Aasland group
Functional annotation of proteins and protein domains
The majority of proteins have a modular architechture: they are composed of one or more globular domains and other more or less structured modules. Globular domains can often be associated with a particular molecular function. Therefore, functional annotation of individual proteins as well as whole proteomes relies, to a large extent, on prediction of globular domains and transfer of functional annotation by homology.
A second aerea of bioinformatics which is poorly developed is the
prediction and annotation of functional sites in proteins: short
linear motifs that are associated with molecular function. Functional
sites are both biochemically hard to determine and bioinformatically
hard to predict. The prediction problem stems from the fact that
the functional sites are short (typically 5-10 residues) and many
of them have evolved by mechanisms different from proteins and protein
domains. Prediction of most functional sites therefore results in
severe overprediction. To meet this challenge, we participate in
the EU-funded ELM consortium which has developed a novel resource
for improved prediction of functional sites. In ELM we combine traditional
detection methods based on experimentally verified sites with contextual
information that is used to evaluate the relevance of the predictions.
The current version of ELM uses three aspects of context: the site
must be in (i) a relevant cellular compartment; (ii) a relevant
organism and (iii) it must be accessible and thus outside globular
domains.
We have recently developed a tool for visualising the linear motifs in multiple alignments while
simultaneously keeping track of phylogeny. This tool will allow us to distinguish which sites have
emerged or been lost during the course of evolution (Hughes, Puntervoll and Aasland, in prep)
Please refer to my MBI home page for information on my molecular biological research interests and group at MBI.
Selected publications:
- Gould, CM, Diella F, Via A, Puntervoll P, Bryne JC, Hughes T, et al., and Aasland R, Helmer-Citterich M, Linding R, Gibson TJ. (2010) ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Res. 38:D167-D180.
- Slagsvold T, Aasland R, Hirano S, Bache KG, Raiborg C, Trambaiolo D, Wakatsuki S, Stenmark H. (2005) Eap45 in mammalian ESCRT-II binds ubiquitin via a phosphoinositide-interacting GLUE domain. J Biol Chem. 280(20):19600-19606
- Puntervoll P, Linding R, Gemund C, Chabanis-Davidson S, Mattingsdal M, et al., and Aasland R, Gibson TJ. (2003) ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res. 31:3625-3630.
- Brehm A, Tufteland KR, Aasland R, Becker PB. (2004) The many colours of chromodomains. BioEssays. 26:133-40.
- Conklin D, Jonassen I, Aasland R, Taylor WR. (2002) Association of nucleotide patterns with gene function classes: application to human 3' untranslated sequences. Bioinformatics. 18:182-189
- Gaullier JM, Simonsen A, D'Arrigo A, Bremnes B, Aasland R., Stenmark H, (1998) FYVE fingers bind PtdIns(3)P. Nature 394:432-433
- Aasland, R., Gibson, T. J., and Stewart, A. F. (1995). The PHD-finger: implications for chromatin-mediated transcriptional regulation. Trends Biochem. Sci. 20, 56-59.
