Aliphatic Index Research Articles

Epidemiology and molecular characterization of chikungunya virus from human cases in North India, 2016.

Chikungunya virus (CHIKV), an arthropod-borne Alphavirus is responsible for chikungunya disease. Arthralgia and arthritis are the major symptom. Some patients recover early while others for a very long time. This study provides, epidemiology and molecular characterization of three whole-genome sequences of CHIKV and assessed phylogenetic analysis, physiological properties, antigenicity, and B-cell epitope prediction by in silico. We report the clinical epidemiology of 325 suspected patients. Of these, 118 (36.30%) were confirmed CHIKV positive by either PCR or ELISA. Clinical analysis showed joint pain, joint swelling and headache were frequent and significant features. Phylogenie analysis showed the currently circulating strain is in close clustring to Africa, Uganda, and Singapore CHIKV strains. Molecular characterization by WGS was done. Thirty eight amino acid changes in the nonstructural proteins were found with respect to the S27 (ECSA) strain. Of these five located in nsP2. Similarly, 34 amino acid changes in structural proteins were observed. The major change was notice; in E3 protein hydropathicity -0.281 to -0.362, in E2 isoelectric point (pI) 8.24 to 8.37, instability index 66.08 to 71.062, aliphatic index varied from 74.69 to 68.59 and E3 75.79 to 70.05. In nsP1 protein pI varies from 6.62 to 8.04, while no other change was observed in structural and nonstructural protein. The linear B-cell epitopes, position, and number varied with the mutation. The molecular characterizations of WGS demonstrate the observation of protein, antigenicity with respect to the mutation.

Immunoinformatic Analysis of Calcium-Dependent Protein Kinase 7 (CDPK7) Showed Potential Targets for Toxoplasma gondii Vaccine.

Apicomplexan parasites, including Toxoplasma gondii (T. gondii), express different types of calcium-dependent protein kinases (CDPKs), which perform a variety of functions, including attacking and exiting the host cells. In the current bioinformatics study, we have used several web servers to predict the basic features and specifications of the CDPK7 protein. The findings showed that CDPK7 protein has 2133 amino acid residues with an average molecular weight (MW) of 219085.79 D. The aliphatic index with 68.78 and grand average of hydropathicity (GRAVY) with -0.331 score were estimated. The outcomes of current research showed that the CDPK7 protein included 502 alpha-helix, 1311 random coils, and 320 extended strands with GOR4 method. Considering the Ramachandran plot, the favored region contains more than 92% of the amino acid residues. In addition, evaluation of antigenicity and allergenicity showed that CDPK7 protein has immunogenic and nonallergenic nature. The present research provides key data for more animal-model study on the CDPK7 protein to design an efficient vaccine against toxoplasmosis in the future.

New insights about the EptA protein and its correlation with the pmrC gene in polymyxin resistance in Pseudomonas aeruginosa.

Nowadays, clinical and scientific interest in antibiotics, as polymyxin, has increased due to the large number of reports of multiresistant Gram-negative bacteria, as Pseudomonas aeruginosa. The aim of this study was to investigate a related group of proteins for resistance to polymyxins, encoded by P. aeruginosa genome, through in silico analysis. The mobilized colistin resistance 1 (MCR1) protein from Escherichia coli was used for comparison. Similar sequences to the protein MCR1 in P. aeruginosa were analysed for physicochemical properties. 31 protein isoforms in P. aeruginosa (EptA) were found able to confer resistance to polymyxin showing protein lengths between 551 and 572 amino acids, with molecular mass values between 61.36 - 62. 80kDa, isoelectric point between 6.10 to 7.17, instability index between 33.76 to 41.87, aliphatic index between 98.67 to 102.63 and the hydropathyindex between - 0.008 to 0.094. These proteins belong to the DUF1705 superfamily with bit-score values between 559.81 and 629.78. A high degree of similarity between EpTAs in P. aeruginosa was observed in relation to other proteins that confer resistance to polymyxins, present in Gram-negative bacteria species of clinical interest. Although, further studies are needed to identify the actual contribution of EptAs in P. aeruginosa species.

