mojtaba mortezavi

The 2019 novel coronavirus (2019-nCoV/SARS-CoV-2) initially appeared as part of an important prevalence of respiratory disease centered in Hubei province, China. Now, it is a pandemic globally and is a significant public health concern. Taxonomically, SARS-CoV-2 was revealed to be a Beta coronavirus (lineage B) related to SARS-CoV and SARS-related bat coronaviruses closely, and it has been stated to have a similar receptor with SARS-CoV (ACE-2). Here, we carried out the codon usage bias (CUB) by analyzing the codon bias index (CBI), codon adaptation index (CAI), and an effective number of codons (ENC) besides phylogenetic analysis of Coronaviridae and also structural modeling of the SARS-CoV-2 spike glycoprotein. We observed that 2019-nCoV has a rich composition of AT nucleotides that strongly affects its codon usage, which seems to be not optimized for the human hosts. Moreover, a close evolutionary phylogenetic relationship was detected between SARS-CoV-2/human/IRIN/ and SARS-CoV-2/human/CHN/WH-09/2020. By in silico modeling of spike glycoprotein, an I-TASSER server, the 3Dstructure of it was also evaluated. This type of analysis would be beneficial for exploring a virus adaptation to host, and evolution and is therefore of value to developing vaccine design and pharmaceutical agents.

Codon usage and rare codons have mixed results on the protein structure and function. An increasing amount of data is shown that replacing the rare codons with frequently synonymous ones has diverse results as a decrease in a protein’s specific activity, changing the folding pathway, and reducing protein solubility. In this study, we investigated the situation of codon usage of the Lampyridae family luciferases using computational databases. For this, the codon feature of these luciferases was studied, bioinformatically. Also, in silico analyses of this enzyme were conducted by structural modeling on the I-TASSER web server. The status of these rare codons in these structural models was studied using SPDBV and PyMOL software. Finally, the binding site properties were studied using the AutoDock Vina. Using molecular modeling, two rare codons (Arg533 and Arg536) were analyzed that may have a critical role in the structure and function of these luciferases. AutoDock Vina was used in molecular docking that recognizes some residues that yield closely related to luciferyl-adenylate binding sites. These analyses created a new understanding of the sequence and structure of these luciferases, and our findings can be used in some fields of clinical and industrial biotechnology. This bioinformatics analysis plays an essential role in the design of new drugs.

The 2019 novel coronavirus (2019-nCoV/SARS-CoV-2) initially appeared as part of an important prevalence of respiratory disease centered in Hubei province, China. Now, it is a pandemic globally and is a significant public health concern. Taxonomically, SARS-CoV-2 was revealed to be a Beta coronavirus (lineage B) related to SARS-CoV and SARS-related bat coronaviruses closely, and it has been stated to have a similar receptor with SARS-CoV (ACE-2). Here, we carried out the codon usage bias (CUB) by analyzing the codon bias index (CBI), codon adaptation index (CAI), and an effective number of codons (ENC) besides phylogenetic analysis of Coronaviridae and also structural modeling of the SARS-CoV-2 spike glycoprotein. We observed that 2019-nCoV has a rich composition of AT nucleotides that strongly affects its codon usage, which seems to be not optimized for the human hosts. Moreover, a close evolutionary phylogenetic relationship was detected between SARS-CoV-2/human/IRIN/ and SARS-CoV-2/human/CHN/WH-09/2020. By in silico modeling of spike glycoprotein, an I-TASSER server, the 3Dstructure of it was also evaluated. This type of analysis would be beneficial for exploring a virus adaptation to host, and evolution and is therefore of value to developing vaccine design and pharmaceutical agents.

Codon usage and rare codons have mixed results on the protein structure and function. An increasing amount of data is shown that replacing the rare codons with frequently synonymous ones has diverse results as a decrease in a protein’s specific activity, changing the folding pathway, and reducing protein solubility. In this study, we investigated the situation of codon usage of the Lampyridae family luciferases using computational databases. For this, the codon feature of these luciferases was studied, bioinformatically. Also, in silico analyses of this enzyme were conducted by structural modeling on the I-TASSER web server. The status of these rare codons in these structural models was studied using SPDBV and PyMOL software. Finally, the binding site properties were studied using the AutoDock Vina. Using molecular modeling, two rare codons (Arg533 and Arg536) were analyzed that may have a critical role in the structure and function of these luciferases. AutoDock Vina was used in molecular docking that recognizes some residues that yield closely related to luciferyl-adenylate binding sites. These analyses created a new understanding of the sequence and structure of these luciferases, and our findings can be used in some fields of clinical and industrial biotechnology. This bioinformatics analysis plays an essential role in the design of new drugs.

