Limits...
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.

Show MeSH

Related in: MedlinePlus

The distribution of physicochemical properties of residues around methyllysine and non-methyllysine.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


getmorefigures.php?uid=PMC3376144&req=5

pone-0038772-g002: The distribution of physicochemical properties of residues around methyllysine and non-methyllysine.G1 is hydrophobic residue, G2 is polar residue, G3 is positively charged residue, and G4 is negatively charged residue.

Mentions: While compared with non-methyllysine, the ratios of four different attributive residues around methyllysine have not changed much, as shown in Figure 2, which indicates that the incorporation of methyl groups to the lysine side chain changes the physicochemical properties of the affected residues only slightly. It is worth noting that the ratios of polar residues surrounding methyllysine were 2.81% to 6.03% higher than those of non-methyllysine from −5 to −2 positions (P≤8.46e-04). Most enzymes bind the methyllysine in a polar environment, which resembles the ‘carbonyl cage’ of SET domains rather than the hydrophobic pockets of chromo domain-related motifs [40]. The methyl groups are coordinated by a set of electrostatic interactions between polar residues of the protein and the trimethylammonium. CH…O-H bonds form between oxygen on the enzyme's sidechains and methyl groups of the methyllysine [41]. These interactions cumulatively position one of the methyl groups in the vicinity of the iron for hydroxylation to occur [24]. All these researches strengthen the role of surrounding sites in the enzymes' reorganization.


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 methyllysine and non-methyllysine.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-g002: The distribution of physicochemical properties of residues around methyllysine and non-methyllysine.G1 is hydrophobic residue, G2 is polar residue, G3 is positively charged residue, and G4 is negatively charged residue.
Mentions: While compared with non-methyllysine, the ratios of four different attributive residues around methyllysine have not changed much, as shown in Figure 2, which indicates that the incorporation of methyl groups to the lysine side chain changes the physicochemical properties of the affected residues only slightly. It is worth noting that the ratios of polar residues surrounding methyllysine were 2.81% to 6.03% higher than those of non-methyllysine from −5 to −2 positions (P≤8.46e-04). Most enzymes bind the methyllysine in a polar environment, which resembles the ‘carbonyl cage’ of SET domains rather than the hydrophobic pockets of chromo domain-related motifs [40]. The methyl groups are coordinated by a set of electrostatic interactions between polar residues of the protein and the trimethylammonium. CH…O-H bonds form between oxygen on the enzyme's sidechains and methyl groups of the methyllysine [41]. These interactions cumulatively position one of the methyl groups in the vicinity of the iron for hydroxylation to occur [24]. All these researches strengthen the role of surrounding sites in the enzymes' reorganization.

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