Phospholipase A2 (PLA2) Sequences in Rattus norvegicus Genome

Phospholipase A2 is enzyme that hydrolyses phospholipids at sn-2 position. This class of enzymes are significant due to their ability to cleave membrane phospholipids and hence causing inflammation. The PLA2 enzymes present in Rattus norvegicus is extensively studied to predict its properties. The Protparam analysis was performed to predict the physical properties like number of amino acids, Theoretical pH, stability index value, aliphatic index value and GRAVY value. The SOPMA analysis predicted its structural properties like the number of alpha-helices and beta-strands. Hence the focus of the present study was to perform a preliminary in silico analysis to identify the PLA2 protein sequences in the genome of Rattus norvegicus.

Transformation of Resinous Components of the Ashalcha Field Oil during Catalytic Aquathermolysis in the Presence of a Cobalt-Containing Catalyst Precursor

The aim of this work was to study the fractional composition of super-viscous oil resins from the Ashalcha field, as well as the catalytic aquathermolysis product in the presence of a cobalt-containing catalyst precursor and a hydrogen donor. The study was conducted at various durations of thermal steam exposure. In this regard, the work enabled the identification of the distribution of resin fractions. These fractions, obtained by liquid adsorption chromatography, were extracted with individual solvents and their binary mixtures in various ratios. The results of MALDI spectroscopy revealed a decrease in the molecular mass of all resin fractions after catalytic treatment, mainly with a hydrogen donor. However, the elemental analysis data indicated a decrease in the H/C ratio for resin fractions as a result of removing alkyl substituents in resins and asphaltenes. Moreover, the data of 1H NMR spectroscopy of resin fractions indicated an increase in the aliphatic hydrogen index during catalytic aquathermolysis at the high molecular parts of the resins R3 and R4. Finally, a structural group analysis was carried out in this study, and hypothetical structures of the initial oil resin molecules and aquathermolysis products were constructed as well.

In silico Structural, Functional and Phylogenetic Analyses of cellulase from Ruminococcus albus

BackgroundCellulose is the primary component of the plant cell wall and an important source of energy for the ruminant and microbial protein synthesis in the rumen. Cell wall content is digested by anaerobic fermentation activity mainly of bacteria belonging to species Fibrobacter succinogenes, Ruminicoccus albus, Ruminococcus flavefaciens, and Butyrivibrio fibrisolvens. Bacteria belonging to the species Ruminococcus albus contain cellulosomes that enable it to adhere to and digest cellulose, and its genome encodes cellulases and hemicellulases.This study aimed to perform an in silico comparative characterization and functional analysis of cellulase from Ruminococcus albus to explore physicochemical properties and to estimate primary, secondary, and tertiary structure using various bio-computational tools.The protein sequences of cellulases belonging to 6 different Ruminococcus albus strains were retrieved using UniProt. In in silico composition of amino acids, basic physicochemical characteristics were analyzed using ProtParam and Protscale. Multiple sequence alignment of retrieved sequences was performed using Clustal Omega and the phylogenetic tree was constructed using Mega X software. Bioinformatics tools are used to better understand and determine the 3D structure of cellulase. The predicted model was refined by ModRefiner. Structure alignment between the best-predicted model and the template is applied to evaluate the similarity between structures. ResultsIn this study are demonstrated several physicochemical characteristics of the cellulase enzyme. The instability index values indicate that the proteins are highly stable. Proteins are dominated by random coils and alpha helixes. The aliphatic index was higher than 71 providing information that the proteins are highly thermostable. No transmembrane domain was found in the protein, and the enzyme is extracellular and moderately acidic. The best tertiary structure model of the enzyme was obtained by the use of Raptor X, which was refined by ModRefiner. Raptor X suggested the 6Q1I_A as one of the best homologous templates for the predicted 3D protein structure. Ramachandran plot analysis showed that 90.1% of amino acid residues are within the most favored regions. ConclusionsThis study provides for the first time insights about the physicochemical properties, structure, and function of cellulase, from Ruminococcus albus, that will help for detection and identification of such enzyme in vivo or in silico.

