title: Exploring the sequence context of phosphorylatable amino acids: the contribution of the upgraded MAPRes tool.
abstract: Several models that predict where post-translational modifications are likely to occur and formulate the corresponding association rules are available to analyze the functional potential of a protein sequence, but an algorithm incorporating the functional groups of the involved amino acids in the sequence analyses process is not yet available. In its previous version, MAPRes was utilized to investigate the influence of the surrounding amino acids of post- translationally and co-translationally modifiable sites. The MAPRes has been upgraded to take into account the different biophysical and biochemical properties of the amino acids that have the potential to influence different post- translational modifications (PTMs). In the present study, the upgraded version of MAPRes was implemented on phosphorylated Ser/Thr/Tyr data by considering the polarity and charge of the surrounding amino acids. The patterns mined by MAPRes incorporating structural information on polarity and charge of amino acids suggest distinct structure-function relationships for phosphorylated serines in a multifunctional protein such as the insulin-receptor substrate-1 (IRS-1) protein. The new version of MAPRes is freely available at http://www.imsb.edu.pk/Database.htm.
authors.affiliation: Institute of Molecular Sciences and Bioinformatics, Lahore, Pakistan.
authors.forename: Zeeshan
authors.initials: Z
authors.lastname: Iqbal
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Hoessli
authors.forename: Wajahat M
authors.initials: WM
authors.lastname: Qazi
authors.forename: Munir
authors.initials: M
authors.lastname: Ahmad
authors.forename: Abdul Rauf
authors.initials: AR
authors.lastname: Shakoori
authors.lastname: Nasir-ud-Din
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry* / Q000378:metabolism*; D057225:Data Mining; D030562:Databases, Protein; D006801:Humans; D055504:Insulin Receptor Substrate Proteins / Q000737:chemistry; D010766:Phosphorylation; D010768:Phosphoserine / Q000378:metabolism; D015203:Reproducibility of Results; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D000596:Amino Acids; D055504:Insulin Receptor Substrate Proteins; D010768:Phosphoserine
keywords: ASSOCIATION RULE MINING; INSULIN-RECEPTOR SUBSTRATE PROTEIN 1; MAPRes; PHOSPHORYLATION; PHOSPHORYTABLE ANMINO ACIDS; POLARITY AND CHARGE; POST- TRANSLATIONAL MODIFICATIONS