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Article
Biochemistry & Molecular Biology
Wanwisa Dejnirattisai et al.
Summary: On November 24, 2021, the sequence of a new SARS-CoV-2 variant, Omicron-B.1.1.529, was announced. Compared to previous variants, Omicron has a higher number of mutations in the Spike (S) protein. Serum neutralization of Omicron by individuals vaccinated or previously infected with Alpha, Beta, Gamma, or Delta variants is significantly reduced or ineffective. Third vaccine doses can boost neutralization titers against Omicron, and high titers are observed in both vaccinated individuals and those infected with the Delta variant. Most potent monoclonal antibodies and antibodies under development are unable to effectively neutralize Omicron due to mutations in its Spike protein. Omicron has structural changes compared to earlier viruses and utilizes mutations that enhance its binding to ACE2, allowing for immune escape. This results in a large number of mutations in the ACE2 binding site and a rebalancing of receptor affinity similar to earlier pandemic viruses.
Article
Biochemistry & Molecular Biology
Pengcheng Han et al.
Summary: The study found that the omicron variant, unlike other variants, has a similar affinity to the human receptor ACE2 as the prototype variant. Multiple mutations in the omicron variant may compensate for both immune escape and transmissibility. The complex structures of the omicron and delta variants binding to ACE2 provide insights into how specific mutations affect the binding.
Article
Biochemistry & Molecular Biology
Zhen Cui et al.
Summary: The Omicron variant of SARS-CoV-2 is spreading rapidly worldwide due to its increased fitness, with spike structures that maintain stability for receptor recognition but compromise viral fusion efficiency. By altering amino acids and structures, it evades recognition by most antibodies, facilitating immune escape. The research sheds light on conserved regions for the development of broad-spectrum vaccines.
Article
Multidisciplinary Sciences
Delphine Planas et al.
Summary: The Omicron variant of SARS-CoV-2, identified in November 2021, has spread rapidly worldwide and shows resistance to most therapeutic monoclonal antibodies and vaccine-elicited antibodies. However, it can be neutralized by antibodies generated by a booster vaccine dose.
Article
Multidisciplinary Sciences
Elisabetta Cameroni et al.
Summary: The Omicron variant of SARS-CoV-2 has raised concerns due to its 37 amino acid substitutions in the spike protein, particularly in the receptor-binding domain (RBD), leading to increased binding affinity with human ACE2. Neutralizing activity against Omicron was greatly reduced in convalescent and vaccinated individuals compared to the ancestral virus, but this decrease was less significant after a third vaccine dose. Broadly neutralizing monoclonal antibodies recognizing conserved RBD epitopes may be crucial in combating the Omicron variant and future zoonotic transmissions.
Article
Multidisciplinary Sciences
Lihong Liu et al.
Summary: The B.1.1.529/Omicron variant of SARS-CoV-2, initially detected in southern Africa, has rapidly spread globally and is expected to become dominant due to its enhanced transmissibility in the coming weeks. This variant poses a threat to the efficacy of current COVID-19 vaccines and antibody therapies due to its significant antibody resistance. Even individuals who have received vaccines and booster doses may have reduced neutralizing activity against B.1.1.529.
Article
Multidisciplinary Sciences
Dhiraj Mannar et al.
Summary: The newly reported Omicron variant shows new salt bridges and hydrogen bonds formed by mutated residues in the receptor binding domain, compensating for reduced ACE2 binding affinity. It also exhibits increased antibody evasion, which likely contributes to its rapid spread.
Article
Multidisciplinary Sciences
Wanchao Yin et al.
Summary: The structures of the Omicron spike trimer and its interactions with ACE2 and an anti-Omicron antibody are reported. Most mutations in Omicron are located on the spike protein surface, altering binding to many existing antibodies. Compensating mutations in the ACE2-binding site enhance binding to ACE2. The therapeutic antibody JMB2002 maintains neutralizing activity against Omicron and inhibits ACE2 binding.
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
Biochemistry & Molecular Biology
Cheng Li et al.
Summary: This study identifies two highly conserved regions on the Omicron variant receptor-binding domain that are recognized by broadly neutralizing antibodies, and generates a bispecific antibody that can simultaneously bind these regions, showing excellent therapeutic efficacy and neutralization breadth.
Article
Biochemistry & Molecular Biology
Darren P. Martin et al.
Summary: This study found 13 rare mutations among the 30 non-synonymous nucleotide substitutions in the Omicron S-gene, which may impact important regions and functions of the S-gene. The mutations were predicted to decrease the fitness of the virus they occurred in prior to the emergence of Omicron. The study also suggests that the mutations in each cluster interact cooperatively to alter the function of Spike. Understanding how these complex and highly adaptive mutation constellations were assembled in the Omicron S-gene, and why they went undetected in the early stages, is crucial.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Sophie M-C Gobeil et al.
