Computational analysis of transition temperatures (Tts) of proteins fused to elastin-like polypeptide (ELP): deep fake evaluation of proteins, linkers, and trailers features

The phase transition temperature (Tt) prediction of the Elastin-like polypeptides (ELPs) is not trivial because it is related to complex sets of variables such as composition, sequence length, hydrophobic characterization, hydrophilic characterization, the sequence order in the fused proteins, linkers and trailer constructs. In this paper, two unique quantitative models are presented for the prediction of the Tt of a family of ELPs that could be fused to different proteins, linkers, and trailers. The lack of need to use multiple software, peptide information, such as PDB file, as well as knowing the second and third structures of proteins are the advantages of this model besides its high accuracy and speed. One of our models could predict the Tt values of the fused ELPs by entering the protein, linker, and trailer features with R2=99%. Also, another model is able to predict the Tt value by entering the fused protein feature with R2=96%. For more reliability, our method is enriched by Artificial Intelligence (AI) to generate similar proteins. In this regard, Generative Adversarial Network (GAN) is our AI method to create fake proteins and similar values. The experimental results show that our strategy for prediction of Tt is reliable in large data.

A Review of Biopolymers’ Utility as Emulsion Stabilizers

Polysaccharides, polynucleotides, and polypeptides are basic natural polymers. They have various applications based on their properties. This review mostly discusses the application of natural polymers as emulsion stabilizers. Natural emulsion stabilizers are polymers of amino acid, nucleic acid, carbohydrate, etc., which are derived from microorganisms, bacteria, and other organic materials. Plant and animal proteins are basic sources of natural emulsion stabilizers. Pea protein-maltodextrin and lentil protein feature entrapment capacity up to 88%, (1–10% concentrated), zein proteins feature 74–89% entrapment efficiency, soy proteins in various concentrations increase dissolution, retention, and stability to the emulsion and whey proteins, egg proteins, and proteins from all other animals are applicable in membrane formation and encapsulation to stabilize emulsion/nanoemulsion. In pharmaceutical industries, phospholipids, phosphatidyl choline (PC), phosphatidyl ethanol-amine (PE), and phosphatidyl glycerol (PG)-based stabilizers are very effective as emulsion stabilizers. Lecithin (a combination of phospholipids) is used in the cosmetics and food industries. Various factors such as temperature, pH, droplets size, etc. destabilize the emulsion. Therefore, the emulsion stabilizers are used to stabilize, preserve and safely deliver the formulated drugs, also as a preservative in food and stabilizer in cosmetic products. Natural emulsion stabilizers offer great advantages because they are naturally degradable, ecologically effective, non-toxic, easily available in nature, non-carcinogenic, and not harmful to health.

Empirical Study of Protein Feature Representation on Deep Belief Networks Trained with Small Data for Secondary Structure Prediction

Small data training approach using Deep Belief Networks applied to two different types of protein feature representation

Empirical Study of Protein Feature Representation on Deep Belief Networks Trained with Small Data for Secondary Structure Prediction

Small data training approach using Deep Belief Networks applied to two different types of protein feature representation

Molecular basis for the adaptive evolution of environment sensing by H-NS proteins

The DNA-binding protein H-NS is a pleiotropic gene regulator in gram-negative bacteria. Through its capacity to sense temperature and other environmental factors, H-NS allows pathogens like Salmonella to adapt their gene expression to their presence inside or outside warm-blooded hosts. To investigate how this sensing mechanism may have evolved to fit different bacterial lifestyles, we compared H-NS orthologs from bacteria that infect humans, plants, and insects, and from bacteria that live on a deep-sea hypothermal vent. The combination of biophysical characterization, high-resolution proton-less NMR spectroscopy and molecular simulations revealed, at an atomistic level, how the same general mechanism was adapted to specific habitats and lifestyles. In particular, we demonstrate how environment-sensing characteristics arise from specifically positioned intra- or intermolecular electrostatic interactions. Our integrative approach clarified the exact modus operandi for H-NS–mediated environmental sensing and suggests that this sensing mechanism resulted from the exaptation of an ancestral protein feature.

Proteomic profiling of breast cancer cell lines and models

We performed quantitative proteomics on 60 human-derived breast cancer cell lines to a depth of ~13,000 proteins. The resulting high-throughput datasets were assessed for quality and reproducibility. We used the datasets to identify and characterize the subtypes of breast cancer and showed that they conform to known transcriptional subtypes, revealing that molecular subtypes are preserved even in under-sampled protein feature sets. All datasets are freely available as public resources on the LINCS portal. We anticipate that these datasets, either in isolation or in combination with complimentary measurements such as genomics, transcriptomics and phosphoproteomics, can be mined for the purpose of predicting drug response, informing cell line specific context in models of signalling pathways, and identifying markers of sensitivity or resistance to therapeutics.

Molecular Basis for the Adaptive Evolution of Environment Sensing by H-NS Proteins

The DNA-binding protein H-NS is a pleiotropic gene regulator in gram-negative bacteria. Through its capacity to sense temperature and other environmental factors, H-NS allows pathogens like Salmonella to adapt their gene expression, and hence toxicity and biological responses, to their presence inside or outside warm-blooded hosts. To investigate how this sensing mechanism may have evolved to fit different bacterial lifestyles, we compared H-NS orthologs from bacteria that infect humans, plants, and insects, and from bacteria that live on a deep-sea hypothermal vent. The combination of biophysical characterization, high-resolution proton-less NMR spectroscopy and molecular simulations revealed, at an atomistic level, how the same general mechanism was adapted to specific habitats and lifestyles. In particular, we demonstrate how environment-sensing characteristics arise from specifically positioned intra- or intermolecular electrostatic interactions. Our integrative approach clarified the mechanism for H-NS–mediated environmental sensing and suggests that it resulted from the exaptation of an ancestral protein feature.