Computational characterizations of GDP-mannose 4,6-dehydratase (NoeL) Rhizobial proteins.

A growing body of evidence suggests that Nod Factors molecules are the critical structural components in nitrogen fixation. These molecules have been implicated in plant-microbe signaling. Many enzymes involved in Nod factors biosynthesis; however, the enzymes that decorate (modify) nod factor main structure play a vital role. Here, the computational analysis of GDP-mannose 4,6-dehydratase (NoeL) proteins with great impact in modification of nod factor structure in four genomes of agriculturally important rhizobia (Bradyrhizobium, Mesorhizobium, Rhizobium, Sinorhizobium) presented. The NoeL number of amino acids was in the range of 147 (M5AMF5) to 372 (A0A023XWX0, Q89TZ1). The molecular weights were around 41 KDa. The results showed that the strain-specific purification strategy should apply as the pI of the sequences varied significantly (in the range of 5.59 to 9.12). The enzyme sequences and eight 3-dimensional structures predicted with homology modeling and machine learning representing the phylogenetic tree revealed the stability of enzymes in different conditions (Instability and Aliphatic index); however, this stability is also strain-specific. Disulphide bonds were observed in some species; however, the pattern was not detected in all members of the same species. Alpha helix was the dominant secondary structure predicted in all cytoplasmic NoeL. All models were homo-tetramer with acceptable sequence identity, GMEAN and coverage (60, - 1.80, 88, respectively). Additionally, Ramachandran maps showed that more than 94% of residues are in favored regions. We also highlight several key characterizations of NoeL from four rhizobia genomes annotation. These findings provide novel insights into the complexity and diversity of NoeL enzymes among important rhizobia and suggest considering a broader framework of biofilm for future research.

Transcriptome-wide and expression analysis of the NAC gene family in pepino (Solanum muricatum) during drought stress.

Solanum muricatum (Pepino) is an increasingly popular solanaceous crop and is tolerant of drought conditions. In this study, 71 NAC transcription factor family genes of S. muricatum were selected to provide a theoretical basis for subsequent in-depth study of their regulatory roles in the response to biological and abiotic stresses, and were subjected to whole-genome analysis. The NAC sequences obtained by transcriptome sequencing were subjected to bioinformatics prediction and analysis. Three concentration gradient drought stresses were applied to the plants, and the target gene sequences were analyzed by qPCR to determine their expression under drought stress. The results showed that the S. muricatum NAC family contains 71 genes, 47 of which have conserved domains. The protein sequence length, molecular weight, hydrophilicity, aliphatic index and isoelectric point of these transcription factors were predicted and analyzed. Phylogenetic analysis showed that the S. muricatum NAC gene family is divided into seven subfamilies. Some NAC genes of S. muricatum are closely related to the NAC genes of Solanaceae crops such as tomato, pepper and potato. The seedlings of S. muricatum were grown under different gradients of drought stress conditions and qPCR was used to analyze the NAC expression in roots, stems, leaves and flowers. The results showed that 13 genes did not respond to drought stress while 58 NAC genes of S. muricatum that responded to drought stress had obvious tissue expression specificity. The overall expression levels in the root were found to be high. The number of genes at extremely significant expression levels was very large, with significant polarization. Seven NAC genes with significant responses were selected to analyze their expression trend in the different drought stress gradients. It was found that genes with the same expression trend also had the same or part of the same conserved domain. Seven SmNACs that may play an important role in drought stress were selected for NAC amino acid sequence alignment of Solanaceae crops. Four had strong similarity to other Solanaceae NAC amino acid sequences, and SmNAC has high homology with the Solanum pennellii. The NAC transcription factor family genes of S. muricatum showed strong structural conservation. Under drought stress, the expression of NAC transcription factor family genes of S. muricatum changed significantly, which actively responded to and participated in the regulation process of drought stress, thereby laying foundations for subsequent in-depth research of the specific functions of NAC transcription factor family genes of S. muricatum.