Summary: The SARS-CoV-2 Omicron variant, aided by extensive spike protein mutation, has surpassed the previously dominant Delta variant. Cryo-EM structures of the Omicron and Delta spikes reveal the conformational impacts of mutations, with the Omicron spike showing a tightly packed RBD organization and increased flexibility at the fusion peptide site.
Article
Multidisciplinary Sciences
Qin Hong et al.
Summary: This study used cryo-electron microscopy to reveal the structural features of the Omicron variant spike protein and its interactions with the ACE2 receptor and antibodies, providing important insights for further research and design of vaccines targeting this variant.
Article
Multidisciplinary Sciences
Matthew McCallum et al.
Summary: The SARS-CoV-2 Omicron variant evades antibody-mediated immunity and exhibits enhanced affinity for host cells due to accumulation of spike mutations and remodeling of interactions with the ACE2 receptor.
Article
Multidisciplinary Sciences
Tongqing Zhou et al.
Summary: In this study, the cryo-electron microscopy structures of the B.1.1.529 (Omicron) variant of SARS-CoV-2 were determined, and receptor binding domain (RBD) antibodies were evaluated for their ability to bind and neutralize this variant. The study found that certain monoclonal antibodies still retained substantial inhibitory activity and identified combinations of antibodies with synergistic neutralization.
Article
Multidisciplinary Sciences
Cathrine Scheepers et al.
Summary: Global genomic surveillance of SARS-CoV-2 has identified a new variant, PANGO lineage C.1.2, which has been detected in low prevalence in South Africa and eleven other countries. It has a high substitution rate and includes changes within the spike protein that have been associated with increased transmissibility or reduced neutralization sensitivity. Similar to the Beta and Delta variants, C.1.2 shows reduced neutralization sensitivity to plasma from vaccinees. However, convalescent donors infected with Beta or Delta show high plasma neutralization against C.1.2. This suggests that the efficacy of vaccines against C.1.2 will be similar to Beta and Delta, and prior infection with Beta or Delta may offer protection against C.1.2. The emergence and neutralization sensitivity of the SARS-CoV-2 PANGO lineage C.1.2 has been monitored by global health authorities.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Jun Zhang et al.
Summary: The Omicron variant of SARS-CoV-2 has a high number of mutations, which requires a higher level of ACE2 receptor for membrane fusion and shows increased resistance to neutralizing antibodies. This suggests that Omicron has acquired the ability to evade host immunity through excessive mutations.
Article
Biology
Marco A. Diaz-Salinas et al.
Summary: This study reveals the effects of ACE2 and antibody binding on the conformational dynamics of SARS-CoV-2 spike protein. The D614G mutation and antibodies targeting diverse epitopes are found to modulate the energetics of the receptor-binding domain (RBD) position and enhance ACE2 binding. These findings offer insights into the development of therapeutic antibody cocktails.
Article
Chemistry, Physical
Md Lokman Hossen et al.
Summary: In this study, we computationally examined the impact of omicron RBD mutations on its structure and interactions with surrounding domains in the spike trimer as well as with ACE2. Our findings suggest that these mutations facilitate a more efficient RBD down to up conformation and ACE2 attachment compared to WT and delta, which, along with antibody evasion, may contribute to omicron's dominance over delta.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
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
Biophysics
Takaharu Mori et al.
Summary: This study conducted molecular dynamics simulations on glycosylated S-proteins to investigate conformational stability and transition mechanisms. Key determinants of stability in each form were found to be N-glycans and interacting residues, while electrostatic interactions and hydrogen bonds drove the conformational transitions.
BIOPHYSICAL JOURNAL
(2021)
Article
Chemistry, Physical
Gennady M. Verkhivker et al.
Summary: This study investigated the molecular mechanisms underlying conformational and dynamic changes in SARS-CoV-2 spike mutant trimers, revealing how mutations can differentially affect dynamics and allosteric signaling in distinct functional states. Key functional regions and regulatory centers that govern collective dynamics, allosteric interactions, and control signal transmission in the SARS-CoV-2 spike proteins were identified. The study also provided insights into allosteric regulatory mechanisms of SARS-CoV-2 spike proteins, proposing a plausible strategy for therapeutic intervention by targeting specific hotspots of allosteric interactions and communications.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Letter
Infectious Diseases
Simona Fiorentini et al.
LANCET INFECTIOUS DISEASES
(2021)
Article
Multidisciplinary Sciences
Cong Xu et al.
