A method to distinguish between lysine acetylation and lysine methylation from protein sequences.
Lysine acetylation and methylation are two major post-translational modifications of lysine residues. They play vital roles in both biological and pathological processes. Specific lysine residues in H3 histone protein tails appear to be targeted for either acetylation or methylation. Hence it is very challenging to distinguish between acetylated and methylated lysine residues using computational methods. This work presents a method that incorporates protein sequence information, secondary structure and amino acid properties to differentiate acetyl-lysine from methyl-lysine. We apply an encoding scheme based on grouped weight and position weight amino acid composition to extract sequence information and physicochemical properties around lysine sites. The proposed method achieves an accuracy of 93.3% using a jackknife test. Feature analysis demonstrates that the prediction model with multiple features can take full advantage of the supplementary information from different features to improve classification performance and prediction robustness. Analysis of the characteristics of lysine residues which can be either methylated or acetylated shows that they are more similar to methyl-lysine than to acetyl-lysine.
Department of Chemistry, Nanchang University, Nanchang 330031, China.
Shao-Ping
SP
Shi
Jian-Ding
JD
Qiu
Xing-Yu
XY
Sun
Sheng-Bao
SB
Suo
Shu-Yun
SY
Huang
Ru-Ping
RP
Liang
D000107:Acetylation; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000378:metabolism; D030562:Databases, Protein; D008239:Lysine / Q000378:metabolism*; D008745:Methylation; D008969:Molecular Sequence Data; D056510:Position-Specific Scoring Matrices; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D060388:Support Vector Machine
D000596:Amino Acids; D011506:Proteins; D008239:Lysine