標題: Propensity Scores for Prediction and Characterization of Bioluminescent Proteins from Sequences
作者: Huang, Hui-Ling
生物科技學系
生物資訊及系統生物研究所
Department of Biological Science and Technology
Institude of Bioinformatics and Systems Biology
公開日期: 14-五月-2014
摘要: Bioluminescent proteins (BLPs) are a class of proteins with various mechanisms of light emission such as bioluminescence and fluorescence from luminous organisms. While valuable for commercial and medical applications, identification of BLPs, including luciferases and fluorescent proteins (FPs), is rather challenging, owing to their high variety of protein sequences. Moreover, characterization of BLPs facilitates mutagenesis analysis to enhance bioluminescence and fluorescence. Therefore, this study proposes a novel methodological approach to estimating the propensity scores of 400 dipeptides and 20 amino acids in order to design two prediction methods and characterize BLPs based on a scoring card method (SCM). The SCMBLP method for predicting BLPs achieves an accuracy of 90.83% for 10-fold cross-validation higher than existing support vector machine based methods and a test accuracy of 82.85%. A dataset consisting of 269 luciferases and 216 FPs is also established to design the SCMLFP prediction method, which achieves training and test accuracies of 97.10% and 96.28%, respectively. Additionally, four informative physicochemical properties of 20 amino acids are identified using the estimated propensity scores to characterize BLPs as follows: 1) high transfer free energy from inside to the protein surface, 2) high occurrence frequency of residues in the transmembrane regions of the protein, 3) large hydrophobicity scale from the native protein structure, and 4) high correlation coefficient (R = 0.921) between the amino acid compositions of BLPs and integral membrane proteins. Further analyzing BLPs reveals that luciferases have a larger value of R (0.937) than FPs (0.635), suggesting that luciferases tend to locate near the cell membrane location rather than FPs for convenient receipt of extracellular ions. Importantly, the propensity scores of dipeptides and amino acids and the identified properties facilitate efforts to predict, characterize, and apply BLPs, including luciferases, photoproteins, and FPs. The web server is available at http://iclab.life.nctu.edu.tw/SCMBLP/index.html.
URI: http://dx.doi.org/10.1371/journal.pone.0097158
http://hdl.handle.net/11536/24717
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0097158
期刊: PLOS ONE
Volume: 9
Issue: 5
結束頁: 
顯示於類別:期刊論文


文件中的檔案:

  1. 000336857400060.pdf