Corpus overview


Overview

MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

NSP11 (3)

ProteinN (2)

ProteinS (2)

ORF3a (2)

NSP15 (1)


Filter

Genes
Diseases
SARS-CoV-2 Proteins
    displaying 1 - 3 records in total 3
    records per page




    NSP 11 of SARS-CoV-2 is an Intrinsically Disordered Protein

    Authors: Kundlik Gadhave; Prateek Kumar; Ankur Kumar; Taniya Bhardwaj; Neha Garg; Rajanish Giri; Agnel Praveen Joseph; Luise Kandler; Oliver Kippes; Ferdinand Kirsten; Konstantin Müller; Kristopher Nolte; Alexander Payne; Matthew G. Reeves; Jane Richardson; Gianluca Santoni; Sabrina Stäb; Dale Tronrud; Christopher Williams; Andrea Thorn; Lorenzo Depau; Jlenia Brunetti; Luisa Bracci; Emanuele Montomoli; Claudia Sala; Giuseppe Ippolito; Rino Rappuoli

    doi:10.1101/2020.10.07.330068 Date: 2020-10-07 Source: bioRxiv

    The intrinsically disordered proteins/regions (IDPs/IDPRs) are known to be responsible for multiple cellular processes and are associated with many chronic diseases MESHD. In viruses, the existence of disordered proteome is also proven and are related with its conformational dynamics inside the host. The SARS-CoV-2 virus has a large proteome, in which, structure and functions of many proteins are not known as of yet. Previously, we have investigated the dark proteome of SARS-CoV-2. However, the disorder status of NSP11 PROTEIN was not possible because of very small in size, just 13 amino acid long, and for most of the IDP predictors the protein size should be at least 30 amino acid long. Also, the structural dynamics and function status of NSP11 PROTEIN was not known. Hence, we have performed the extensive experimentation on NSP11 PROTEIN. Our results based on the Circular dichroism spectroscopy gives characteristic disordered spectrum for IDPs. Further, we investigated the conformational behaviour of nsp11 in the presence of membrane mimetic environment, alpha helix inducer, and natural osmolyte. In presence of negatively charged and neutral liposomes, nsp11 remain disordered. However, with SDS micelle, it adopted an -helical conformation, suggesting the helical propensity of NSP11 PROTEIN. At the end, we again confirmed the IDP behaviour of nsp11 using molecular dynamics simulations.

    Temporal landscape of mutation accumulation in SARS-CoV-2 genomes from Bangladesh: possible implications from the ongoing outbreak in Bangladesh

    Authors: Otun Saha; Rokaiya Nurani Shatadru; Nadira Naznin Rakhi; Israt Islam; Md. Shahadat Hossain; Md. Mizanur Rahaman; Leo C James; Madeline A Lancaster; Zhu Shu; Zhiming Yuan; Lei Tong; Han Xia; Jingzhe Pan; Natalie Garton; Manish Pareek; Michael Barer; Craig J Smith; Stuart M Allan; Michelle M. Lister; Hannah C. Howson-Wells; Edward C Holmes; Matthew W. Loose; Jonathan K. Ball; C. Patrick McClure; - The COVID-19 Genomics UK consortium study group; Shi Chen

