Analysis using top‐k skyline query of protein‐protein interaction reveals alpha‐synuclein as the most important protein in Parkinson’s disease

Parkinson’s disease is the second‐most‐common neurodegenerative disorder and can reduce patients’ quality of life. The disease is caused by abnormalities in dopaminergic neurons, such as reactive oxygen species (ROS) imbalance leading to programmed cell death, protein misfolding, and vesicle trafficking. Protein‐protein interaction (PPI) analysis has been demonstrated to understand better candidate proteins that might contribute to multifactorial neurodegenerative diseases, particularly in Parkinson’s disease. PPI analysis can be obtained from experiments and computational predictions. However, experiment data is often limited in interactome coverage. Therefore, additional computational prediction methods are required to provide more comprehensive PPI information. PPI can be represented as protein‐protein networks and analyzed based on centrality measures. The previous study has shown that top‐k skyline query, a method using dominance rule‐based centrality measures, reveals important protein candidates in Parkinson’s diseases. This study applied the top‐k skyline query to PPIs containing experiment and prediction data to find important proteins in Parkinson’s disease. The result shows that alpha‐synuclein (SNCA) is the most important protein and is expected to be a potential biomarker candidate for Parkinson’s disease.

Controlling the adsorption of osteopontin for mediating cell behaviour by using self-assembled monolayers with varying surface chemistry

Osteopontin (OPN) is an important protein for mediating cell behaviour on biomaterials.

Computational identification of human ubiquitination sites using convolutional and recurrent neural networks

Ubiquitination is a very important protein post-translational modification in human, which is closely related to many human diseases such as cancers. Although some methods have been elegantly proposed to predict...

Collagen and the Effect of Poly-L-lactic Acid based Materials on its Synthesis

Collagen is an important protein in various biological functions such as providing elasticity and waterproofing to the skin, structural stability to the cells in connective tissues (e.g. tendons, and bone)...

Structure Basis for Inhibition of SARS-CoV-2 by the Feline Drug GC376

The pandemic of SARS-CoV-2 coronavirus disease-2019 (COVID-19) caused by SARS-COV-2 continues to ravage many countries in the world. Mpro is an indispensable protein for viral translation in SARS-CoV-2 and a potential target in high-specificity anti-SARS-CoV-2 drug screening. In this study, to explore potential drugs for treating COVID-19, we elucidated the structure of SARS-CoV-2 Mpro and explored the interaction between Mpro and GC376, an antiviral drug used to treat a range of coronaviruses in Feline via inhibiting Mpro. The availability and safety of GC376 were proved by biochemical and cell experiments in vitro. We determined the structure of an important protein, Mpro, in SARS-CoV-2, and revealed the interaction of GC376 with the viral substrate and inhibition of the catalytic site of SARS-CoV-2 Mpro.

Predominant cleavage of proteins N-terminal to serines and threonines using scandium(III) triflate

Proteolytic digestion prior to LC–MS analysis is a key step for the identification of proteins. Digestion of proteins is typically performed with trypsin, but certain proteins or important protein sequence regions might be missed using this endoproteinase. Only few alternative endoproteinases are available and chemical cleavage of proteins is rarely used. Recently, it has been reported that some metal complexes can act as artificial proteases. In particular, the Lewis acid scandium(III) triflate has been shown to catalyze the cleavage of peptide bonds to serine and threonine residues. Therefore, we investigated if this compound can also be used for the cleavage of proteins. For this purpose, several single proteins, the 20S immune-proteasome (17 proteins), and the Universal Proteomics Standard UPS1 (48 proteins) were analyzed by MALDI–MS and/or LC–MS. A high cleavage specificity N-terminal to serine and threonine residues was observed, but also additional peptides with deviating cleavage specificity were found. Scandium(III) triflate can be a useful tool in protein analysis as no other reagent has been reported yet which showed cleavage specificity within proteins to serines and threonines. Graphic abstract

A Review of the Role of Amelogenin Protein in Enamel Formation and Novel Experimental Techniques to Study its Function

: Amelognein protein plays a vital role in the formation and mineralization of enamel matrix. Amelogenin structure is complex in nature and researchers have studied it with different experimental techniques. Considering its important role, there is a need to understand this important protein, which has been discussed in detail in this review. In addition, various experimental techniques to study amelogenin protein used previously have been tackled along with their advantages and disadvantages. A selection of 67 relevant articles/book chapters was included in this study. The review concluded that amelogenins act as nanospheres or spacers for the growth of enamel crystals. Various experimental techniques can be used to study amelogenins, however, their advantages and drawbacks should be kept in mind before performing analysis.

Whole-Genome Sequencing of Nontyphoidal Salmonella enterica Isolates Obtained from Various Meat Types in Ghana

Here, we report the draft genome sequences of 16 nontyphoidal Salmonella enterica isolates obtained from locally produced meats in Tamale, Ghana, which are commonly consumed by most natives as an important protein source. The draft genomes will help provide a molecular snapshot of Salmonella enterica isolates found in these retail meats in Tamale.