The fatty-acid profile of the vegetable oils determines its properties and nutritional value. Palm-oil obtained from the African oil-palm [Elaeis guineensis Jacq. (Tenera)] contains 44% palmitic acid (C16:0), but, palm-oil obtained from the American oilpalm [Elaeis oleifera] contains only 25% C16:0. In part, the b-ketoacyl-[ACP] synthase II (KASII) [EC: 2.3.1.179] protein is responsible for the high level of C16:0 in palm-oil derived from the African oil-palm. To understand more about E. guineensis KASII (EgKASII) and E. oleifera KASII (EoKASII) proteins, it is essential to know its structures. Hence, this study was undertaken.
Beta-glucosidase (3.2.1.21) plays an essential role in the removal of non-reducing terminal glucosyl residues from glycosides. Recently, beta-glucosidase has been of interest for biomass conversion that acts in synergy with two other enzymes, endoglucanase and exo-glucanase. However, there is not much information available on the catalytic interactions of beta-glucosidase with its substrates. Thus, this study reports on the binding modes between beta-glucosidase from glycoside hydrolase family 1 namely BglB with cellobiose, cellotetraose and cellotetriose via molecular docking simulation. From the results, the binding affinities of BglB-cellobiose, BglB-cellotetraose, and BglB-cellotetriose complexes were reported to be -6.2kJ/mol , -5.68 kJ/mol and -5.63 kJ/mol, respectively. The detail interactions were also been investigated that revealed the key residues involved in forming hydrogen bonds (h-bond) with the substrates. These findings may provide valuable insigths in designing beta-glucosidase with higher cellobiose-hydrolyzing efficiency.
A great challenge is posed to the treatment of tuberculosis due to the evolution of multidrug-resistant (MDR) and extensively drugresistant (XDR) strains of Mycobacterium tuberculosis in recent times. The complex cell envelope of the bacterium contains unusual structures of lipids which protects the bacterium from host enzymes and escape immune response. To overcome the drug resistance, targeting "drug targets" which have a critical role in growth and virulence factor is a novel approach for better tuberculosis treatment. The enzyme Phosphopantetheinyl transferase (PptT) is an attractive drug target as it is primarily involved in post translational modification of various types-I polyketide synthases and assembly of mycobactin, which is required for lipid virulence factors. Our in silico studies reported that the structural model of M.tuberculosis PptT characterizes the structure-function activity. The refinement of the model was carried out with molecular dynamics simulations and was analyzed with root mean square deviation (RMSD), and radius of gyration (Rg). This confirmed the structural behavior of PptT in dynamic system. Molecular docking with substrate coenzyme A (CoA) identified the binding pocket and key residues His93, Asp114 and Arg169 involved in PptT-CoA binding. In conclusion, our results show that the M.tuberculosis PptT model and critical CoA binding pocket initiate the inhibitor design of PptT towards tuberculosis treatment.
A hidden Markov model (HMM) has been utilized to predict and generate artificial secretory signal peptide sequences. The strength of signal peptides of proteins from different subcellular locations via Lactococcus lactis bacteria correlated with their HMM bit scores in the model. The results show that the HMM bit score +12 are determined as the threshold for discriminating secreteory signal sequences from the others. The model is used to generate artificial signal peptides with different bit scores for secretory proteins. The signal peptide with the maximum bit score strongly directs proteins secretion.
Functional genomics has proven to be an efficient tool in identifying genes involved in various biological functions. However the availability of commercially important seaweed Eucheuma denticulatum functional resources is still limited. EuDBase is the first seaweed online repository that provides integrated access to ESTs of Eucheuma denticulatum generated from samples collected from Kudat and Semporna in Sabah, Malaysia. The database stored 10,031 ESTs that are clustered and assembled into 2,275 unique transcripts (UT) and 955 singletons. Raw data were automatically processed using ESTFrontier, an in-house automated EST analysis pipeline. Data was collected in MySQL database. Web interface is implemented using PHP and it allows browsing and querying EuDBase through search engine. Data is searchable via BLAST hit, domain search, Gene Ontology or KEGG Pathway. A user-friendly interface allows the identification of sequences either using a simple text query or similarity search. The development of EuDBase is initiated to store, manage and analyze the E. denticulatum ESTs and to provide accumulative digital resources for the use of global scientific community. EuDBase is freely available from http://www.inbiosis.ukm.my/eudbase/.
