Genome Research

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supplemental Research Data
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Müller, A.
Right arrow Articles by Sternberg, M. J.E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Müller, A.
Right arrow Articles by Sternberg, M. J.E.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Vol. 12, Issue 11, 1625-1641, November 2002

Structural Characterization of the Human Proteome

Arne Müller,1 Robert M. MacCallum,1,4 and Michael J.E. Sternberg1,2,3

1 Biomolecular Modelling Laboratory, Cancer Research UK, London, United Kingdom; 2 Department of Biological Sciences, Structural Bioinformatics Group, Imperial College of Science, Technology and Medicine, South Kensington, London, United Kingdom

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 of their globular domains together with a general sequence-based study. We show that 39% of the human proteome can be assigned to known structures. We estimate that for 77% of the proteome, there is some functional annotation, but only 26% of the proteome can be assigned to standard sequence motifs that characterize function. Of the human protein sequences, 13% are transmembrane proteins, but only 3% of the residues in the proteome form membrane-spanning regions. There are substantial differences in the composition of globular domains of transmembrane proteins between the proteomes we have analyzed. Commonly occurring structural superfamilies are identified within the proteome. The frequencies of these superfamilies enable us to estimate that 98% of the human proteome evolved by domain duplication, with four of the 10 most duplicated superfamilies specific for multicellular organisms. The zinc-finger superfamily is massively duplicated in human compared to fly and worm, and occurrence of domains in repeats is more common in metazoa than in single cellular organisms. Structural superfamilies over- and underrepresented in human disease genes have been identified. Data and results can be downloaded and analyzed via web-based applications at http://www.sbg.bio.ic.ac.uk.

[Supplemental material is available online at http://www.genome.org.]

3 Present address: Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden.

4 Corresponding author.

12:1625-1641 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 Proc. Natl. Acad. Sci. USAHome page
K.-J. Hwang, F. Mahmoodian, J. A. Ferretti, E. D. Korn, and J. M. Gruschus
Intramolecular interaction in the tail of Acanthamoeba myosin IC between the SH3 domain and a putative pleckstrin homology domain
PNAS, January 16, 2007; 104(3): 784 - 789.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
V. Kunin, S. A. Teichmann, M. A. Huynen, and C. A. Ouzounis
The properties of protein family space depend on experimental design
Bioinformatics, June 1, 2005; 21(11): 2618 - 2622.
[Abstract] [Full Text] [PDF]

Home page
 J. Leukoc. Biol.Home page
I. C. Nicholson, M. Ayhan, N. J. Hoogenraad, and H. Zola
In silico evaluation of two mass spectrometry-based approaches for the identification of novel human leukocyte cell-surface proteins
J. Leukoc. Biol., February 1, 2005; 77(2): 190 - 198.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. J. McGuffin, S. A. Street, K. Bryson, S.-A. Sorensen, and D. T. Jones
The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms
Nucleic Acids Res., January 1, 2004; 32(90001): D196 - 199.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Fleming, A. Muller, R. M. MacCallum, and M. J. E. Sternberg
3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes
Nucleic Acids Res., January 1, 2004; 32(90001): D245 - 250.
[Abstract] [Full Text] [PDF]

Home page
 ScienceHome page
C. Chothia, J. Gough, C. Vogel, and S. A. Teichmann
Evolution of the Protein Repertoire
Science, June 13, 2003; 300(5626): 1701 - 1703.
[Abstract] [Full Text] [PDF]


Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.