scholarly journals Toxoplasma gondii Tyrosine-Rich Oocyst Wall Protein: A Closer Look through an In Silico Prism

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Ali Asghari ◽  
Hamidreza Majidiani ◽  
Taher Nemati ◽  
Mohammad Fatollahzadeh ◽  
Morteza Shams ◽  
...  
Keyword(s):  
Toxoplasma Gondii ◽  
T Lymphocyte ◽  
Signal Peptide ◽  
In Silico ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Transmembrane Domain ◽  
Protein A ◽  
Oocyst Wall ◽  
In Silico Study

Toxoplasmosis is a global threat with significant zoonotic concern. The present in silico study was aimed at determination of bioinformatics features and immunogenic epitopes of a tyrosine-rich oocyst wall protein (TrOWP) of Toxoplasma gondii. After retrieving the amino acid sequence from UniProt database, several parameters were predicted including antigenicity, allergenicity, solubility and physico-chemical features, signal peptide, transmembrane domain, and posttranslational modifications. Following secondary and tertiary structure prediction, the 3D model was refined, and immunogenic epitopes were forecasted. It was a 25.57 kDa hydrophilic molecule with 236 residues, a signal peptide, and significant antigenicity scores. Moreover, several linear and conformational B-cell epitopes were present. Also, potential mouse and human cytotoxic T-lymphocyte (CTL) and helper T-lymphocyte (HTL) epitopes were predicted in the sequence. The findings of the present in silico study are promising as they render beneficial characteristics of TrOWP to be included in future vaccination experiments.

In Silico Study of Potential Cross-Kingdom Plant MicroRNA Based Regulation in Chronic Myeloid Leukemia

2020 ◽  
Vol 17 (2) ◽  
pp. 125-132
Author(s):  
Marjanu Hikmah Elias ◽  
Noraziah Nordin ◽  
Nazefah Abdul Hamid
Keyword(s):  
Targeted Therapy ◽  
In Silico ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Target Prediction ◽  
In Silico Analysis ◽  
Microrna Target ◽  
Good Target

Background: Chronic Myeloid Leukaemia (CML) is associated with the BCRABL1 gene, which plays a central role in the pathogenesis of CML. Thus, it is crucial to suppress the expression of BCR-ABL1 in the treatment of CML. MicroRNA is known to be a gene expression regulator and is thus a good candidate for molecularly targeted therapy for CML. Objective: This study aims to identify the microRNAs from edible plants targeting the 3’ Untranslated Region (3’UTR) of BCR-ABL1. Methods: In this in silico analysis, the sequence of 3’UTR of BCR-ABL1 was obtained from Ensembl Genome Browser. PsRNATarget Analysis Server and MicroRNA Target Prediction (miRTar) Server were used to identify miRNAs that have binding conformity with 3’UTR of BCR-ABL1. The MiRBase database was used to validate the species of plants expressing the miRNAs. The RNAfold web server and RNA COMPOSER were used for secondary and tertiary structure prediction, respectively. Results: In silico analyses revealed that cpa-miR8154, csi-miR3952, gma-miR4414-5p, mdm-miR482c, osa-miR1858a and osa-miR1858b show binding conformity with strong molecular interaction towards 3’UTR region of BCR-ABL1. However, only cpa-miR- 8154, osa-miR-1858a and osa-miR-1858b showed good target site accessibility. Conclusion: It is predicted that these microRNAs post-transcriptionally inhibit the BCRABL1 gene and thus could be a potential molecular targeted therapy for CML. However, further studies involving in vitro, in vivo and functional analyses need to be carried out to determine the ability of these miRNAs to form the basis for targeted therapy for CML.

Do Toxoplasma gondii apicoplast proteins have antigenic potential? An in silico study

2020 ◽  
Vol 84 ◽  
pp. 107158 ◽  
Author(s):  
Hüseyin Can ◽  
Sedef Erkunt Alak ◽  
Ahmet Efe Köseoğlu ◽  
Mert Döşkaya ◽  
Cemal Ün
Keyword(s):  
Toxoplasma Gondii ◽  
In Silico ◽  
In Silico Study

Cloning and Prokaryotic Expression and Structure Prediction of Prx II the Differentially Expressed Gene under AFB1 Stress

2011 ◽  
Vol 236-238 ◽  
pp. 1078-1082
Author(s):  
Zhen Hong Zhuang ◽  
Feng Zhang ◽  
Yan Yun Li ◽  
Jun Yuan ◽  
Yan Ling Yang ◽  
...  
Keyword(s):  
Signal Peptide ◽  
Prokaryotic Expression ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Differentially Expressed Gene ◽  
Protein Molecule ◽  
Helix 69 ◽  
Prokaryotic Expression Vector ◽  
Mice Liver ◽  
Α Helix

The gene, prx II, in mice liver was found to be up-regulated under the stress of AFB1 in our previous study. In this study, the total RNA from the mice liver was extracted, and followed by the synthesis of cDNA with the RNA as template by the method of reverse transcription. Then, prx II gene fragment was amplified by PCR with the cDNA as template. After double-digestion and ligation reaction, the prokaryotic expression vector pET28a (+)-prx II was successfully constructed and was transformed into E. coli BL21 (DE3). The protein- Prx II was successfully expressed when induced byIPTG, and finally, Prx II was purified by Ni2+-NTA affinity chromatography. The molecule structure of Prx II, including its signal peptide, hydrophobicity, and its secondary and tertiary structure, was predicted by bioinformatics analysis. The results showed that no signal peptide was predicted in the molecule of Prx II; Five hydrohpobic domains were predicted in the protein molecule, and the average predictive value for its hydrophobicity was -0.151; There were 35% α-helix (69 residues) and 21% β-pleated sheet (42 residues) in the molecule; The tertiary structure of the protein was constituted by seven α-helices and seven β-pleated sheets.

