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Posttranslational modification is the chemical-modification of a protein after translation, which is one of the essential later steps in protein maturation for many proteins. Post-translational modifications such as methylation, acylation, glycosylation, phosphorylation, and sulfation, to name a few, serve many functions. As a consequence, the analysis of proteins and their post-translational modifications is particularly important for the study of complex diseases where multiple genes are to be involved, such as heart disease, cancer and diabetes. Protein methylation, which is one of most important post-translational modification, typically takes place on arginine or lysine residues in the protein sequence. Arginine can be methylated once (mono-methylated Arg) or twice, with either both methyl groups on one terminal nitrogen (asymmetric dimethylated Arg) or one on both nitrogens (symmetric dimethylated Arg) by peptidylarginine methyltransferases (PRMTs); while Lysine can be methylated once, twice or three times by lysine methyltransferases.
Relative research traced back to 1959, Ambler and Rees  first discovered e-N-methyllysine in the flagella protein of S. typhimurium and, subsequently, during the early 1960s Murray  found methylation in the acid-hydrolysates of histones isolated from calf thymus, wheat germ and various rabbit organs. Nowadays, protein methylation has been most well studied in the histones. The methyl groups from S-adenosyl methionine transfer to histones catalyzed by histone methyltransferases, which can act epigenetically to repress or activate gene expression[4, 5]. Protein methylation is a reversible type of posttranslational modification, just like phosphorylation and sumoylation. It has been reported that that LSD1 (lysine-specific demethylase 1) is responsible for the demethylation of histone H3 K4, JHDM1 (JmjC domain-containing histone demethylase 1) is responsible for the demethylation of K36. Most histone lysine methylation, with the exception of histone H3 K79, has been shown to be catalyzed exclusively by the conserved SET domain superfamily proteins[8, 9].
The full extent of regulatory roles of protein methylation is still under elusive investigation. Importantly, identification of methylated proteins with specific methylation sites will be a foundation of understanding the molecular mechanism of protein methylation. Besides the experimental methods, such as mutagenesis of potential methylated residues, methylation-specific antibodies  and mass-spectrometry[11, 12], in silico prediction of methylation sites is much more desirable for its much more convenience and fast speed. Up to now, a few of previous methods were published for protein methylation site prediction. Such as MeMo, a protein methylation site prediction online tool for based on Support Vector Machines (SVMs); while another group developed another novel approach called Bi-profile Bayes also based on SVMs algorithm.
In this paper, we present a new generation algorithm predicting methylation sites based on Position-Specific Iterated BLAST (PSIBLAST) program and with optimized by Position-Specific Scoring Matrices (PSSM)[16-18] plus multivariate statistical analyses of a large number of amino acid attributes to resolve this sequence metric problem. Our analysis results obtained from cross-validation experiments and test on independent data sets indicate more effectiveness than Bi-profile Bayes or Memo. This method is a novel general arginine and lysine methylation tool and can provide probability information for prediction results than provided before.
Protein methylation, one of most important post-translational modification, typically takes place on arginine or lysine amino acid residues in the protein sequence. Due to this issue, we analysis the arginine or lysine methylation diagrams separately. Based on our results, the lysine methylation surrounding sites play an important role in determining the methylation, especially for the -2 to +2 site. The PSSM results show a little bit different, including -4 and +4 sites. In the 506 physical-chemistry parameters, the amino acid composition contributes most and secondary structure properties the second in determining the methylation. Regarding protein-lysine methylation, the bulk of recent research references have primarily been focused on histone methylation[20, 21]. This is undoubtedly a result of the lure that histone possess, as components of the nucleosome, in controlling genetic expression. The mechanisms and biological importance of DNA methylation at each particular lysine residue in the H3 and H4 histone subunits continue to be unraveled. Methylation of several lysine residues in the H3 subunit (Lys36 and Lys79) are linked with euchromatin and transcriptional activation, whereas methylation of other residues in H3 and H4 (H3 Lys4, H3 Lys9, H3 Lys27 and H4 Lys20) are associated with heterochromatin and transcriptional repression[22, 23]. The reaction requires iron and a-ketoglutarate as cofactors. Structural analyses reveal that methylated histones are bound predominantly through backbone interactions. The catalytic center locate in a deep pocket and the peptide chain must be bent to fit into this cavity. As a result, the enzyme motif secondary structure is essential for that targeting reaction. Extensive site-directed mutagenesis shows that this binding motif critically depends on the presence of flexible amino acid residues, allowing proper peptide bending to achieve a catalytically productive position. The amino acid composition for the enzymes reaction site is also understandable. Most enzymes bind the methylated lysine in a polar environment, which resembles the 'carbonyl cage' of SET domains rather than the hydrophobic pockets of chromo domain-related motifs. The methyl-groups are cooperated by a set of electrostatic interactions between polar residues of the protein and the trimethylammonium. CHâˆ™âˆ™âˆ™O-H-bonds form between oxygen on the enzyme's side-chains and methyl-groups of the methyl-lysine[26, 27]. These interactions cumulatively locate one of the methyl-groups in vicinity of the iron for hydroxylation to occur. All this data strengthen the role of surrounding sites the enzymes reorganization.
The surrounding positional sites role of arginine methylation shows a little difference[28, 29]. The -1− +2 positions especially +1 for recognition of the substrate arginine. The PSSM results show a little bit different, including -2 and +2 sites. Arginine is unique among 20 amino acids as its guanidino group has five potential hydrogen bond donors that are positioned for favorable interactions with biological hydrogen bond acceptors. In protein-DNA complexes, Arg residues are the most frequent hydrogen bond donors to backbone phosphate groups and to thymine, adenine, and guanine bases. The context of methylated residues in these proteins differs from the original consensus for asymmetrically dimethylated proteins, suggesting the importance of residues in the -1 to -2 positions for recognition of the substrate arginine. In the 506 physical-chemistry parameters, electrostatic charge, the amino acid composition and secondary structure properties contribute a lot in determining the methylation assurances. PRMT, formerly named as protein methylase I, is not only specific for Gly-Arg-Gly or Gly-Ala-Arg primary sequences but is also highly specific for the higher structure of proteins. The diversity of these enzymes superfamilies is enhanced by alternative splicing reactions that lead to amino acid sequence variants. The mammalian PRMT family currently contains nine highly conservative members; all harbor signature motifs I, post-I, II, and III and the conserved THW loop in the secondary structure. Based on the known substrates, few of clear recognition consensuses have identified. Crystal structures of the conserved core region of PRMT have been published for Hmt1, PRMT3, and PRMT1, in some cases in complex with S adenosylhomocysteine and/or some substrate peptides, show that the core region consists of two domains folded together into an integral structure. The N-terminal half of the core, containing a typical Rossman fold and two α-helices, is the AdoMet-binding domain, the most highly conserved region among PRMTs and also partially conserved in other types of AdoMet-dependent methyltransferases The C-terminal half of the core forms a barrel-like structure, unique to the PRMT family, which folds against the N-terminal AdoMetbinding region. The results provides a cleft between protein substrate binding site and the catalysis site. All these relative publications stress the essential role in secondary structure. The three-dimensional structure analysis is also consistence with which our parameters including electrostatic charge and secondary structural properties are essential for the enzymatic activity. Mutation of dimer contact residues of Hmt1 or deletion of the PRMT1 dimerization arm eliminates the enzymatic activity, which enhance the role of amino acid composition to the enzyme activity function.