A random forest method has been selected to perform both gene selection and classification of the microarray data. In this embedded method, the selection of smallest possible sets of genes with lowest error rates is the key factor in achieving highest classification accuracy. Hence, improved gene selection method using random forest has been proposed to obtain the smallest subset of genes as well as biggest subset of genes prior to classification. The option for biggest subset selection is done to assist researchers who intend to use the informative genes for further research. Enhanced random forest gene selection has performed better in terms of selecting the smallest subset as well as biggest subset of informative genes with lowest out of bag error rates through gene selection. Furthermore, the classification performed on the selected subset of genes using random forest has lead to lower prediction error rates compared to existing method and other similar available methods.
Laccase belongs to the family of blue multi-copper oxidases and are capable of oxidizing a wide range of aromatic compounds. Laccases have industrial applications in paper pulping or bleaching and hydrocarbon bioremediation as a biocatalyst. We describe the design of a laccase with broader substrate spectrum in bioremediation. The application of evolutionary trace (ET) analysis of laccase at the ligand binding site for optimal design of the enzyme is described. In this attempt, class specific sites from ET analysis were mapped onto known crystal structure of laccase. The analysis revealed 162PHE as a critical residue in structure function relationship studies.
The formation of protein homodimer complexes for molecular catalysis and regulation is fascinating. The homodimer formation through 2S (2 state), 3SMI (3 state with monomer intermediate) and 3SDI (3 state with dimer intermediate) folding mechanism is known for 47 homodimer structures. Our dataset of forty-seven homodimers consists of twenty-eight 2S, twelve 3SMI and seven 3SDI. The dataset is characterized using monomer length, interface area and interface/total (I/T) residue ratio. It is found that 2S are often small in size with large I/T ratio and 3SDI are frequently large in size with small I/T ratio. Nonetheless, 3SMI have a mixture of these features. Hence, we used these parameters to develop a decision tree model. The decision tree model produced positive predictive values (PPV) of 72% for 2S, 58% for 3SMI and 57% for 3SDI in cross validation. Thus, the method finds application in assigning homodimers with folding mechanism.
Normal blood glucose level depends on the availability of insulin and its ability to bind insulin receptor (IR) that regulates the downstream signaling pathway. Insulin sequence and blood glucose level usually vary among animals due to species specificity. The study of genetic variation of insulin, blood glucose level and diabetics symptoms development in Aves is interesting because of its optimal high blood glucose level than mammals. Therefore, it is of interest to study its evolutionary relationship with other mammals using sequence data. Hence, we compiled 32 Aves insulin from GenBank to compare its sequence-structure features with phylogeny for evolutionary inference. The analysis shows long conserved motifs (about 14 residues) for functional inference. These sequences show high leucine content (20%) with high instability index (>40). Amino acid position 11, 14, 16 and 20 are variable that may have contribution to binding to IR. We identified functionally critical variable residues in the dataset for possible genetic implication. Structural models of these sequences were developed for surface analysis towards functional representation. These data find application in the understanding of insulin function across species.
Rubisco is a very large, complex and one of the most abundant proteins in the world and comprises up to 50% of all soluble protein in plants. The activity of Rubisco, the enzyme that catalyzes CO2 assimilation in photosynthesis, is regulated by Rubisco activase (Rca). In the present study, we searched for hypothetical protein of Vitis vinifera which has putative Rubisco activase function. The Arabidopsis and tobacco Rubisco activase protein sequences were used as seed sequences to search against Vitis vinifera in UniprotKB database. The selected hypothetical proteins of Vitis vinifera were subjected to sequence, structural and functional annotation. Subcellular localization predictions suggested it to be cytoplasmic protein. Homology modelling was used to define the three-dimensional (3D) structure of selected hypothetical proteins of Vitis vinifera. Template search revealed that all the hypothetical proteins share more than 80% sequence identity with structure of green-type Rubisco activase from tobacco, indicating proteins are evolutionary conserved. The homology modelling was generated using SWISS-MODEL. Several quality assessment and validation parameters computed indicated that homology models are reliable. Further, functional annotation through PFAM, CATH, SUPERFAMILY, CDART suggested that selected hypothetical proteins of Vitis vinifera contain ATPase family associated with various cellular activities (AAA) and belong to the AAA+ super family of ring-shaped P-loop containing nucleoside triphosphate hydrolases. This study will lead to research in the optimization of the functionality of Rubisco which has large implication in the improvement of plant productivity and resource use efficiency.
Proteins can interact in various ways, ranging from direct physical relationships to indirect interactions in a formation of protein-protein interaction network. Diagnosis of the protein connections is critical to identify various cellular pathways. Today constructing and analyzing the protein interaction network is being developed as a powerful approach to create network pharmacology toward detecting unknown genes and proteins associated with diseases. Discovery drug targets regarding therapeutic decisions are exciting outcomes of studying disease networks. Protein connections may be identified by experimental and recent new computational approaches. Due to difficulties in analyzing in-vivo proteins interactions, many researchers have encouraged improving computational methods to design protein interaction network. In this review, the experimental and computational approaches and also advantages and disadvantages of these methods regarding the identification of new interactions in a molecular mechanism have been reviewed. Systematic analysis of complex biological systems including network pharmacology and disease network has also been discussed in this review.
