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Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin
2009
BMC Biology
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We estimate that 27% of the total human proteome are alpha-helical transmembrane proteins and provide an extended classification together with in-depth investigations of the membrane proteome's functional ...
Membrane proteins form key nodes in mediating the cell's interaction with the surroundings, which is one of the main reasons why the majority of drug targets are membrane proteins. ...
Acknowledgements We thank Professor Gunnar von Heijne at Stockholm University for valuable comments on the manuscript, and Michele Clamp in Erik Landers lab at Broad Institute of Massachusetts Institute ...
doi:10.1186/1741-7007-7-50
pmid:19678920
pmcid:PMC2739160
fatcat:x6wuncn6e5gjlevmfjsauxjwla
Page 697 of The Journal of Investigative Dermatology Vol. 123, Issue 4
[page]
2004
The Journal of Investigative Dermatology
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of the plasma membrane proteome of the human epidermis. ...
Based on these simplistic assumptions, the number of proteins identified in this study may represent at least 25-35% of the membrane proteome of human epi- dermis, and most likely more when the cellular ...
LOCATE: a mammalian protein subcellular localization database
2007
Nucleic Acids Research
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The proteome annotated in LOCATE is from the RIKEN FANTOM Consortium Isoform Protein Sequence sets which contains 58 128 mouse and 64 637 human protein isoforms. ...
LOCATE is a curated, web-accessible database that houses data describing the membrane organization and subcellular localization of mouse and human proteins. ...
Funding to pay the Open Access publication charges for this article was provided by The University of Queensland. ...
doi:10.1093/nar/gkm950
pmid:17986452
pmcid:PMC2238969
fatcat:rh5sf5cp35aclbdt7fmdwkoohe
Structural Characterization of the Human Proteome
2002
Genome Research
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Of the human protein sequences, 13% are transmembrane proteins, but only 3% of the residues in the proteome form membrane-spanning regions. ...
This paper reports an analysis of the encoded proteins (the proteome) of the genomes of human, fly, worm, yeast, and representatives of bacteria and archaea in terms of the three-dimensional structures ...
The size of the human proteome is estimated at the number of protein sequences in the ENSEMBL dataset (∼29,000). ...
doi:10.1101/gr.221202
pmid:12421749
pmcid:PMC187559
fatcat:hb4hceo4endulcckxk23yjuxza
Correcting mistakes in predicting distributions
2018
Bioinformatics
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Motivation: Many applications monitor predictions of a whole range of features for biological datasets, e.g. the fraction of secreted human proteins in the human proteome. ...
As proof-of-principle, the correction was applied to a two-class (membrane/not) and to a seven-class (localization) prediction. ...
Conflict of Interest: none declared. ...
doi:10.1093/bioinformatics/bty346
pmid:29762646
fatcat:r4m5twjpzraglbnx7k5x6g7bii
Comparing function and structure between entire proteomes
2001
Protein Science
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We predicted that ∼15%-30% of all proteins contained transmembrane helices. We could not find a correlation between the content of membrane proteins and the complexity of the organism. ...
In particular, we did not find significantly higher percentages of helical membrane proteins in eukaryotes than in prokaryotes or archae. ...
The publication costs of this article were defrayed in part by payment of page charges. ...
doi:10.1110/ps.10101
pmid:11567088
pmcid:PMC2374214
fatcat:ksxod7tslvburobrldaoy26zo4
Proteomics and Phosphoproteomics Analysis of Human Lens Fiber Cell Membranes
2013
Investigative Ophthalmology and Visual Science
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The purpose of this study was to characterize the lens fiber cell membrane proteome and phosphoproteome from human lenses. ...
The results presented herein significantly expand the characterized proteome and phosphoproteome of the human lens fiber cell and provide a valuable reference for future research in studies of lens development ...
Acknowledgments The authors thank Phil Wilmarth for his helpful discussions. ...
doi:10.1167/iovs.12-11168
pmid:23349431
pmcid:PMC3567755
fatcat:hmaqofsu5jgahefbpvwaoiq65u
Characterization of the Mouse Brain Proteome Using Global Proteomic Analysis Complemented with Cysteinyl-Peptide Enrichment
2006
Journal of Proteome Research
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Approximately 26% of the identified proteins with gene ontology (GO) annotations were membrane proteins, with 1447 proteins predicted to have transmembrane domains, and many of the membrane proteins were ...
The proteomic approach presented here may have broad applications for rapid proteomic analyses of various mouse models of human brain diseases. ...
