Deep mutational scanning of CYP2C19 reveals a substrate specificity-abundance tradeoff DOI Creative Commons
Gabriel Boyle,

Katherine A. Sitko,

Jared Galloway

и другие.

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

Опубликована: Окт. 8, 2023

Abstract Cytochrome P450s (CYPs) are a family of enzymes responsible for metabolizing nearly 80% small molecule drugs. Variants in CYPs can substantially alter drug metabolism, which may result improper dosing and severe adverse reactions. have low sequence conservation, making it difficult to anticipate whether variant effects measured one CYP extend others based on alone. Even closely related CYPs, like CYP2C9 its closest homolog CYP2C19, distinct phenotypic properties despite sharing 92% amino acid identity. Thus, we used Variant Abundance by Massively Parallel sequencing (VAMP-seq) measure the steady-state protein abundance, proxy stability, 7,660 missense variants CYP2C19 expressed cultured human cells. Our results confirmed positions structural features critical function revealed how at conserved across all eukaryotic influence abundance. We jointly analyzed 4,670 whose abundance was both CYP2C9, finding that homologs different abundances substrate recognition sites within hydrophobic core, substitutions some regions reduced but not CYP2C9. also single multiple WT exchanges between While most had no effect, site 4 (SRS4) CYP2C19. When nearby acids were exchanged double triple mutants, found interactions revealing region is partially difference thermodynamic stability two homologs. Since these important determining specificity, there be an evolutionary tradeoff altered enzymatic function. Finally, our data analyze 368 previously unannotated variants, 43% decreased comparing genes, uncovered underlying their functional differences paved way more complete understanding versatile families enzymes.

Язык: Английский

Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455–456 synergistically enhances antibody evasion and ACE2 binding DOI Creative Commons
Fanchong Jian, Leilei Feng, Sijie Yang

и другие.

PLoS Pathogens, Год журнала: 2023, Номер 19(12), С. e1011868 - e1011868

Опубликована: Дек. 20, 2023

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) XBB lineages have achieved dominance worldwide and keep on evolving. Convergent evolution of the receptor-binding domain (RBD) L455F F456L is observed, resulting in variants with substantial growth advantages, such as EG.5, FL.1.5.1, XBB.1.5.70, HK.3. Here, we show that neutralizing antibody (NAb) evasion drives convergent F456L, while epistatic shift caused by enables subsequent convergence through ACE2 binding enhancement further immune evasion. evade RBD-targeting Class 1 public NAbs, reducing neutralization efficacy breakthrough infection (BTI) reinfection convalescent plasma. Importantly, single substitution significantly dampens receptor binding; however, combination forms an adjacent residue flipping, which leads to enhanced NAbs resistance affinity. The perturbed mode exceptional NAb evasion, revealed structural analyses. Our results indicate flexibility contributed epistasis cannot be underestimated, potential SARS-CoV-2 RBD remains high.

Язык: Английский

Процитировано

72
Spike deep mutational scanning helps predict success of SARS-CoV-2 clades DOI Creative Commons
Bernadeta Dadonaite,

Jack Brown,

Teagan McMahon

и другие.

Nature, Год журнала: 2024, Номер 631(8021), С. 617 - 626

Опубликована: Июль 3, 2024

SARS-CoV-2 variants acquire mutations in the spike protein that promote immune evasion

Язык: Английский

Процитировано

47
Deep mutational scanning of H5 hemagglutinin to inform influenza virus surveillance DOI Creative Commons
Bernadeta Dadonaite, Jenny Ahn, Jordan T. Ort

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 24, 2024

H5 influenza is a potential pandemic threat. Previous studies have identified molecular phenotypes of the viral hemagglutinin (HA) protein that contribute to risk, including cell entry, receptor preference, HA stability, and reduced neutralization by polyclonal sera. Here we use pseudovirus deep mutational scanning measure how all mutations clade 2.3.4.4b affect each phenotype. We identify allow better bind a2-6-linked sialic acids, show some viruses already carry stabilize HA. also recent strains with sera elicited candidate vaccine virus. Overall, systematic nature combined safety pseudoviruses enables comprehensive characterization inform surveillance influenza.

Язык: Английский

Процитировано

9
Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 synergistically enhances antibody evasion and ACE2 binding DOI Creative Commons
Fanchong Jian, Leilei Feng, Sijie Yang

и другие.

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

Опубликована: Авг. 31, 2023

Summary Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) XBB lineages have achieved dominance worldwide and keep on evolving. Convergent evolution of the receptor-binding domain (RBD) L455F F456L is observed, resulting in variants like EG.5, FL.1.5.1, XBB.1.5.70, HK.3. Here, we show that neutralizing antibody (NAb) evasion drives convergent F456L, while epistatic shift caused by enables subsequent convergence through ACE2 binding enhancement further immune evasion. evade Class 1 NAbs, reducing neutralization efficacy breakthrough infection (BTI) reinfection convalescent plasma. Importantly, single substitution significantly dampens receptor binding; however, combination forms an adjacent residue flipping, which leads to enhanced NAbs resistance affinity. The perturbed mode exceptional NAb evasion, as revealed structural analyses. Our results indicate flexibility contributed epistasis cannot be underestimated, potential SARS-CoV-2 RBD remains high.

