Deep2Pep: A deep learning method in multi-label classification of bioactive peptide.

Functional peptides are easy to absorb and have low side effects, which has attracted increasing interest from pharmaceutical scientists. However, due to the limitations in the laboratory funding and human resources, it is difficult to screen the functional peptides from a large number of peptides with unknown functions. With the development of machine learning and Deep learning, the combination of computational methods and biological information provides an effective method for identifying peptide functions. To explore the value of multi-functional active peptides, a new deep learning method named Deep2Pep (Deep learning to Peptides) was constructed, which was based on sequence encoding, embedding, and language tokenizer. It can achieve predictions of peptides on antimicrobial, antihypertensive, antioxidant and antihyperglycemic by converting sequence information into digital vectors, combined BiLSTM, attention-residual algorithm, and BERT Encoder. The results showed that Deep2Pep had a Hamming Loss of 0.095, subset Accuracy of 0.737, and Macro F1-Score of 0.734. which outperformed other models. BiLSTM played a primary role in Deep2Pep, which BERT encoder was in an auxiliary position. Deep learning algorithms was used in this study to accurately predict the four active functions of peptides, and it was expected to provide effective references for predicting multi-functional peptides.

New insight into the mechanism by which antifreeze peptides regulate the physiological function of Streptococcus thermophilus subjected to freezing stress.

INTRODUCTION: Antifreeze peptides regulate the physiological functions of frozen cells and even their apoptosis; however, the mechanisms by which antifreeze peptides regulate these processes remain unclear, although the interactions between cell membranes and ice are well known to be important in this process. OBJECTIVES: Our study aims to investigate how antifreeze peptides regulate cell physiological functions during the freezing process. METHODS: We investigated the cryoprotective effect of rsfAFP on the physiological functions of S. thermophilus under freezing stress by measuring cellular metabolism activity, intracellular enzyme activity, cell membrane characterization, and cell apoptosis. The mechanism by which rsfAFP impacts S. thermophilus physiological functions under freezing stress was investigated using multispectral techniques and cryo-TEM. RESULTS: We show that a recombinant antifreeze peptide (rsfAFP) interacts with the extracellular capsular polysaccharides and peptidoglycan of Streptococcus thermophilus and ice to cover the outer layer of the membrane, forming a dense protective layer that regulates the molecular structure of extracellular ice crystals, which results in reduced extracellular membrane damage, depressed apoptosis and increased intracellular metabolic activity. This interaction mechanism was indicated by the fact that S. thermophilus better maintained its permeability barrier, membrane fluidity, membrane structural integrity, and cytoplasmic membrane potential during freezing stress with rsfAFP treatment. CONCLUSION: These results provide new insights into the mechanism by which rsfAFP regulates frozen cellphysiological functionsand apoptosis under freezing stress.

Effects of simultaneous and sequential cofermentation of Wickerhamomyces anomalus and Saccharomyces cerevisiae on physicochemical and flavor properties of rice wine.

Microorganism species and inoculation fermentation methods have great influence on physicochemical and flavor properties of rice wine. Thus, this work investigated microbial interactions and physicochemical and aroma changes of rice wine through different inoculation strategies of Wickerhamomyces anomalus (W. anomalus) and Saccharomyces cerevisiae (S. cerevisiae). The results underlined that inoculation strategies and non-Saccharomyces yeasts all affected the volatile acidity, total acidity, and alcohol content of rice wine. The sequential cofermentation consumed relatively more sugar and resulted in the higher ethanol content, causing reduced thiols and increased alcohols, esters, phenylethyls, and terpenes, which was more conducive to improve rice wine flavor than simultaneous cofermentation. Moreover, simultaneous cofermentation increased fatty aroma of rice wine, while sequential cofermentation increased mellow and cereal-like flavor. These results confirmed that sequential cofermentation of S. cerevisiae and W. anomalus was a choice for the future production of rice wine with good flavor and quality.

Citral stabilization and characterization of nanoemulsions stabilized by a mixture of gelatin and Tween 20 in an acidic system.

BACKGROUND: Citral is one of the most important flavor compounds in fresh juice and lemon oil. Unfortunately, citral is chemically unstable and degrades over time in aqueous solutions. Here, citral nanoemulsions including a mixture of gelatin and Tween 20 as emulsifiers were produced in an effort to maintain the stability of citral in an acidic system. RESULTS: The mean droplet size and polydispersity index of the citral nanoemulsion were 467.83 nm and 0.259 respectively when the mass ratio of gelatin/Tween 20 was 3:1 and the total emulsifier concentration of the emulsion system was 10 g kg-1 . The citral nanoemulsion remained stable during storage for 14 days at 30 °C. Therefore this nanoemulsion system effectively protected citral from degradation and decreased the formation of off-flavor compounds (e.g. p-cymene, p-cresol and p-methylacetophenone) relative to a single emulsifier. CONCLUSION: The mixture of gelatin and Tween 20 enhanced the stability of citral under acidic conditions and could be used as an effective emulsifier to protect citral from degradation under acidic environments in the food industry. © 2016 Society of Chemical Industry.

