Inductive inference of novel protein-molecule interactions using Heterogeneous Graph Transformer (HGT) AutoEncoder

Protein-molecule interactions are promoted by the physicochemical characteristics of the actors involved, but structural information alone does not capture expression patterns, localization and pharmacokinetics. In this work we propose an integrative strategy for protein-molecule interaction discovery that combines different layers of information through the use of convolutional operators on graph, and frame the problem as missing link prediction task on an heterogeneous graph constituted by three node types: 1) molecules 2) proteins 3) diseases. Physicochemical information of the actors are encoded using shallow embedding techniques (SeqVec, Mol2Vec, Doc2Vec respectively) and are supplied as feature vectors to a Graph AutoEncoer (GAE) that uses a Heterogeneous Graph Transformer (HGT) in the encoder module. We show in this work that HGT Autoencoder can be used to accurately recapitulate the protein-molecule interactions set and propose novel relationships in inductive settings that are grounded in biological and functional information extracted from the graph.

Sequence based prediction of protein phase separation into disordered condensates using machine learning

Several proteins which are responsible for neuro-degenrerative disorders (Alzheimers, Parkinsons etc) are shown to undergo a mechanism known as liquid liquid phase separation (LLPS). We in this research build a predictor which would answer whether a protein molecule would undergo LLPS or not. For this we used some protein sequences for which we already knew the answer. The ones who undergo LLPS were considered as the positive set and the ones who do not, were taken as the negative set. Depending on the knowledge of amino-acid sequences we identified some relevant variables in the context of LLPS e.g. number of amino acids, length of the best pairings, average register shifts. Using these variables we built a number of scoring functions which were basically analytic functions involving these variables and we also combined some scores already existing in the literature. We considered a total of 43636 protein sequences, among them only 121 were positive. We applied logistic regression and performed cross validation, where 25% of the data were used as the training set and the performance of the obtained results were tested on the remaining 75% of the data. In the training process, we used Simplex algorithm to maximize area under the curve (AUC) in receiver operator characteristics (ROC) space for each of the scores we defined. The optimised parameters were then used to evaluate AUC on the test set to check the accuracy. The best performing score was identified as the predicting model to answer the question whether a protein chain would undergo phase separating behavior or not.

Role of Disulfide Bonds and Sulfhydryl Blocked by N-Ethylmaleimide on the Properties of Different Protein-Stabilized Emulsions

To investigate the role of sulfhydryl groups and disulfide bonds in different protein-stabilized emulsions, N-ethylmaleimide (NEM) was used as a sulfhydryl-blocking agent added in the emulsion. The addition of NEM to block the sulfhydryl groups resulted in a reduction in disulfide bond formation, which enabled the internal structure of the protein molecule to be destroyed, and then decreased the restriction of protein membrane on the oil droplets. Furthermore, with the NEM content increasing in the emulsion, a reduction in the protein emulsifying activity and emulsion stability also occurred. At the same time, the intermolecular interaction of the protein on the oil droplet interface membrane was destroyed, and the emulsion droplet size increased with the NEM content in the emulsion. Although NEM blocking sulfhydryl groups from forming disulfide bonds has similar effects on three types of protein emulsion, the degree of myofibrillar protein (MP), egg-white protein isolate (EPI), and soybean protein isolate (SPI) used as emulsifiers had a subtle difference.

Development of the Composition and Technology for Obtaining Paclitaxel Nanoscale Formulation Consisting of a Conjugate of Polymer Particles with a Protein Vector Molecule

Introduction. The use of the anticancer drug paclitaxel is limited due to its high toxicity and lipophilicity. A new polymer composition of paclitaxel has been proposed, which provides targeted transport of the drug into tumor cells and improves its safety.Aim. Method development for preparation of a novel paclitaxel formulation consisting of a conjugate of PLGA nanoparticles with the third domain of alpha-fetoprotein.Materials and methods. The object of this study is paclitaxel-loaded nanoparticles based on a copolymer of lactic and glycolic acids, the surface of which is modified with a vector molecule - the recombinant third domain of alpha-fetoprotein. Nanoparticles were obtained by single emulsification method and precipitation. Conjugation with a protein molecule was performed by the carbodiimide method. The analysis of the obtained nanoparticles was carried out using dynamic and electrophoretic light scattering, high performance liquid chromatography, dialysis membrane method.Results and discussion. Synthesis of paclitaxel-loaded nanoparticles based on a copolymer of lactic and glycolic acids and its conjugation optimization under varying a wide range of conditions have been carried out. The resulting conjugate had an average diameter of 280 ± 12 nm. The conjugation efficiency was 95 %. The release of paclitaxel from the polymer matrix in the release medium was 65 % in 220 h.Conclusions. A method of obtaining and substantiating the composition of the original nanosized form of paclitaxel is proposed. The possibility of prolonged release of paclitaxel from the polymer matrix has been shown.

