An insight into SARS-CoV-2 Membrane protein interaction with Spike, Envelope, and Nucleocapsid proteins

Kumar, Amit; Kumar, Prateek; Garg, Neha; Giri, Rajanish

doi:10.1101/2020.10.30.363002

Cited by 10 publications

(8 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A variety of proteinprotein interactions are essential for SARS-CoV-2 replication and viral assembly. Such is the case for the virus structural proteins, which have been reported to interact with each other [38]. In the hemin-agarose eluate, the M protein was identified in band 7 at a higher relative molecular mass position than its predicted molecular mass of 25 kDa.…”

Section: Discussionmentioning

confidence: 89%

“…Human alpha-S1-casein (P47710) was used as negative control and human haptoglobin (P00738-2) as a positive control. A library of 15 amino acid peptides with a 5-residues overlap was designed to represent the entire coding region of RBD (aa 319-541), NTD (aa 1-303), and partial sequence of haptoglobin (121-127; 226-234; 253-267; 283-289; 318-327) and alpha-S1-casein (31)(32)(33)(34)(35)(36)(37)(38)(39)(40). Peptides were synthesized onto cellulose membranes using an Auto-Spot Robot ASP-222 (Intavis Bioanalytical Instruments, AG, Köln, Germany) [69,70].…”

Section: Spot-synthesismentioning

confidence: 99%

See 1 more Smart Citation

SARS-CoV-2 Proteins Bind to Hemoglobin and Its Metabolites

Lechuga

Souza-Silva

Sacramento

et al. 2021

IJMS

View full text Add to dashboard Cite

(1) Background: coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been linked to hematological dysfunctions, but there are little experimental data that explain this. Spike (S) and Nucleoprotein (N) proteins have been putatively associated with these dysfunctions. In this work, we analyzed the recruitment of hemoglobin (Hb) and other metabolites (hemin and protoporphyrin IX-PpIX) by SARS-Cov2 proteins using different approaches. (2) Methods: shotgun proteomics (LC–MS/MS) after affinity column adsorption identified hemin-binding SARS-CoV-2 proteins. The parallel synthesis of the peptides technique was used to study the interaction of the receptor bind domain (RBD) and N-terminal domain (NTD) of the S protein with Hb and in silico analysis to identify the binding motifs of the N protein. The plaque assay was used to investigate the inhibitory effect of Hb and the metabolites hemin and PpIX on virus adsorption and replication in Vero cells. (3) Results: the proteomic analysis by LC–MS/MS identified the S, N, M, Nsp3, and Nsp7 as putative hemin-binding proteins. Six short sequences in the RBD and 11 in the NTD of the spike were identified by microarray of peptides to interact with Hb and tree motifs in the N protein by in silico analysis to bind with heme. An inhibitory effect in vitro of Hb, hemin, and PpIX at different levels was observed. Strikingly, free Hb at 1mM suppressed viral replication (99%), and its interaction with SARS-CoV-2 was localized into the RBD region of the spike protein. (4) Conclusions: in this study, we identified that (at least) five proteins (S, N, M, Nsp3, and Nsp7) of SARS-CoV-2 recruit Hb/metabolites. The motifs of the RDB of SARS-CoV-2 spike, which binds Hb, and the sites of the heme bind-N protein were disclosed. In addition, these compounds and PpIX block the virus’s adsorption and replication. Furthermore, we also identified heme-binding motifs and interaction with hemin in N protein and other structural (S and M) and non-structural (Nsp3 and Nsp7) proteins.

show abstract

Section: Discussionmentioning

confidence: 89%

Section: Spot-synthesismentioning

confidence: 99%

SARS-CoV-2 Proteins Bind to Hemoglobin and Its Metabolites

Lechuga

Souza-Silva

Sacramento

et al. 2021

IJMS

View full text Add to dashboard Cite

show abstract

“…It delineates the shape of the viral envelope by forming the homotypic interaction between them. It often interacts with the envelope E protein present in the host cell membrane budding compartment, produces the viral envelope and accountable for constructing virus-like particles (VLPs) [72] , [73] . During the assembly and budding process, M protein is performing a dominant aspect in retaining the S protein by its interaction.…”