Exploring the Catalytic Significant Residues of Serine Protease Using Substrate-Enriched Residues and a Peptidase Inhibitor

Serine proteases are the most versatile proteolytic enzymes with tremendous applications in various industrial processes. This study was designed to investigate the biochemical properties, critical residues, and the catalytic potential of alkaline serine protease using in-silico approaches. The primary sequence was analyzed using ProtParam, SignalP, and Phyre2 tools to investigate biochemical properties, signal peptide, and secondary structure, respectively. The three-dimensional structure of the enzyme was modeled using the MODELLER program present in Discovery Studio followed by Molecular Dynamics simulation using GROMACS 5.0.7 package with CHARMM36m force field. The proteolytic potential was measured by performing docking with casein- and keratin-enriched residues, while the effect of the inhibitor was studied using phenylmethylsulfonyl fluoride, (PMSF) applying GOLDv5.2.2. Molecular weight, instability index, aliphatic index, and isoelectric point for serine protease were 39.53 kDa, 27.79, 82.20 and 8.91, respectively. The best model was selected based on the lowest MOLPDF score (1382.82) and DOPE score (-29984.07). The analysis using ProSA-web revealed a Z-score of -9.7, whereas 88.86% of the residues occupied the most favored region in the Ramachandran plot. Ser327, Asp138, Asn261, and Thr326 were found as critical residues involved in ligand binding and execution of biocatalysis. Our findings suggest that bioengineering of these critical residues may enhance the catalytic potential of this enzyme.

Validation of Safety Guidelines Adopted for COVID – 19 in Nigeria: The Guidance and Counseling Perspective

Background: This paper adopted scientific approach to validate the WHO/NCDC safety counseling guidelines to prevent the spread of the SARS-COV 2 coronaviruses in Nigeria in the guidance and counseling perspectives using the sequence characteristics of SARS-COV 2 in Nigeria as validation criterion.
 Methods: Five hypotheses were used to validate the safety counseling guidelines currently operational globally. Bioinformatics analysis of retrieved RdRP sequences was adopted.
 Results: All alternate hypotheses were accepted indicating the validity of each of the criterion. Indicators validated included the use of soap (foam) can dissolve the fatty layer of the virus protein coat through regular washing of hands. Heat (high temperature) above 26°C can melt the virus protect as well as hot water. Alkaline water or basic solution with high pH was found to destroy the virus protein coat. Alcohols based sanitizers was also found to dissolve the fat especially the outer lipid layer. High ultra violet light (extinction coefficient) exposures on any object harboring the virus was found to breakdown the viral protein coat while high molecular weight of the coronaviruses confines them to the nose mask or face shield on infected patients. Hence the advocacy for the use of personal protective equipment and the nose mask. The study also validated and revealed that coronavirus strain in Nigeria (MT159778.1) shows a high molecular weight (16289.82g/mol), Total number of negatively charged amino acid residues (11), Total number of positively charged amino acid residues (14), aliphatic index (95.45%), instability index (49.67%), G-C content (38.34%), Half-life (1.2 hrs), alpha helix (49.66%), extinction coefficient (15065m/mol), isoelectric point (8.33) and Hydropathicity (0.106).
 Conclusion: These are the validities that constitutes’ the guidance and counseling perspective on the WHO/NCDC issued safety guidelines towards preventing the spread of the COVID – 19 coronaviruses globally.