Enriching limited information on rare diseases from heterogeneous networks for drug repositioning

Background The historical data of rare disease is very scarce in reality, so how to perform drug repositioning for the rare disease is a great challenge. Most existing methods of drug repositioning for the rare disease usually neglect father–son information, so it is extremely difficult to predict drugs for the rare disease. Method In this paper, we focus on father–son information mining for the rare disease. We propose GRU-Cooperation-Attention-Network (GCAN) to predict drugs for the rare disease. We construct two heterogeneous networks for information enhancement, one network contains the father-nodes of the rare disease and the other network contains the son-nodes information. To bridge two heterogeneous networks, we set a mapping to connect them. What’s more, we use the biased random walk mechanism to collect the information smoothly from two heterogeneous networks, and employ a cooperation attention mechanism to enhance repositioning ability of the network. Result Comparing with traditional methods, GCAN makes full use of father–son information. The experimental results on real drug data from hospitals show that GCAN outperforms state-of-the-art machine learning methods for drug repositioning. Conclusion The performance of GCAN for drug repositioning is mainly limited by the insufficient scale and poor quality of the data. In future research work, we will focus on how to utilize more data such as drug molecule information and protein molecule information for the drug repositioning of the rare disease.

Role of Disulfide Bonds and Sulfhydryl Blocked by N-Ethylmaleimide on the Properties of Different Protein-Stabilized Emulsions

To investigate the role of sulfhydryl groups and disulfide bonds in different protein-stabilized emulsions, N-ethylmaleimide (NEM) was used as sulfhydryl-blocking agent to be added in the emulsion. The addition of NEM to block the sulfhydryl groups resulted in a reduction of the content of disulfide bonds formation, which enabled destruction of the internal structure of the protein molecule, and then decreased the restriction of protein membrane on the oil droplets. Furthermore, with NEM content increasing in the emulsion, a reduction of protein emulsifying activity and emulsion stability also occurred. At the same time, the intermolecular interaction of the protein on the oil droplet interface membrane was destroyed, and the emulsion droplet size increased with the NEM content in the emulsion. Although NEM blocking sulfhydryl groups not to form disulfide bonds has similar effects on three types of protein emulsion, the degree of myofibrillar protein (MP), egg-white protein isolate (EPI), and soybean protein isolate (SPI) as emulsifier had a subtle difference.

Calling the Amino Acid Sequence of a Protein/Peptide from the Nanospectrum Produced by a Sub-nanometer Diameter Pore

The blockade current that develops when a protein translocates across a thin membrane through a sub-nanometer diameter pore (i.e., a nanospectrum) informs with extreme sensitivity on the sequence of amino acids that constitute the protein. Whereas mass spectrometry (MS) is still the dominant technology for protein identification, it suffers limitations. In proteome-wide studies, MS fails to sequence proteins de novo, but merely classifies a protein and it is not very sensitive requiring about a femtomole to do that. Compared with MS, a sub-nanometer diameter pore (i.e. a sub-nanopore) directly reads the amino acids constituting a single protein molecule, but efficient computational tools are still required for processing and interpreting the blockade current. Here, we delineate computational methods for processing sub-nanopore nanospectra and predicting electrical blockade currents from protein sequences, which are essential for protein identification.

The Influence of Various Factors and Changes in the Concentration of the Substrate on the Action Enzymes of Microbial Origin

