Equivalence of the Transition Heat Capacities of Proteins and DNA

It has been reported for many globular proteins that the native heat capacity at 25°C, per gram, is the same. This has been interpreted to indicate that heat capacity is a fundamental property of native proteins that provides important information on molecular structure and stability. Heat capacities for both proteins and DNA has been suggested to be related to universal effects of hydration/solvation on native structures. Here we report on results from thermal denaturation analysis of two well-known proteins, human serum albumin and lysozyme, and a short DNA hairpin. The transition heat capacities at the Tm for the three molecules were quantitatively evaluated by differential scanning calorimetry. When normalized per gram rather than per mol the transition heat capacities were found to be precisely equivalent. This observation for the transition heat capacities of the proteins is consistent with previous reports. However, an identical transition heat capacity for DNA has not been reported and was unexpected. Further analysis of the collected data suggested a mass dependence of hydration effects on thermal denaturation that is preserved at the individual protein amino acid and DNA base levels. Equivalence of transition heat capacities suggests the possibility of a universal role of hydration effects on the thermal stability of both proteins and DNA.

Revisiting rustrela virus - new cases of encephalitis and a solution to the capsid enigma

Rustrela virus (RusV, species Rubivirus strelense) is a recently discovered relative of rubella virus (RuV) that has been detected in cases of encephalitis across a wide spectrum of mammals, including placental and marsupial animals. Here we diagnosed two additional cases of fatal RusV-associated meningoencephalitis in a South American coati (Nasua nasua) and a Eurasian otter (Lutra lutra) that were detected in a zoological garden with history of prior RusV infections. Both animals showed abnormal movement or unusual behaviour and their brains tested positive for RusV using specific RT-qPCR and RNA in situ hybridization. As previous sequencing of RusV proved to be very challenging, we employed a sophisticated target-specific capture enrichment with specifically designed RNA baits to generate complete RusV genome sequences from both detected encephalitic animals and apparently healthy wild yellow-necked field mice (Apodemus flavicollis). Furthermore, the technique was used to revise three previously published RusV genomes from two encephalitic animals and a wild yellow-necked field mouse. Virus-to-host sequence ratio and thereby sequence coverage improved markedly using the enrichment method as compared to standard procedures. When comparing the newly generated RusV sequences to the previously published RusV genomes, we identified a previously undetected stretch of 309 nucleotides predicted to represent the intergenic region and the sequence encoding the N-terminus of the capsid protein. This indicated that the original RusV sequence was likely incomplete due to misassembly of the genome at a region with an exceptionally high G+C content of >80 mol%, which could not be resolved even by enormous sequencing efforts with standard methods. The updated capsid protein amino acid sequence now resembles those of RuV and ruhugu virus in size and harbours a predicted RNA binding domain that was not encoded in the original RusV genome version. The new sequence data indicate that RusV has the largest overall genome (9,631 nucleotides), intergenic region (290 nucleotides) and capsid protein-encoding sequence (331 codons) within the genus Rubivirus.

Homocysteinylation and sulfhydration in diseases

: Homocysteine (Hcy) is an important intermediate in methionine metabolism and generation of one-carbon unit, and its dysfunction is associated with many pathological states. Although Hcy is a non-protein amino acid, many studies have demonstrated protein-related homocysteine metabolism and possible mechanisms underlying homocysteinylation. Homocysteinylated proteins lose their original biological function and have a negative effect on the various disease phenotypes. Hydrogen sulfide (H2S) has been recognized as an important gaseous signaling molecule with mounting physiological properties. H2S modifies small molecules and proteins via sulfhydration, which is supposed to be essential in the regulation of biological functions and signal transduction in human health and disorders. This review briefly introduces Hcy and H2S, further discusses pathophysiological consequences of homocysteine modification and sulfhydryl modification, and ultimately makes a prediction that H2S might exert a protective effect on the toxicity of homocysteinylation of target protein via sulfhydration. The highlighted information here yields new insights for the role of protein modification by Hcy and H2S in diseases.