Fucoxanthin (Fx) is an active compound commonly found in the many types of seaweed with numerous biological activities. The main goal of this investigation is to explore the effect of Fx against the cell proliferation, apoptotic induction and oxidative stress in the oral squamous (KB) cell line. Cytotoxicity of Fx was determined by MTT assay. The intracellular ROS production, mitochondrial membrane potential (MMP) and apoptosis induction in KB cells were examined through DCFH-DA, Rhodamine-123 and DAPI, and dual staining techniques. Effect of Fx on the antioxidant enzymes and lipid peroxidation in the KB cells was studied through the standard procedures. Fx treated KB cells showed morphological changes and reduced cell survival, which is exhibited by the cytotoxic activity of 50 µM/ml (IC50) Fx against the KB cells. The Fx treatment considerably induced the apoptotosis cells (EB/AO) and decreased the MMP (Rh-123) in KB cells. Further, it was pointed out that there was an increased lipid peroxidation (LPO) with decreased antioxidants (CAT, SOD and GSH). These results concluded that Fx has the cytotoxic effect against KB cells and has the potential to induce the apoptosis via increased oxidative stress. Hence, the Fx can be a promising agent for the treatment of oral cancer and it may lead to the development of cancer therapeutics.
Plants are very complex organisms that produce medicinally important natural products. The Star-fruit producing plant (Averrhoa carambola L.) is a species of woody plant in the family Oxalidaceae native to the Philippines, Indonesia, Malaysia, Vietnam, India, Bangladesh and Sri Lanka; but, cultivated in many parts of the world. Star-fruits are popular tropical fruits and used commonly in Ayurvedic and Traditional Chinese Medicines (TCM) in India, China, and Brazil to relieve ailments such as chronic headache, fever, cough, gastro-enteritis, diarrhoea, ringworm infections, and skin inflammations. However, this fruit contains high amount of oxalate, which is hazardous for uremic patients, and caramboxin (CBX), which is neurotoxic. The aim of this review is to highlight the nutritional, medicinal and toxicological traits of the star-fruits.
Mitogen-activated protein kinase 4 (MPK4) interacts with the (Mitogen-activated protein kinase kinase kinase 1) MEKK1/ Mitogenactivated protein kinase kinase 1 (MKK1)/ Mitogen-activated protein kinase kinase 2 (MKK2) complex to affect its function in plant development or against pathogen attacks. The KEGG (Kyoto Encyclopedia of Genes and Genomes) network analysis of Arabidopsis thaliana revealed close interactions between those four genes in the same plant-pathogen interaction pathway, which warrants further study of these genes due to their evolutionary conservation in different plant species. Through targeting the signature sequence in MPK4 of papaya using orthologs from Arabidopsis, the predicted sequence of MPK4 was studied using a comparative in silico approach between different plant species and the MAP cascade complex of MEKK1/MKK1/MKK2. This paper reported that MPK4 was highly conserved in papaya with 93% identical across more than 500 bases compared in each species predicted. Slight variations found in the MEKK1/MKK1/MKK2 complex nevertheless still illustrated sequence similarities between most of the species. Localization of each gene in the cascade network was also predicted, potentiating future functional verification of these genes interactions using knock out or/and gene silencing tactics.
The innovations and developments in microbiology, biomedical sciences, and biotechnology come along with the challenges of biological risk (biorisk). Biorisk is defined as the "combination of the probability of occurrence of harm and the severity of that harm where the source of harm is a biological agent or toxin." Biorisk is a borderless challenge to the global community. Hence, all universities, colleges, centers of bio-excellence, and institutions of higher learning can and should do their bit to educate technical members, academicians, students and stakeholders (LASS) for the efficient and comprehensive biorisk management (BRM) for our and future generations safety and sustainability.
