Atomistic Simulations and In Silico Mutational Profiling of Protein Stability and Binding in the SARS-CoV-2 Spike Protein Complexes with Nanobodies: Molecular Determinants of Mutational Escape Mechanisms

Article Biochemistry & Molecular Biology

Bi-paratopic and multivalent VH domains block ACE2 binding and neutralize SARS-CoV-2

Colton J. Bracken et al.

Summary: This study presents a strategy to rapidly identify and assemble synthetic human VH domains for neutralizing SARS-CoV-2, which was proven to be effective through experimental validation.

NATURE CHEMICAL BIOLOGY (2021)

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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)

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Article Chemistry, Physical

Dynamic Network Modeling of Allosteric Interactions and Communication Pathways in the SARS-CoV-2 Spike Trimer Mutants: Differential Modulation of Conformational Landscapes and Signal Transmission via Cascades of Regulatory Switches

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)

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Article Multidisciplinary Sciences

Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape

Paul-Albert Koenig et al.

Summary: In this study, new neutralizing nanobodies targeting the SARS-CoV-2 spike protein were developed, showing enhanced neutralizing activity through engineering technology and successfully suppressing the emergence of escape mutants. The findings suggest that nanobodies can neutralize through receptor binding competition and also render virions noninfectious.

SCIENCE (2021)

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Review Virology

Structural Analysis of Neutralizing Epitopes of the SARS-CoV-2 Spike to Guide Therapy and Vaccine Design Strategies

Maxwell T. Finkelstein et al.

Summary: This review summarizes recent studies focusing on the development of monoclonal antibodies and vaccines against SARS-CoV-2. By studying the structural details of the virus, important information for the treatment and prevention of COVID-19 can be obtained.

VIRUSES-BASEL (2021)

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Article Multidisciplinary Sciences

Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM

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.

SCIENCE ADVANCES (2021)

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Review Biochemistry & Molecular Biology

Binding Revisited-Avidity in Cellular Function and Signaling

Simon Erlendsson et al.

Summary: Avidity is a term used to describe the accumulated strength of multiple interactions between biomolecules, covering both specific and nonspecific interactions. Unlike affinity, which focuses on individual binding events, avidity is a macroscopic parameter linked to various microscopic events and can be influenced by reduced dimensionality and hindered diffusion. In biological systems, avidity plays a role in explaining discrepancies between cellular and in vitro binding strengths, and its effects on intracellular signaling processes are also important to consider.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

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Article Microbiology

Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies

Allison J. Greaney et al.

Summary: The evolution of SARS-CoV-2 may impact the recognition of the virus by human antibody-mediated immunity, with mutations affecting antibody binding varying significantly among individuals and within the same individual over time. Despite this variability, mutations that greatly reduce antibody binding usually occur at specific sites in the RBD, with E484 being the most crucial. These findings can inform surveillance efforts for SARS-CoV-2 evolution in the future.

CELL HOST & MICROBE (2021)

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Article Multidisciplinary Sciences

Detection of a SARS-CoV-2 variant of concern in South Africa

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.

NATURE (2021)

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Article Biochemistry & Molecular Biology

Sixteen novel lineages of SARS-CoV-2 in South Africa

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.

NATURE MEDICINE (2021)

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Article Biochemistry & Molecular Biology

Comparative Perturbation-Based Modeling of the SARS-CoV-2 Spike Protein Binding with Host Receptor and Neutralizing Antibodies: Structurally Adaptable Allosteric Communication Hotspots Define Spike Sites Targeted by Global Circulating Mutations

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.

BIOCHEMISTRY (2021)

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Article Biophysics

A multiscale coarse-grained model of the SARS-CoV-2 virion

Alvin Yu et al.

Summary: This article presents the current status and ongoing development of a largely bottom-up coarse-grained (CG) model of the SARS-CoV-2 virion. The CG model was constructed using data from cryo-electron microscopy, x-ray crystallography, and computational predictions to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into the complete virion model. The CG model allows for capturing viral behavior that is difficult to observe in atomistic simulations and can be iteratively improved with new data.

BIOPHYSICAL JOURNAL (2021)

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Article Chemistry, Physical

Critical Interactions Between the SARS-CoV-2 Spike Glycoprotein and the Human ACE2 Receptor

Elhan Taka et al.

Summary: By performing molecular dynamics simulations, researchers identified key interactions between the receptor-binding domain of the S protein and ACE2, suggesting that blocking the hydrophobic surface of the RBD could be an effective strategy to inhibit S-ACE2 interactions and prevent SARS-CoV-2 infection. The hydrophobic end of the RBD serves as the main anchor site and is the last to unbind from ACE2 under force, indicating its importance in the binding process.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

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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)

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Article Multidisciplinary Sciences

Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7

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.

