A conserved oligomerization domain in the disordered linker of coronavirus nucleocapsid proteins DOI Creative Commons
Huaying Zhao, Di Wu, Sergio A. Hassan

и другие.

Science Advances, Год журнала: 2023, Номер 9(14)

Опубликована: Апрель 5, 2023

The nucleocapsid (N-)protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a key role in viral assembly and scaffolding the RNA. It promotes liquid-liquid phase separation (LLPS), forming dense droplets that support ribonucleoprotein particles with as-of-yet unknown macromolecular architecture. Combining biophysical experiments, molecular dynamics simulations, analysis mutational landscape, we describe heretofore oligomerization site contributes to LLPS, is required for higher-order protein-nucleic acid complexes, coupled large-scale conformational changes N-protein upon nucleic binding. self-association interface located leucine-rich sequence intrinsically disordered linker between folded domains formed by transient helices assembling into trimeric coiled-coils. Critical residues stabilizing hydrophobic electrostatic interactions adjacent are highly protected against mutations viable SARS-CoV-2 genomes, motif conserved across related coronaviruses, thus presenting target antiviral therapeutics.

Язык: Английский

Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-CoV-2 virus-like particles DOI Creative Commons
Abdullah M. Syed, Alison Ciling, Mir M. Khalid

и другие.

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2021, Номер unknown

Опубликована: Дек. 21, 2021

Abstract The Omicron SARS-CoV-2 virus contains extensive sequence changes relative to the earlier arising B.1, B.1.1 and Delta variants that have unknown effects on viral infectivity response existing vaccines. Using virus-like particles (SC2-VLPs), we examined mutations in all four structural proteins found showed 3-fold higher capsid assembly cell entry Delta, a property conferred by S N protein mutations. Thirty-eight antisera samples from individuals vaccinated with Pfizer/BioNTech, Moderna, Johnson & vaccines convalescent sera unvaccinated COVID-19 survivors had 15-fold lower efficacy prevent transduction VLPs containing ancestral B.1 spike protein. A third dose of Pfizer vaccine elicited substantially neutralization titers against Omicron, resulting detectable neutralizing antibodies 8 out subjects compared 1 pre-boost. Furthermore, monoclonal antibody therapeutics Casirivimab Imdevimab robust activity or but no VLPs. Our results suggest is more efficient at triggered previous infection, least prior boost, will limited ability neutralize Omicron. In addition, some currently available not be useful treating Omicron-infected patients. One-Sentence Summary enhanced only weakly neutralized vaccination without boost therapeutics.

Язык: Английский

Процитировано

62
Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein DOI Creative Commons
Huaying Zhao,

Ai Nguyen,

Di Wu

и другие.

PNAS Nexus, Год журнала: 2022, Номер 1(2)

Опубликована: Май 1, 2022

Abstract Worldwide SARS-CoV-2 sequencing efforts track emerging mutations in its spike protein, as well characteristic other viral proteins. Besides their epidemiological importance, the observed sequences present an ensemble of viable protein variants, and thereby a source information on structure function. Charting mutational landscape nucleocapsid (N) that facilitates assembly, we observe variability exceeding with more than 86% residues can be substituted, average by three to four different amino acids. However, exhibit uneven distribution tracks known structural features but also reveals highly protected stretches unknown One these conserved regions is central disordered linker proximal N-G215C mutation has become dominant Delta variant, outcompeting G215 variants without further or N-protein substitutions. Structural models suggest G215C stabilizes transient helices serving protein–protein interaction interfaces. Comparing variant ancestral version biophysical experiments, find significantly compact less structure. exhibits substantially stronger self-association, shifting unliganded from dimeric tetrameric oligomeric state, which leads enhanced coassembly nucleic This suggests sequence mirrored high plasticity properties, hypothesize exploited achieve greater efficiency infectivity.

Язык: Английский

Процитировано

56
A proteome-scale map of the SARS-CoV-2–human contactome DOI Creative Commons
Dae‐Kyum Kim, Benjamin Weller, Chung-Wen Lin

и другие.

Nature Biotechnology, Год журнала: 2022, Номер 41(1), С. 140 - 149

Опубликована: Окт. 10, 2022

Abstract Understanding the mechanisms of coronavirus disease 2019 (COVID-19) severity to efficiently design therapies for emerging virus variants remains an urgent challenge ongoing pandemic. Infection and immune reactions are mediated by direct contacts between viral molecules host proteome, vast majority these virus–host (the ‘contactome’) have not been identified. Here, we present a systematic contactome map severe acute respiratory syndrome 2 (SARS-CoV-2) with human encompassing more than 200 binary intraviral protein–protein interactions. We find that proteins genetically associated comorbidities illness long COVID enriched in SARS-CoV-2 targeted network communities. Evaluating contactome-derived hypotheses, demonstrate NSP14 activates nuclear factor κB (NF-κB)-dependent transcription, even presence cytokine signaling. Moreover, several tested proteins, genetic knock-down substantially reduces replication. Additionally, show USP25 this effect is phenocopied small-molecule inhibitor AZ1. Our results connect architecture COVID-19 offer potential therapeutic targets.

Язык: Английский

Процитировано

47
Fitness effects of mutations to SARS-CoV-2 proteins DOI Creative Commons
Jesse D. Bloom, Richard A. Neher

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Янв. 31, 2023

Knowledge of the fitness effects mutations to SARS-CoV-2 can inform assessment new variants, design therapeutics resistant escape, and understanding functions viral proteins. However, experimentally measuring is challenging: we lack tractable lab assays for many proteins, comprehensive deep mutational scanning has been applied only two Here develop an approach that leverages millions publicly available sequences estimate mutations. We first calculate how independent occurrences each mutation are expected be observed along phylogeny in absence selection. then compare these observations actual effect mutation. These estimates correlate well with measurements. For most genes, synonymous nearly neutral, stop-codon deleterious, amino-acid have a range effects. some accessory proteins under little no provide interactive visualizations all (https://jbloomlab.github.io/SARS2-mut-fitness/). The framework describe applicable any virus which number sufficiently large neutral observed.

Язык: Английский

Процитировано

32
A conserved oligomerization domain in the disordered linker of coronavirus nucleocapsid proteins DOI Creative Commons
Huaying Zhao, Di Wu, Sergio A. Hassan

и другие.

Science Advances, Год журнала: 2023, Номер 9(14)

Опубликована: Апрель 5, 2023

The nucleocapsid (N-)protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a key role in viral assembly and scaffolding the RNA. It promotes liquid-liquid phase separation (LLPS), forming dense droplets that support ribonucleoprotein particles with as-of-yet unknown macromolecular architecture. Combining biophysical experiments, molecular dynamics simulations, analysis mutational landscape, we describe heretofore oligomerization site contributes to LLPS, is required for higher-order protein-nucleic acid complexes, coupled large-scale conformational changes N-protein upon nucleic binding. self-association interface located leucine-rich sequence intrinsically disordered linker between folded domains formed by transient helices assembling into trimeric coiled-coils. Critical residues stabilizing hydrophobic electrostatic interactions adjacent are highly protected against mutations viable SARS-CoV-2 genomes, motif conserved across related coronaviruses, thus presenting target antiviral therapeutics.

Язык: Английский

Процитировано

32