The Effects of Dietary Protein Supplementation on Exercise-Induced Inflammation and Oxidative Stress: A Systematic Review of Human Trials

This systematic review examined the effects of whole protein and commonly consumed amino acid supplements on markers of exercise-induced inflammation and oxidative stress and was reported according to the PRISMA guidelines. MEDLINE and SPORTDiscus were searched from inception until June 2021. The inclusion criteria were randomized clinical trials in humans, healthy adult participants (≥18 years), dietary protein/amino acid interventions, and measurements of oxidative stress/the redox status or inflammation post-exercise. The Cochrane Collaboration risk of bias 2 tool was used to critically appraise the studies. Data extracted from thirty-four studies were included in the systematic review (totaling 757 participants with only 10 females; age range 19–40 years). The included trials examined five types of whole protein and seven different amino acids supplements; most studies (n = 20) failed to identify statistically significant effects on markers of inflammation or oxidative stress after exercise; some (n = 14) showed either anti-inflammatory or antioxidant effects on some, but not all, markers. In conclusion, we found weak and inconsistent evidence that dietary protein/amino acid interventions can modify exercise-induced changes in oxidative stress and inflammation. However, given that these were not the primary outcomes in many of the included studies and many had design limitations, further research is warranted (Open Science Framework registration number: 10.17605/OSF.IO/AGUR2).

Passage of SARS-CoV-2 in cells expressing human and mouse ACE2 selects for mouse-adapted and ACE2-independent viruses

Human ACE2 (hACE2) is required for cell attachment and entry of SARS-CoV-2. Mouse ACE2 (mACE2) does not support infection of early SARS-CoV-2 isolates. Herein we describe a new system for generating mouse-adapted SARS-CoV-2 in vitro by serial passaging virus in co-cultures of cell lines expressing hACE2 and mACE2. Mouse-adapted viruses emerged with a series of spike protein amino acid changes, all of which have been reported in human isolates. Mouse-adapted viruses replicated to high titers in C57BL/6J mouse lungs and nasal turbinates, and caused severe lung histopathology. Remarkably, one mouse-adapted virus was able to replicate efficiently in ACE2-negative cell lines, a characteristic not described for any SARS-CoV-2 variants. ACE2-independent entry by SARS-CoV-2 represents a new biology for SARS-CoV-2 with potential widespread implications for disease and intervention development.

Phenotypic effects from the expression of a deregulated AtGAD1 transgene and GABA pathway suppression mutants in maize

Glutamate decarboxylase (GAD; EC 4.1.1.15) catalyzes the irreversible decarboxylation of glutamate to produce γ-aminobutyric acid (GABA); a ubiquitous non-protein amino acid involved in the regulation of several aspects of plant metabolism and physiology. To study the function of GAD and GABA in maize, we have; 1) introduced native and deregulated forms of AtGAD1 into maize with the intent of increasing the synthesis of GABA and 2) introduced constructs into maize designed to suppress the activity of several GABA shunt, GABA transport and GABA pathway genes. Maize plants expressing the deregulated AtGAD1 exhibit a severe chlorosis and retarded growth phenotype and have high levels of GABA, and Ca++/CaM-independent GAD activity. Plants expressing the suppression constructs for GABA biosynthetic and transport pathway genes had no observable phenotype whereas a knockout of GABA catabolic pathway genes led to growth and developmental defects under standard growth conditions. The implications of this study to our understanding of the action and function of GABA and GAD in crops are discussed.

Identification of a novel immunological epitope on Hexon of fowl adenovirus serotype 4

Fowl adenovirus serotype 4 (FAdV-4), the causative agent of hepatitis-hydropericardium syndrome (HHS), distributed widely in the poultry farms in China. Hexon is one of the major capsid proteins associated with viral species or serotypes. However, the epitopes of Hexon protein remain largely unknown. In this study, a monoclonal antibody (mAb) specific to Hexon protein of FAdV-4, designated as 3G8, was generated. Subsequently, the linear peptide recognized by 3G8 was mapped and identified as 213AYGAYVK219 using a series of overlapping peptides generated from Hexon protein. Amino acid sequence analysis revealed that the epitope recognized by 3G8 was highly conserved across all the FAdVs. The epitope was immunogenic and could be recognized by FAdV-4 positive chicken serum samples. These findings will enrich our knowledge regarding the epitope on Hexon and provide valuable information for further characterization of the antigenicity of Hexon protein.