    doi:10.1101/2020.08.20.259721 Date: 2020-08-21 Source: bioRxiv

    Along with intrinsic evolution, adaptation to selective pressure in new environments might have resulted in the circulatory SARS-CoV-2 strains in response to the geoenvironmental conditions of a country and the demographic profile of its population. Thus the analysis of genomic mutations of these circulatory strains may give an insight into the molecular basis of SARS-CoV-2 pathogenesis and evolution favoring the development of effective treatment and containment strategies. With this target, the current study traced the evolutionary route and mutational frequency of 198 Bangladesh originated SARS-CoV-2 genomic sequences available in the GISAID platform over a period of 13 weeks as of 14 July 2020. The analyses were performed using MEGA 7, Swiss Model Repository, Virus Pathogen Resource and Jalview visualization. Our analysis identified that majority of the circulating strains in the country belong to B and/or L type among cluster A to Z and strikingly differ from both the reference genome and the first sequenced genome from Bangladesh. Mutations in Nonspecific protein 2 ( NSP2 PROTEIN NSP2 HGNC), NSP3 PROTEIN NSP3 HGNC, RNA dependent RNA polymerase PROTEIN ( RdRp PROTEIN), Helicase HGNC, Spike, ORF3a PROTEIN, and Nucleocapsid (N) protein PROTEIN were common in the circulating strains with varying degrees and the most unique mutations(UM) were found in NSP3 HGNC NSP3 PROTEIN (UM-18). But no or limited changes were observed in NSP9 PROTEIN, NSP11 PROTEIN, E (Envelope), NSP7a, ORF 6, and ORF 7b suggesting the possible conserved functions of those proteins in SARS-CoV-2 propagation. However, along with D614G mutation, more than 20 different mutations in the Spike protein PROTEIN were detected basically in the S2 domain. Besides, mutations in SR-rich region of N protein PROTEIN and P323L in RDRP PROTEIN were also present. However, the mutation accumulation showed an association with sex and age of the COVID-19 MESHD positive cases. So, identification of these mutational accumulation patterns may greatly facilitate drug/ vaccine development deciphering the age and the sex dependent differential susceptibility to COVID-19 MESHD.

    A Systemic and Molecular Study of Subcellular Localization of SARS-CoV-2 Proteins

    Authors: Jing Zhang; Ruth Cruz-cosme; Meng-Wei Zhuang; Dongxiao Liu; Yuan Liu; Shaolei Teng; Pei-Hui Wang; Qiyi Tang

    doi:10.1101/2020.08.02.233023 Date: 2020-08-02 Source: bioRxiv

    Coronavirus possesses the largest RNA genome among all the RNA viruses. Its genome encodes about 29 proteins. Most of the viral proteins are non-structural proteins (NSP) except envelop (E), membrane (M), nucleocapsid (N PROTEIN) and Spike (S) proteins PROTEIN that constitute the viral nucleocapsid, envelop and surface. We have recently cloned all the 29 SARS-CoV-2 genes into vectors for their expressions in mammalian cells except NSP11 PROTEIN that has only 14 amino acids (aa). We are able to express all the 28 cloned SARS-CoV-2 genes in human cells to characterize their subcellular distributions. The proteins of SARS-CoV-2 are mostly cytoplasmic but some are both cytoplasmic and nuclear. Those punctate staining proteins were further investigated by immunofluorescent assay (IFA) using specific antibodies or by co-transfection with an organelle marker-expressing plasmid. As a result, we found that NSP15 PROTEIN, ORF6 PROTEIN, M and ORF7a PROTEIN are related to Golgi apparatus, and that ORF7b PROTEIN, ORF8 PROTEIN and ORF10 PROTEIN colocalize with endoplasmic reticulum (ER). Interestingly, ORF3a PROTEIN distributes in cell membrane, early endosome, endosome, late endosome and lysosome, which suggests that ORF3a PROTEIN might help the infected virus to usurp endosome and lysosome for viral use. Furthermore, we revealed that NSP13 PROTEIN colocalized with SC35 HGNC, a protein standing for splicing compartments in the nucleus. Our studies for the first time visualized the subcellular locations of SARS-CoV-2 proteins MESHD and might provide novel insights into the viral proteins biological functions.

The ZB MED preprint Viewer preVIEW includes all COVID-19 related preprints from medRxiv and bioRxiv, from ChemRxiv, from ResearchSquare, from arXiv and from Preprints.org and is updated on a daily basis (7am CET/CEST).
The web page can also be accessed via API.

Sources


Annotations

All
None
MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


Export subcorpus as...

This service is developed in the project nfdi4health task force covid-19 which is a part of nfdi4health.

nfdi4health is one of the funded consortia of the National Research Data Infrastructure programme of the DFG.