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PMeS: prediction of methylation sites based on enhanced feature encoding scheme.

Shi SP, Qiu JD, Sun XY, Suo SB, Huang SY, Liang RP - PLoS ONE (2012)

Bottom Line: Protein methylation is predominantly found on lysine and arginine residues, and carries many important biological functions, including gene regulation and signal transduction.Thus, identification of methylation sites can be very helpful for the drug designs of various related diseases.The enhanced feature encoding scheme was composed of the sparse property coding, normalized van der Waals volume, position weight amino acid composition and accessible surface area.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Nanchang University, Nanchang, People's Republic of China.

ABSTRACT
Protein methylation is predominantly found on lysine and arginine residues, and carries many important biological functions, including gene regulation and signal transduction. Given their important involvement in gene expression, protein methylation and their regulatory enzymes are implicated in a variety of human disease states such as cancer, coronary heart disease and neurodegenerative disorders. Thus, identification of methylation sites can be very helpful for the drug designs of various related diseases. In this study, we developed a method called PMeS to improve the prediction of protein methylation sites based on an enhanced feature encoding scheme and support vector machine. The enhanced feature encoding scheme was composed of the sparse property coding, normalized van der Waals volume, position weight amino acid composition and accessible surface area. The PMeS achieved a promising performance with a sensitivity of 92.45%, a specificity of 93.18%, an accuracy of 92.82% and a Matthew's correlation coefficient of 85.69% for arginine as well as a sensitivity of 84.38%, a specificity of 93.94%, an accuracy of 89.16% and a Matthew's correlation coefficient of 78.68% for lysine in 10-fold cross validation. Compared with other existing methods, the PMeS provides better predictive performance and greater robustness. It can be anticipated that the PMeS might be useful to guide future experiments needed to identify potential methylation sites in proteins of interest. The online service is available at http://bioinfo.ncu.edu.cn/inquiries_PMeS.aspx.

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The distribution of physicochemical properties of residues around methylarginine and non-methylarginine.G1 is hydrophobic residue, G2 is polar residue, G3 is positively charged residue, and G4 is negatively charged residue.
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pone-0038772-g001: The distribution of physicochemical properties of residues around methylarginine and non-methylarginine.G1 is hydrophobic residue, G2 is polar residue, G3 is positively charged residue, and G4 is negatively charged residue.

Mentions: As mentioned above, the SPC feature is mainly based on the hydrophobicity and charged character of amino acid residue. To determine whether methylation and non-methylation sites have distinct physiochemical properties, we calculated statistically significant differences in the distribution of physicochemical properties of amino acid residues surrounding methylation and non-methylation sites based on the paired Welch's t-test. As shown in Figure 1, from −7 to +7 positions, the ratios of hydrophobic amino acids around methylarginine were 2.3% to 29.2% higher than those of non-methylarginine with P-value ≤3.59e-02 (see Table S6). Especially for the +1 position, hydrophobic residues around methylarginine account for 77.3%, about 29.2% higher than those of non-methylarginine (P  = 3.84e-09). From −7 to +7 positions, polar and negatively charged residues surrounding non-methylarginine were 1.15% to 7.12% higher than those of methylarginine (P<0.05). This analysis reveals that methylarginine and non-methylarginine have distinct physiochemical properties. In fact, some studies suggested that the arginine residue becomes more hydrophobic due to addition of methyl groups and may engage in more van der Waal interactions [8].


PMeS: prediction of methylation sites based on enhanced feature encoding scheme.

Shi SP, Qiu JD, Sun XY, Suo SB, Huang SY, Liang RP - PLoS ONE (2012)

The distribution of physicochemical properties of residues around methylarginine and non-methylarginine.G1 is hydrophobic residue, G2 is polar residue, G3 is positively charged residue, and G4 is negatively charged residue.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3376144&req=5

pone-0038772-g001: The distribution of physicochemical properties of residues around methylarginine and non-methylarginine.G1 is hydrophobic residue, G2 is polar residue, G3 is positively charged residue, and G4 is negatively charged residue.
Mentions: As mentioned above, the SPC feature is mainly based on the hydrophobicity and charged character of amino acid residue. To determine whether methylation and non-methylation sites have distinct physiochemical properties, we calculated statistically significant differences in the distribution of physicochemical properties of amino acid residues surrounding methylation and non-methylation sites based on the paired Welch's t-test. As shown in Figure 1, from −7 to +7 positions, the ratios of hydrophobic amino acids around methylarginine were 2.3% to 29.2% higher than those of non-methylarginine with P-value ≤3.59e-02 (see Table S6). Especially for the +1 position, hydrophobic residues around methylarginine account for 77.3%, about 29.2% higher than those of non-methylarginine (P  = 3.84e-09). From −7 to +7 positions, polar and negatively charged residues surrounding non-methylarginine were 1.15% to 7.12% higher than those of methylarginine (P<0.05). This analysis reveals that methylarginine and non-methylarginine have distinct physiochemical properties. In fact, some studies suggested that the arginine residue becomes more hydrophobic due to addition of methyl groups and may engage in more van der Waal interactions [8].

Bottom Line: Protein methylation is predominantly found on lysine and arginine residues, and carries many important biological functions, including gene regulation and signal transduction.Thus, identification of methylation sites can be very helpful for the drug designs of various related diseases.The enhanced feature encoding scheme was composed of the sparse property coding, normalized van der Waals volume, position weight amino acid composition and accessible surface area.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Nanchang University, Nanchang, People's Republic of China.

ABSTRACT
Protein methylation is predominantly found on lysine and arginine residues, and carries many important biological functions, including gene regulation and signal transduction. Given their important involvement in gene expression, protein methylation and their regulatory enzymes are implicated in a variety of human disease states such as cancer, coronary heart disease and neurodegenerative disorders. Thus, identification of methylation sites can be very helpful for the drug designs of various related diseases. In this study, we developed a method called PMeS to improve the prediction of protein methylation sites based on an enhanced feature encoding scheme and support vector machine. The enhanced feature encoding scheme was composed of the sparse property coding, normalized van der Waals volume, position weight amino acid composition and accessible surface area. The PMeS achieved a promising performance with a sensitivity of 92.45%, a specificity of 93.18%, an accuracy of 92.82% and a Matthew's correlation coefficient of 85.69% for arginine as well as a sensitivity of 84.38%, a specificity of 93.94%, an accuracy of 89.16% and a Matthew's correlation coefficient of 78.68% for lysine in 10-fold cross validation. Compared with other existing methods, the PMeS provides better predictive performance and greater robustness. It can be anticipated that the PMeS might be useful to guide future experiments needed to identify potential methylation sites in proteins of interest. The online service is available at http://bioinfo.ncu.edu.cn/inquiries_PMeS.aspx.

Show MeSH
Related in: MedlinePlus