NATURE (2021)

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Article Multidisciplinary Sciences

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

Erik Volz et al.

Summary: Genetic and testing data from England indicate that the SARS-CoV-2 variant B.1.1.7 has a transmission advantage over other lineages, showing a rapid expansion during autumn 2020. Analysis of S gene target failures (SGTF) in community-based diagnostic PCR testing suggests that B.1.1.7 is more transmissible than non-variant of concern lineages and has a significant transmission advantage, with a reproduction number 50% to 100% higher. Additionally, cases of B.1.1.7 appear to include a larger share of under 20-year-olds compared to non-variant cases.

NATURE (2021)

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Article Biochemistry & Molecular Biology

Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies

Delphine Planas et al.

Summary: The ability of convalescent sera from individuals with coronavirus disease 2019 and those vaccinated with BNT162b2 to neutralize SARS-CoV-2 variants B1.1.7 and B.1.351 decreases, but increases after two vaccine doses. The study found that the B.1.1.7 and B.1.351 variants may have acquired partial resistance to neutralizing antibodies generated by natural infection or vaccination, particularly in individuals with low antibody levels. This suggests that the B.1.351 variant may pose a greater risk of infection in immunized individuals.

NATURE MEDICINE (2021)

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Article Multidisciplinary Sciences

Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice

Phillip Pymm et al.

Summary: Neutralizing antibodies, particularly nanobodies, play a crucial role in immunity against SARS-CoV-2 and in the development of therapeutics for COVID-19. Researchers have identified high-affinity nanobodies that effectively disrupt the interaction between the virus and the human host cell receptor ACE2, offering promising prophylactic potential against SARS-CoV-2. Studies have shown that nanobody-Fc fusions can block viral engagement with host cells and significantly reduce viral loads in infected mice, suggesting their use as preventive agents against COVID-19.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Biochemical Research Methods

Computational epitope map of SARS-CoV-2 spike protein

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)

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Article Infectious Diseases

Neutralization of SARS-CoV-2 by highly potent, hyperthermostable, and mutation-tolerant nanobodies

Thomas Guettler et al.

Summary: This study introduces the use of single-domain (VHH) antibodies as an alternative for combating SARS-CoV-2, showing their ability to neutralize the virus, inhibit its infectivity, and tolerate immune-escape mutations. The research also suggests that this approach may simplify vaccine production and adapt to viral escape mutations.

LANCET INFECTIOUS DISEASES (2021)

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Article Chemistry, Physical

Dynamic Profiling of Binding and Allosteric Propensities of the SARS-CoV-2 Spike Protein with Different Classes of Antibodies: Mutational and Perturbation-Based Scanning Reveals the Allosteric Duality of Functionally Adaptable Hotspots

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)

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Article Multidisciplinary Sciences

In vivo monoclonal antibody efficacy against SARS-CoV-2 variant strains

Rita E. Chen et al.

Summary: Cell culture experiments showed reduced or abrogated neutralizing activity of monoclonal antibodies against SARS-CoV-2 variant strains, but low prophylactic doses of antibody combinations protected against infection in vivo without resistance emergence. Higher doses of several monoclonal antibody cocktails also provided protection against viruses with a B.1.351 spike gene in vivo. Many antibody products with Emergency Use Authorization should therefore retain substantial efficacy against prevailing variant strains of SARS-CoV-2.

NATURE (2021)

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Article Multidisciplinary Sciences

Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants

Jianliang Xu et al.

Summary: The study found that camelid nanobodies can effectively circumvent vaccine escape caused by mutations in the novel coronavirus. These nanobodies are able to neutralize SARS-CoV-2 variants through two mechanisms, demonstrating promising potential in preventing COVID-19 mortality when vaccines are compromised.

NATURE (2021)

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Article Chemistry, Multidisciplinary

A glycan gate controls opening of the SARS-CoV-2 spike protein

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.

NATURE CHEMISTRY (2021)

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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)

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Article Multidisciplinary Sciences

SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma

Emanuele Andreano et al.

Summary: Research suggests that SARS-CoV-2 has the potential to generate variants resistant to neutralizing antibodies, and computational modeling predicts that these variants may prevent binding of neutralizing antibodies. Therefore, the development of vaccines and antibodies capable of controlling emerging variants is crucial.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Multidisciplinary Sciences

Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting diverse and conserved epitopes

Dapeng Sun et al.

