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Article
Multidisciplinary Sciences
Lorenz Ulrich et al.
Summary: Experimental assessments of major VOCs show that Alpha and Beta variants have a higher affinity for the human ACE2 receptor compared to the progenitor variant. Competition experiments demonstrate that Alpha has a clear fitness advantage over wt-S-614G in ferrets and mouse models.
Article
Microbiology
Ziwei Yang et al.
Summary: The variants of concern of SARS-CoV-2 have mutations that enhance transmission and reduce the effectiveness of COVID-19 vaccines and treatments. These variants have a higher propensity to bind to the human receptor and exhibit slower transitions between receptor-bound states. These findings provide insights into the adaptation strategies of SARS-CoV-2.
Article
Biology
Hisham M. Dokainish et al.
Summary: The Spike protein plays a crucial role in neutralization and vaccine development for SARS-CoV-2. Its inherent flexibility provides essential information for designing antiviral drugs and vaccines.
Article
Multidisciplinary Sciences
Jessica A. Plante et al.
Summary: The D614G substitution in the SARS-CoV-2 spike protein enhances viral replication and infectivity in human lung epithelial cells, primary airway tissues, and hamsters. This variant may increase transmission in the upper respiratory tract and doesn't seem to significantly reduce vaccine efficacy. Further research on therapeutic antibodies targeting the circulating G614 virus is recommended.
Article
Microbiology
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
Chemistry, Multidisciplinary
Jaewoon Jung et al.
Summary: This paper addresses the high performance extreme-scale molecular dynamics algorithm in the GENESIS software for cellular-scale MD simulations, achieving a performance of 8.30 ns/day on Fugaku supercomputer with a system containing 1.6 billion atoms, extending the size and time of MD simulations.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2021)
Article
Cell Biology
Sophie M-C Gobeil et al.
Summary: The study found that the mutation variant G614 of SARS-CoV-2 leads to significant changes in the protein structure, resulting in altered positioning ratio of RBD, which may have implications for vaccine design.
Article
Multidisciplinary Sciences
Dhiman Ray et al.
Summary: Researchers are focusing on the correlation between the RBD region of the SARS-CoV-2 virus and residues distant from it to understand molecular recognition events and predict key mutations for therapeutics. Their model can identify multiple residues with long-distance coupling with the RBD opening and successfully predict some key mutations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Pengfei Wang et al.
Summary: The COVID-19 pandemic has had global repercussions, with promising vaccines and monoclonal antibody therapies. However, newly detected variants of SARS-CoV-2 present challenges to these treatment options.
Article
Multidisciplinary Sciences
Jun Zhang et al.
Summary: The Delta variant of SARS-CoV-2 is more efficient at fusing membranes at low levels of cellular receptor ACE2, possibly contributing to its heightened transmissibility. Each variant shows different rearrangement of the antigenic surface of the S protein, but only the changes in the RBD make it a better target for therapeutic antibodies.
Article
Multidisciplinary Sciences
Matthew McCallum et al.
Summary: The transmission of SARS-CoV-2 leads to the emergence of variants, such as the B.1.617.2 (Delta) variant, which dampens the in vitro potency of vaccine-elicited serum neutralizing antibodies. Mutations in the B.1.617.1 (Kappa) and Delta spike glycoproteins alter key antigenic sites, affecting the recognition by monoclonal antibodies. The angiotensin-converting enzyme 2 binding affinities of Kappa and Delta are comparable to the Wuhan-Hu-1 isolate, while Delta+ exhibits significantly reduced affinity.
Article
Multidisciplinary Sciences
Donald J. Benton et al.
Summary: Studies indicate that the G614 mutant spike adopts more open conformations, which may facilitate binding to the SARS-CoV-2 receptor ACE2 and the subsequent structural rearrangements required for viral membrane fusion.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Seiya Ozono et al.
Summary: The naturally occurring mutations of SARS-CoV-2 spike protein can affect cell entry, with the D614G mutation resulting in increased cell entry and maintaining susceptibility to neutralization by antisera against prototypic viruses. Further global surveillance is needed to understand the transmissibility of SARS-CoV-2 among humans.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Zharko Daniloski et al.
Summary: A novel variant of SARS-CoV-2 virus with mutation D614G has been found to be more effective at transducing human cells and showing increased infectivity in human cells compared to the wild-type variant.
Article
Virology
Jun Zhang et al.
Summary: The COVID-19 pandemic, caused by SARS-CoV-2, has led to millions of deaths and devastating socio-economic consequences worldwide. Understanding the structure-function relationships of viral proteins and host factors is crucial for developing intervention strategies. The trimeric spike protein is a key target for diagnostics, therapeutics, and vaccines, and rapid progress in its structural biology has advanced our understanding of the viral entry process.
CURRENT OPINION IN VIROLOGY
(2021)
Article
Multidisciplinary Sciences
Jun Zhang et al.
