title: Exploring proteome-wide occurrence of clusters of charged residues in eukaryotes.
abstract: Clusters of charged residues are one of the key features of protein primary structure since they have been associated to important functions of proteins. Here, we present a proteome wide scan for the occurrence of Charge Clusters in Protein sequences using a new search tool (FCCP) based on a score-based methodology. The FCCP was run to search charge clusters in seven eukaryotic proteomes: Arabidopsis thaliana, Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Homo sapiens, Mus musculus, and Saccharomyces cerevisiae. We found that negative charge clusters (NCCs) are three to four times more frequent than positive charge clusters (PCCs). The Drosophila proteome is on average the most charged, whereas the human proteome is the least charged. Only 3 to 8% of the studied protein sequences have negative charge clusters, while 1.6 to 3% having PCCs and only 0.07 to 0.6% have both types of clusters. NCCs are localized predominantly in the N-terminal and C-terminal domains, while PCCs tend to be localized within the functional domains of the protein sequences. Furthermore, the gene ontology classification revealed that the protein sequences with negative and PCCs are mainly binding proteins.
authors.affiliation: Laboratory of Molecular and Cellular Screening Processes, Centre De Biotechnologie De Sfax, Bioinformatics Group, PoBox '1177,'3018 Sfax, Tunisia.
authors.forename: Sabrine
authors.initials: S
authors.lastname: Belmabrouk
authors.affiliation: Laboratory of Molecular and Cellular Screening Processes, Centre De Biotechnologie De Sfax, Bioinformatics Group, PoBox '1177,'3018 Sfax, Tunisia.
authors.forename: Najla
authors.initials: N
authors.lastname: Kharrat
authors.affiliation: Laboratory of Molecular and Cellular Screening Processes, Centre De Biotechnologie De Sfax, Bioinformatics Group, PoBox '1177,'3018 Sfax, Tunisia.
authors.forename: Riadh
authors.initials: R
authors.lastname: Benmarzoug
authors.affiliation: Laboratory of Molecular and Cellular Screening Processes, Centre De Biotechnologie De Sfax, Bioinformatics Group, PoBox '1177,'3018 Sfax, Tunisia.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Rebai
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D017360:Arabidopsis / Q000737:chemistry; D017173:Caenorhabditis elegans / Q000737:chemistry; D002352:Carrier Proteins / Q000737:chemistry*; D004331:Drosophila melanogaster / Q000737:chemistry; D063990:Gene Ontology; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D020543:Proteome / Q000737:chemistry*; D040901:Proteomics / Q000706:statistics & numerical data*; D012441:Saccharomyces cerevisiae / Q000737:chemistry; D055672:Static Electricity; D015027:Zebrafish / Q000378:metabolism
chemical_list: D002352:Carrier Proteins; D020543:Proteome
keywords: algorithm; charge cluster; program; protein sequence analysis; proteome screening