A comprehensive review of protein-centric predictors for biomolecular interactions: from proteins to nucleic acids and beyond.

Proteins interact with diverse ligands to perform a large number of biological functions, such as gene expression and signal transduction. Accurate identification of these protein-ligand interactions is crucial to the understanding of molecular mechanisms and the development of new drugs. However, traditional biological experiments are time-consuming and expensive. With the development of high-throughput technologies, an increasing amount of protein data is available. In the past decades, many computational methods have been developed to predict protein-ligand interactions. Here, we review a comprehensive set of over 160 protein-ligand interaction predictors, which cover protein-protein, protein-nucleic acid, protein-peptide and protein-other ligands (nucleotide, heme, ion) interactions. We have carried out a comprehensive analysis of the above four types of predictors from several significant perspectives, including their inputs, feature profiles, models, availability, etc. The current methods primarily rely on protein sequences, especially utilizing evolutionary information. The significant improvement in predictions is attributed to deep learning methods. Additionally, sequence-based pretrained models and structure-based approaches are emerging as new trends.

[Polyclonal antibody and immunomagnetic beads preparation technology for type A trichothecenes].

OBJECTIVE: Preparing immunomagnetic beads for enrichment and purification of mask type A trichothecenes. METHODS: Through immunizing New Zealand white rabbits with family A toxin artificial antigen 3-Ac-NEOS-HS-BSA, the polyclonal antibodies of type A trichothecenes( type A family) were isolated, as well as its antibody titre were determinated and purified. The coupling condition of high titer antibody and immunomagnetic beads were optimized and applied. RESULTS: After 5 times of immunization with type A trichothecene family toxin, the rabbit serum inhibited the highest antibody titer( 1 : 64 000). The optimal coupling condition of antibody and immunomagnetic beads were: temperature = 24 ℃, rotation capture in pH 7. 4, 0. 02 mol/L PBS buffer solution with 10% methanol in 24 h. CONCLUSION: The establishment of preparation method of type A single family toxin polyclonal antibody and immunomagnetic beads can make a standard for enrichment and purification of type A matrix complex single family toxins.

A sensitive and validated immunomagnetic-bead based enzyme-linked immunosorbent assay for analyzing total T-2 (free and modified) toxins in shrimp tissues.

Accurate analyses of total T-2 (free and modified) in aquatic organisms including shrimp are important as the hazard caused by T-2 has been caught increasing attention. Therefore, acurate analysis of free T-2 especially of modified T-2 in shrimp tissues is important. A rapid, sensitive, and validated method for quantitative determination of free T-2 and modified T-2 toxin was developed using immunomagnetic-bead based enzyme-linked immunosorbent assay (IMB-ELISA). Super paramagnetic particles with a carboxyl group activated by an ester method coupled with envelope antigen 3- acetylneosolaniol- hemisuccinate - ovalbumin (3-Ac-NEOS-HS-OVA) was used to form immunomagnetic beads which could bind to T-2 skeletal structure antibodies. The conditions for magnetic bead coating of T-2 skeletal structure antibodies, and the concentrations of the polyclonal antibody and HRP-labeled goat anti-rabbit antibody were optimized. A good linear relationship with T-2 concentrations ranging from 5-75ng/mL (R2 =0.9965) was observed. The detection limit of different shrimp tissues of the IMB-ELISA ranged from 2.53 to 3.20ng/mL. And the IC50 was 63ng/mL. The recovery varied from 86% to 99% with a standard deviation of 2.8-5.8%. The application of this method to study the distribution in tissues showed that the total T-2 concentration in hepatopancreas was 26.7µg/kg > blood > head > muscle in the highest dose group of 12.2mg/kg. Our research showed a combination of ELISA and immunomagnetic bead technology provide a new, convenient approach to significantly improve the accuracy and sensitivity of total T-2 measurement in shrimp tissues.

Effects of T-2 Toxin on Pacific White Shrimp Litopenaeus vannamei: Growth, and Antioxidant Defenses and Capacity and Histopathology in the Hepatopancreas.

Modified-masked T-2 toxin (mT-2) formed during metabolism in edible aquatic animals may go undetected by traditional analytical methods, thereby underestimating T-2 toxicity. The effects of T-2 on growth and antioxidant capacity and histopathological changes in the hepatopancreas were studied in Pacific white shrimp Litopenaeus vannamei exposed for 20 d to 0, 0.5, 1.2, 2.4, 4.8, and 12.2 mg/kg of T-2 in their feed. The concentration of mT-2 in the hepatopancreas was detected by liquid chromatography-tandem mass spectrophotometry before and after trifluoroacetic acid (TFA) treatment that converted mT-2 to free T-2. A dose-dependent increase in mT-2 concentration was observed in the hepatopancreas. Dietary exposure to T-2 significantly decreased (P < 0.05) shrimp growth and survival rate compared with the controls. The malondialdehyde (MDA) concentration was significantly increased in shrimp exposed to feed with ≥2.4 mg/kg T-2 (P < 0.05). The antioxidant enzymes, superoxide dismutase (SOD) and glutathione peroxidase (GPx), total antioxidant capacity (T-AOC), and also glutathione (GSH) content increased in shrimp dosed with 2.4-4.8 mg/kg T-2 but declined at the highest dose (12.2 mg/kg), probably indicating an inability to cope with high concentrations of reactive oxygen species (ROS) as evident from a marked increase in MDA (P < 0.05) culminating in cellular toxicity. Histopathological changes in the hepatopancreas were dose dependent, with cell autophagy evident at the highest exposure dose. This is the first report in shrimp of a dose-dependent increase in ROS, SOD enzyme activity, and T-AOC at low T-2 exposures, and associated histopathological changes in the hepatopancreas, in response to dietary T-2. Received January 26, 2016; accepted October 9, 2016.