Prediction of Prospective Mutational Landscape of SARS-CoV-2 Spike ssRNA and Evolutionary Basis of Its Host Interaction.

Booster doses are crucial against severe COVID-19, as rapid virus mutations and variant emergence prolong the pandemic crisis. The virus's quick evolution, short generation-time, and adaptive changes impact virulence and evolvability, helping predictions about variant of concerns' (VOCs') landscapes. Here, in this study, we used a new computational algorithm, to predict the mutational pattern in SARS-CoV-2 ssRNA, proteomics, structural identification, mutation stability, and functional correlation, as well as immune escape mechanisms. Interestingly, the sequence diversity of SARS Coronavirus-2 has demonstrated a predominance of G- > A and C- > U substitutions. The best validation statistics are explored here in seven homologous models of the expected mutant SARS-CoV-2 spike ssRNA and employed for hACE2 and IgG interactions. The interactome profile of SARS-CoV-2 spike with hACE2 and IgG revealed a strong correlation between phylogeny and divergence time. The systematic adaptation of SARS-CoV-2 spike ssRNA influences infectivity and immune escape. Data suggest higher propensity of Adenine rich sequence promotes MHC system avoidance, preferred by A-rich codons. Phylogenetic data revealed the evolution of SARS-CoV-2 lineages' epidemiology. Our findings may unveil processes governing the genesis of immune-resistant variants, prompting a critical reassessment of the coronavirus mutation rate and exploration of hypotheses beyond mechanical aspects.

Screening of Prospective Antiallergic Compound as FcεRI Inhibitors and Its Antiallergic Efficacy Through Immunoinformatics Approaches.

The occurrence of allergy, a type I hypersensitivity reaction, is rising exponentially all over the world. Sometimes, allergy proves to be fatal for atopic patients, due to the occurrence of anaphylaxis. This study is aimed to find an anti-allergic agent that can inhibit the binding of IgE to Human High Affinity IgE Receptor (FCεRI), thereby preventing the degranulation of mast cells. A considerable number of potential anti-allergic compounds were assessed for their inhibitory strength through ADMET studies. AUTODOCK was used for estimating the binding energy between anti-allergic compounds and FCεRI, along with the interacting amino acids. The docked pose showing favorable binding energy was subjected to molecular dynamics simulation study. Marrubiin, a diterpenoid lactone from Lamiaceae, and epicatechin-3-gallate appears to be effective in blocking the Human High Affinity IgE Receptor (FCεRI). This in-silico study proposes the use of marrubiin and epicatechin-3-gallate, in the downregulation of allergic responses. Due to the better inhibition constant, future direction of this study is to analyze the safety and efficacy of marrubiin in anti-allergic activities through in-vivo clinical human trials.

Substrate level optimization for better yield of oyster mushroom (Pleurotus ostreatus) production, using different ratio of rice straw and sugarcane bagasse.

Mushroom cultivation has been identified as a cost-effective technique for converting lignocellulosic wastes. This study utilized a combination of two distinct agro-wastes as a substrate for better Pleurotus ostreatus cultivation. Oyster mushroom has been cultivated on substrates made up of rice straw and sugarcane bagasse with different ratios. This technique gives a significant difference between mycelium running, fruit body formation, yield, biological efficiency, and better-quality taste of Pleurotus ostreatus mushroom. A minimum of 19 days were required for 1st harvesting from bag number T4 where substrate ratio was used at 3:2. The maximum yield was found as T4 (886 g/kg) in bag number on the dry substrate from the first flushing. According to proximate analyses, protein contents were increased in treatment bags compared with the control. Anyhow, the enrichment of L-glutamine content in the fruit body was found at 11.8 mg/g from 1st flushing in T4 bag, among the other bags and the flavour was changed due to the substrate level composition. According to the study, 3:2 is an ideal substrate ratio for the development of oyster mushrooms cultivation. According to this ratio, it helps the farmer for minimum time to grow the mushroom fruit body and reduce the lignocellulosic waste materials from the environmental pollution along with increasing the flavour in the fruitbody compared with commonly produced mushroom substrate (T6). Therefore, more research should be conducted to assess the consequences of combining different substrates and decreasing the lignocellulosic biomass by converting a protein-rich edible product through the oyster mushroom.