Summary: Substitution of aspartic acid (D) with glycine (G) at position 614 in the spike protein of SARS-CoV-2 enhances viral spread. Cryo-electron microscopy structures reveal that the G614 strain has increased infectivity compared to the D614 strain. These findings provide insights for vaccine development and understanding viral entry mechanisms.
Article
Chemistry, Multidisciplinary
Yury Valdes-Balbin et al.
Summary: The development of recombinant COVID-19 vaccines has been accelerated by scientific progress in 2020. Studies have shown that the recombinant spike glycoprotein induces a potent antibody response in animals and there is a good correlation between antibody response and neutralization in convalescent sera. This review provides insights into the molecular aspects of the interaction between SARS-CoV-2 RBD and ACE2, epitopes involved in neutralizing activity, and the impact of virus mutations.
ACS CENTRAL SCIENCE
(2021)
Article
Multidisciplinary Sciences
Rachael A. Mansbach et al.
Summary: The emergence of the G-form variant of COVID-19 has led to a more infectious strain with increased viral loads, likely due to changes in protein energetics favoring infection-capable states and enhanced exposure of the receptor binding domain. These findings are crucial for vaccine design.
Article
Chemistry, Multidisciplinary
Terra Sztain et al.
Summary: Through simulations, the study reveals the mechanism of spike protein receptor binding domain (RBD) opening in SARS-CoV-2 infection, highlighting the crucial role of N-glycan in facilitating RBD opening. This research represents a milestone in ensemble pathway simulations and provides a foundation for understanding the fundamental mechanisms of viral entry and infection.
Review
Microbiology
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
Multidisciplinary Sciences
Meng Yuan et al.
Summary: Mutations in the RBS residues of new variant strains of the coronavirus can affect the binding and neutralizing effects of antibodies, but have little impact on antibodies targeting more conserved neutralizing sites.
Article
Multidisciplinary Sciences
Matthew McCallum et al.
Summary: The novel CAL.20C (B.1.427/B.1.429) variant carries spike protein mutations, resulting in reduced neutralizing titers in vaccinated individuals and convalescent individuals. The L452R mutation reduces neutralizing activity in RBD-specific monoclonal antibodies, while the S13I and W152C mutations lead to the total loss of neutralization in NTD-specific antibodies due to antigenic supersite remodeling.
Article
Multidisciplinary Sciences
Sophie M-C Gobeil et al.
Summary: SARS-CoV-2 variants with multiple spike mutations have increased transmission and resistance to antibodies. Research showed that these variants have enhanced receptor binding and a preference for receptor binding domain up states. Different variants exhibit different mechanisms for resistance to neutralizing antibodies, which helps explain their transmission and resistance.
Review
Cell Biology
Chenxi Wang et al.
Summary: COVID-19 caused by SARS-CoV-2, which emerged in December 2019, has led to over 140 million infections worldwide by the end of April 2021. The prevalent D614G variant, with glycine substitution at position 614 in the spike glycoprotein, became a dominant strain globally due to its high contagiousness. Extensive studies have characterized the epidemiological features of this variant and revealed its underlying mechanisms.
JOURNAL OF MOLECULAR CELL BIOLOGY
(2021)
Letter
Biochemistry & Molecular Biology
Xiantao Zhang et al.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2021)
Review
Microbiology
Philip V'kovski et al.
Summary: This review discusses key aspects of coronavirus biology and their implications for SARS-CoV-2 infections, treatment, and prevention strategies. Understanding virus-host interactions at the molecular level is crucial for developing effective intervention strategies. Summarizing the discoveries of SARS-CoV-2 infection and comparing it with other coronaviruses will support future preparedness and combat strategies.
NATURE REVIEWS MICROBIOLOGY
(2021)
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Multidisciplinary Sciences
Renhong Yan et al.
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Multidisciplinary Sciences
Daniel Wrapp et al.
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Biochemistry & Molecular Biology
Qihui Wang et al.
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Jian Shang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
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Yasunori Watanabe et al.
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Biochemistry & Molecular Biology
Qianqian Li et al.
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Biochemistry & Molecular Biology
Bette Korber et al.
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Chemistry, Physical
Hyeonuk Woo et al.
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
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Biochemistry & Molecular Biology
Leonid Yurkovetskiy et al.
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Biochemistry & Molecular Biology
Rory Henderson et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2020)
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Biochemistry & Molecular Biology
Antoni G. Wrobel et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2020)
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Multidisciplinary Sciences
Yongfei Cai et al.
Article
Microbiology
Tongqing Zhou et al.
CELL HOST & MICROBE
(2020)
Article
Multidisciplinary Sciences
Lizhou Zhang et al.
NATURE COMMUNICATIONS
(2020)
Letter
Biochemistry & Molecular Biology
Xiaoyi Jiang et al.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2020)
Article
Biology
Yiska Weisblum et al.
Article
Biochemical Research Methods
Jing Huang et al.
Article
Chemistry, Multidisciplinary
Chigusa Kobayashi et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2017)
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Chemistry, Physical
Jumin Lee et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2016)
