Chain Amino Acids Research Articles

Clinical characteristics and genetic analysis of a Chinese pedigree affected with tuberous sclerosis complex

To explore the genetic basis for a Chinese pedigree affected with tuberous sclerosis complex (TSC). The TSC1 and TSC2 genes were sequenced. Candidate variant was verified by Sanger sequencing of the proband and her family members. Pathogenicity of the variant was predicted based on the American College of Medical Genetics and Genomics (ACMG) guidelines. The proband was found to harbor a heterozygous c.52delC frameshift variant of the TSC2 gene, which may result in synthesis of amino acid chain starting from the 18th amino acid Leu and terminating at the 28th amino acid (p.Leu18CysfsTer28). The variant was unreported in the public database. Mutation Taster software predicted that the variant is harmful. Both parents of the proband were of the wild type, suggesting that the variant has occurred de novo. Based on the ACMG guidelines, the variant was predicted to be likely pathogenic (PVS1 +PM2). A novel pathogenic variant of the TSC2 gene c.52delC (p.Leu18CysfsTer28) was identified, which has enriched the mutational spectrum of TSC2 and provided a basis for genetic counseling for this pedigree.

Immuno-dominant dengue NS1 peptides as antigens for production of monoclonal antibodies.

Synthetic peptides have recently become common as antigens for antibody production. Peptides are short chains of amino acids that can be used to elicit an immune response. The immunogenicity of the peptide antigens varies depending on the length, charge, solubility, and amino acids contained in the peptide sequence. Dengue NS1 protein is an important target antigen in the early detection of dengue infection. In this study, peptides corresponding to a highly conserved region from the dengue NS1 region were designed and synthesized. Balb/C mice were immunized against each peptide and spleen cells extracted from the immunized mice were fused with NS0 murine myeloma cells. Hybridoma clones obtained from the fusions were tested against peptides using ELISA. Out of 1,830 growing clones, 28 clones produced antibodies reacting with dengue NS1 peptides. A purified monoclonal antibody reacting with all four peptides was tested for reactivity with dengue NS1 native protein using dengue-confirmed serum and urine samples. The monoclonal antibody shows significant reactivity with both serum and urine. The findings of the current research can be used to detect dengue infection using urine, which ultimately results in the prevention of dengue epidemics through painless diagnosis, following treatment, and patient management to safeguard human and economic wellness.

A-Heal® in the Management of Chronic Nonhealing Ulcers

Background and Objective: The aim of this study is to assess the efficacy of A-Heal® in the treatment of nonhealing ulcers (NHU). Patients and Methods: This is a case–control study involving 12 patients who applied A-Heal® 10 mg twice a day on an NHU till the complete healing of the ulcer. The control group had the standard treatment. A-Heal® is a 13 amino acid chain, which was initially isolated from the human placenta, is now synthesized, and has shown to be a powerful angiogenesis factor. Before starting the trial, morphologic features of the ulcers were noted including, size, shape, location, and associated diseases. The follow-up period was set at 6 months. Results: The average age of the treated patients was 52.5 ± 5.3 years in the study group and 51.9 ± 4.7 years in the control group. The mean duration of the ulcer was 13.7 ± 5.3 weeks. All the ulcers were located in the lower limbs. In 9 (75%) patients, there was total healing of ulcers in 22 days and three patients showed signs of wound healing with a reduction in wound size and required an additional 1 week for total healing of the ulcer. Regarding the secondary outcomes of preliminary efficacy, total healing and significant reduction of the area were observed in all patients. There were no adverse events recorded. Conclusion: This case series shows that A-Heal® has proved to be safe with a good preliminary efficacy to heal NHUs, according to the protocol and doses used. A larger clinical trial is needed to verify our results.

Post-Translational Modifications of cGAS-STING: A Critical Switch for Immune Regulation.