Vaccinomic approach for novel multi epitopes vaccine against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)

BackgroundThe spread of a novel coronavirus termed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in China and other countries is of great concern worldwide with no effective vaccine. This study aimed to design a novel vaccine construct against SARS-CoV-2 from the spike S protein and orf1ab polyprotein using immunoinformatics tools. The vaccine was designed from conserved epitopes interacted against B and T lymphocytes by the combination of highly immunogenic epitopes with suitable adjuvant and linkers.ResultsThe proposed vaccine composed of 526 amino acids and was shown to be antigenic in Vaxigen server (0.6194) and nonallergenic in Allertop server. The physiochemical properties of the vaccine showed isoelectric point of 10.19. The instability index (II) was 31.25 classifying the vaccine as stable. Aliphatic index was 84.39 and the grand average of hydropathicity (GRAVY) was − 0.049 classifying the vaccine as hydrophilic. Vaccine tertiary structure was predicted, refined and validated to assess the stability of the vaccine via Ramachandran plot and ProSA-web servers. Moreover, solubility of the vaccine construct was greater than the average solubility provided by protein sol and SOLpro servers indicating the solubility of the vaccine construct. Disulfide engineering was performed to reduce the high mobile regions in the vaccine to enhance stability. Docking of the vaccine construct with TLR4 demonstrated efficient binding energy with attractive binding energy of − 338.68 kcal/mol and − 346.89 kcal/mol for TLR4 chain A and chain B respectively. Immune simulation significantly provided high levels of immunoglobulins, T-helper cells, T-cytotoxic cells and INF-γ. Upon cloning, the vaccine protein was reverse transcribed into DNA sequence and cloned into pET28a(+) vector to ensure translational potency and microbial expression.ConclusionA unique vaccine construct from spike S protein and orf1ab polyprotein against B and T lymphocytes was generated with potential protection against the pandemic. The present study might assist in developing a suitable therapeutics protocol to combat SARSCoV-2 infection.

In silico analysis of carbohydrate-binding pockets in the lectin genes from various species of Canavalia

Legumes are endowed with an opulent class of proteins called lectins that can detect tenuous variations in carbohydrate structures and bind them reversibly with high affinity and specificity. The genus Canavalia, in the family of Leguminosae, is considered to be an affluent source of lectin. An effort has been made to analyse the sequences encoded by the lectin gene and its carbohydrate binding pockets from three species of Canavalia, including C. virosa, C. rosea, and C. pubescens. Crude seed extract showed highest haemagglutination titer against buffalo RBCs and has high affinity to mannose and trehalose. Amplification of the lectin gene by gene-specific primers showed the presence of an 870 bp amplicon. Physicochemical characterization using various bioinformatic tools showed that the isoelectric point was below 7, suggesting that lectin molecules were acidic. A high aliphatic index and high instability index were observed, which indicated that lectin molecules were stable towards a wide range of temperatures. The occurrence of N-glycosylation sites at two sites was also identified in all three species. Prediction of secondary structure showed that approximately 59.05 %, 56.76 % and 54.88 % of the elements were random coils in the case of C. virosa, C. pubescens and C. rosea, respectively. Comparative modelling of the proteins and docking of hypothetical models with sugar moieties that inhibited the agglutination activity suggested that asparagine, serine, alanine, valine, tyrosine and threonine were the major residues involved in hydrogen bonding and other stacking interactions. This can further provide insights on its prospective antibiosis property.

Adaptation and convergence in circadian\u2010related genes in Iberian freshwater fish