Использование ферментных препаратов микробного происхождения в промышленности имеет устойчивую тенденцию к увеличению, при этом 2/3 текущего объема составляют ферменты для пищевой промышленности, а их основная доля приходится на спиртовую отрасль. При этом потребность спиртовой отрасли России в комплексных ферментных препаратах составляет около 7 тыс. т, доля отечественных препаратов составляет менее 15%. Объектами исследований служили ферменты микробного происхождения, плесневые грибы, затор спиртового производства. Осахаривание проводили при температуре 57…58 °С, длительность брожения при этом составляла 62 ч. Установлено, что для достижения максимального действия фермента, при других постоянных условиях, требуется сравнительно большая концентрация субстрата. У большинства ферментов вне клетки она выше, чем концентрация данного вещества в организме, то есть фермент действует менее эффективно, чем в искусственно созданных условиях, где он насыщается субстратом. В зависимости от активности расход грибной культуры может колебаться в определенных пределах. Скорость и глубина гидролиза углеводов сырья определяются активностью глубинной культуры плесневого гриба. Таким образом, свойства ферментов определяются главным образом особыми свойствами белков. При этом в молекуле белка изменяется укладка пептидных цепей, что приводит к потере характерных свойств белка. Способность ферментов в благоприятных условиях пережить материнские клетки и проявлять свое действие вне клетки позволяет широко использовать биологические катализаторы в различных отраслях пищевой промышленности. The use of enzyme preparations of microbial origin in industry has a steady tendency to increase, with 2/3 of the current volume being enzymes for the food industry, and their main share is in the alcohol industry. At the same time, the need of the alcohol industry in Russia for complex enzyme preparations is about 7 thousand tons, the share of domestic preparations is less than 15%. The objects of research were enzymes of microbial origin, mold fungi, mash of alcohol production. Saccharification was carried out at a temperature of 57…58 °C, the duration of fermentation was 62 hours. It was found that to achieve the maximum effect of the enzyme, under other constant conditions, a relatively high concentration of the substrate is required. For most enzymes outside the cell, it is higher than the concentration of a given substance in the body, so the enzyme acts less efficiently than in artificially created conditions, where it is saturated with a substrate. Depending on the activity, the consumption of the mushroom culture can fluctuate within certain limits. The rate and depth of hydrolysis of raw carbohydrates are determined by the activity of the deep culture of the mold. Thus, the properties of enzymes are determined mainly by the special properties of proteins. In this case, the folding of peptide chains in the protein molecule changes, which leads to the loss of the characteristic properties of the protein. The ability of enzymes to survive mother cells under favorable conditions and to exert their action outside the cell makes it possible to widely use biological catalysts in various branches of the food industry.

SpCrus2 Glycine-Rich Region Contributes Largely to the Antiviral Activity of the Whole-Protein Molecule by Interacting with VP26, a WSSV Structural Protein

Crustins are cysteine-rich cationic antimicrobial peptides with diverse biological functions including antimicrobial and proteinase inhibitory activities in crustaceans. Although a few crustins reportedly respond to white spot syndrome virus (WSSV) infection, the detailed antiviral mechanisms of crustins remain largely unknown. Our previous research has shown that SpCrus2, from mud crab Scylla paramamosain, is a type II crustin containing a glycine-rich region (GRR) and a cysteine-rich region (CRR). In the present study, we found that SpCrus2 was upregulated in gills after WSSV challenge. Knockdown of SpCrus2 by injecting double-stranded RNA (dsSpCrus2) resulted in remarkably increased virus copies in mud crabs after infection with WSSV. These results suggested that SpCrus2 played a critical role in the antiviral immunity of mud crab. A GST pull-down assay showed that recombinant SpCrus2 interacted specifically with WSSV structural protein VP26, and this result was further confirmed by a co-immunoprecipitation assay with Drosophila S2 cells. As the signature sequence of type II crustin, SpCrus2 GRR is a glycine-rich cationic polypeptide with amphipathic properties. Our study demonstrated that the GRR and CRR of SpCrus2 exhibited binding activities to VP26, with the former displaying more potent binding ability than the latter. Interestingly, pre-incubating WSSV particles with recombinant SpCrus2 (rSpCrus2), rGRR, or rCRR inhibited virus proliferation in vivo; moreover, rSpCrus2 and rGRR possessed similar antiviral abilities, which were much stronger than those of rCRR. These findings indicated that SpCrus2 GRR contributed largely to the antiviral ability of SpCrus2, and that the stronger antiviral ability of GRR might result from its stronger binding activity to the viral structural protein. Overall, this study provided new insights into the antiviral mechanism of SpCrus2 and the development of new antiviral drugs.

Targeted Protein Degradation: Current Status and Future Prospects

The protein degradation is a well-controlled, highly selective mechanism for intracellular protein degradation and its turnover. There are several proteins in our body but among them some goes for degradation at a time. Proteins which are going to be degraded are identified by a 76 amino acid polypeptide known as ubiquitin and the process is known as ubiquitination. Ubiquitation means the attachment of many ubiquitin molecules to the target protein molecule that need to be broken down. During the ubiquitination procedure iso peptide bonds are formed. And these iso peptide bonds are formed between the nitrogen molecule of the lysine residue from the target protein and the carbon molecule of the ubiquitin molecule. Through this endogenous ubiquitin-proteasome machinery, disease responsible proteins can be permanently removed. Energy is required for this process and that’s why ATP is employed in this process. This targeted protein degradation plays a very crucial role for cancer and other diseases. Through this review we just enlighten the significant points if the targeted protein degradation and its significance.