Innate immune mechanisms initiate immune responses via pattern-recognition receptors (PRRs). Cyclic GMP-AMP synthase (cGAS), a member of the PRRs, senses diverse pathogenic or endogenous DNA and activates innate immune signaling pathways, including the expression of stimulator of interferon genes (STING), type I interferon, and other inflammatory cytokines, which, in turn, instructs the adaptive immune response development. This groundbreaking discovery has rapidly advanced research on host defense, cancer biology, and autoimmune disorders. Since cGAS/STING has enormous potential in eliciting an innate immune response, understanding its functional regulation is critical. As the most widespread and efficient regulatory mode of the cGAS-STING pathway, post-translational modifications (PTMs), such as the covalent linkage of functional groups to amino acid chains, are generally considered a regulatory mechanism for protein destruction or renewal. In this review, we discuss cGAS-STING signaling transduction and its mechanism in related diseases and focus on the current different regulatory modalities of PTMs in the control of the cGAS-STING-triggered innate immune and inflammatory responses.

A Biomimetic Basalt Fiber/Epoxy Helical Composite Spring with Hierarchical Triple-Helix Structures Inspired by the Collagen Fibers in Compact Bone.

The lightweight property of helical composite spring (HCS) applied in the transportation field has attracted more and more attention recently. However, it is difficult to maintain stiffness and fatigue resistance at the same time. Herein, inspired by collagen fibers in bone, a bionic basalt fiber/epoxy resin helical composite spring is manufactured. The collagen fibers consist of nanoscale hydroxyapatite (increases stiffness) and collagen molecules composed of helical amino acid chains (can increase fatigue resistance). Such a helical structure of intercalated crystals ensures that bone has good resistance to fracture. Specifically, we first investigated the effect of adding different contents of NS to basalt fibers on the stiffness and fatigue properties of an HCS. The results show that the optimal NS content of 0.4 wt% resulted in 52.1% and 43.5% higher stiffness and fatigue properties of an HCS than those without NS, respectively. Then, two braided fiber bundles (TS-BFB) and four braided fiber bundles (FS-BFB) were designed based on the helical structure of amino acid chains, and the compression tests revealed that the maximum load resistance of TS-BFB and FS-BFB was increased by 29.2% and 44%, respectively, compared with the conventional single fiber bundle (U-BFB). The superior mechanical performance of TS-BFB and FS-BFB is attributed to the more adequate bonding of 0.4 wt% NS to the epoxy resin and the multi-fiber bundles that increase the transverse fiber content of the spring. The findings in this work introduce the bionic collagen fiber structure into the design for an HCS and provide a new idea to improve the spring performance.

SP-A binding to the SARS-CoV-2 spike protein using hybrid quantum and classical in silico modeling and molecular pruning by Quantum Approximate Optimization Algorithm (QAOA) Based MaxCut with ZDOCK.

The pulmonary surfactant protein A (SP-A) is a constitutively expressed immune-protective collagenous lectin (collectin) in the lung. It binds to the cell membrane of immune cells and opsonizes infectious agents such as bacteria, fungi, and viruses through glycoprotein binding. SARS-CoV-2 enters airway epithelial cells by ligating the Angiotensin Converting Enzyme 2 (ACE2) receptor on the cell surface using its Spike glycoprotein (S protein). We hypothesized that SP-A binds to the SARS-CoV-2 S protein and this binding interferes with ACE2 ligation. To study this hypothesis, we used a hybrid quantum and classical in silico modeling technique that utilized protein graph pruning. This graph pruning technique determines the best binding sites between amino acid chains by utilizing the Quantum Approximate Optimization Algorithm (QAOA)-based MaxCut (QAOA-MaxCut) program on a Near Intermediate Scale Quantum (NISQ) device. In this, the angles between every neighboring three atoms were Fourier-transformed into microwave frequencies and sent to a quantum chip that identified the chemically irrelevant atoms to eliminate based on their chemical topology. We confirmed that the remaining residues contained all the potential binding sites in the molecules by the Universal Protein Resource (UniProt) database. QAOA-MaxCut was compared with GROMACS with T-REMD using AMBER, OPLS, and CHARMM force fields to determine the differences in preparing a protein structure docking, as well as with Goemans-Williamson, the best classical algorithm for MaxCut. The relative binding affinity of potential interactions between the pruned protein chain residues of SP-A and SARS-CoV-2 S proteins was assessed by the ZDOCK program. Our data indicate that SP-A could ligate the S protein with a similar affinity to the ACE2-Spike binding. Interestingly, however, the results suggest that the most tightly-bound SP-A binding site is localized to the S2 chain, in the fusion region of the SARS-CoV-2 S protein, that is responsible for cell entry Based on these findings we speculate that SP-A may not directly compete with ACE2 for the binding site on the S protein, but interferes with viral entry to the cell by hindering necessary conformational changes or the fusion process.