Summary: The recent global health emergency caused by SARS-CoV-2 outbreak is mediated by the interaction between the SARS-CoV-2 trimeric spike glycoprotein and the human ACE2 receptor. The SARS-CoV-2 S trimer is more sensitive to ACE2 receptor compared to SARS-CoV S trimer, potentially contributing to its superior infectivity. Research findings depict the mechanism of ACE2-induced conformational transitions in S trimer structure, aiding in the development of anti-SARS-CoV-2 vaccines and therapeutics.
Article
Biochemistry & Molecular Biology
Daming Zhou et al.
Summary: The race to develop vaccines against SARS-CoV-2 variants, such as B.1.1.7, B.1.351, and P.1, is ongoing as these variants have mutations in the spike protein, potentially leading to immune escape. A structure-function analysis of B.1.351 revealed tighter ACE2 binding and widespread evasion from monoclonal antibody neutralization, particularly driven by the E484K mutation.
Article
Biochemistry & Molecular Biology
Kamyab Javanmardi et al.
Summary: The Spike Display platform characterized 200 variant SARS-CoV-2 spikes, revealing a public epitope in the N-terminal domain loops that is recognized by most NTD-binding nAbs. Mutations in NTDs of variants like B.1.1.7, B.1.351, B.1.1.28, B.1.427/B.1.429, and B.1.617.2 impact spike expression and escape most NTD-targeting nAbs. Certain variants like B.1.351 and B.1.1.28 completely evade binding by a potent ACE2 mimic.
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
Houriiyah Tegally et al.
Summary: The article describes a newly emerged lineage of SARS-CoV-2, 501Y.V2, characterized by eight mutations in the spike protein, which may result in increased transmissibility or immune escape. This lineage originated in South Africa and quickly became dominant in Eastern Cape, Western Cape, and KwaZuluNatal provinces within weeks.
Article
Biochemistry & Molecular Biology
Houriiyah Tegally et al.
Summary: The study identified 16 new lineages of SARS-CoV-2 in South Africa between March and August 2020, with unique mutations not found elsewhere. Three lineages (B.1.1.54, B.1.1.56, and C.1) dominated during the country's first wave, accounting for approximately 42% of all infections. The C.1 lineage, with 16 nucleotide mutations including the D614G spike protein change, became the most geographically widespread by August 2020. Genomic surveillance played a crucial role in identifying the 501Y.V2 variant in South Africa in December 2020.
Article
Multidisciplinary Sciences
Nicholas G. Davies et al.
Summary: A new variant of SARS-CoV-2 has emerged in England, with a higher reproduction number and potential for large resurgences of COVID-19 cases. Without stringent control measures, it is projected that COVID-19 hospitalizations and deaths in England for the first 6 months of 2021 will exceed those in 2020. The variant has spread globally and exhibited similar transmission increases in Denmark, Switzerland, and the United States.
Article
Multidisciplinary Sciences
Alexander Muik et al.
Summary: A new SARS-CoV-2 lineage B.1.1.7 has emerged in the UK, which is more transmissible and faster spreading than other strains. However, a study found that the BNT162b2 vaccine offers largely preserved protection against the B.1.1.7 lineage, despite some reduced neutralizing titers.
Article
Biochemistry & Molecular Biology
Gennady M. Verkhivker et al.
Summary: This study identified key residues within the SARS-CoV-2 spike protein that play crucial roles in binding with ACE2 host receptor, and demonstrated their impact on long-range communication in complexes through allosteric interactions. The research suggests that mutational variants and antibody-escaping mutations tend to target structurally plastic and energetically adaptable centers to modulate interactions within the complexes.
Article
Chemistry, Physical
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
Multidisciplinary Sciences
Nicholas G. Davies et al.
Summary: Studies have shown that the SARS-CoV-2 B.1.1.7 lineage is more transmissible and may cause more severe illness compared to pre-existing variants.
Article
Biochemistry & Molecular Biology
Sophia F. Mersmann et al.
Summary: ProteinLens is an interactive web application for investigating allosteric signaling in biomolecular structures based on atomistic graph-theoretical methods. It allows systematic analysis of signaling in biomolecular structures to aid in the detection of allosteric sites and pathways.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Mateusz Sikora et al.
Summary: The spike protein of the SARS-CoV-2 virus plays a crucial role in infection and is the primary target for antibodies. Through molecular dynamics simulations and bioinformatics analyses, accessible epitopes have been identified for potential vaccine development. The extensive and flexible glycan coat covering the spike protein presents challenges in antibody binding but also reveals promising epitope candidates for structure-based vaccine design.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biophysics
Zhen-lu Li et al.
Summary: Nrp1 plays a crucial role in the entry of SARS-CoV-2 into cells, enhancing virus infectivity by facilitating the separation of S1 and S2. The study reveals how Nrp1 affects the binding and separation of S1 and S2, providing insights for potential therapeutic interventions targeting the Nrp1-assisted viral infection mechanism.
