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Sci Rep. 2016 Jun 16;6:28249. doi: 10.1038/srep28249.

GPS-Lipid: a robust tool for the prediction of multiple lipid modification sites.

Xie Y1, Zheng Y1, Li H1, Luo X1, He Z1, Cao S1, Shi Y1, Zhao Q1,2,3, Xue Y4, Zuo Z1,2, Ren J1,2,3.

Author information

1
State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.
2
Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.
3
Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha 410073, China.
4
Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.

Abstract

As one of the most common post-translational modifications in eukaryotic cells, lipid modification is an important mechanism for the regulation of variety aspects of protein function. Over the last decades, three classes of lipid modifications have been increasingly studied. The co-regulation of these different lipid modifications is beginning to be noticed. However, due to the lack of integrated bioinformatics resources, the studies of co-regulatory mechanisms are still very limited. In this work, we developed a tool called GPS-Lipid for the prediction of four classes of lipid modifications by integrating the Particle Swarm Optimization with an aging leader and challengers (ALC-PSO) algorithm. GPS-Lipid was proven to be evidently superior to other similar tools. To facilitate the research of lipid modification, we hosted a publicly available web server at http://lipid.biocuckoo.org with not only the implementation of GPS-Lipid, but also an integrative database and visualization tool. We performed a systematic analysis of the co-regulatory mechanism between different lipid modifications with GPS-Lipid. The results demonstrated that the proximal dual-lipid modifications among palmitoylation, myristoylation and prenylation are key mechanism for regulating various protein functions. In conclusion, GPS-lipid is expected to serve as useful resource for the research on lipid modifications, especially on their co-regulation.

PMID:
27306108
PMCID:
PMC4910163
DOI:
10.1038/srep28249
[Indexed for MEDLINE]
Free PMC Article

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