Biocomputational characterisation of MBO_200107 protein of Mycobacterium tuberculosis variant caprae: a molecular docking and simulation study

The principal objective of this study was to delineate the potentiality of the MBO_200107 protein from the Mycobacterium tuberculosis variant caprae in cancer research. It is a cytoplasmic protein, comprised of a 354-long amino acid chain, alkaline, had a molecular weight of 39089.37 Da, an isoelectric point of 9.62 and a grand average of hydropathicity of −0.345. One of the functional domains was predicted as Gammaglutamylcyclotransferase (GGCT). Among tertiary structures, the Modeller and Phyre2 model satisfied all the quality parameters, though they are truncated; contrarily, the I-TASSER model is full length and contains the sequence for the GGCT domain, though it did not meet all the quality parameters. It also has significant sequence similarities (47.5% by EMBOSS Water and 72.4% by EMBOSS Matcher) with a human GGCT, and the conserved sequences are confined to the GGCT domain of the MBO_200107. According to molecular docking analyses, the protein has a binding affinity of −4.8 kcal/mol by Autodock Vina and −56.465 kcal/mol by HPEPDOCK to the human glutathione (GSH), an essential metabolite for GGCT metabolism. The Molecular dynamic simulation of the docked complex showed the binding efficiency of the GSH to MBO_200107 with a minimal structural alteration. The in silico findings mentioned above revealed that the protein could be used as a supplementary tool in cancer research, such as designing vaccines or drugs where the role of GGCT has been implicated. Further, we recommend fully characterising the protein and conducting essential in vitro and in vivo experiments to determine its detailed usefulness. Communicated by Ramaswamy H. Sarma

A Review of Natural Gas Hydrate Formation with Amino Acids

Natural gas is a kind of low-carbon energy source with abundant reserves globally and high calorific value. It is cleaner and more efficient than oil and coal. Enlarging the utilization of natural gas is also one of the important ways to reduce carbon emissions in the world. Solidified natural gas technology (SNG) stores natural gas in solid hydrates, which is a prospective, efficient, safe and environmental-friendly strategy of natural gas storage and transport. However, the slow growth rate and randomness of nucleation during natural gas hydrate formation in pure water hinder the industrial application of this technology. As a kind of new and potential additives, biodegradable amino acids can be adopted as favorable kinetic promoters for natural gas hydrate synthesis. Compared with other frequently used chemical additives, amino acids are usually more friendly to the environment, and are capable of avoiding foam formation during complete decomposition of gas hydrates. In this paper, we have reviewed the research progress of gas hydrate generation under the promotion of amino acids. The formation systems in which amino acids can enhance the growth speed of gas hydrates are summarized, and the impact of the concentration in different systems and the side chains of amino acids on hydrate growth have been illustrated. The thermodynamic and kinetic behaviors as well as the morphology properties of hydrate formation with amino acids are summarized, and the promotion mechanism is also analyzed for better selection of this kind of potential additives in the future.

Computational Design of Extraordinarily Stable Peptide Structures through Side-Chain-Locked Knots.

Extraordinarily stable protein and peptide structures are critically demanded in many applications. Typical approaches to enhance protein and peptide stability are strengthening certain interactions. Here, we develop a very different approach: stabilizing peptide structures through side-chain-locked knots. More specifically, a peptide core consists of a knot, which is prevented from unknotting and unfolding by large side chains of amino acids at knot boundaries. These side chains impose free energy barriers for unknotting. The free energy barriers are quantified using all-atom and coarse-grained simulations. The barriers become infinitely high for large side chains and tight knot cores, resulting in stable peptide structures, which never unfold unless one chemical bond is broken. The extraordinary stability is essentially kinetic stability. Our new approach lifts the thermodynamic restriction in designing peptide structures, provides extra freedom in selecting sequence and structural motifs that are thermodynamically unstable, and should expand the functionality of peptides. This work also provides a bottom-up understanding of how knotting enhances protein stability.

