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SwissPalm: Protein Palmitoylation database.

Blanc M, David F, Abrami L, Migliozzi D, Armand F, Bürgi J, van der Goot FG - F1000Res (2015)

Bottom Line: Systems analysis of the palmitoyl-proteome screens indicate that 10% or more of the human proteome is susceptible to S-palmitoylation.Moreover, ontology and pathway analyses of the human palmitoyl-proteome reveal that key biological functions involve this reversible lipid modification.Through the compilation of data and continuous updates, SwissPalm will provide a powerful tool to unravel the global importance of protein S-palmitoylation.

View Article: PubMed Central - PubMed

Affiliation: Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland.

ABSTRACT
Protein S-palmitoylation is a reversible post-translational modification that regulates many key biological processes, although the full extent and functions of protein S-palmitoylation remain largely unexplored. Recent developments of new chemical methods have allowed the establishment of palmitoyl-proteomes of a variety of cell lines and tissues from different species.  As the amount of information generated by these high-throughput studies is increasing, the field requires centralization and comparison of this information. Here we present SwissPalm ( http://swisspalm.epfl.ch), our open, comprehensive, manually curated resource to study protein S-palmitoylation. It currently encompasses more than 5000 S-palmitoylated protein hits from seven species, and contains more than 500 specific sites of S-palmitoylation. SwissPalm also provides curated information and filters that increase the confidence in true positive hits, and integrates predictions of S-palmitoylated cysteine scores, orthologs and isoform multiple alignments. Systems analysis of the palmitoyl-proteome screens indicate that 10% or more of the human proteome is susceptible to S-palmitoylation. Moreover, ontology and pathway analyses of the human palmitoyl-proteome reveal that key biological functions involve this reversible lipid modification. Comparative analysis finally shows a strong crosstalk between S-palmitoylation and other post-translational modifications. Through the compilation of data and continuous updates, SwissPalm will provide a powerful tool to unravel the global importance of protein S-palmitoylation.

No MeSH data available.


Related in: MedlinePlus

Additional information.A: (upper) Global alignment of isoform sequences highlighting all cysteine residues. (lower) When available, information on protein topology, disulfide bond involvement and prediction scores from CSS-Palm 4.0 and PalmPred are provided for each cysteine residue in the different isoform sequences.B: Global alignment of orthologs sequences show conserved cysteine residues (502 and 503 in human calnexin) across species.
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f4: Additional information.A: (upper) Global alignment of isoform sequences highlighting all cysteine residues. (lower) When available, information on protein topology, disulfide bond involvement and prediction scores from CSS-Palm 4.0 and PalmPred are provided for each cysteine residue in the different isoform sequences.B: Global alignment of orthologs sequences show conserved cysteine residues (502 and 503 in human calnexin) across species.

Mentions: Protein information page. A system of summary boxes gives a quick overview on the main information related to S-palmitoylated proteins. This includes the number of times the protein is cited in proteome or targeted studies, information on experimental sites, and high confidence predictions from CSS-Palm 4.0 and PalmPred (Figure 3B). Other information includes a global alignment of isoform sequences highlighting all cysteine residues (Figure 4A), protein topology, disulfide bond positions and prediction scores (Figure 4B), information on orthologous proteins and an alignment of them (Figure 3D), as well as GO terms and references (cell types, techniques, subcellular localization).


SwissPalm: Protein Palmitoylation database.

Blanc M, David F, Abrami L, Migliozzi D, Armand F, Bürgi J, van der Goot FG - F1000Res (2015)

Additional information.A: (upper) Global alignment of isoform sequences highlighting all cysteine residues. (lower) When available, information on protein topology, disulfide bond involvement and prediction scores from CSS-Palm 4.0 and PalmPred are provided for each cysteine residue in the different isoform sequences.B: Global alignment of orthologs sequences show conserved cysteine residues (502 and 503 in human calnexin) across species.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4544385&req=5

f4: Additional information.A: (upper) Global alignment of isoform sequences highlighting all cysteine residues. (lower) When available, information on protein topology, disulfide bond involvement and prediction scores from CSS-Palm 4.0 and PalmPred are provided for each cysteine residue in the different isoform sequences.B: Global alignment of orthologs sequences show conserved cysteine residues (502 and 503 in human calnexin) across species.
Mentions: Protein information page. A system of summary boxes gives a quick overview on the main information related to S-palmitoylated proteins. This includes the number of times the protein is cited in proteome or targeted studies, information on experimental sites, and high confidence predictions from CSS-Palm 4.0 and PalmPred (Figure 3B). Other information includes a global alignment of isoform sequences highlighting all cysteine residues (Figure 4A), protein topology, disulfide bond positions and prediction scores (Figure 4B), information on orthologous proteins and an alignment of them (Figure 3D), as well as GO terms and references (cell types, techniques, subcellular localization).

Bottom Line: Systems analysis of the palmitoyl-proteome screens indicate that 10% or more of the human proteome is susceptible to S-palmitoylation.Moreover, ontology and pathway analyses of the human palmitoyl-proteome reveal that key biological functions involve this reversible lipid modification.Through the compilation of data and continuous updates, SwissPalm will provide a powerful tool to unravel the global importance of protein S-palmitoylation.

View Article: PubMed Central - PubMed

Affiliation: Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland.

ABSTRACT
Protein S-palmitoylation is a reversible post-translational modification that regulates many key biological processes, although the full extent and functions of protein S-palmitoylation remain largely unexplored. Recent developments of new chemical methods have allowed the establishment of palmitoyl-proteomes of a variety of cell lines and tissues from different species.  As the amount of information generated by these high-throughput studies is increasing, the field requires centralization and comparison of this information. Here we present SwissPalm ( http://swisspalm.epfl.ch), our open, comprehensive, manually curated resource to study protein S-palmitoylation. It currently encompasses more than 5000 S-palmitoylated protein hits from seven species, and contains more than 500 specific sites of S-palmitoylation. SwissPalm also provides curated information and filters that increase the confidence in true positive hits, and integrates predictions of S-palmitoylated cysteine scores, orthologs and isoform multiple alignments. Systems analysis of the palmitoyl-proteome screens indicate that 10% or more of the human proteome is susceptible to S-palmitoylation. Moreover, ontology and pathway analyses of the human palmitoyl-proteome reveal that key biological functions involve this reversible lipid modification. Comparative analysis finally shows a strong crosstalk between S-palmitoylation and other post-translational modifications. Through the compilation of data and continuous updates, SwissPalm will provide a powerful tool to unravel the global importance of protein S-palmitoylation.

No MeSH data available.


Related in: MedlinePlus