fluid, as well as eight lung adenocarcinoma tissues ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400274w
更新日期：2013-08-02 00:00:00
abstract：:Cooperia oncophora is one of the most common intestinal parasitic nematodes in cattle worldwide. To date, C. oncophora infections are treated using broad-spectrum anthelmintics. However, during the past decade, reports of anthelmintic resistance in this parasite species have emerged worldwide, necessitating new avenue...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400114y
更新日期：2013-09-06 00:00:00
abstract：:Histones are subjected to extensive post-translational modifications (PTMs) that are known to play key roles in many biological processes. In this study, we report a fast, efficient, highly reproducible, and easily automated method involving ultra-high performance liquid chromatography (UHPLC) coupled to a high resolu...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100497a
更新日期：2010-10-01 00:00:00
abstract：:New mass-tagging reagents for quantitative proteomics measurements have been designed using solid phase peptide synthesis technology. The solid phase mass tags have been used to accurately measure the relative amounts of cysteine-containing peptides in model peptide mixtures as well as in mixtures of tryptic digests i...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr034081k
更新日期：2004-01-01 00:00:00
abstract：:The enormous challenges of mass spectrometry-based metaproteomics are primarily related to the analysis and interpretation of the acquired data. This includes reliable identification of mass spectra and the meaningful integration of taxonomic and functional meta-information from samples containing hundreds of unknown ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr501246w
更新日期：2015-03-06 00:00:00
abstract：:We recently developed a novel method for analysis of collagen O-glycosylations, which include galactosyl-hydroxylysine (GHL) and glucosyl-galactosyl-hydroxylysine (GGHL), using hydrazide chemistry (Taga, Y., Mol. Cell. Proteomics 2012, 11 (6), M111.010397). Here we investigated an overglycosylation model of collagen p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400079d
更新日期：2013-05-03 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300280t
更新日期：2012-06-01 00:00:00
abstract：:The Chromosome-Centric Human Proteome Project (C-HPP) aims to identify "missing" proteins in the neXtProt knowledgebase. We present an in-depth proteomics analysis of the human sperm proteome to identify testis-enriched missing proteins. Using protein extraction procedures and LC-MS/MS analysis, we detected 235 protei...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00400
更新日期：2016-11-04 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050137u
更新日期：2005-11-01 00:00:00
abstract：:Fulminant type 1 diabetes (FT1DM) is a relatively new clinical entity featured by acute destruction of pancreatic beta cells. Clinical consequences of FT1DM could be fatal when timely medications are not provided, suggesting the particular importance of rapid and accurate diagnosis. Here we report a serum metabonomics...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300523x
更新日期：2012-09-07 00:00:00
abstract：:Hepatocellular carcinoma (HCC) causes more than half a million annual deaths worldwide. Understanding the mechanisms contributing to HCC development is highly desirable for improved surveillance, diagnosis, and treatment. Liver tissue metabolomics has the potential to reflect the physiological changes behind HCC devel...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00185
更新日期：2019-08-02 00:00:00
abstract：:A major challenge in the life sciences is the extraction of detailed molecular information from plants and animals that are not among the handful of exhaustively studied "model organisms." As a consequence, certain species with novel phenotypes are often ignored due to the lack of searchable databases, tractable genet...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050306a
更新日期：2006-04-01 00:00:00
abstract：:The SEQUEST program was the first and remains one of the most widely used tools for assigning a peptide sequence within a database to a tandem mass spectrum. The cross correlation score is the primary score function implemented within SEQUEST and it is this score that makes the tool particularly sensitive. Unfortunate...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800420s
更新日期：2008-10-01 00:00:00
abstract：:Post-translational nitration of proteins was analyzed by capillary reversed-phase high-performance liquid chromatography (RP-HPLC) on-line interfaced to electrospray ionization mass spectrometry (ESI--MS) or tandem mass spectrometry (ESI--MS/MS). Both methods were compared using a tryptic digest of bovine serum albumi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr034034s
更新日期：2003-09-01 00:00:00
abstract：:In Thailand, diabetes mellitus is the most significant risk factor for melioidosis, a severe disease caused by Burkholderia pseudomallei. In this study, neutrophils isolated from healthy or diabetic subjects were infected with B. thailandensis E555, a variant strain with a B. pseudomallei-like capsular polysaccharide ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00166
更新日期：2019-07-05 00:00:00
abstract：:Russell and colleagues deserve credit for being the first to use a QconCAT standard to simultaneously quantify both the wild-type and mutant peptides of a protein (i.e., CYP2B6) ( J. Proteome Res. 2013, 12 (12), 5934-5942. DOI: 10.1021/pr400279u). However, the rationale of their study was entirely different from ours ...
journal_title：Journal of proteome research
pub_type： 评论,杂志文章
doi：10.1021/acs.jproteome.8b00940
更新日期：2019-03-01 00:00:00
abstract：:We have explored the potential of commercial polystyrene-divinylbenzene monolithic capillary nanoLC-MS/MS for identifying Sinorhizobium fredii HH103 nodulation outer proteins. Monolithic nanoLC with off-line MALDI-TOF/TOF and on-line ESI-q-oTOF is fast and robust, generating complementary data and offering high-confid...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060519f
更新日期：2007-03-01 00:00:00
