Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy

摘要：

　　Motivation:Favorable interaction between the regulatory subunit of the cAMP.dependent protein kinase (PKA) and a peptide in A-kinase anchoring proteins (AKAPs) is critical for transtocating PKA to the subcellular sites where the enzyme phosphorylates its substrates.It is very hard to identify AKAPs peptides binding to PKA due to the high sequence diversity of AKAPs.Results:We propose a hierarchical and efficient approach,which combines molecular dynamics (MD) simulations,free energy calculations,virtual mutagenesis (VM) and bioinformatics analyses,to predict peptides binding to the PKA RIIα regulatory subunit in the human proteome systematically.Our approach successfully retrieved 15 out of 18 documented RIIα-binding peptides.Literature curation supported that many newty predicted peptides might be true AKAPs.Here,we present the first systematic search for AKAP peptides in the human proteome,which is useful to further experimental identification of AKAPs and functional analysis of their biological roles.

作者: Tingjun Hou Youyong Li Wei Wang

作者单位: Institute of Functional Nano & Soft Materials(FUNSOM)and Jiangsu Key Laboratory for Carbon-Based Fun Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093-

会议类型: 国际会议

会议名称: The 6th International Conference of Molecular Simulations and Applied Informatics Technologies(第六届国际分子模拟与信息技术应用学术会议(ICMS&I))

会议地点: 南京

会议语种:英文

页码: 408-415

在线出版日期: 2012-05-13（万方平台首次上网日期，不代表论文的发表时间）