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Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events.

Fortelny N, Yang S, Pavlidis P, Lange PF, Overall CM - Nucleic Acids Res. (2014)

Bottom Line: New features include the mapping of protein termini and cleavage entries across protein isoforms and significantly, the mapping of protein termini originating from alternative transcription and alternative translation start sites.Neo-termini are also linked to associated proteases.In re-capitulating the major findings originally performed manually, this validates the utility of these new resources.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada Centre for High Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada.

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Biological processes leading to differences in termini in proteins and databases containing corresponding information.
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Figure 1: Biological processes leading to differences in termini in proteins and databases containing corresponding information.

Mentions: Three independent processes form protein species that differ in the extent of their sequence and hence termini. First, RNA splicing can lead to the selection of alternative exons encoding the N- or C-terminus (Figure 1). Second, use of alternative translation initiation sites leads to protein species with either shorter or longer sequence and hence alternate protein N-termini (Figure 1). Third, post-translational modification by proteolytic processing truncates the protein and leads to the formation of shorter stable protein chains with a unique neo N- or neo C-terminus (Figure 1) (1,2). Recent analyses show that proteolytic processing of proteins in vivo in tissues (3) or specialized enucleate cells, the erythrocyte (4) and platelet (5), is remarkably high at 49%, 68% and 77%, respectively. Such analyses reveal the formation of stable protein species by proteolytic processing as a pervasive phenomenon in proteomes and hence one that needs to be considered in interpreting biological processes.


Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events.

Fortelny N, Yang S, Pavlidis P, Lange PF, Overall CM - Nucleic Acids Res. (2014)

Biological processes leading to differences in termini in proteins and databases containing corresponding information.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383881&req=5

Figure 1: Biological processes leading to differences in termini in proteins and databases containing corresponding information.
Mentions: Three independent processes form protein species that differ in the extent of their sequence and hence termini. First, RNA splicing can lead to the selection of alternative exons encoding the N- or C-terminus (Figure 1). Second, use of alternative translation initiation sites leads to protein species with either shorter or longer sequence and hence alternate protein N-termini (Figure 1). Third, post-translational modification by proteolytic processing truncates the protein and leads to the formation of shorter stable protein chains with a unique neo N- or neo C-terminus (Figure 1) (1,2). Recent analyses show that proteolytic processing of proteins in vivo in tissues (3) or specialized enucleate cells, the erythrocyte (4) and platelet (5), is remarkably high at 49%, 68% and 77%, respectively. Such analyses reveal the formation of stable protein species by proteolytic processing as a pervasive phenomenon in proteomes and hence one that needs to be considered in interpreting biological processes.

Bottom Line: New features include the mapping of protein termini and cleavage entries across protein isoforms and significantly, the mapping of protein termini originating from alternative transcription and alternative translation start sites.Neo-termini are also linked to associated proteases.In re-capitulating the major findings originally performed manually, this validates the utility of these new resources.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada Centre for High Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada.

Show MeSH