Gene Ontology Capsule GAN: an improved architecture for protein function prediction.

Proteins are the core of all functions pertaining to living things. They consist of an extended amino acid chain folding into a three-dimensional shape that dictates their behavior. Currently, convolutional neural networks (CNNs) have been pivotal in predicting protein functions based on protein sequences. While it is a technology crucial to the niche, the computation cost and translational invariance associated with CNN make it impossible to detect spatial hierarchies between complex and simpler objects. Therefore, this research utilizes capsule networks to capture spatial information as opposed to CNNs. Since capsule networks focus on hierarchical links, they have a lot of potential for solving structural biology challenges. In comparison to the standard CNNs, our results exhibit an improvement in accuracy. Gene Ontology Capsule GAN (GOCAPGAN) achieved an F1 score of 82.6%, a precision score of 90.4% and recall score of 76.1%.

Studying folding leftrightarrow unfolding dynamics of solvated alanine polypeptides using molecular dynamics

The atomistic description of the folding process of a structureless chain of amino acids to a functioning protein is still considered to be a challenge for computational biophysics. An in-depth understanding of protein-folding can be achieved through atomistic dynamics accounting for the solvent effects, combined with the theoretical description of conformational changes in shorter polypeptide chains. The present paper studies the folding transitions in short polypeptide chains consisting of 11 alanine residues in explicit solvent employing all-atom molecular dynamics. The multiple observed folding leftrightarrow unfolding events of the peptide are interpreted as a dynamic process and rationalised through the analysis of the potential energy surface of the system. It is demonstrated that alanine polypeptide folding dynamics is governed by the backbone dihedral angles and involves the formation of spontaneously folded alpha -helices which emerge and live for ca. 1–20 picoseconds. The helical content within the polypeptide at different temperatures was quantified through a statistical mechanics approach, which showed a reasonable agreement with the results of molecular dynamics simulations and experiments performed for alanine-rich peptides.Graphical abstract

Innovative swine blood hydrolysates as promising ingredients for European seabass diets: Impact on growth performance and resistance to Tenacibaculum maritimum infection

Hydrolysates from high-protein coproducts are rich in bioactive peptides (small amino acid chains with properties beyond their nutritional value). When included in aquafeeds, they may promote fish robustness while increasing animal blood value and minimizing waste, contributing to a circular economy. This work assessed how innovatively produced blood hydrolysates (BH) included in plant-based diets for European seabass (Dicentrarchus labrax) affected growth performance and resistance to Tenacibaculum maritimum infection. Three fractions of swine BH obtained by autohydrolysis (AH) or enzymatically were selected. AH fraction was oven-dried, whilst the enzymatically obtained BH were further submitted to a micro (RMF) and nanofiltration (RNF) and the respective retentates freeze-dried. A commercially based diet was formulated, where 50% of fishmeal was replaced by vegetable proteins, and used as negative control (NC). Each BH fraction was then added at 3% to the NC and further compared to a fishmeal-based diet (positive control, PC); all diets remained isolipidic and isoproteic. Diets were assigned to triplicate groups of European seabass juveniles (12.3 ± 1.4 g) and fed three times daily until apparent satiation in a recirculating saltwater system. After a 12-week growth trial, fish were bath challenged with T. maritimum and cumulative mortality followed for 8 days. A digestibility trial was also performed in parallel. Hydrolysates-containing diets had a significantly lower apparent digestibility coefficient (ADC) of dry matter compared to the PC, but RNF did not differ from the NC. RMF and AH had lower lipid ADCs than both controls, while the RNF only differed from the PC. Mineral ADCs of PC, NC and RNF were similar. Calcium ADC in RMF and AH was significantly lower than all other diets; RMF also displayed lower copper and potassium ADCs. Fish fed PC had the highest final weight, followed by NC and RNF. Daily growth index and feed conversion ratio (FCR) of RNF was similar to both controls. RMF induced the lowest final weight, highest FCR and reduced villus length in anterior intestine. This diet has also resulted in increased plasmatic peroxidase, but lower lysozyme, compared to all other treatments, showing the lowest disease resistance. Results clearly show that the RNF was the only test diet that significantly reduced European seabass mortality after T. maritimum infection, without affecting fish growth in relation to a practical plant-protein based diet, highlighting its high potential for aquafeeds supplementation.