Summary: Highly potent neutralizing nanobodies (Nbs) targeting the receptor binding domain (RBD) of the SARS-CoV-2 spike protein show effectiveness against circulating variants of concern. Structural analysis of the Nbs provides insights into their high-affinity and broadly neutralizing activity against the virus.

NATURE COMMUNICATIONS (2021)

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Article Cell Biology

One-shot identification of SARS-CoV-2 S RBD escape mutants using yeast screening

Irene M. Francino-Urdaniz et al.

Summary: This study reveals the presence of escape mutants for five nAbs targeting the S receptor binding site, predominantly located on the periphery of the ACE2 recognition site. The research team provides libraries, methods, and software as an openly available community resource to expedite the development of new therapeutic strategies against SARS-CoV-2.

CELL REPORTS (2021)

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Article Biochemistry & Molecular Biology

Neutralization of SARS-CoV-2 by highly potent, hyperthermostable, and mutation-tolerant nanobodies

Thomas Guettler et al.

Summary: Monoclonal anti-SARS-CoV-2 immunoglobulins are effective in treating COVID-19, but their production in mammalian cells is not scalable. This study isolated 45 infection-blocking VHH antibodies from alpaca immune libraries, with one particularly effective VHH antibody capable of neutralizing the virus at low concentrations and showing strong binding to the Spike protein in different conformations. Additionally, the research identified VHH antibodies that can tolerate immune-escape mutations, as well as fold-promoting nanobodies that could simplify vaccine production and adaptation to viral mutations.

EMBO JOURNAL (2021)

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Article Virology

Receptor recognition by novel coronavirus from Wuhan: An analysis based on decade-long structural studies of SARS

Yushun Wan et al.

JOURNAL OF VIROLOGY (2020)

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Article Multidisciplinary Sciences

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

Daniel Wrapp et al.

SCIENCE (2020)

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Article Biochemistry & Molecular Biology

Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2

Qihui Wang et al.

CELL (2020)

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Article Biochemistry & Molecular Biology

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

Alexandra C. Walls et al.

CELL (2020)

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Article Immunology

Characterization of the receptor-binding domain (RBD) of 2019 novel coronavirus: implication for development of RBD protein as a viral attachment inhibitor and vaccine

Wanbo Tai et al.

CELLULAR & MOLECULAR IMMUNOLOGY (2020)

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Article Immunology

Key residues of the receptor binding motif in the spike protein of SARS-CoV-2 that interact with ACE2 and neutralizing antibodies

Chunyan Yi et al.

CELLULAR & MOLECULAR IMMUNOLOGY (2020)

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Article Multidisciplinary Sciences

A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2

Yan Wu et al.

SCIENCE (2020)

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Article Multidisciplinary Sciences

Site-specific glycan analysis of the SARS-CoV-2 spike

Yasunori Watanabe et al.

SCIENCE (2020)

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Article Multidisciplinary Sciences

A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV

Meng Yuan et al.

SCIENCE (2020)

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Article Multidisciplinary Sciences

A human monoclonal antibody blocking SARS-CoV-2 infection

Chunyan Wang et al.

NATURE COMMUNICATIONS (2020)

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Article Multidisciplinary Sciences

Vulnerabilities in coronavirus glycan shields despite extensive glycosylation

Yasunori Watanabe et al.

NATURE COMMUNICATIONS (2020)

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Article Multidisciplinary Sciences

A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2

Rui Shi et al.

NATURE (2020)

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Article Multidisciplinary Sciences

Human neutralizing antibodies elicited by SARS-CoV-2 infection

Bin Ju et al.

NATURE (2020)

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Article Multidisciplinary Sciences

Cross-neutralization ofSARS-CoV-2 by a human monoclonal SARS-CoV antibody

Dora Pinto et al.

NATURE (2020)

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Article Biochemistry & Molecular Biology

Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding

Tyler N. Starr et al.

CELL (2020)

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Article Microbiology

Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike

Jiandong Huo et al.

CELL HOST & MICROBE (2020)

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Article Chemistry, Physical

Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane

Hyeonuk Woo et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2020)

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Article Biochemistry & Molecular Biology

Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy

Shuo Du et al.

CELL (2020)

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Article Biochemistry & Molecular Biology

Controlling the SARS-CoV-2 spike glycoprotein conformation

Rory Henderson et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2020)

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Article Biochemistry & Molecular Biology

A thermostable, closed SARS-CoV-2 spike protein trimer

Xiaoli Xiong et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2020)

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Article Biochemistry & Molecular Biology

Structure-guided covalent stabilization of coronavirus spike glycoprotein trimers in the closed conformation

Matthew McCallum et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2020)

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Article Biochemistry & Molecular Biology

Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2

Jiangdong Huo et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2020)

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Article Multidisciplinary Sciences

A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2

Xiangyang Chi et al.