BackgroundThe circadian clock is a biological timing system that improves the ability of organisms to deal with environmental fluctuations. At the molecular level it consists of a network of transcription-translation feedback loops, involving genes that activate (bmal and clock – positive loop) and repress expression (cryptochrome (cry) and period (per) – negative loop). This is regulated by daily alternations of light but can also be affected by temperature. Fish, as ectothermic, depend on the environmental temperature and thus are good models to study its integration within the circadian system. Here, we studied the molecular evolution of circadian genes in four Squalius freshwater fish species, distributed across Western Iberian rivers affected by two climatic types with different environmental conditions (e.g., light and temperature). S. carolitertii and S. pyrenaicus inhabit the colder northern region under Atlantic climate type, while S. torgalensis, S. aradensis and some populations of S. pyrenaicus inhabit the warmer southern region affected by summer droughts, under Mediterranean climate type.ResultsWe identified 16 circadian-core genes in the Squalius species using a comparative transcriptomics approach. We detected evidence of positive selection in 12 of these genes using methods based on dN/dS. Positive selection was mainly found in cry and per genes of the negative loop, with 55 putatively adaptive substitutions, 16 located on protein domains. Evidence for positive selection is predominant in southern populations affected by the Mediterranean climate type. By predicting protein features we found that changes at sites under positive selection can impact protein thermostability by changing their aliphatic index and isoelectric point. Additionally, in nine genes, the phylogenetic clustering of species that belong to different clades but inhabit southern basins with similar environmental conditions indicated evolutionary convergence. We found evidence for increased nonsynonymous substitution rate in convergent lineages, likely due to positive selection at 27 sites, mostly in cry genes.ConclusionsOur results support that temperature may be a selective pressure driving the evolution of genes involved in the circadian system. By integrating sequence-based functional protein prediction with dN/dS-based methods to detect selection we uncovered adaptive convergence in the southern populations, probably related to their similar thermal conditions.

The bioinformatics of projected acetyl-CoA carboxylase genes in Hevea brasiliensis

This study clarified the variation and role of physical and chemical characteristics of the H. brasiliensis projected acetyl-CoA carboxylase genes. The detectable similarity and joining projected acetyl-CoA carboxylase genes of H. brasiliensis in the dendrogram may be the outcome of tropical environmental. Six projected acetyl-CoA carboxylase genes from H. Brasiliensis collected from NCBI. The NCBI locus number of the protein sequence utilized in this study was determined. The physical and chemical properties of acetyl-CoA carboxylase from H.brasiliensis. The factors were calculated the designate number of protein, number of amino acids, molecular weight, theoretical isoelectric point values, the total number of atoms, extinction coefficients, estimated half-life, instability index, aliphatic index and grand average of hydropathicity.

Can soybean lipoxygenases be real models for mammalian lipoxygenases? A bioinformatics approach

Soybean lipoxygenases (soybean lipoxygenase-1) has been a well-studied enzyme because it is considered as a model enzyme for mammalian lipoxygenases. In general, the soybean lipoxygenase-1 is used in the test of inhibitory activities of various compounds. The present study provides a bioinformatics approach for comparison of various lipoxygenases in the databases. Their various physical and chemical parameters such as molecular weight, theoretical pI, amino acid composition, aliphatic index and grand average of hydropathicity and the multiple sequence alignments of the lipoxygenases were computed by using several bioinformatics tools. In order to see phylogenetic relation among lipoxygenases, a phylogenetic tree was constructed. The first three most abundant amino acids in soybean lipoxygenase-1 and 15-lipoxygenase (human) are L (10.3 %), S (7.4 %), A (6.7 %) and L (13.3 %), G (7.4 %), V (7.1 %), respectively. According to the phylogenetic tree, the soybean lipoxygenases are within separate clade compared to the mammalian lipoxygenases. In conclusion, soybean lipoxygenase-1 may not fully characterise the human lipoxygenase-15 since there are remarkable sequence-based differences, which are obtained by using bioinformatics tools between soybean lipoxygenase-1 and lipoxygenases from other sources especially from human. In this context, the researchers aware of the problems described above and having similar concerns have begun to use recombinant DNA technology to produce recombinant h-15-LOX enzyme in Escherichia coli.