In silico comparative structural and functional analysis of arsenite methyltransferase from bacteria, fungi, fishes, birds, and mammals.

BACKGROUND: Arsenic, a ubiquitous toxic metalloid, is a threat to the survival of all living organisms. Bioaccumulation of arsenic interferes with the normal physiological pathway. To overcome arsenic toxicity, organisms have developed arsenite methyltransferase enzyme, which methylates inorganic arsenite to organic arsenic MMA (III) in the presence of S-adenosylmethionine (SAM). Bacteria-derived arsM might be horizontally transported to different domains of life as arsM or as3mt (animal ortholog). A systematic study on the functional diversity of arsenite methyltransferase from various sources will be used in arsenic bioremediation. RESULTS: Several arsenite methyltransferase protein sequences of bacteria, fungi, fishes, birds, and mammals were retrieved from the UniProt database. In silico physicochemical studies confirmed the acidic, hydrophilic, and thermostable nature of these enzymes. Interkingdom relationships were revealed by performing phylogenetic analysis. Homology modeling was performed by SWISS-MODEL, and that was validated through SAVES-v.6.0. QMEAN values ranged from - 0.93 to - 1.30, ERRAT score (83-96), PROCHECK (88-92%), and other parameters suggested models are statistically significant. MOTIF and PrankWeb discovered several functional motifs and active pockets within the proteins respectively. The STRING database showed protein-protein interaction networks. CONCLUSION: All of our in silico studies confirmed the fact that arsenite methyltransferase is a cytosolic stable enzyme with conserved sequences over a wide range of organisms. Thus, because of its stable and ubiquitous nature, arsenite methyltransferase could be employed in arsenic bioremediation.

Stress adaptation signature into the functional units of spike, envelope, membrane protein and ssRNA of SARS-CoV-2.

Pandemic coronavirus causes respiratory, enteric and sometimes neurological diseases. Proteome data of individual coronavirus strains were already reported. Here we investigated of SARS-CoV-2 ssRNA and protein of spike, envelope and membrane to determine stress adaptation profile. Thermodynamic properties, Physicochemical behaviour and, amino acid composition along with their RMSD value was analysed. Thermodynamic index of SARS-CoV2 spike, envelope and membrane ssRNA is unstable in higher temperature. Presence of higher proportion of polar with positive and negative charged amino acid residues into spike (S), envelope (E) and membrane (M) protein indicate the lower stress adaptability pattern. Our study represented several unstable pockets into S, E and M proteins of SARS-CoV-2 against different abiotic stresses, specifically higher in spike protein. Contact with heat through solvent may denature the architectural network of SARS-CoV-2 spike, envelope and membrane ssRNA and structural protein. The stress instability index of SARS-CoV-2 and the interactome profile of its transmembrane proteins may help to reveal novel factors for inhibiting SARS-CoV-2 growth.

Structural Phylogeny of Different Allergens May Reveal Common Epitopic Footprint.

BACKGROUND: The incidence of allergy has been increasing at an alarming rate over the last few decades. OBJECTIVE: Our present study aims to find out the structurally homologous motifs present in different proteinaceous allergens. METHODS: Significant number of protein sequences and their corresponding structures of various pollen, fungal, bacterial, and food allergens were retrieved and the sequence and structural identity were analyzed. RESULTS: Intra- and inter-sequence along with their structural analysis of the proteinaceous allergens revealed that no significant relationships exist among them. A few, but not the negligible number of high structural similarities, were observed within different groups of allergens from fungus, angiosperms, and animals (Aves and Mammalia). CONCLUSION: Our in silico study on thirty-six different allergens showed a significant level of structural similarities among themselves, regardless of their sequences.