Smith) for support of this research and the Environmental Molecular Sciences Laboratory (EMSL) for use of the instrumentation applied in this research. EMSL is a U.S. ...
doi:10.1021/pr0503681
pmid:16457602
pmcid:PMC1850945
fatcat:p4dgeh5nirephb2ny36hno5q2y
Analyzing the Platelet Proteome
2004
Seminars in Thrombosis and Hemostasis
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This technology can be used to analyze the protein content (i.e., the proteome) of any cell or tissue and complements the powerful field of genomics. ...
During the last 10 years, mass spectrometry (MS) has become a key tool for protein analysis and has underpinned the emerging field of proteomics. ...
The extent of coverage of the platelet proteome achieved to date is difficult to say because it is difficult to estimate the total number of proteins within a platelet. ...
doi:10.1055/s-2004-833483
pmid:15354269
fatcat:jeflbd5h2rhabbqbhkaawdoxvq
A Survey of Membrane Proteins in Human Serum
2012
Proteomics Insights
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Serum and membrane proteins are two of the most attractive targets for proteomic analysis. ...
In this study, an analysis of membrane proteins in normal human serum was carried out. ...
human plasma Peptide Atlas by researchers participating in the Plasma Proteome Project of the Human Proteome Organization (HUPO). 4 Comparative studies of the plasma have revealed many potential markers ...
doi:10.4137/pri.s9374
pmid:25288886
pmcid:PMC4177280
fatcat:a3ohws3xv5cmdejubvvw2legym
The Zebrafish Secretome
2008
Zebrafish
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About 16.5% of the zebrafish proteome and 17.0% of the human proteome possessed predicted N-terminal signal sequences. ...
The secretome is a functionally rich proteome subset, including cellular membrane and extracellular proteins processed through the secretory pathway. ...
Stephen Ekker for his continued involvement in providing insight into the needs and values associated with the zebrafish and zebrafish community. ...
doi:10.1089/zeb.2008.0529
pmid:18554177
pmcid:PMC2738611
fatcat:k6selxhpubetri7fm5wf6zp7zq
Do more complex organisms have a greater proportion of membrane proteins in their genomes?
2000
Proteins: Structure, Function, and Bioinformatics
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Using optimized hydropathy analysis of proteins in several, diverse proteomes, we show that organisms of the three domains of life-Eukarya, Eubacteria, and Archaea-have similar proportions of ␣-helical ...
membrane proteins within their genomes and that these are matched by the complexity of the aqueous components. ...
I The Estimated Percent of Membrane Proteins and Proteome Sizes for the Organisms Studied † Organism
Percent
membrane
proteins
Proteins
studied
Size of
proteome
Percent
genome
sequenced ...
doi:10.1002/(sici)1097-0134(20000601)39:4<417::aid-prot140>3.0.co;2-y
pmid:10813823
fatcat:gylcfbgmdvchjc7g3p6sgpo6aq
Deep Coverage Mouse Red Blood Cell Proteome
2008
Molecular & Cellular Proteomics
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Recently we presented an in-depth proteome for the human RBC. ...
All proteins were identified, validated, and categorized in terms of subcellular localization, protein family, and function, and in comparison with the human RBC, were classified as orthologs, family-related ...
Comparative Analysis of Mouse and Human RBC Proteomes Membrane Proteins-40 membrane proteins (93 including proteins in the membrane/soluble fraction) were identified on initial MS analysis of digested ...
doi:10.1074/mcp.m700458-mcp200
pmid:18344233
fatcat:7hyzqtriprgu5c7t3dzmp7zcu4
Identification of a membrane proteomic signature for human embryonic stem cells independent of culture conditions
2008
Stem Cell Research
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In conclusion, we describe the first membrane proteome profile of hESC that is independent of culture conditions. ...
Proteomic profiling of human embryonic stem cells (hESC) can identify cell fate determination and self-renewal biomarkers. ...
Nielsen for advice on FT handling, and Morten Bern of Proxeon Biosystems A/S for the use of software analysis tools. The access to the PepMapper program of Dr. ...
doi:10.1016/j.scr.2008.06.001
pmid:19383402
fatcat:hbpgorjxeja3pjgbzxnkz7wgay
Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Quantitative Comparison of the Membrane Proteomes of Self-renewing and Differentiating Human Embryonic Stem Cells
2009
Molecular & Cellular Proteomics
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We determined and quantitatively compared the membrane proteomes of the self-renewing versus differentiating cells of two distinct human embryonic stem cell lines. ...
Of the 811 identified membrane proteins, six displayed significantly higher expression levels in the undifferentiated state compared with differentiating cells. ...
Acknowledgments-We thank all members from the Center for ...
doi:10.1074/mcp.m800287-mcp200
pmid:19151416
pmcid:PMC2689770
fatcat:2qj7pkrgibbphjxlmzdqgca2uu
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