From Plantation to Cup: Changes in Bioactive Compounds during Coffee Processing

Coffee is consumed not just for its flavor, but also for its health advantages. The quality of coffee beverages is affected by a number of elements and a series of processes, including: the environment, cultivation, post-harvest, fermentation, storage, roasting, and brewing to produce a cup of coffee. The chemical components of coffee beans alter throughout this procedure. The purpose of this article is to present information about changes in chemical components and bioactive compounds in coffee during preharvest and postharvest. The selection of the appropriate cherry maturity level is the first step in the coffee manufacturing process. The coffee cherry has specific flavor-precursor components and other chemical components that become raw materials in the fermentation process. During the fermentation process, there are not many changes in the phenolic or other bioactive components of coffee. Metabolites fermented by microbes diffuse into the seeds, which improves their quality. A germination process occurs during wet processing, which increases the quantity of amino acids, while the dry process induces an increase in non-protein amino acid γ-aminobutyric acid (GABA). In the roasting process, there is a change in the aroma precursors from the phenolic compounds, especially chlorogenic acid, amino acids, and sugars found in coffee beans, to produce a distinctive coffee taste.

Influence of non-protein amino-acid mimosine in peptide conformational propensities from novel Amber force field parameters

Mimosine is a non-protein amino acid derived from plants known for its ability to bind to divalent or trivalent metal cations such as Zn$^{2+}$, Ni$^{2+}$, Fe$^{2+}$ or Al$^{3+}$. This results in interesting antimicrobial and anti-cancer properties, which make mimosine a promising candidate for therapeutic applications. One possibility is to incorporate mimosine into synthetic short peptide drugs. However, our understanding of how this amino acid affects peptide structure is still limited, reducing our ability to design effective therapeutic compounds. In this work, we used computer simulations to understand this question. We first build parameters for the mimosine residue to be used in combination with two classical force fields of the Amber family. Then, we used atomistic molecular dynamics simulations with the resulting parameter sets to evaluate the influence of mimosine in the structural propensities for this amino acid. We compared the results of these simulations with identical peptides where mimosine is replaced by either phenylalanine or tyrosine. We found that the strong dipole in mimosine induces a preference for conformations where the amino acid rings are stacked over more traditional conformations. We validated our results using quantum mechanical calculations, which provide a robust foundation to the outcome of our classical simulations.

Determining the optimal parameters of ultra-high-frequency treatment of chickpeas for the production of gluten-free flour

This paper describes the materials and results of studying the properties of such a leguminous crop as the chickpea variety Miras 07 of Kazakhstan selection in order to obtain gluten-free flour and further process it to produce confectionery products. The research involved the ultra-high-frequency (UHF) treatment of chickpea grain to improve quality indicators and reduce anti-alimentary factors. A change in the protein fraction of chickpeas was determined under exposure to ultra-high-frequency processing. The study has proven the effectiveness of ultra-high-frequency treatment of chickpea for 180 seconds. Based on chemical analysis, it was found that the exposure to ultra-high-frequency treatment fully preserved the vitamin and mineral complex, compared with untreated chickpeas. When chickpea grain is heated for 180 seconds, up to 20 % of the starch contained in the grain passes into dextrin, which is easily absorbed by humans while the toxic substances are destroyed. The change in the protein fraction of chickpeas during ultra-high-frequency processing was determined. With ultra-high-frequency treatment of chickpea flour at 180 seconds of exposure, the protein fraction content remains unchanged at 79.8 %. The result based on the IR spectrum data indicates that ultra-high-frequency processing did not affect the protein-amino acid composition of the examined Miras 07 chickpea variety. The current study has confirmed the effectiveness of ultra-high-frequency chickpea treatment, which leads to the intensification of biochemical processes in the processed product due to the resonant absorption of energy by protein molecules and polysaccharides. Under the influence of ultra-high-frequency treatment, there is a decrease in the microbiological contamination of raw materials while the organoleptic indicators improve. According to the microbiological indicators of chickpea flour, the content of microorganisms was 1×103 CFU/g, which meets the requirements for sanitary and hygienic safety