Arsenic and Its Effect on Nutritional Properties of Oyster Mushrooms with Reference to Health Risk Assessment.

Arsenic (As) contamination is endemic in West Bengal, India. Arsenic exposure through mushroom is lethal to health. Pleurotus sp. is globally consumed as food for its medicinal and nutritional values. This study was performed to evaluate the arsenic accumulation in mushroom through arsenic biomagnified rice straw substrate in relation to health risk assessment. Arsenic concentrations were higher in P. ostreatus (12.577 mg/kg DW) and Pleurotus sp. (12.446 mg/kg DW) cultivated in arsenic biomagnified rice straw as compared with P. ostreatus (0.472 mg/kg DW) and Pleurotus sp. (0.434 mg/kg DW) cultivated in non-contaminant rice straw; respectively. The bio-concentration factor (BCF) value of arsenic was highest in stem at 3rd flush for both P. ostreatus and Pleurotus sp. The health risk index (HRI) based on dietary intake of these arsenic biomagnified mushrooms was found moderately higher in both the species, so higher intake of these mushrooms will put people at health risk.

In Silico Analyses of Burial Codon Bias Among the Species of Dipterocarpaceae Through Molecular and Phylogenetic Data.

INTRODUCTION: DNA barcode, a molecular marker, is used to distinguish among the closely related species, and it can be applied across a broad range of taxa to understand ecology and evolution. MaturaseK gene (matK) and rubisco bisphosphate carboxylase/oxygenase form I gene (rbcL) of the chloroplast are highly conserved in a plant system, which are used as core barcode. This present endeavor entails the comprehensive examination of the under threat plant species based on success of discrimination on DNA barcode under selection pressure. RESULT: The family Dipterocarpaceae comprising of 15 genera is under threat due to some factors, namely, deforestation, habitat alteration, poor seed, pollen dispersal, etc. Species of this family was grouped into 6 clusters for matK and 5 clusters and 2 sub-clusters for rbcL in the phylogenetic tree by using neighbor-joining method. Cluster I to cluster VI of matK and cluster I to cluster V of rbcL genes were analyzed by various codon and substitution bias tools. Mutational pressure guided the codon bias which was favored by the avoidance of higher GC content and significant negative correlation between GC12 and GC3 (in sub-cluster I of cluster I [0.03 < P], cluster I [0.00001 < P], and cluster II [0.01 < P] of rbcL, and cluster IV [0.013 < P] of matK). After refining the results, it could be speculated that the lower null expectation values (R = 0.5 or <0.5) were less divergent from the evolutionary perspective. Apart from that, the higher null expectation values (R = >0.85) also showed the same result, which possibly could be due to the negative impact of very high and low transition rate than transversion. CONCLUSION: Through the analysis of inter-generic, inter/intra-specific variation and phylogenetic data, it was found that both selection and mutation played an important role in synonymous codon choice in these genes, but they acted inconsistently on the genes, both matK and rbcL. In vitro stable proteins of both matK and rbcL were selected through natural selection rather than mutational selection. matK gene had higher individual discrimination and barcode success compared with rbcL. These discriminatory approaches may describe the problem related to the extinction of plant species. Hence, it becomes very imperative to identify and detect the under threat plant species in advance.

Molecular Mechanism of Antibiotic Resistance: The Untouched Area of Future Hope.