Phytase hydrolyzes phytic acid. Phytic acid is the main form of phosphorus storage in plant seeds in cereals, legumes, and oilseeds. In addition, phytic acid chelates essential minerals and binds to amino acids and proteins and prevents the action of digestive enzymes leads to decrease in the digestibility of proteins. Monogastric animals are unable to hydrolyze phytic acid due to the lack of phytase in their digestive system. In the current study, based on the docking results and DynaMut webserver predictions, T312R and F260R mutants, were chosen. Then, using Quick-Change PCR, the two residues in the active site of phytase from Yersinia intermedia phytase were mutated to Arg. Moreover, a double mutant F260R/ T312R was generated. Afterwards, the recombinant mutant and wild-type phytases were expressed in bacterial host, purified and their activities were measured. According to the results, the activities of T312R and F260R almost remained unchanged; however, that of T312R/ F260R was increased about 2.35 folds compared with the wild-type. This indicated that incorporation of two positively-charged arginine residues in the active site led to more interactions of these residues with the negatively charged-rich substrate and increased the phytase activity. In conclusion, highly active T312R/ F260R double mutant can be used as feed additive in feed industries.

Late embryonic accumulating proteins (LEAs) are proteins that involved in reducing Cellular injuries associated with dehydration and preventing cellular proteins from aggregation due to osmotic stress and freezing. Increased expression of some genes encoding these proteins has led to increased resistance to stresses such as dehydration, cold and salinity in many plants. Analysis of biological data with the using of bioinformatics tools plays an important role in the study of genes and proteins and predicts their function in response to the stress.

In this study, in order to study of LEA proteins in two important grasses (tolerant and sensitive to drought), the interest sequences are obtained from different data bases and the phylogeny tree are drown using ClustalW software. After the investigation of classes in different groups, the short sequences deleted and some sequences were selected. The information about sequence characteristics, their motifs, prediction of intracellular location, analysis of hydrogen and non-hydrogen bands and prediction of biological process and molecular activity obtained using ProtParam, EXPASY, MEME and SMART, Wolf PSORT, PIC, WHAT IF databases and Blast2GO software. The 3D structure of these proteins was modeled using Discovery studio, HyperChem, MODELLER v10 and SPDBV software.

The results were grouped the proteins into seven distinct groups with the highest number of sequences in dehydrin group. Most proteins had small size with less than 30 kDa. Also, the most sequences showed high surface charge, because of their hydrophilicity and flexible structure to form a chaperone structure to protect the cell membrane from stress. The study of intracellular location showed that most of proteins are located in the cell nucleus. Also, the motif study demonstrated the conserved sequences among members of the same group. The prediction of molecular activity and biology indicated the role of these proteins in the tolerance to the stress including drought and protein folding through bindings or catalytic activity.  

Barley as a stress-resistant plant mainly involved the dehydrin sequences and rice as a stress-sensitive plant mainly contains the LEA4 and LEA2 sequences.

In order to investigate the activity of antioxidant enzymes of 14 tea clones under normal and drought stress conditions, two separate experiments were carried out in a randomized complete block design with two replications in 2017 at Fashalem Tea Research Station in Rasht. Irrigation in both designs was carried out routinely until July 22 followed by a drought stress treatment for one plot until August 22 when tea leaves were harvested. Tea leaves from each plot of the both experiments were then removed and transferred to a freezer at -80 °C. The activity of the antioxidant such as ascorbate peroxidase, superoxide dismutase, catalase, peroxidase, phenylalanine ammoniaase, lipid peroxidase, malondialdehyde, β-carotene, and lycopene were measured. The results showed that drought stress increased the activity of antioxidant enzymes. Based on the results obtained from the mean comparisons, clones 100, 399 and Bazri, had the highest activity for ascorbate peroxidase, superoxide dismutase, catalase, peroxidase, phenylalanine ammoniaase, and lipid peroxidase under drought stress conditions. On the other hand, these clones had the lowest contents of malondialdehyde. Clones 278 and 276 on the other hand, had the least values of antioxidant enzymes under drought stress conditions (except malondialdehyde) and were considered as sensitive clones.

Luciferase enzymes are involved in the bioluminescence reaction (light emission by living organisms). The bioluminescence process is a widespread phenomenon in the Nature. These enzymes are identified in some domains of life, but the luciferases from lampyrid genus are considered of for biological applications. The molecular cloning of a new type of firefly luciferase from Luciola lateralis was reported, previously. Here, we study its substrate binding site and rare codon with molecular docking and bioinformatics studies. By molecular modelling, some rare codons were identified that may have a critical role in structure and function of this luciferase. AutoDock Vina was used in the molecular docking that recognizes some residues that yield closely related with luciferin and AMP binding site. These types of studies help in the discovery of the light production reaction. Evaluation of these hidden information’s can improve the knowledge of luciferases folding and protein expression challenges and help in design of new drugs.