BIOPHYSICAL JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Yafei Liu et al.
Summary: The research found that antibodies against different domains of the SARS-CoV-2 spike protein have different effects, with some antibodies inducing an open conformation of the RBD and enhancing the virus infectivity. Structural and mutational analysis revealed the mechanisms of these antibodies, and infectivity-enhancing antibodies were detected at higher levels in severe patients.
Article
Cell Biology
Wei Hu et al.
Summary: The spike protein of SARS-CoV-2 recognizes host receptors through mechanical force, accelerating viral entry and fusion. Mutations can strengthen viral binding and detachment speed, while certain antibodies derived from recovered patients show potential for therapeutic strategies.
Article
Chemistry, Medicinal
Gennady M. Verkhivker et al.
Summary: The computational framework developed in this study allows for comprehensive and rapid mutational scanning of binding energetics and residue interaction networks in the SARS-CoV-2 spike protein complexes. The research reveals the key regions of structural plasticity, mutational impact, and functional response, emphasizing the importance of dynamic crosstalk between binding affinities and structural stability with conformational adaptability for resilience.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Physical
Gennady Verkhivker et al.
Summary: The study investigates how SARS-CoV-2 spike proteins interact with different classes of antibodies through atomistic simulations and scanning approaches, revealing their functional adaptability and regulatory mechanisms. The research also explores how antibody binding modulates allosteric propensities of spike protein residues, identifying versatile allosteric centers targeted by circulating mutations that can elicit resistance to antibody binding.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Multidisciplinary
Lucy Fallon et al.
Summary: The SARS-CoV-2 coronavirus spike protein plays a crucial role in viral entry and is a target for neutralizing antibodies. By using simulations, interactions influencing spike protein dynamics can be identified for potential therapeutic targeting. Small molecules binding to specific pockets may modulate the spike protein equilibrium and shed light on its conformational changes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
M. Alejandra Tortorici et al.
Summary: The emergence of SARS-CoV-2 variants and recurrent spillovers of coronaviruses into the human population emphasize the need for broadly neutralizing antibodies to prevent future zoonotic infections. The human monoclonal antibody S2X259 has shown promising results in neutralizing various forms of SARS-CoV-2 and potentially zoonotic sarbecoviruses by inhibiting the binding of ACE2 to the receptor-binding domain. This antibody targets a key antigenic site and may guide the design of vaccines effective against all sarbecoviruses.
Article
Chemistry, Multidisciplinary
Maxwell Zimmerman et al.
Summary: Researchers utilized the Folding@home project to simulate the viral proteome of SARS-CoV-2 and discovered 'cryptic' epitopes, with spike variants affecting the balance between receptor binding and immune evasion. The data and models generated provide valuable insight for the design of antiviral drugs.
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.
Article
Biochemistry & Molecular Biology
Tzu-Jing Yang et al.
Summary: The spike protein of the SARS-CoV-2 B.1.1.7 variant exhibits mutations that affect virus binding to the host ACE2 receptor and immune evasion. The A570D and N501Y mutations have been shown to impact the stability of the spike protein structure, and an introduced neutralizing antibody can effectively neutralize different strains of the virus.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2021)
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.
Article
Multidisciplinary Sciences
Yongfei Cai et al.
Summary: The study found that the B.1.1.7 variant has increased receptor binding affinity, while the B.1.351 variant has developed resistance to some neutralizing antibodies by reshaping antigenic surfaces on the spike protein.
Article
Biology
Michael Barton et al.
Summary: The study analyzed the effects of mutations in the Spike protein of SARS-CoV-2 on its interaction with ACE2, finding that most mutations increased affinity with ACE2. Two ACE2 mutations were also found to enhance binding with the Spike protein.
Article
Immunology
Catherine A. Hogan et al.
Summary: This study evaluated the relative contribution of VOCs in nearly 67,000 infections in British Columbia during the first 16 weeks of 2021, finding that B.1.1.7, B.1.351, and P.1 showed different spreading patterns in the region. While B.1.1.7 and P.1 increased in proportion, P.1 expanded rapidly, while B.1.351 remained a minority.
EMERGING INFECTIOUS DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Cody B. Jackson et al.
Summary: The D614G spike mutation in SARS-CoV-2 virus leads to more efficient infection of cells and animals, without affecting the affinity of the S protein for ACE2. This mutation is significant in the current global pandemic.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
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Chemistry, Multidisciplinary
Kazuki Akisawa et al.
Summary: The spike protein plays a crucial role in SARS-CoV-2 infection, and its structural properties and interaction with receptor proteins or neutralizing antibodies are of great interest. The open structure of the spike protein exhibits significant stabilization energy losses, especially in the receptor binding domain of chain-B. Binding with ACE2 or antibodies partially compensates for this loss.
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