Contact map dependence of a T-cell receptor binding repertoire.

The T-cell arm of the adaptive immune system provides the host protection against unknown pathogens by discriminating between host and foreign material. This discriminatory capability is achieved by the creation of a repertoire of cells each carrying a T-cell receptor (TCR) specific to non-self-antigens displayed as peptides bound to the major histocompatibility complex (pMHC). The understanding of the dynamics of the adaptive immune system at a repertoire level is complex, due to both the nuanced interaction of a TCR-pMHC pair and to the number of different possible TCR-pMHC pairings, making computationally exact solutions currently unfeasible. To gain some insight into this problem, we study an affinity-based model for TCR-pMHC binding in which a crystal structure is used to generate a distance-based contact map that weights the pairwise amino acid interactions. We find that the TCR-pMHC binding energy distribution strongly depends both on the number of contacts and the repeat structure allowed by the topology of the contact map of choice; this in turn influences T-cell recognition probability during negative selection, with higher variances leading to higher survival probabilities. In addition, we quantify the degree to which neoantigens with mutations in sites with higher contacts are recognized at a higher rate.

Tandem mass tag labeled quantitative proteomic analysis of differential protein expression on total alkaloid of Aconitum flavum Hand.-Mazz. against melophagus ovinus.

Melophagus ovinus disease is a common ectoparasitosis, which can lead to a decrease in animal production performance, product quality, and even death. Aconitum flavum Hand.-Mazz. has many pharmacological activities including insecticidal, heat-clearing, analgesic, and dehumidifying. However, there are few researches focused on the effects and related mechanism of Aconitum flavum Hand.-Mazz. in killing Melophagus ovinus. In this study, 11 alkaloids of Aconitum flavum Hand.-Mazz. were detected, and its total alkaloid activity was determined. The results showed when the total alkaloid concentration was 64 mg/ml and the treatment time was 16 h, the killing rate of Melophagus ovinus reached 100%. Through the observation of the differences in the surface of Melophagus ovinus in each experimental group, it was found that the morphology of the posterior end of the female Melophagus ovinus in the alkaloid treatment group was significantly different from that of the blank and positive control groups, and most of the epidermal tissue was obsessive and missing. Moreover, the enzyme activity determination results of 64 mg/ml group were significantly different when compared with the normal control group, while there was no significant difference in other groups. Then, the Melophagus ovinus gene library was established by the unreferenced genome transcriptome sequencing, the proteomic comparison was performed using tandem mass tag labeled protein detection technology, and finally, the samples were quantitatively analyzed by liquid chromatography-mass spectrometry tandem and bioinformatics methods. Based on the above experimental results, it was speculated that Aconitum flavum Hand.-Mazz. total alkaloids may cause the imbalance of protein disulfide isomerase expressions by affecting the regulation of Hsp40 cellular protein homeostasis and the oxidation of protein disulfide isomerase and related proteins. This would affect the selective recognition of signal sequence, the targeted transport of Sec 61, and the correct folding of the three-dimensional structure of amino acid chain, weakening the clearance of amino acid chains that cannot be correctly folded and eventually resulting in the killing of Melophagus ovinus. This study preliminarily revealed the mechanism of Aconitum flavum Hand.-Mazz. total alkaloids against Melophagus ovinus and provided a theoretical basis for the screening of Melophagus ovinus action targets and the development of new veterinary drugs.

