4.6 Article

Computational decomposition reveals reshaping of the SARS-CoV-2-ACE2 interface among viral variants expressing the N501Y mutation

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study

Budheswar Dehury et al.

Summary: Recent studies have shown the role of ACE2 in mediating SARS-CoV-2 entry into host cells and the impact of mutations on molecular interactions. Computational simulations and experimental analyses provide detailed insight into the crucial interaction between RBD and ACE2.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2021)

Article Biochemistry & Molecular Biology

Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity

Sandipan Chakraborty

Summary: The study identifies selective SARS-CoV2 spike RBD variants through evolutionary analysis and protein docking calculations, showing differential binding affinities with ACE2. Some variants exhibit reduced ACE2 affinity, while others demonstrate increased affinity towards ACE2.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2021)

Article Biophysics

Biomechanical characterization of SARS-CoV-2 spike RBD and human ACE2 protein-protein interaction

Wenpeng Cao et al.

Summary: This study utilizes single-molecule force spectroscopy and molecular dynamics simulations to quantify the interactions between SARS-CoV-2 or SARS-CoV-1 RBD and ACE2, revealing that the N-linked glycan interaction plays a crucial role in the binding difference between the two viruses. The study uncovers the mechanism behind ACE2 binding disparity and provides insights for developing new strategies to inhibit SARS-CoV-2 entry.

BIOPHYSICAL JOURNAL (2021)

Article Virology

Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications

Jasdeep B. Singh et al.

Summary: The SARS-CoV-2 virus has undergone multiple mutations during its global circulation, leading to the emergence of three new lineages in the UK, South Africa, and Brazil. These mutations impact crucial proteins such as spike, ORF8, and nucleocapsid, potentially affecting host receptor affinity and antibody resistance.

VIRUSES-BASEL (2021)

Article Multidisciplinary Sciences

An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants

Kui K. Chan et al.

Summary: The study suggests that engineered decoy receptors can tightly bind to the S protein of SARS-related viruses, and are expected to be effective against future coronavirus outbreaks.

SCIENCE ADVANCES (2021)

Article Biochemistry & Molecular Biology

Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies

Xing Zhu et al.

Summary: The UK variant of SARS-CoV-2 with the N501Y mutation shows increased infectivity due to tighter binding with the ACE2 receptor, but without significant structural changes. Important neutralization epitopes in the spike receptor binding domain are retained.

PLOS BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide

Eileen Socher et al.

Summary: The B.1.1.7 variant of SARS-CoV-2 virus exhibits enhanced infectivity compared to the wild type virus, affecting the interaction interfaces with the ACE2 receptor. The mutations within B.1.1.7 lead to increased flexibility around the fusion peptide and alter the RBD-ACE2 interface, resulting in reduced binding affinity.

BIOMEDICINES (2021)

Review Biochemistry & Molecular Biology

Structural Evaluation of the Spike Glycoprotein Variants on SARS-CoV-2 Transmission and Immune Evasion

Mohd Zulkifli Salleh et al.

Summary: The emergence of SARS-CoV-2 has posed significant challenges worldwide, resulting in millions of deaths. Mutations in the spike (S) glycoprotein may impact vaccine efficacy. Variants such as Alpha, Beta, Gamma have mutations in their spike proteins that enhance viral fitness.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Review Microbiology

SARS-CoV-2 variants, spike mutations and immune escape

William T. Harvey et al.

Summary: The evolution of SARS-CoV-2 has been characterized by the emergence of mutations and variants that impact virus characteristics. Manufacturers are preparing for possible updates to vaccines in response to changes in the virus population, and it is crucial to monitor genetic and antigenic changes alongside experiments to understand the impacts of mutations.

NATURE REVIEWS MICROBIOLOGY (2021)

Article Biochemistry & Molecular Biology

A Multibasic Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells

Markus Hoffmann et al.

MOLECULAR CELL (2020)

Article Microbiology

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

Andrew Rambaut et al.

NATURE MICROBIOLOGY (2020)

Article Multidisciplinary Sciences

Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion

Donald J. Benton et al.

NATURE (2020)

Article Multidisciplinary Sciences

Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor

Jinsung Yang et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2

Thomas W. Linsky et al.

SCIENCE (2020)

Article Chemistry, Physical

Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning

Chad W. Hopkins et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

James A. Maier et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Biochemistry & Molecular Biology

The Conformational Stability of Nonfibrillar Amyloid-β Peptide Oligomers Critically Depends on the C-Terminal Peptide Length

Eileen Socher et al.

ACS CHEMICAL NEUROSCIENCE (2014)

Article Multidisciplinary Sciences

Host cell entry of Middle East respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein

Jean Kaoru Millet et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Computer Science, Interdisciplinary Applications

SPFP: Speed without compromise-A mixed precision model for GPU accelerated molecular dynamics simulations

Scott Le Grand et al.

COMPUTER PHYSICS COMMUNICATIONS (2013)

Article Chemistry, Physical

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

Daniel R. Roe et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Physical

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

Romelia Salomon-Ferrer et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Physical

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

Andreas W. Goetz et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

Article Multidisciplinary Sciences

Activation of the SARS coronavirus spike protein via sequential proteolytic cleavage at two distinct sites

Sandrine Belouzard et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Multidisciplinary Sciences

Protease-mediated enhancement of severe acute respiratory syndrome coronavirus infection

S Matsuyama et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Biochemistry & Molecular Biology

The FoldX web server: an online force field

J Schymkowitz et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Chemistry, Multidisciplinary

UCSF chimera - A visualization system for exploratory research and analysis

EF Pettersen et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)