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Using core hydrophobicity to identify phosphorylation sites of human G protein-coupled receptors

Author:
Huang, Jian-Hua, Cao, Dong-Sheng, Yan, Jun, Xu, Qing-Song, Hu, Qian-Nan, Liang, Yi-Zeng
Source:
Biochimie 2012 v.94 no.8 pp. 1697-1704
ISSN:
0300-9084
Subject:
G-protein coupled receptors, amino acid sequences, amino acids, biotechnology, correlation, drugs, humans, hydrophobicity, phosphorylation, prediction, signal transduction, support vector machines
Abstract:
As the most frequent drug target, G protein-coupled receptors (GPCRs) are a large family of seven trans-membrane receptors that sense molecules outside the cell and activate inside signal transduction pathways. The activity and lifetime of activated receptors are regulated by receptor phosphorylation. Therefore, investigating the exact positions of phosphorylation sites in GPCRs sequence could provide useful clues for drug design and other biotechnology applications. Experimental identification of phosphorylation sites is expensive and laborious. Hence, there is significant interest in the development of computational methods for reliable prediction of phosphorylation sites from amino acid sequences. In this article, we presented a simple and effective method to recognize phosphorylation sites of human GPCRs by combining amino acid hydrophobicity and support vector machine. The prediction accuracy, sensitivity, specificity, Matthews correlation coefficient and area under the curve values for phosphoserine, phosphothreonine, and phosphotyrosine were 0.964, 0.790, 0.999, 0.866, 0.941; 0.954, 0.800, 0.985, 0.828, 0.958; and 0.976, 0.820, 0.993, 0.861, 0.959, respectively. The establishment of such a fast and accurate prediction method will speed up the pace of identifying proper GPCRs sites to facilitate drug discovery.
Agid:
902183