scholarly journals Structural and Functional Annotation of Uncharacterized Protein NCGM946K2_146 of Mycobacterium Tuberculosis: An In-Silico Approach

Proceedings ◽  
2020 ◽  
Vol 66 (1) ◽  
pp. 13
Author(s):  
Abu Saim Mohammad Saikat ◽  
Rabiul Islam ◽  
Shahriar Mahmud ◽  
Md. Abu Sayeed Imran ◽  
Mohammad Shah Alam ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
In Silico ◽  
Functional Annotation ◽  
Tertiary Structure ◽  
Human Pathogen ◽  
Ramachandran Plot ◽  
Uncharacterized Protein ◽  
Trehalose Synthase ◽  
Z Scores ◽  
Human Death

The human pathogen Mycobacterium tuberculosis (MTB) is indeed one of the renowned, important, longtime infectious diseases, tuberculosis (TB). Interestingly, MTB infection has become one of the world’s leading causes of human death. In trehalose synthase, the protein NCGM 946K2 146 found in MTB has an important role. For carbohydrate transport and metabolism, trehalose synthase is required. The protein is not clarified yet, though. In this research, an in silico approach was, therefore, formulated for functional and structural documentation of the uncharacterized protein NCGM946K2_146.Three distinct servers, including Modeller, Phyre2, and Swiss Model, were used to evaluate the predicted tertiary structure. The top materials are selected using structural evaluations conducted with the analysis of Ramachandran Plot, Swiss-Model Interactive Workplace, ProSA-web, Verify 3D, and Z scores. This analysis aimed to uncover the value of the NCGM946K2_146 protein of MTB. This research will, therefore, improve our pathogenesis awareness and give us a chance to target the protein compound.

scholarly journals Structural and Functional Annotation of Uncharacterized Protein NCGM946K2_146 of Mycobacterium tuberculosis: An In-Silico Approach

2020 ◽  
Author(s):  
Abu Saim Mohammad Saikat
Keyword(s):  
Mycobacterium Tuberculosis ◽  
In Silico ◽  
Functional Annotation ◽  
Tertiary Structure ◽  
Human Pathogen ◽  
Ramachandran Plot ◽  
Uncharacterized Protein ◽  
Trehalose Synthase ◽  
Z Scores ◽  
Human Death

The human pathogen <i>Mycobacterium tuberculosis</i> ( MTB) is indeed one of the renowned important longtime infectious diseases that cause tuberculosis (TB). Interestingly, MTB infection has become one of the world's leading causes of human death. In trehalose synthase, the protein NCGM 946K2 146 found in MTB has an important role. For carbohydrate transport and metabolism, trehalose synthase is required. The protein is not clarified yet, however. In this research, an <i>in silico</i> approach was therefore formulated for functional and structural documentation of the uncharacterized protein NCGM946K2 146. Three different servers, including the Modeller, the Phyre2, and the Swiss Model, were used to evaluate the predicted tertiary structure. The top materials are selected using structural evaluations conducted with the analysis of Ramachandran Plot, Swiss-Model Interactive Workplace, Prosa-web, Verify 3D, and Z scores. This analysis aimed to uncover the value of the NCGM946K2 146 protein of MTB. This research will, therefore, improve our pathogenesis awareness and give us a chance to target the protein compound.

scholarly journals Structural and Functional Annotation of Uncharacterized Protein NCGM946K2_146 of Mycobacterium tuberculosis: An In-Silico Approach

2020 ◽  
Author(s):  
Abu Saim Mohammad Saikat
Keyword(s):  
Mycobacterium Tuberculosis ◽  
In Silico ◽  
Functional Annotation ◽  
Tertiary Structure ◽  
Human Pathogen ◽  
Ramachandran Plot ◽  
Uncharacterized Protein ◽  
Trehalose Synthase ◽  
Z Scores ◽  
Human Death

The human pathogen <i>Mycobacterium tuberculosis</i> ( MTB) is indeed one of the renowned important longtime infectious diseases that cause tuberculosis (TB). Interestingly, MTB infection has become one of the world's leading causes of human death. In trehalose synthase, the protein NCGM 946K2 146 found in MTB has an important role. For carbohydrate transport and metabolism, trehalose synthase is required. The protein is not clarified yet, however. In this research, an <i>in silico</i> approach was therefore formulated for functional and structural documentation of the uncharacterized protein NCGM946K2 146. Three different servers, including the Modeller, the Phyre2, and the Swiss Model, were used to evaluate the predicted tertiary structure. The top materials are selected using structural evaluations conducted with the analysis of Ramachandran Plot, Swiss-Model Interactive Workplace, Prosa-web, Verify 3D, and Z scores. This analysis aimed to uncover the value of the NCGM946K2 146 protein of MTB. This research will, therefore, improve our pathogenesis awareness and give us a chance to target the protein compound.

