Phosphoproteome sequence analysis and significance: mining association patterns around phosphorylation sites utilizing MAPRes.
Phosphorylation, one of the most common protein post-translational modifications (PTMs) on hydroxyl groups of S/T/Y is catalyzed by kinases and involves the presence or absence of certain amino acid residues in the vicinity of the phosphorylation sites. Using MAPRes, we have analyzed the substrate proteins of Phospho.ELM 7.0 and found that there are both general and specific requirements for the presence or absence of particular amino acids in the vicinity of phosphorylated S/T/Y for both of the phosphorylation data, whether or not kinase information was taken into account. Patterns extracted by MAPRes for kinase-specific data have been utilized to find the consensus sequence motifs for various kinases required to catalyze the process of phosphorylation on S/T/Y. These consensus sequences for different kinase groups, families, and individual members are consistent with those described earlier with some novel consensus reported for the first time. A comparison study for the patterns mined by MAPRes with the results of existing prediction methods was performed by searching for these patterns in the vicinity of phosphorylation sites predicted by different available method. This comparison resulted in 87-98% conformity with the results of the predictions by available methods. Additionally, the patterns mined by MAPRes for substrate sites included 61 kinases, the highest number analyzed so far.
Ahmad
Ishtiaq
I
Institute of Molecular Sciences and Bioinformatics, Lahore, Pakistan.
Mehmood
Abid
A
Khurshid
Ahmed
A
Qazi
Wajahat M
WM
Hoessli
Daniel C
DC
Walker-Nasir
Evelyne
E
Shakoori
Abdul Rauf
AR
D030562:Databases, Protein; D010750:Phosphoproteins / Q000737:chemistry*; D010766:Phosphorylation; D011494:Protein Kinases / Q000737:chemistry* / Q000378:metabolism; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000378:metabolism*; D020539:Sequence Analysis, Protein
D010750:Phosphoproteins; D020543:Proteome; D011494:Protein Kinases