The treatment of bacterial infections is becoming increasingly ineffective due to rapid mutation which leads to antibiotic resistant and resistant bacteria become more prevalent. As a result the existing antibiotics are gradually obsolete and again new drugs are needed to be designed for the same threat. However, the prediction of evolutionary processes/antibiotic resistance is uncertain. Still, the understanding of mode of evolution of resistance in bacteria is a determining step in the preclinical development of new antibiotics, because drug developers assess the risk of resistance arising against a drug during preclinical development. Multidrug efflux pump systems play an important role for making multidrug resistance to a range of clinically important antibiotics in gram-negative bacteria like Pseudomonas aeruginosa, which lower the intracellular drug concentration by exporting incoming antibiotics across the membranes. We tried to show that the wild type susceptible bacteria P. aeruginosa modified its genetic makeup at mutational hotspots under stress. This strain may either become multidrug resistant or remain susceptible depending on position of amino acid changes in regulatory proteins of efflux pump. Multidrug resistant strain made significant changes at the amino acid positions, 103rd (G → A) and 126th (E → V) through the mutation on the nucleotide position of 308th (G → C); both 377th (A → T) and 378th (G → T), respectively in mexR, a repressor of mexAB-oprM efflux pump. This mutant protein showed low affinity with their operator. But the alteration at 103th position (G → A) in mexR may provide almost similar structural and functional stability as wild type. It was found that mutation was seemed to be well regulated within the limit and position specific under stress which might be back to its original form by supplying counter stress unless addition or deletion takes place.

Modification of drug-binding proteins associated with the efflux pump in MDR-MTB in course of evolution: an unraveled clue based on in silico approach.

Mycobacterium tuberculosis (MTB) is commonly resistant to various drugs. Multidrug-resistant tuberculosis (MDR-MTB) is mostly caused by mutation in drug-binding proteins and protein folding. The aim of the study was to identify the pattern of mutations in embC, inhA and rpoB proteins and investigate its interactions with available drug such as rifampicin, ethambutol and isoniazid, using a computer docking method. The evolution of drugs resistant mechanisms of MTB was analyzed using an in silico approach. The model proteins were considered to be in a protein-protein interaction network among the twenty transmembrane proteins. The changes in structural conformation may describe the significance of the proton pumps system. The docking analysis revealed that unlike isoniazid, both rifampicin and ethambutol, bound to the same residues in mutant and wild forms. Moreover, multiple-sequence alignment (MSA) showed mutational hotspot regions where the substitution of amino acids in these three target proteins was position specific under stress. The molecular basis of drug resistance in M. tuberculosis can be represented by a protein network which is a well-regulated system for efflux pump activation by popularly used drugs. Ethambutol and rifampicin form stable complexes with EmbC and RpoB, respectively. Isoniazid shows no binding affinity to mutant InhA (2015). Analysis of the cellular network associated with drug regulatory proteins suggest that mmpl3, Rv1634 and Rv1258c play a major role by altering the protein pump to remove the active drug compounds from the bacterial cell.

Higher peptide nonplanarity (ω) close to protein carboxy-terminal and its positive correlation with ψ dihedral-angle is evolved conferring protein thermostability.

BACKGROUND: Thermostability conferred by ensembles of several weak-interactions results in compactness-rigidity in proteins that impairs their flexibility/function. Understanding of protein's structural modification under stress is important. METHOD: In this study, randomly selected 54 nonhomologous and variedly thermostable (0-20 °C/21-40 °C/41-60 °C/61-80 °C/81-100 °C) proteins were investigated to elucidate their thermostability utilizing multiple bioinformatics-tools. Important physico-chemical factors/peptide-nonplanarity(ω) and Ramachandran-plot were analyzed from the proteins' PDB-structure by SPSS-programme. RESULT: Our ANOVA results suggest that temperature exerted significant and periodic influences on ω (F = 5.81/p = 0.0001) and ψ (F = 6.52/p = 0.0001) dihedral-angles in proteins where peptide nonplanarity obviously favored thermostability. The Pearson-correlation and further goodness of-fit model from ordinal-regression analysis suggest that nonplanarity is increasingly abundant in protein carboxy-terminal (χ2 = 37.9/p = 0.0001) at higher temperatures. Moreover, the ω is found to be highly correlated with ψ (r = 0.289/p = 0.0001) but not ɸ (r = -0.071/p = 0.365) which is supported by the regression-analysis (R2 = 0.085/F = 7.623/p < 0.001). Consistent and paradoxical decrease in the protein-size is linked to protein-thermostability. Hydrophobicity/hydrophilicity/protein phosphorylation and iso-electric point/charge were found to be grossly increasing with the protein-thermostability. However, outlier/disallowed residue-number (mean ±â€¯SD) was lower in moderate- and hyper-thermostable proteins, indicating temperature as a better purifying naturalselection-pressure to generate consistent allelic-fitness. CONCLUSIONS: In the current study, irrespective to the protein homology, nonplanarity has been demonstrated as a significant determinant of protein-thermostability.