In silico characterization of bacterial chitinase: illuminating its relationship with archaeal and eukaryotic cousins

BackgroundChitin is one of the most abundant biopolymers on Earth, only trailing second after cellulose. The enzyme chitinase is responsible for the degradation of chitin. Chitinases are found to be produced by wide range of organisms ranging from archaea to higher plants. Though chitin is a major component of fungal cell walls and invertebrate exoskeletons, bacterial chitinase can be industrially generated at low cost, in facile downstream processes at high production rate. Microbial chitinases are more stable, active, and economically practicable compared to the plant- and animal-derived enzymes. ResultsIn the present study, computationally obtained results showed functional characteristics of chitinase with particular emphasis on bacterial chitinase which is fulfilling all the required qualities needed for commercial production. Sixty-two chitinase sequences from four different groups of organisms were collected from the RCSB Protein Data Bank. Considering one suitable exemplary sequence from each group is being compared with others. Primary, secondary, and tertiary structures are determined by in silico models. Different physical parameters, viz., pI, molecular weight, instability index, aliphatic index, GRAVY, and presence of functional motifs, are determined, and a phylogenetic tree has been constructed to elucidate relationships with other groups of organisms. ConclusionsThis study provides novel insights into distribution of chitinase among four groups and their characterization. The results represent valuable information toward bacterial chitinase in terms of the catalytic properties and structural features, can be exploited to produce a range of chitin-derived products.

Structural-Genetic Characterization Of Novel Butaryl co-A Dehydrogenase and Proposition of Butanol Biosynthesis Pathway in Pusillimonas ginsengisoli SBSA.

Despite extensive use in the biofuel industry, only butyryl co-A dehydrogenase enzymes from the Clostridia group have undergone extensive structural and genetic characterization.The present study, portrays the characterization of structural, functional and phylogenetic properties of butyryl co-A dehydrogenase identified within the genome of Pusillimonas ginsengisoli SBSA. In silico characterization, homology modelling and docking data indicates that this protein is a homo-tetramer and 388 amino acid residue long, rich in alanine and leucine residue; having molecular weight of 42347.69 dalton. Its isoelectric point value is 5.78; indicate its neutral nature while 38.38 instability index value indicate its stable nature. Its thermostable nature evidenced by its high aliphatic index (93.14); makes its suitable for industry-based use. The secondary structure prediction analysis of butyryl co-A dehydrogenase unveiled that the proteins has secondary arrangements of 54% α-helix, 13% β-stand and 5% disordered conformation. However, phylogenetic analysis clearly indicates that probably horizontal gene transfer is the primary mechanism of spreading of this gene in this organism. Notably, multiple sequence alignment study of phylogenetically diverse butyryl co-A dehydrogenase sequence highlighted the presence of conserved amino acid residues i.e. YXV/LGXKXWXS/T. Physicochemical characterization of other relevant proteins involved in butanol metabolism of SBSA also has been carried out. However, metabolic construction of functional butanol biosynthesis pathway in SBSA, enlightened its cost-effective potential use in biofuel industry as an alternate to Clostridia system.

Validation of Isolate Stability Status and in silico Characterization of SARS-COV 2 Partial CdsRdRP Gene Sequences

Background and Objective: In December 2019, patients diagnosed with viral pneumonia due to an unidentified microbial agent were reported in Wuhan, China. A novel coronavirus was subsequently identified as the causative pathogen, provisionally named 2019 novel coronavirus (COVID 19). The article aimed to unmask the genetic stability and nature of the viruses and validated the safety guidelines adopted for the coronaviruses currently causing the global pandemic. Materials and Methods: This study uses in silico approach and bioinformatics tools to validate the stability status and characteristics of the novel SARS-COV 2 coronaviruses by retrieving nucleotide sequences isolated and deposited in the NCBI. Results: The results have revealed that 11 out of 12 isolates studied are genetically and thermally unstable. The aliphatic index ranged from 52.98-112.07 in MT187977.1-MT127116.1, respectively. The instability index among the sequences ranged from 39.58-73.65 in MT187977.1-MT152900.1 isolate, respectively. The G-C contents range from 37.28-49.26% in MN938385.1-MT187977.1, respectively. Phylogenetically, isolates MT127116.1, MT159778.1, MT050414.1 and MT042777.1 showed the same genetic and mutation pathway with an evolutionary distance of 0.4 and 0.8 divergence times relative to the last common ancestor. Conclusion: There is a need for concerted effort in studying and understanding the genetic and thermal stability status and other characteristics of the viruses to be able to find a suitable therapy and drug design for the pandemic and biosecurity of humans against the virus now and in the future.