A novel family of non-secreted tridecaptin lipopeptide produced by Paenibacillus elgii.

Bacteria from the genus Paenibacillus make a variety of antimicrobial compounds, including lipopeptides produced by a non-ribosomal synthesis mechanism (NRPS). In the present study, we show the genomic and phenotypical characterization of Paenibacillus elgii AC13 which makes three groups of small molecules: the antimicrobial pelgipeptins and two other families of peptides that have not been described in P. elgii. A family of lipopeptides with [M + H]+ 1664, 1678, 1702, and 1717m/z was purified from the culture cell fraction. Partial characterization revealed that they are similar to tridecaptin from P. terrae. However, they present amino acid chain modifications in positions 3, 7, and 10. These new variants were named tridecaptin G1, G2, G3, and G4. Furthermore, a gene cluster was identified in P. elgii AC13 genome, revealing high similarity to the tridecaptin-NRPS gene cluster from P. terrae. Tridecaptin G1 and G2 showed in vitro antimicrobial activity against Escherichia coli, Klebsiella pneumonia (including a multidrug-resistant strain), Staphylococcus aureus, and Candida albicans. Tri G3 did not show antimicrobial activity against S. aureus and C. albicans at all tested concentrations. An intriguing feature of this family of lipopeptides is that it was only observed in the cell fraction of the P. elgii AC13 culture, which could be a result of the amino acid sequence modifications presented in these variants.

Role of a bacterial glycolipid in Sec-independent membrane protein insertion

Non-proteinaceous components in membranes regulate membrane protein insertion cooperatively with proteinaceous translocons. An endogenous glycolipid in the Escherichia coli membrane called membrane protein integrase (MPIase) is one such component. Here, we focused on the Sec translocon-independent pathway and examined the mechanisms of MPIase-facilitated protein insertion using physicochemical techniques. We determined the membrane insertion efficiency of a small hydrophobic protein using solid-state nuclear magnetic resonance, which showed good agreement with that determined by the insertion assay using an in vitro translation system. The observed insertion efficiency was strongly correlated with membrane physicochemical properties measured using fluorescence techniques. Diacylglycerol, a trace component of E. coli membrane, reduced the acyl chain mobility in the core region and inhibited the insertion, whereas MPIase restored them. We observed the electrostatic intermolecular interactions between MPIase and the side chain of basic amino acids in the protein, suggesting that the negatively charged pyrophosphate of MPIase attracts the positively charged residues of a protein near the membrane surface, which triggers the insertion. Thus, this study demonstrated the ingenious approach of MPIase to support membrane insertion of proteins by using its unique molecular structure in various ways.

The Association of Circulating Amino Acids and Dietary Inflammatory Potential with Muscle Health in Chinese Community-Dwelling Older People.

Amino acids (AAs) and dietary inflammatory potential play essential roles in muscle health. We examined the associations of dietary inflammatory index (DII) of habitual diet with serum AA profile, and ascertained if the associations between DII and muscle outcomes were mediated by serum AAs, in 2994 older Chinese community-dwelling men and women (mean age 72 years) in Hong Kong. Higher serum branched chain AAs (BCAAs), aromatic AAs and total glutathione (tGSH) were generally associated with better muscle status at baseline. A more pro-inflammatory diet, correlating with higher serum total homocysteine and cystathionine, was directly (90.2%) and indirectly (9.8%) through lower tGSH associated with 4-year decline in hand grip strength in men. Higher tGSH was associated with favorable 4-year changes in hand grip strength, gait speed and time needed for 5-time chair stands in men and 4-year change in muscle mass in women. Higher leucine and isoleucine were associated with decreased risk of sarcopenia in men; the associations were abolished after adjustment for BMI. In older men, perturbations in serum sulfur AAs metabolism may be biomarkers of DII related adverse muscle status, while the lower risk of sarcopenia with higher BCAAs may partly be due to preserved BMI.