Protein Thermostability Is Owing to Their Preferences to Non-Polar Smaller Volume Amino Acids, Variations in Residual Physico-Chemical Properties and More Salt-Bridges.

INTRODUCTION: Protein thermostability is an important field for its evolutionary perspective of mesophilic versus thermophilic relationship and for its industrial/ therapeutic applications. METHODS: Presently, a total 400 (200 thermophilic and 200 mesophilic homologue) proteins were studied utilizing several software/databases to evaluate their amino acid preferences. Randomly selected 50 homologous proteins with available PDB-structure of each group were explored for the understanding of the protein charges, isoelectric-points, hydrophilicity, hydrophobicity, tyrosine phosphorylation and salt-bridge occurrences. These 100 proteins were further probed to generate Ramachandran plot/data for the gross secondary structure prediction in and comparison between the thermophilic and mesophilic proteins. RESULTS: Present results strongly suggest that nonpolar smaller volume amino acids Ala (χ2 = 238.54, p<0.001) and Gly (χ2 = 73.35, p<0.001) are highly and Val moderately (χ2 = 144.43, p<0.001) occurring in the 85% of thermophilic proteins. Phospho-regulated Tyr and redox-sensitive Cys are also moderately distributed (χ2~20.0, p<0.01) in a larger number of thermophilic proteins. A consistent lower distribution of thermophilicity and discretely higher distribution of hydrophobicity is noticed in a large number of thermophilic versus their mesophilic protein homolog. The mean differences of isoelectric points and charges are found to be significantly less (7.11 vs. 6.39, p<0.05 and 1 vs. -0.6, p<0.01, respectively) in thermophilic proteins compared to their mesophilic counterpart. The possible sites for Tyr phosphorylation are noticed to be 25% higher (p<0.05) in thermophilic proteins. The 60% thermophiles are found with higher number of salt bridges in this study. The average percentage of salt-bridge of thermophiles is found to be higher by 20% than their mesophilic homologue. The GLU-HIS and GLU-LYS salt-bridge dyads are calculated to be significantly higher (p<0.05 and p<0.001, respectively) in thermophilic and GLU-ARG is higher in the mesophilic proteins. The Ramachandran plot/ data suggest a higher abundance of the helix, left-handed helix, sheet, nonplanar peptide and lower occurrence of cis peptide, loop/ turn and outlier in thermophiles. Pearson's correlation result suggests that the isoelectric points of mesophilic and thermophilic proteins are positively correlated (r = 0.93 and 0.84, respectively; p<0.001) to their corresponding charges. And their hydrophilicity is negatively associated with the corresponding hydrophobicity (r = -0.493, p<0.001 and r = -0.324, p<0.05) suggesting their reciprocal evolvement. CONCLUSIONS: Present results for the first time with this large amount of datasets and multiple contributing factors suggest the greater occurrence of hydrophobicity, salt-bridges and smaller volume nonpolar residues (Gly, Ala and Val) and lesser occurrence of bulky polar residues in the thermophilic proteins. A more stoichiometric relationship amongst these factors minimized the hindrance due to side chain burial and increased compactness and secondary structural stability in thermophilic proteins.