Section: Genome and Structure Of Sars-cov-2mentioning

confidence: 99%

COVID-19: A review of newly formed viral clades, pathophysiology, therapeutic strategies and current vaccination tasks

Murugan

Ramamoorthy

Kuppuswamy

et al. 2021

International Journal of Biological Macromolecules

View full text Add to dashboard Cite

Today, the world population is facing an existential threat by an invisible enemy known as severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) or COVID-19. It is highly contagious and has infected a larger fraction of human population across the globe on various routes of transmission. The detailed knowledge of the SARS-CoV-2 structure and clinical aspects offers an important insight into the evolution of infection, disease progression and helps in executing the different therapies effectively. Herein, we have discussed in detail about the genome structure of SARS-CoV-2 and its role in the proteomic rational spread of different muted species and pathogenesis in infecting the host cells. The mechanisms behind the viral outbreak and its immune response, the availability of existing diagnostics techniques, the treatment efficacy of repurposed drugs and the emerging vaccine trials for the SARS-CoV-2 outbreak also have been highlighted. Furthermore, the possible antiviral effects of various herbal products and their extracted molecules in inhibiting SARS-CoV-2 replication and cellular entry are also reported. Finally, we conclude our opinion on current challenges involved in the drug development, bulk production of drug/vaccines and their storage requirements, logistical procedures and limitations related to dosage trials for larger population.

show abstract

“…This approach increased the overall identification of proteins, and after purification, the N protein was the most abundant protein identified by mass spectrometry in the 45 kDa band. A variety of protein-protein interactions are essential for SARS-CoV-2 replication and viral assembly, such as its structural proteins that have been reported to interact with each other [37]. In the heminagarose eluate, the M protein was identified in band 7 at a higher relative molecular mass position than its predicted molecular mass of 25 kDa.…”

Section: Discussionmentioning

confidence: 97%

SARS-CoV-2 proteins bind heme and hemoglobin

De-Simone

Lechuga

Souza-Silva

et al. 2021

Preprint

View full text Add to dashboard Cite

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome virus 2 (SARS-CoV-2), has led to a global crisis that included collapsing healthcare systems and shut-down communities, producing considerable economic burden. Despite the number of effective vaccines quickly implemented, the emergence of new variants is a primary concern. The scientific community undertook a rapid response to better study this new virus. However, critical questions about viral protein-protein interactions and mechanisms of its physiopathology are still unclear. Although severe COVID-19 was associated with hematological dysfunctions, scarce experimental data were produced about iron dysmetabolism and the viral proteins’ possible interaction with hemoglobin (Hb) chains. This work demonstrates the binding of SARS-CoV-2 proteins to hemin and Hb using a multimethodological approach. In silico analysis indicated binding motifs between a cavity in the viral nucleoprotein and hemoglobin’s porphyrin coordination region. Different hemin binding capacities of mock and SARS-CoV-2-infected culture extracts were noticed using gel electrophoresis and TMB staining. Hemin-binding proteins were isolated from SARS-CoV-2-infected cells by affinity chromatography and identified by shotgun proteomics, indicating that structural (nucleoprotein, spike, and membrane protein) and non-structural (Nsp3 and Nsp7) viral proteins interact with hemin. In vitro analyses of virus adsorption to host cells and viral replication studies in Vero cells demonstrated inhibitory activities - at different levels - by hemin, protoporphyrin IX (PpIX) Hb. Strikingly, free Hb at 1mM suppressed viral replication (99 %), and its interaction with SARS-CoV-2 was localized to the RBD region of the Spike protein. The findings showed clear evidence of new avenues to disrupt viral replication and understand virus physiopathology that warrants further investigation.

show abstract

An insight into SARS-CoV-2 Membrane protein interaction with Spike, Envelope, and Nucleocapsid proteins

Cited by 10 publications

References 58 publications

SARS-CoV-2 Proteins Bind to Hemoglobin and Its Metabolites

SARS-CoV-2 Proteins Bind to Hemoglobin and Its Metabolites

COVID-19: A review of newly formed viral clades, pathophysiology, therapeutic strategies and current vaccination tasks

SARS-CoV-2 proteins bind heme and hemoglobin

Contact Info

Product

Resources

About