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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

Markus Almén, Karl JV Nordström, Robert Fredriksson, Helgi B Schiöth
2009 BMC Biology  
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  
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

J. Sprenger, J. Lynn Fink, S. Karunaratne, K. Hanson, N. A. Hamilton, R. D. Teasdale
2007 Nucleic Acids Research  
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

A. Muller
2002 Genome Research  
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

Valérie Marot-Lassauzaie, Michael Bernhofer, Burkhard Rost
2018 Bioinformatics  
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

Jinfeng Liu, Burkhard Rost
2001 Protein Science  
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

Zhen Wang, Jun Han, Larry L. David, Kevin L. Schey
2013 Investigative Ophthalmology and Visual Science  
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

Haixing Wang, Wei-Jun Qian, Mark H. Chin, Vladislav A. Petyuk, Richard C. Barry, Tao Liu, Marina A. Gritsenko, Heather M. Mottaz, Ronald J. Moore, David G. Camp, Arshad H. Khan, Desmond J. Smith (+1 others)
2006 Journal of Proteome Research  
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

Angel García, Nicole Zitzmann, Steve P Watson
2004 Seminars in Thrombosis and Hemostasis  
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

Nguyen Tien Dung, Phan Van Chi
2012 Proteomics Insights  
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

Eric W. Klee
2008 Zebrafish  
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?

Timothy J. Stevens, Isaiah T. Arkin
2000 Proteins: Structure, Function, and Bioinformatics  
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>;2-y pmid:10813823 fatcat:gylcfbgmdvchjc7g3p6sgpo6aq

Deep Coverage Mouse Red Blood Cell Proteome

Erica M. Pasini, Morten Kirkegaard, Doris Salerno, Peter Mortensen, Matthias Mann, Alan W. Thomas
2008 Molecular & Cellular Proteomics  
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

Linda Harkness, Helle Christiansen, Jan Nehlin, Torben Barington, Jens S. Andersen, Moustapha Kassem
2008 Stem Cell Research  
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

Tatyana A. Prokhorova, Kristoffer T. G. Rigbolt, Pia T. Johansen, Jeanette Henningsen, Irina Kratchmarova, Moustapha Kassem, Blagoy Blagoev
2009 Molecular & Cellular Proteomics  
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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