4.7 Article

Shortening Epitopes to Survive: The Case of SARS-CoV-2 Lambda Variant

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Microbiology

Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition

Allison J. Greaney et al.

Summary: Antibodies targeting the SARS-CoV-2 spike receptor-binding domain (RBD) are key in neutralizing antibody responses, and a deep mutational scanning method was used to assess the impact of all amino-acid mutations in the RBD on antibody binding with 10 human monoclonal antibodies. The study identified the clustered escape mutations in different surfaces of the RBD that correspond to structurally defined antibody epitopes, showing that even antibodies targeting the same surface can have distinct escape mutations.

CELL HOST & MICROBE (2021)

Article Multidisciplinary Sciences

Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies

Dami A. Collier et al.

Summary: The B.1.1.7 variant of SARS-CoV-2 exhibited reduced neutralization by vaccines and antibodies from recovered COVID-19 patients, with a more substantial loss seen when introducing the E484K mutation. This mutation poses a threat to the efficacy of the BNT162b2 vaccine.

NATURE (2021)

Article Biochemistry & Molecular Biology

N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2

Matthew McCallum et al.

Summary: The study identifies 41 human monoclonal antibodies that recognize the N-terminal domain of the SARS-CoV-2 spike protein and exhibit strong neutralizing activity. These antibodies inhibit cell-to-cell fusion, activate effector functions, and protect animals from virus challenge, highlighting the importance of NTD-specific neutralizing antibodies for protective immunity and vaccine development. Several SARS-CoV-2 variants with mutations in the NTD supersite suggest ongoing selective pressure on the virus.
Article Biochemistry & Molecular Biology

SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies

Markus Hoffmann et al.

Summary: The emerging SARS-CoV-2 variants may exhibit resistance to existing neutralizing antibodies and treatments, which could have significant implications for pandemic containment efforts.
Article Chemistry, Physical

Integrated Biophysical Modeling of the SARS-CoV-2 Spike Protein Binding and Allosteric Interactions with Antibodies

Gennady M. Verkhivker et al.

Summary: The study investigates the molecular mechanisms underlying the modulation of dynamics and allosteric signaling in the SARS-CoV-2 spike proteins induced by binding to antibodies using coevolutionary analysis, molecular simulations, and perturbation-based hierarchical network modeling. Through these methods, the study identifies highly coevolving hotspots and functional clusters that enable cross-talk between distant allosteric regions in the spike complexes with antibodies, demonstrating how antibodies can induce specific and functionally relevant changes in the spike proteins by modulating their allosteric propensities and collective dynamics. The findings provide insights into the regulatory mechanisms of SARS-CoV-2 spike proteins and how antibody-escaping mutations may target energy hotspots and allosteric effector centers to control functional movements and allosteric communication in the complexes.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

Article Virology

SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate?

Stefano Pascarella et al.

Summary: Lineage B.1.617+, also known as G/452R.V3 and denoted by WHO as delta and kappa, is a newly described SARS-CoV-2 variant first identified in India in October 2020. Three sublineages, B.1.617.1 (kappa), B.1.617.2 (delta), and B.1.617.3, have been identified, with their potential impact on the current pandemic under investigation. This variant with 13 amino acid changes, including E484Q, L452R, and P681R, is characterized by a significant alteration in the surface electrostatic potential of the spike protein receptor-binding domain, particularly noticeable in the delta sublineage. The enhanced electrostatic potential change may facilitate the interaction between the B.1.617+ RBD and the ACE2 receptor, potentially increasing virus transmission.

JOURNAL OF MEDICAL VIROLOGY (2021)

Article Multidisciplinary Sciences

BNT162b2-elicited neutralization of B.1.617 and other SARS-CoV-2 variants

Jianying Liu et al.

Summary: Serum samples from individuals vaccinated with the BNT162b2 vaccine can neutralize various SARS-CoV-2 variants, indicating mass immunization as a central strategy to end the global COVID-19 pandemic.

NATURE (2021)

Article Multidisciplinary Sciences

SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape

Tyler N. Starr et al.

Summary: An ideal therapeutic anti-SARS-CoV-2 antibody should have resistance to viral escape, activity against diverse sarbecoviruses, and provide high protection through viral neutralization and effector functions. Studies have found a trade-off between in vitro neutralization potency and breadth of sarbecovirus binding in SARS-CoV-2 antibodies targeting the RBD, but identified some antibodies with exceptional sarbecovirus breadth and resistance to SARS-CoV-2 escape.

NATURE (2021)

Article Medicine, Research & Experimental

Dominance of Alpha and Iota variants in SARS-CoV-2 vaccine breakthrough infections in New York City

Ralf Duerr et al.

Summary: The study found that breakthrough infections still occur after receiving COVID-19 mRNA vaccines, but the vaccines have high efficacy against B.1.1.7 and B.1.526 variants.

JOURNAL OF CLINICAL INVESTIGATION (2021)

Editorial Material Public, Environmental & Occupational Health

A call to research: the relationship between SARS-2-CoV, ACE 2 and antihypertensives COMMENT

Antonio Cassone et al.

PATHOGENS AND GLOBAL HEALTH (2020)

Article Virology

Evidence for mutations in SARS-CoV-2 Italian isolates potentially affecting virus transmission

Domenico Benvenuto et al.

JOURNAL OF MEDICAL VIROLOGY (2020)

Article Biochemical Research Methods

Molecular Simulations and Network Modeling Reveal an Allosteric Signaling in the SARS-CoV-2 Spike Proteins

Gennady M. Verkhivker

JOURNAL OF PROTEOME RESEARCH (2020)

Article Biochemistry & Molecular Biology

SWISS-MODEL: homology modelling of protein structures and complexes

Andrew Waterhouse et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Nuala A. O'Leary et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemical Research Methods

PRODIGY: a web server for predicting the binding affinity of protein-protein complexes

Li C. Xue et al.

BIOINFORMATICS (2016)

Article Biochemistry & Molecular Biology

UniProt: a hub for protein information

Alex Bateman et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemical Research Methods

Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking

Jens Vindahl Kringelum et al.

PLOS COMPUTATIONAL BIOLOGY (2012)

Article Biochemistry & Molecular Biology

DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein-protein interactions

Dennis M. Krueger et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemical Research Methods

Prediction of glycosylation sites using random forests

Stephen E. Hamby et al.

BMC BIOINFORMATICS (2008)

Article Chemistry, Multidisciplinary

UCSF chimera - A visualization system for exploratory research and analysis

EF Pettersen et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)