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

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Anila Hoda ◽  
Myqerem Tafaj ◽  
Enkelejda Sallaku
Keyword(s):  
Cell Wall ◽  
Physicochemical Properties ◽  
In Silico ◽  
Plant Cell Wall ◽  
Tertiary Structure ◽  
Transmembrane Domain ◽  
Physicochemical Characteristics ◽  
Structure Alignment ◽  
Ruminococcus Albus ◽  
Predicted Model

Abstract Background Cellulose 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. Results In 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. Conclusions This 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.

In silico Proteome analysis of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Preprint)

2020 ◽  
Author(s):  
Chittaranjan Baruah ◽  
PAPARI DEVI ◽  
DHIRENDRA K SHARMA
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
In Silico ◽  
Structure Prediction ◽  
Active Sites ◽  
Tertiary Structure ◽  
Functional Characterization ◽  
Protein Structures ◽  
Reference Sequence ◽  
Significant Similarity ◽  
Drug Designing

BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense, single-stranded RNA coronavirus. The virus is the causative agent of coronavirus disease 2019 (COVID-19) and is contagious through human-to-human transmission. The RNA genome of SARS-CoV-2 encodes 29 proteins, though one may not get expressed. 15 proteins are not yet having experimental structures for investigation on possible drug targets. OBJECTIVE The present study reports sequence analysis, complete coordinate tertiary structure prediction and in silico sequence-based and structure-based functional characterization of full SARS-CoV-2 proteome based on the NCBI reference sequence NC_045512 (29903 bp ss-RNA). METHODS A total of 25 polypeptides have been analyzed out of which 15 proteins are not yet having experimental structures and only 10 are having experimental structures with known PDB IDs. Out of 15 newly predicted structures six (6) were predicted using comparative modeling and nine (09) proteins having no significant similarity with so far available PDB structures were modeled using ab-initio modeling. QMEANDisCo 4.0.0 and ProQ3 for global and local (per-residue) quality estimates is used for structure verification. RESULTS The all-atom model of tertiary structure of high quality and may be useful for structure-based drug designing targets. The study has identified along with nine major targets sixteen nonstructural proteins (NSPs), which may be equally important from the drug design angle. Tunnel analysis revealed the presence of large number of tunnels in NSP3, ORF 6 protein and membrane glycoprotein indicating a large number of transport pathways for small ligands influencing their reactivity. CONCLUSIONS The 15 theoretical structures would perhaps be useful for the scientific community for advanced computational analysis on interactions of each protein for detailed functional analysis of active sites towards structure based drug designing or to study potential vaccines, if at all, towards preventing epidemics and pandemics in absence of complete experimental structure. CLINICALTRIAL The protein structures have been deposited to ModelArchive.

scholarly journals Bioinformatics Analysis of JAZF1 Gene in Broilers with Ascites Syndrome

2021 ◽  
Vol 41 (01) ◽  
pp. 19-24
Author(s):  
FengPing Guo
Keyword(s):  
Signal Peptide ◽  
Protein Function ◽  
Vascular Remodeling ◽  
Tertiary Structure ◽  
Transmembrane Domain ◽  
Phosphorylation Site ◽  
Glycosylation Site ◽  
Random Coil ◽  
Pulmonary Vascular Remodeling ◽  
Ascites Syndrome

Pulmonary vascular remodeling (PVR) is the main characteristic lesion of ascites syndrome (AS) in broilers. JAZF1 plays an important role in PVR, but there is no study on its protein function and structure. In this study, the physical and chemical properties, hydrophilicity/hydrophobicity and transmembrane domain, phosphorylation site and glycosylation site, subcellular localization and signal peptide, secondary and tertiary structure, antigen peptide and conserved domain and phylogenetic relationship of JAZF1 protein were predicted online by bioinformatics tools. The results showed that the number of amino acids of JAZF1 was 243aa, the theoretical isoelectric point was 8.63, the instability index was 58.1, and the average coefficient of hydrophilicity was -0.674. It was found to be a hydrophilic protein having 35 phosphorylation sites and a N-glycosylation site with no transmembrane domain. The protein is expressed in the nucleus, there is no signal peptide distribution in the whole sequence and the secondary structure is mainly composed of random coil and α- helix. There were 7 B cell epitopes, 7 conserved domains and compared with other birds, JAZF1 is 95.61% similar. In summary, from the analysis we came to conclude that the amino acid sequence 64-80aa, 91-108aa, 136-151aa and 179-187aa can be selected as antigen sites and among which 136-151aa may be the best. This study lays a good foundation for follow-up experiments, which then provides powerful conditions for pathological detection of pulmonary vascular remodeling and gene drug therapy of ascites syndrome in broilers.

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