[Post-translational modification (PTM) bioinformatics in China: progresses and perspectives].

Post-translational modifications (PTMs) are essential for regulating conformational changes, activities and functions of proteins, and are involved in almost all cellular pathways and processes. Identification of protein PTMs is the basis for understanding cellular and molecular mechanisms. In contrast with labor-intensive and time-consuming experiments, the PTM prediction using various bioinformatics approaches can provide accurate, convenient, and efficient strategies and generate valuable information for further experimental consideration.

Improving the accuracy of predicting disulfide connectivity by feature selection.

Disulfide bonds are primary covalent cross-links formed between two cysteine residues in the same or different protein polypeptide chains, which play important roles in the folding and stability of proteins. However, computational prediction of disulfide connectivity directly from protein primary sequences is challenging due to the nonlocal nature of disulfide bonds in the context of sequences, and the number of possible disulfide patterns grows exponentially when the number of cysteine residues increases. In the previous studies, disulfide connectivity prediction was usually performed in high-dimensional feature space, which can cause a variety of problems in statistical learning, such as the dimension disaster, overfitting, and feature redundancy.

A novel method of analyzing proline synonymous codons in E. coli.

Proline is a special imino acid in protein and the isomerization of the prolyl peptide bond has notable biological significance and influences the final structure of protein greatly, so the correlation between proline synonymous codon usage and local amino acid, the correlation between proline synonymous codon usage and the isomerization of the prolyl peptide bond were both investigated in the Escherichia coli genome by using a novel method based on information theory. The results show that in peptide chain, the residue at the first position C-terminal influences the usage of proline synonymous codon greatly and proline synonymous codons contain some factors influencing the isomerization of the prolyl peptide bond.

Cooperativity of the oxidization of cysteines in globular proteins.

Based on the 639 non-homologous proteins with 2910 cysteine-containing segments of well-resolved three-dimensional structures, a novel approach has been proposed to predict the disulfide-bonding state of cysteines in proteins by constructing a two-stage classifier combining a first global linear discriminator based on their amino acid composition and a second local support vector machine classifier. The overall prediction accuracy of this hybrid classifier for the disulfide-bonding state of cysteines in proteins has scored 84.1% and 80.

Prediction of the disulfide-bonding state of cysteines in proteins based on dipeptide composition.

In this paper, a novel approach has been introduced to predict the disulfide-bonding state of cysteines in proteins by means of a linear discriminator based on their dipeptide composition. The prediction is performed with a newly enlarged dataset with 8114 cysteine-containing segments extracted from 1856 non-homologous proteins of well-resolved three-dimensional structures. The oxidation of cysteines exhibits obvious cooperativity: almost all cysteines in disulfide-bond-containing proteins are in the oxidized form.