Phyllanthus amarus Schumach. and Thonn. is a wide spread medicinal herb with various traditional uses. It is well documented for its antioxidant, anti-inflammatory, and hepatoprotective activities. Therefore, it is of interest to evaluate the 80% ethanol extract of Phyllanthus amarus (PA) on spatial memory using the 8-radial arm maze (8-RAM) in mice after induction of neuro inflammation by lipopolysaccharide (LPS) in a 14- and 28-days treatment study. LC-MS/MS was performed to profile the chemical composition in PA extract. Mice were treated orally with 5% v/v tween 20, PA extract (100, 200 and 400 mg/kg), or ibuprofen (IBF 40 mg/kg) for 14 and 28 days. All groups were challenged with LPS (1 mg/kg) via intraperitoneal (i.p.) injection a day prior to the 8-RAM task except for the negative control group which received an i.p. injection of saline. Data obtained were analyzed with one-way ANOVA followed by post hoc Dunnett's test (comparison of all groups against vehicle control). Analysis of LC-MS/MS data revealed the presence of 16 compounds in the PA extract. Administration of PA extract at 200 and 400 mg/kg for 14 and 28 days significantly (*P<0.05) decreased the working and reference memory errors against LPS-induced spatial memory impairment. The observed protective action is possibly due to the putative antineuroinflammatory effects of PA. In conclusion, PA extract possess neuroprotective effects against spatial memory impairment mediated by LPS.
Design and development of effective anti-virals in combating CoVid-19 is a great challenge worldwide. Known drugs such as chloroquine, lopinavir, favipiravir and remdesivir are used in the management of CoVid - 19. It is known that Ivermectin and remdesivir both are effective against filoviruses, paramyxo viruses. Available data also shows that ivermectin and remedesivir repress the replication of SARS-CoV-2. Thus, we document the potential use of ivermectin and remdesivir in the management of CoVid -19.
Kinase Suppressor of Ras (KSR) is a molecular scaffold that interacts with the core kinase components of the ERK cascade, Raf, MEK, ERK to provide spatial and temporal regulation of Ras-dependent ERK cascade signaling. Interruption of this mechanism can have a high influence in inhibiting the downstream signaling of the mutated tyrosine kinase receptor kinase upon ligand binding. Still none of the studies targeted to prevent the binding of Raf, MEK binding on kinase suppressor of RAS. In that perspective the cysteine rich C1 domain of scaffold proteins kinase suppressor of Ras-1 was targeted rather than its ATP binding site with small ligand molecules like flavones and anthocyanidins and analyzed through insilico docking studies. The binding energy evaluation shows the importance of hydroxyl groups at various positions on the flavone and anthocyanidin nucleus. Over all binding interaction shows these ligands occupied the potential sites of cysteine rich C1 domain of scaffold protein KSR.
There is a shred of evidence to suggest that Emblica officinalis Gaertn, the botanical name for amla seeds, has greater medicinal potential than amla fruit. We conducted this work to assess the anti-inflammatory, antibacterial, and antioxidant capacities of E. officinalis seed extracts. The bioactive components from the seeds were fractionated using chloroform, hexane, methanol, and diethyl ether, according to the polarity of the solvents. The total amount of phenolic and flavonoid was estimated. Both the reducing power and antioxidant capacities of the extracts were evaluated using the DPPH (1,1-diphenyl-2-picryl-hydrazyl) technique. 15-lipoxygenase (LOX) was inhibited by seed extracts at doses ranging from 5 to 25 micrograms. In silico docking was employed to assess the results. Some human pathogenic microorganisms were tested for their antibacterial activity using the agar disc diffusion method. Escherichia coli, Proteus vulgaris, and Klebsiella pneumonia were inhibited by a methanolic extract with an IC50 value of 58g, making it the most common organic solvent extract. Methanolic extracts also showed good antioxidant and antibacterial activity. Our investigation led us to discover that amla seeds have anti-inflammatory, antioxidant, and antibacterial effects.
The immature lymphoid cells with chromosomal structural and numerical abnormalities cause the acute lymphoblastic leukemia (ALL). This hematologic disorder constitutes about 25% of cancer prognosis among children and adolescents. D-Carvone, a monocyclic monoterpene obtained from the essential oils extracted from plants is reported to possess the various biological activities. The present study was aimed to investigate the anticancer potential of D-Carvone against the human leukemic Molt-4 cells. The cytotoxicity of DCarvone was analyzed by MTT assay. The level of lipid peroxidation and antioxidants were determined. The intracellular ROS, MMP and apoptosis were demonstrated by fluorescent staining techniques. The MTT assay revealed that the D-Carvone treatment suppressed the viability of Molt-4 cells and the IC50 was determined at 20 µM/ml. The D-Carvone treatment was increased the oxidative stress and reduced the level of antioxidants in the Molt-4 cell lines. The increased intracellular ROS, apoptotic cell death, and diminished MMP was noted in the D-Carvone treatment. In the Molt-4 cells, D-carvone induced the apoptosis in a time and dose dependent manner by the activation of caspases-8, -9 and -3. Thus, data provide insights for the clinical application of D-Carvone in the treatment of blood cancer Molt-4 cells. Our study suggests the therapeutic potential D-Carvone for the treatment of leukemia in future.