Response of adult domestic cats in Sri Lanka to Acalypha indica root embedded toys and the influence of single nucleotide polymorphisms in olfactory receptor genes on the elicited behavior

Exclusively indoor cats exhibit many behavioral complications due to their reduced activity levels and limited behavioral diversity. Environment enrichment is a tool to stimulate adult indoor cats and make them more active. In this research, we evaluated the feasibility of using a toy embedded with roots of the herbal plant, Acalypha indica, as an environmental enrichment tool in adult domestic short-haired cats and how the single nucleotide polymorphisms (SNPs) in the feline olfactory receptor genes influence the animals’ behavioral response toward the toys. A single-blinded crossover study was conducted to evaluate the behavioral changes of adult cats (n = 38) presented with a stuffed plush toy embedded with Acalypha indica roots (treatment) and an empty toy without Acalypha indica roots (control) for 15 min. Activities were recorded, and an ethogram was constructed. Interaction time percentage, presence or absence of interactive behavior types, and total interactive behavior type counts were calculated. Statistical analyses were performed using RStudio software. Differences between treatment and control groups were evaluated using Mann-Whitney U test. Significant differences in interaction time percentage (P = 0.002) and behavior count (P = 0.001) were shown between treatment and control toy types. McNemar’s Chi-squared test results indicated that the proportion of licking (P = 0.004), chewing (P = 0.008), and face rubbing (P = 0.02) behavior types were significantly higher when cats were given the Acalypha indica toy. Based on these three significant behavior types, responders (n = 10) and non-responders (n = 10) for treatment toys were identified and assessed for variations in OR10K1, OR10V1, and OR2B11 olfactory receptor genes. Seven, five, and two SNPs were identified in the coding regions of OR10K1, OR10V1, and OR2B11 genes, respectively. Allele frequencies of SNPs at 354 bp and 688 bp positions of OR10K1 were considerably different between responders and non-responders, and SNP at 354 bp substituted arginine by a stop codon at site 107 in the amino acid chain. The present study showed that a toy embedded with roots of Acalypha indica holds potential as an environmental enrichment tool in adult domestic cats. However, the variations in olfactory genes, such as OR10K1, could change their behavioral responses toward these olfactory enrichment toys.

Single polysome analysis of mRNP

Eukaryotic translation is a complex process that involves the interplay of various translation factors to convert genetic information into a specific amino acid chain. According to an elegant model of eukaryotic translation initiation, the 3′ poly(A) tail of an mRNA, which is occupied by poly(A)-binding proteins (PABPs), communicates with the 5′-cap bound by eIF4E to enhance translation. Although the circularization of mRNA resulting from the communication is widely understood, it has yet to be directly observed. To explore mRNA circularization in translation, we analyzed the level of colocalization of eIF4E, eIF4G, and PABP on individual mRNAs in polysomal and subpolysomal fractions using single polysome analysis. Our results show that the three tested proteins barely coexist in mRNA in either polysomal or subpolysomal fractions, implying that the closed-loop structure generated by the communication between eIF4E, eIF4G, and PAPB may be transient during translation.

Conformational analysis and water dynamics: a molecular dynamics study on the survival of a β-lactoglobulin peptide in the archaeological record

One of the greatest successes of the application of Palaeoproteomics to Archaeology is its use by a number of authors to track evidence of dairying practice, both in terms of its origin and the selection of animal species. To this end, the whey protein β-lactoglobulin entrapped in pottery and dental calculus is widely studied because it is so frequently recovered but why is it differentially preserved? Hydrolysis plays a big part in the breakdown of proteins. Therefore, it is essential to explore the role of water in degradation to uncover some of the patterns linked to protein survival. One approach to understand the hydrolytic process is to examine the molecular behaviour of this protein and in particular of the peptide most commonly recovered: T125PEVDXEALEK135. In this study, we use Molecular Dynamics, with the Amber14SB forcefield and the SPC/E water model in Gromacs 2020, to first explore the dynamics of this peptide in bulk water. Despite the difficulties in describing reactive processes with classical methods, we were able to identify geometric arrangements between water and protein residues which are similar to the ones described in the literature for protein hydrolysis. These arrangements helped to identify potential sites for hydrolysis along the bovine β-lactoglobulin T125PEVDDEALEK135 amino acid chain.