Cloning and Tissue Expression Analysis of Calcium-dependent Protein Kinase Gene <i>BsCDPK1</i> in <i>Bletilla striata</i>

Calcium-dependent protein kinases (CDPKs) play vital roles in the regulation of plant growth, development, and the response to adversity stress. Studying the sequence information and expression pattern of CDPK gene could lay the foundation for the protein structure, gene functions and signal network of plant stress resistance. The full-length cDNA of BsCDPK1 gene was obtained by RT-PCR and RACE approaches in this study. The physicochemical properties and structural domains of BsCDPK1 protein were analyzed by bioinformatics tools; In addition, amino acid sequence alignment and phylogenetic analysis of BsCDPK1 were performed. The expression pattern of BsCDPK1  gene in the seedling stage of Bletilla striata  was detected by real-time fluorescence quantitative PCR. The result showed that the full cDNA of the cloned BsCDPK1  was 1 981 bp, encoding 496 amino acids. The molecular weight of encoded protein was 55.997 KD, isoelectric point 5.38, aliphatic index 87.50 and instability index 43.54. The BsCDPK1 protein included the typical kinase domain of CDPKs in other plants, autoinhibitory domain, ATP binding site and the four EF-hands were highly conserved, which was more homologous with CDPKs of Dendrobium candidum  and Phalaenopsis equestris , clustered on the same evolutionary branch. The results of qRT-PCR indicated that BsCDPK1  gene was expressed in the roots, stems and leaves in Bletilla striata seedlings. The cloning and sequence characterizing and tissue expression pattern analysis of  BsCDPK1  provided experimental basis for elucidating the function of BsCDPK1  gene in plant growth and development and adversity stress responses.

Variability in linear polypeptide stabilizes proteoglycan than zinc finger protein in vascular smooth muscle cells: An In Silico approach

Background: Structural and physicochemical topologies of proteins play a considerable role in differentiating the functional properties of the biological system. We aimed to study the physicochemical similarities, structural and functional differences of versican (VCAN) and early growth response (Egr) proteins involved in vascular injuries. Methods: For the primary structure prediction, the proteomic tools Expasy's Protparam is used, likewise, for secondary structure and content prediction SOPM and SOPMA tool is used. The transmembrane regions in VCAN and EGR proteins are predicted through SOSUI (Classification and Secondary Structure Prediction of Membrane Proteins) server. The CYSREC tool is used to identify the presence of disulphide bonds in all the VCAN and EGR proteins, additionally through homology modelling the disulphide bonds are visualized and structure of the modelled proteins are validated through Rampage (Ramachandran plot), ProQ (Protein Quality Server) and ProSA (Protein Structure Analysis) server. Results: VCAN and Egr proteins resemble hydrophilic in nature, similarly negative score of the grand average of hydropathicity index confirms hydrophilic nature. The maximum molecular weight for VCAN is observed as 39265 and 61623 Dalton for EGR protein. VCAN proteins showed a higher level of basic residues except Q86W61, while all the Egr proteins were acidic residues. The extinction coefficient (EC) has unique absorbance at 280 nm wavelength. Based on the aliphatic index (AI ≥ 45) and instability index (II ≥ 40) most of the VCAN and Egr proteins were unstable. The Classification and Secondary Structure Prediction of Membrane Proteins server classifies all Egr and few VCAN and proteins are soluble nature. Secondary structure content prediction and SOPM server show most of the VCAN proteins are beta sheets and many Egr proteins are alpha-helical, while few with mixed structures. Besides these differences, the VCAN protein stability was identified by most probable disulfide (SS) bridges using CYS_REC tool and confirmed by homology modeling in tertiary structure. Whereas the probable disulfide bonds in Egr proteins were not identified. Conclusion: The findings with these functional and structural properties will add an extra room in understanding their dual role.