scholarly journals An In silico Approach for Structural and Functional Annotation of Uncharacterized Protein Rv0986 present in Mycobacterium tuberculosis

2020 ◽  
pp. 61-67
Keyword(s):  
Mycobacterium Tuberculosis ◽  
In Silico ◽  
Functional Annotation ◽  
Mycobacterial Infection ◽  
Z Score ◽  
Human Pathogen ◽  
Ramachandran Plot ◽  
Uncharacterized Protein ◽  
Tertiary Structures ◽  
Plot Analysis

Tuberculosis (TB) is an ancient infectious disease caused by Mycobacterium tuberculosis (MTB). MTB is a human pathogen. Surprisingly, TB has become the top disease for its death rate worldwide. The uncharacterized protein Rv0986 is closely related to the transporters of the ATP-binding cassette domain, therefore, take part in the export of macrolide as well as a lipoprotein. Furthermore, it is associated with cell division protein. Hence, the protein has a significant role in mycobacterial infection. But, so far, the uncharacterized protein Rv0986 is not elaborated. As a result, in this study, the structural and functional annotation of the protein is described through in silico approach. The predicted tertiary structures of the protein generated by Swiss Model, Modeller, and Phyre2, and documented by the Ramachandran Plot analysis with PROCHECK, Verify 3D, and Swiss-Model Interactive Workplace. Z-score also applied for the overall structural assessment. This study will unleash the importance of the uncharacterized protein present in MTB, therefore, it provides an opportunity for drug and vaccine targeting against infection by MTB.

scholarly journals Characterization and Functional Annotation of Uncharacterized ABC Transporter ATP-Binding Protein Rv0986 of Mycobacterium tuberculosis (Strain ATCC 25618 / H37Rv)

2020 ◽  
Author(s):  
Abu Saim Mohammad Saikat
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Functional Annotation ◽  
Mycobacterial Infection ◽  
Structural Quality ◽  
Atp Binding ◽  
Model Quality ◽  
Uncharacterized Protein ◽  
Z Scores ◽  
Atp Binding Protein ◽  
Human Death

AbstractThe most significant ancient infectious disease tuberculosis is causes by a human pathogen, Mycobacterium tuberculosis (MTB). Amazingly, tuberculosis (TB) has become one of the major causes of human death worldwide. The protein Rv0986 is associated with the ATP-binding cassette domain of the transporters involved in the export of lipoprotein and macrolide, and cell division protein, therefore, related to mycobacterial infection. But the protein Rv0986 is not yet explored. As a result, identification, characterization, and functional annotation of uncharacterized protein Rv0986 were predicted where the structure modeling was generated by using Modeller, Phyre2, and Swiss Model with the structural quality assessment by Ramachandran Plot (PROCHECK), Verify 3d, and Swiss-Model Interactive Workplace as well. Z-scores obtained from Prosa-web were also applied for overall 3D model quality. This in-silico method will uncover the significance of undiscovered uncharacterized protein Rv0986 present in MTB, and indeed it can accelerate the way to enrich our knowledge in the pathogenesis and drug-targeting opportunity against infection by MTB.

scholarly journals Structural and Functional Annotation of Uncharacterized Protein NCGM946K2_146 of Mycobacterium tuberculosis: An In-Silico Approach

2020 ◽  
Author(s):  
Rabiul Islam ◽  
Abu Saim Mohammad Saikat ◽  
Shahriar Mahmud ◽  
Md. Abu Sayeed Imran ◽  
Mohammad Shah Alam ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
In Silico ◽  
Functional Annotation ◽  
Uncharacterized Protein

scholarly journals An in silico approach for structural and functional annotation of matrix protein of Nipah henipavirus: A protein functional analysis

2021 ◽  
Author(s):  
Apurbo Kumar Paul ◽  
Abu Saim Mohammad Saikat
Keyword(s):  
In Silico ◽  
Functional Annotation ◽  
Matrix Protein ◽  
Tertiary Structure ◽  
Virus Assembly ◽  
Viral Envelope ◽  
Dimensional Structure ◽  
Functional Explanation ◽  
Virus Core ◽  
The Matrix