Язык: Английский

Процитировано

22
Full-spike deep mutational scanning helps predict the evolutionary success of SARS-CoV-2 clades DOI Creative Commons
Bernadeta Dadonaite,

Jack Brown,

Teagan McMahon

и другие.

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

Опубликована: Ноя. 14, 2023

SARS-CoV-2 variants acquire mutations in spike that promote immune evasion and impact other properties contribute to viral fitness such as ACE2 receptor binding cell entry. Knowledge of how affect these phenotypes can provide insight into the current potential future evolution virus. Here we use pseudovirus deep mutational scanning measure >9,000 across full XBB.1.5 BA.2 spikes binding, entry, or escape from human sera. We find outside receptor-binding domain (RBD) have meaningfully impacted during evolution. also neutralization by serum individuals who recently had infections. The strongest are RBD at sites 357, 420, 440, 456, 473-however, antigenic impacts vary individuals. identify strong RBD; however many them decrease suggesting they act modulating conformation. Notably, growth rates clades be explained substantial part measured effects on phenotypes, our data could enable better prediction

Язык: Английский

Процитировано

21
Deep mutational scanning reveals functional constraints and antibody-escape potential of Lassa virus glycoprotein complex DOI Creative Commons
Caleb R. Carr, Katharine H. D. Crawford, Michael Murphy

и другие.

Immunity, Год журнала: 2024, Номер 57(9), С. 2061 - 2076.e11

Опубликована: Июль 15, 2024

Lassa virus is estimated to cause thousands of human deaths per year, primarily due spillovers from its natural host, Mastomys rodents. Efforts create vaccines and antibody therapeutics must account for the evolutionary variability virus's glycoprotein complex (GPC), which mediates viral entry into cells target neutralizing antibodies. To map space accessible GPC, we used pseudovirus deep mutational scanning measure how nearly all GPC amino-acid mutations affected cell neutralization. Our experiments defined functional constraints throughout GPC. We quantified neutralization with a panel monoclonal All antibodies tested were escaped by that existed among lineages. Overall, our work describes biosafety-level-2 method elucidate shows prospective characterization antigenic variation could aid design vaccines.

Язык: Английский

Процитировано

6
Functional and antigenic landscape of the Nipah virus receptor-binding protein DOI Creative Commons
Brendan B. Larsen,

Teagan McMahon,

Jack T. Brown

и другие.

Cell, Год журнала: 2025, Номер unknown

Опубликована: Март 1, 2025

Язык: Английский

Процитировано

0
Deep mutational scanning and CRISPR-engineered viruses: tools for evolutionary and functional genomics studies DOI Creative Commons
Mercedes Paz, Gonzalo Moratorio

mSphere, Год журнала: 2025, Номер unknown

Опубликована: Апрель 24, 2025

ABSTRACT Recent advancements in synthetic biology and sequencing technologies have revolutionized the ability to manipulate viral genomes with unparalleled precision. This review focuses on two powerful methodologies: deep mutational scanning CRISPR-based genome editing, that enable comprehensive mutagenesis detailed functional characterization of proteins. These approaches significantly deepened our understanding molecular determinants driving evolution adaptation. Furthermore, we discuss how these advances provide transformative insights for future vaccine development therapeutic strategies.

Язык: Английский

Процитировано

0
Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex DOI Creative Commons
Caleb R. Carr, Katharine H. D. Crawford, Michael Murphy

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Фев. 6, 2024

Lassa virus is estimated to cause thousands of human deaths per year, primarily due spillovers from its natural host,

Язык: Английский

Процитировано

1
Deep mutational scanning of rabies glycoprotein defines mutational constraint and antibody-escape mutations DOI Creative Commons
Arjun K. Aditham,

Caelan E. Radford,

Caleb R. Carr

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 17, 2024

Abstract Rabies virus causes nearly 60,000 human deaths annually. Antibodies that target the rabies glycoprotein (G) are being developed as post-exposure prophylactics, but mutations in G can render such antibodies ineffective. Here, we use pseudovirus deep mutational scanning to measure how all single amino-acid affect cell entry and neutralization by a panel of antibodies. These measurements identify sites critical for G’s function, define constrained regions attractive epitopes clinical antibodies, including at apex base protein. We provide complete maps escape eight monoclonal some or development. Escape most present natural strains. Overall, this work provides comprehensive information on functional antigenic effects help inform development stabilized vaccine antigens resilient genetic variation.

Язык: Английский

Процитировано

1