The Positively Charged Active Site of the Bacterial Toxin RelE Causes a Large Shift in the General Base pKa

PseAraUbi: predicting arabidopsis ubiquitination sites by incorporating the physico-chemical and structural features

We makes three kinds of important features from Arabidopsis thaliana: protein secondary structure based on the Chou-Fasman parameter, amino acids hydrophobicity and polarity information, and analyze their properties. Ubiquitination modification is an important post-translational modification of proteins, which participates in the regulation of many important life activities in cells. At present, ubiquitination proteomics research is mostly concentrated in animals and yeasts, while relatively few studies have been carried out in plants. It can be said that the calculation and prediction of Arabidopsis thaliana ubiquitination sites is still in its infancy. Based on this, we describe a calculation method, PseAraUbi (Prediction of Arabidopsis thaliana ubiquitination sites using pseudo amino acid composition), that can effectively detect ubiquitination sites on Arabidopsis thaliana using support vector machine learning classifiers. Based on protein sequence information, extract features from the Chou-Fasman parameter, amino acids hydrophobicity features, polarity information and selected for classification with the Boruta algorithm. PseAraUbi achieves promising performances with an AUC score of 0.953 with fivefold cross-validation on the training dataset, which are significantly better than that of the pioneer Arabidopsis thaliana ubiquitination sites method. We also proved the ability of our proposed method on independent test sets, thus gaining a competitive advantage. In addition, we also in-depth analyzed the physicochemical properties of amino acids in the region adjacent to the ubiquitination site. To facilitate the community, the source code, optimal feature subset, ubiquitination sites dataset in the Arbidopsis proteome are available at GitHub ( https://github.com/HNUBioinformatics/PseAraUbi.git ) for interest users.

Structure and chemistry of enzymatic active sites that play a role in the switch and conformation mechanism

Enzymes, which are biological molecules, are constructed from polypeptide chains, and these molecules are activated through reaction mechanisms. It is the role of enzymes to speed up chemical reactions that are used to build or break down cell structures. Activation energy is reduced by the enzymes' selective binding of substrates in a protected environment. In enzyme tertiary structures, the active sites are commonly situated in a "cleft," which necessitates the diffusion of substrates and products. The amino acid residues of the active site may be far apart in the primary structure owing to the folding required for tertiary structure. Due to their critical role in substrate binding and attraction, changes in amino acid structure at or near the enzyme's active site usually alter enzyme activity. At the enzyme's active site, or where the chemical reactions occur, the substrate is bound. Enzyme substrates are the primary targets of the enzyme's active site, which is designed to assist in the chemical reaction. This chapter elucidates the summary of structure and chemistry of enzymes, their active site features, charges and role of water in the structures to clarify the biochemistry of the enzymes in the depth of atomic features.

Synthesis of Oligoribonucleotides Containing a 2'-Amino-5'-S-phosphorothiolate Linkage

Oligoribonucleotides containing a photocaged 2′-amino-5′-S-phophorothiolate linkage have potential applications as therapeutic agents and biological probes to investigate the RNA structure and function. We envisioned that oligoribonucleotides containing a 2′-amino-5′-S-phosphorothiolate linkage could provide an approach to identify the general base within catalytic RNAs by chemogenetic suppression. To enable preliminary tests of this idea, we developed synthetic approaches to a dinucleotide, trinucleotide, and oligoribonucleotide containing a photocaged 2′-amino-5′-S-phosphorothiolate linkage. We incorporated the photocaged 2′-amino-5′-S-phosphorothiolate linkage into an oligoribonucleotide substrate for the hepatitis delta virus (HDV) ribozyme and investigated the pH dependence of its cleavage following UV irradiation both in the presence and absence of the ribozyme. The substrate exhibited a pH-rate profile characteristic of the modified linkage but reacted slower when bound to the ribozyme. Cleavage inhibition by the HDV ribozyme could reflect a non-productive ground-state interaction with the modified substrate’s nucleophilic 2′-NH₂ or a poor fit of the modified transition state at the ribozyme’s active site.