Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks

• Published in: PloS one 2010-06, Vol.5 (6), p.e10972-e10972
• Main Authors: Huang, Tao, Shi, Xiao-He, Wang, Ping, He, Zhisong, Feng, Kai-Yan, Hu, Lele, Kong, Xiangyin, Li, Yi-Xue, Cai, Yu-Dong, Chou, Kuo-Chen
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Amino acids; Analysis; Architectural engineering; Avalanches; Biochemistry/Bioinformatics; Biochemistry/Drug Discovery; Biochemistry/Protein Chemistry; Bioinformatics; Biology; Computation; Computational Biology/Systems Biology; Computer applications; Datasets; Drugs; Experimental methods; Flexibility; Half-life; Health sciences; Hydrophobicity; Influenza; Laboratories; Life sciences; Metabolism; Molecular Sequence Data; Pharmacology/Drug Development; Physicochemical properties; Polarity; Predictions; Properties (attributes); Protein folding; Protein structure; Proteins; Proteins - chemistry; Proteins - metabolism; Redundancy; Secondary structure; Software; Stability analysis; Statistical analysis; Studies; Subcellular Fractions - metabolism
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0010972

The metabolic stability is a very important idiosyncracy of proteins that is related to their global flexibility, intramolecular fluctuations, various internal dynamic processes, as well as many marvelous biological functions. Determination of protein's metabolic stability would provide us with useful information for in-depth understanding of the dynamic action mechanisms of proteins. Although several experimental methods have been developed to measure protein's metabolic stability, they are time-consuming and more expensive. Reported in this paper is a computational method, which is featured by (1) integrating various properties of proteins, such as biochemical and physicochemical properties, subcellular locations, network properties and protein complex property, (2) using the mRMR (Maximum Relevance & Minimum Redundancy) principle and the IFS (Incremental Feature Selection) procedure to optimize the prediction engine, and (3) being able to identify proteins among the four types: "short", "medium", "long", and "extra-long" half-life spans. It was revealed through our analysis that the following seven characters played major roles in determining the stability of proteins: (1) KEGG enrichment scores of the protein and its neighbors in network, (2) subcellular locations, (3) polarity, (4) amino acids composition, (5) hydrophobicity, (6) secondary structure propensity, and (7) the number of protein complexes the protein involved. It was observed that there was an intriguing correlation between the predicted metabolic stability of some proteins and the real half-life of the drugs designed to target them. These findings might provide useful insights for designing protein-stability-relevant drugs. The computational method can also be used as a large-scale tool for annotating the metabolic stability for the avalanche of protein sequences generated in the post-genomic age.