Nipah henipavirus is an emerging RNA virus with increased mortality threatening global security. In South and Southeast Asia, the Nipah virus has caused numerous disease outbreaks. The matrix protein in Nipah henipavirus has an important role, in connecting the viral envelope with the virus core. For virus assembly, linking the viral envelope with the virus core are very crucial. Through functional and structural explanation evaluations, bioinformatics strategies can help us better understanding of the protein. This investigation aims to allocate the structural and functional annotation of protein. Moreover, the investigation attributes physicochemical parameters, three-dimensional structure, and functional annotation of the protein (QBQ56721.1) applying an in silico perspective. The in silico analysis confirmed the protein's hydrophilic nature, with a secondary structure dominated by alpha (α) helices. Based on several quality assessment methodologies, the tertiary-structure model of the protein has been shown to be reasonably consistent. The functional explanation suggested the protein as a structural protein connected to the viral envelope with the virus core, a protein required for virus assembly. This investigation unleashes the significance of the matrix protein (QBQ56721.1) as a functional protein required for Nipah henipavirus.

scholarly journals An in silico approach for structural and functional annotation of matrix protein of Nipah henipavirus: A protein functional analysi

2021 ◽  
Author(s):  
Apurbo Kumar Paul ◽  
Abu Saim Mohammad Saikat
Keyword(s):  
In Silico ◽  
Functional Annotation ◽  
Matrix Protein ◽  
Tertiary Structure ◽  
Virus Assembly ◽  
Viral Envelope ◽  
Dimensional Structure ◽  
Functional Explanation ◽  
Virus Core ◽  
The Matrix

Nipah henipavirus is an emerging RNA virus with increased mortality threatening global security. In South and Southeast Asia, the Nipah virus has caused numerous disease outbreaks. The matrix protein in Nipah henipavirus has an important role, in connecting the viral envelope with the virus core. For virus assembly, linking the viral envelope with the virus core are very crucial. Through functional and structural explanation evaluations, bioinformatics strategies can help us better understanding of the protein. This investigation aims to allocate the structural and functional annotation of protein. Moreover, the investigation attributes physicochemical parameters, three-dimensional structure, and functional annotation of the protein (QBQ56721.1) applying an in silico perspective. The in silico analysis confirmed the protein's hydrophilic nature, with a secondary structure dominated by alpha (α) helices. Based on several quality assessment methodologies, the tertiary-structure model of the protein has been shown to be reasonably consistent. The functional explanation suggested the protein as a structural protein connected to the viral envelope with the virus core, a protein required for virus assembly. This investigation unleashes the significance of the matrix protein (QBQ56721.1) as a functional protein required for Nipah henipavirus.

Exploring PLAC1 Structure and Underlying Mechanisms to Design a Derivative Vaccine Against Breast Cancer Progression; In-Silico Study

2020 ◽  
Vol 17 (5) ◽  
pp. 379-391
Author(s):  
Farzaneh Afzali ◽  
Parisa Ghahremanifard ◽  
Mohammad Mehdi Ranjbar ◽  
Mahdieh Salimi
Keyword(s):  
Breast Cancer ◽  
Cancer Progression ◽  
In Silico ◽  
Tertiary Structure ◽  
Specific Antigen ◽  
Docking Simulation ◽  
Post Translational Modification ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Underlying Mechanisms

Background: The tolerogenic homeostasis in Breast Cancer (BC) can be surpassed by rationally designed immune-encouraging constructs against tumor-specific antigens through immunoinformatics approach. Objective: Availability of high throughput data providing the underlying concept of diseases and awarded computational simulations, lead to screening the potential medications and strategies in less time and cost. Despite the extensive effects of Placenta Specific 1 (PLAC1) in BC progression, immune tolerance, invasion, cell cycle regulation, and being a tumor-specific antigen the fundamental mechanisms and regulatory factors were not fully explored. It is also worth to design an immune response inducing construct to surpass the hurdles of traditional anti-cancer treatments. Methods and Result: The study was initiated by predicting and modelling the PLAC1 secondary and tertiary structures and then engineering the fusion pattern of PLAC1 derived immunodominant predicted CD8+ and B-cell epitopes to form a multi-epitope immunogenic construct. The construct was analyzed considering the physiochemical characterization, safety, antigenicity, post-translational modification, solubility, and intrinsically disordered regions. After modelling its tertiary structure, proteinprotein docking simulation was carried out to ensure the attachment of construct with Toll-Like Receptor 4 (TLR4) as an immune receptor. To guarantee the highest expression of the designed construct in E. coli k12 as an expressional host, the codon optimization and in-silico cloning were performed. The PLAC1 related miRNAs in BC were excavated and validated through TCGA BC miRNA-sequencing and databases; the common pathways then were introduced as other probable mechanisms of PLAC1 activity. Conclusion: Regarding the obtained in-silico results, the designed anti-PLAC1 multi-epitope construct can probably trigger humoral and cellular immune responses and inflammatory cascades, therefore may have the potential of halting BC progression and invasion engaging predicted pathways.

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.

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