Isolation and characterisation of sericin antifreeze peptides and molecular dynamics modelling of their ice-binding interaction.

This study aimed to isolate and characterise a novel sericin antifreeze peptide and investigate its ice-binding molecular mechanism. The thermal hysteresis activity of ice-binding sericin peptides (I-SP) was measured and their activity reached as high as 0.94 °C. A P4 fraction, with high hypothermia protective activity and inhibition activity of ice recrystallisation, was obtained from I-SP, and a purified sericin peptide, named SM-AFP, with the sequence of TTSPTNVSTT and a molecular weight of 1009.50 Da was then isolated from the P4 fraction. Treatment of Lactobacillus delbrueckii Subsp. bulgaricus LB340 LYO with 100 µg/ml synthetic SM-AFP led to 1.4-fold increased survival (p < 0.05). Finally, an SM-AFP/ice binding model was constructed and results of molecular dynamics simulation suggested that the binding of SM-AFP with ice and prevention of ice crystal growth could be attributed to hydrogen bond formation, hydrophobic interaction and non-bond interactions. Sericin peptides could be developed into beneficial cryoprotectants and used in frozen food processing.

Study on structural and spectral properties of isobavachalcone and 4-hydroxyderricin by computational method.

Isobavachalcone and 4-hydroxyderricin, two major chalcone constituents isolated from the roots of Angelica keiskei KOIDZUMI, exhibit numerous biological activities. Quantum chemical methods have been employed to investigate their structural and spectral properties. The ground state structures were optimized using density functional B3LYP method with 6-311G (d, p) basis set in both gas and solvent phases. Based on the optimized geometries, the harmonic vibrational frequency, the (1)H and (13)C nuclear magnetic resonance (NMR) chemical shift using the GIAO method were calculated at the same level of theory, with the aim of verifying the experimental values. Results reveal that B3LYP has been a good method to study their vibrational spectroscopic and NMR spectral properties of the two chalcones. The electronic absorption spectra were calculated using the time-dependent density functional theory (TDDFT) method. The solvent polarity effects were considered and calculated using the polarizable continuum model (PCM). Results also show that substitutions of different electron donating groups can alter the absorption properties and shift the spectra to a higher wavelength region.

A theoretical study on cellular antioxidant activity of selected flavonoids.

The antioxidant capacities of the selected flavonoids quercetin, luteolin and taxifolin have been investigated at density functional level of theory with the aim of verifying the cellular antioxidant activity (CAA) values representative of experimental findings. The selected flavonoids were believed to act through the H-atom transfer mechanism. Their potentiality of hydrogen abstraction was evaluated by computing the OH bond dissociation enthalpy (BDE) in gas-phase and in dimethylsulfoxide solution. Results indicate that the order of antioxidant efficacies calculated in this work is in agreement with that reported by experimental results of CAA. Time-dependent density functional theory (TDDFT) calculations were also performed both in gas-phase and in dimethylsulfoxide to reproduce the electronic UV-vis spectra of the selected flavonoids.

Experimental and theoretical study on the structure and electronic spectra of imiquimod and its synthetic intermediates.

Crystal structure of the imiquimod has been determined by single crystal X-ray analysis, imiquimod crystallizes in orthorhombic space group P2(1)2(1)2(1) and the molecules are linked along the c axis by the strong N-H ... N hydrogen bonds. A density functional theory (DFT) study on the electronic properties of imiquimod and its synthetic intermediates has been performed at B3LYP/6-31G* level, while taking solvent effects into account. Both the single configuration interaction (CIS) method and the time-dependent DFT (TDDFT) approaches have been used to calculate the electronic absorption spectra, and there is a good agreement between the calculated and experimental UV-visible absorption spectra. The fluorescence emission spectra of these three compounds in solution have also been measured, the relatively low fluorescence intensity is attributed to a chlorine-modulated heavy atom effect that enhances intersystem crossing between excited singlet and triplet states, and the relatively high fluorescence intensity of imiquimod results from an extended pi-conjugated system which enhances S(1)-->S(0) radiant transition.