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.

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 Influenza Virus Matrix Protein Is the Major Driving Force in Virus Budding

2000 ◽  
Vol 74 (24) ◽  
pp. 11538-11547 ◽  
Author(s):  
Paulino Gómez-Puertas ◽  
Carmen Albo ◽  
Esperanza Pérez-Pastrana ◽  
Amparo Vivo ◽  
Agustı́n Portela
Keyword(s):  
Virus Particle ◽  
Influenza A ◽  
Matrix Protein ◽  
Virus Assembly ◽  
Microscopic Analysis ◽  
Tubular Structures ◽  
Electron Microscopic ◽  
Particle Assembly ◽  
M1 Protein ◽  
The Matrix

ABSTRACT To get insights into the role played by each of the influenza A virus polypeptides in morphogenesis and virus particle assembly, the generation of virus-like particles (VLPs) has been examined in COS-1 cell cultures expressing, from recombinant plasmids, different combinations of the viral structural proteins. The presence of VLPs was examined biochemically, following centrifugation of the supernatants collected from transfected cells through sucrose cushions and immunoblotting, and by electron-microscopic analysis. It is demonstrated that the matrix (M1) protein is the only viral component which is essential for VLP formation and that the viral ribonucleoproteins are not required for virus particle formation. It is also shown that the M1 protein, when expressed alone, assembles into virus-like budding particles, which are released in the culture medium, and that the recombinant M1 protein accumulates intracellularly, forming tubular structures. All these results are discussed with regard to the roles played by the virus polypeptides during virus assembly.

scholarly journals Tsg101 Is Recruited by a Late Domain of the Nucleocapsid Protein To Support Budding of Marburg Virus-Like Particles

2010 ◽  
Vol 84 (15) ◽  
pp. 7847-7856 ◽  
Author(s):  
Olga Dolnik ◽  
Larissa Kolesnikova ◽  
Lea Stevermann ◽  
Stephan Becker
Keyword(s):  
Matrix Protein ◽  
Virus Assembly ◽  
Recombinant Expression ◽  
Marburg Virus ◽  
Viral Envelope ◽  
Virus Like Particles ◽  
Late Domain ◽  
Transmembrane Glycoprotein ◽  
Late Domains ◽  
The Impact

ABSTRACT The nucleoprotein NP of Marburg virus (MARV) is the major component of the viral nucleocapsid, which also consists of the viral proteins VP35, L, and VP30, as well as the viral genome. During virus assembly at the plasma membrane, the nucleocapsids are enwrapped by the major matrix protein VP40 and the viral envelope, which contains the transmembrane glycoprotein GP. Upon recombinant expression, VP40 alone is able to induce the formation and release of virus-like particles (VLPs) that closely resemble the filamentous morphology of MARV particles. Release of these VP40-induced VLPs is partially dependent on the cellular ESCRT machinery, which interacts with a late-domain motif in VP40. Coexpression with NP significantly enhances the budding of VP40-induced VLPs by an unknown mechanism. In the present study we analyzed the impact of late domains present in NP on the release of VLPs. We observed that the ESCRT I protein Tsg101 was recruited by NP into NP-induced inclusions in the perinuclear region. In the presence of VP40, NP was then recruited to VP40-positive membrane clusters and, in turn, recruited Tsg101 via a C-terminal PSAP late-domain motif in NP. This PSAP motif also mediated a dramatically enhanced incorporation of Tsg101 into VLPs, and its deletion significantly diminished the positive effect of NP on the release of VLPs. Taken together, these data indicate that NP enhances budding of VLPs by recruiting Tsg101 to the VP40-positive budding site through a PSAP late-domain motif.

Association of the nucleocapsid protein N of vesicular stomatitis virus with phospholipids vesicles containing the matrix protein M

1984 ◽  
Vol 62 (11) ◽  
pp. 1174-1180 ◽  
Author(s):  
John Capone ◽  
Hara P. Ghosh
Keyword(s):  
Vesicular Stomatitis Virus ◽  
Nucleocapsid Protein ◽  
Matrix Protein ◽  
Lipid Vesicles ◽  
Viral Envelope ◽  
M Protein ◽  
Phospholipid Vesicles ◽  
N Protein ◽  
The Matrix ◽  
Vesicular Stomatitis

The matrix protein M and the nucleocapsid protein N were isolated from vesicular stomatitis virus and reconstituted into artificial phospholipid vesicles. While the M protein could be reconstituted into phospholipid vesicles, the N protein had no affinity for lipid vesicles. The N protein could, however, associate with phospholipid vesicles in the presence of M protein. Identical results were also obtained when an in vitro system synthesizing M and N proteins was used for reconstitution. The results suggest that M protein is involved in virus maturation by interacting with the viral envelope and the N protein of the nucleoprotein core.

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 The native structure of the full-length, assembled influenza A virus matrix protein, M1

2020 ◽  
Author(s):  
Julia Peukes ◽  
Xiaoli Xiong ◽  
Simon Erlendsson ◽  
Kun Qu ◽  
William Wan ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Matrix Protein ◽  
Virus Assembly ◽  
Full Length ◽  
Terminal Domain ◽  
Intact Virus ◽  
The Matrix ◽  
Matrix Protein M1

Influenza A virus causes millions of severe illnesses during annual epidemics. The most abundant protein in influenza virions is the matrix protein M1 that mediates virus assembly by forming an endoskeleton beneath the virus membrane. The structure of full-length M1, and how it oligomerizes to mediate assembly of virions, is unknown. Here we have determined the complete structure of assembled M1 within intact virus particles, as well as the structure of M1 oligomers reconstituted in vitro. We found that the C-terminal domain of M1 is disordered in solution, but can fold and bind in trans to the N-terminal domain of another M1 monomer, thus polymerising M1 into linear strands which coat the interior surface of the assembling virion membrane. In the M1 polymer, five histidine residues, contributed by three different M1 monomers, form a cluster that can serve as the pH-sensitive disassembly switch after entry into a target cell. These structures therefore provide mechanisms for influenza virus assembly and disassembly.

scholarly journals Viral Protein Determinants of Lassa Virus Entry and Release from Polarized Epithelial Cells

2010 ◽  
Vol 84 (7) ◽  
pp. 3178-3188 ◽  
Author(s):  
Katrin Schlie ◽  
Anna Maisa ◽  
Fabian Freiberg ◽  
Allison Groseth ◽  
Thomas Strecker ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Matrix Protein ◽  
Mdck Cells ◽  
Virus Assembly ◽  
Apical Cell ◽  
Virus Transmission ◽  
Progeny Virus ◽  
Lassa Virus ◽  
Protein Z ◽  
The Matrix

ABSTRACT The epithelium plays a key role in the spread of Lassa virus. Transmission from rodents to humans occurs mainly via inhalation or ingestion of droplets, dust, or food contaminated with rodent urine. Here, we investigated Lassa virus infection in cultured epithelial cells and subsequent release of progeny viruses. We show that Lassa virus enters polarized Madin-Darby canine kidney (MDCK) cells mainly via the basolateral route, consistent with the basolateral localization of the cellular Lassa virus receptor α-dystroglycan. In contrast, progeny virus was efficiently released from the apical cell surface. Further, we determined the roles of the glycoprotein, matrix protein, and nucleoprotein in directed release of nascent virus. To do this, a virus-like-particle assay was developed in polarized MDCK cells based on the finding that, when expressed individually, both the glycoprotein GP and matrix protein Z form virus-like particles. We show that GP determines the apical release of Lassa virus from epithelial cells, presumably by recruiting the matrix protein Z to the site of virus assembly, which is in turn essential for nucleocapsid incorporation into virions.

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