SCIENCE (2020)

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Article Multidisciplinary Sciences

Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies

Alina Baum et al.

SCIENCE (2020)

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Article Multidisciplinary Sciences

Structure-based design of prefusion-stabilized SARS-CoV-2 spikes

Ching-Lin Hsieh et al.

SCIENCE (2020)

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Article Multidisciplinary Sciences

Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail

Johanna Hansen et al.

SCIENCE (2020)

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Article Multidisciplinary Sciences

Structural basis for neutralization of SARS-CoV-2 and SARS-CoV by a potent therapeutic antibody

Zhe Lv et al.

SCIENCE (2020)

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Article Multidisciplinary Sciences

Distinct conformational states of SARS-CoV-2 spike protein

Yongfei Cai et al.

SCIENCE (2020)

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Article Multidisciplinary Sciences

Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability

Philip J. M. Brouwer et al.

SCIENCE (2020)

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Article Multidisciplinary Sciences

Cryo-EM analysis of the post-fusion structure of the SARS-CoV spike glycoprotein

Xiaoyi Fan et al.

NATURE COMMUNICATIONS (2020)

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Article Chemistry, Physical

Conformational transition of SARS-CoV-2 spike glycoprotein between its closed and open states

Mert Gur et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

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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)

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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)

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Article Multidisciplinary Sciences

SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies

Christopher O. Barnes et al.

NATURE (2020)

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Article Multidisciplinary Sciences

Functional plasticity and evolutionary adaptation of allosteric regulation

Megan Leander et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Article Multidisciplinary Sciences

In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges

Beata Turonova et al.

SCIENCE (2020)

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Article Multidisciplinary Sciences

Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms

M. Alejandra Tortorici et al.

SCIENCE (2020)

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Review Immunology

Structural Basis of SARS-CoV-2 and SARS-CoV Antibody Interactions

Edem Gavor et al.

TRENDS IN IMMUNOLOGY (2020)

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Article Chemistry, Multidisciplinary

Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein

Lorenzo Casalino et al.

ACS CENTRAL SCIENCE (2020)

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Editorial Material Chemistry, Multidisciplinary

Fighting COVID-19 Using Molecular Dynamics Simulations

Pablo R. Arantes et al.

ACS CENTRAL SCIENCE (2020)

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Article Microbiology

Real-Time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles

Maolin Lu et al.

CELL HOST & MICROBE (2020)

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Article Multidisciplinary Sciences

Assessment of software methods for estimating protein-protein relative binding affinities

Tawny R. Gonzalez et al.

PLOS ONE (2020)

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Article Multidisciplinary Sciences

An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike

Michael Schoof et al.

SCIENCE (2020)

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Article Multidisciplinary Sciences

Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2

Yufei Xiang et al.

SCIENCE (2020)

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Article Chemistry, Physical

Critical Sequence Hotspots for Binding of Novel Coronavirus to Angiotensin Converter Enzyme as Evaluated by Molecular Simulations

Mahdi Ghorbani et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2020)

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Article Biochemistry & Molecular Biology

Coevolution, Dynamics and Allostery Conspire in Shaping Cooperative Binding and Signal Transmission of the SARS-CoV-2 Spike Protein with Human Angiotensin-Converting Enzyme 2

Gennady Verkhivker

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

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Article Biochemistry & Molecular Biology

Harnessing Avidity: Quantifying the Entropic and Energetic Effects of Linker Length and Rigidity for Multivalent Binding of Antibodies to HIV-1

Tal Einav et al.

CELL SYSTEMS (2019)

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Article Biochemistry & Molecular Biology

The RCSB protein data bank: integrative view of protein, gene and 3D structural information

Peter W. Rose et al.

NUCLEIC ACIDS RESEARCH (2017)

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Article Biochemistry & Molecular Biology

BindProfX: Assessing Mutation-Induced Binding Affinity Change by Protein Interface Profiles with Pseudo-Counts

Peng Xiong et al.

JOURNAL OF MOLECULAR BIOLOGY (2017)

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Article Biochemistry & Molecular Biology

DynOmics: dynamics of structural proteome and beyond

Hongchun Li et al.

NUCLEIC ACIDS RESEARCH (2017)

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Article Multidisciplinary Sciences

Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion

Alexandra C. Walls et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

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Article Biochemistry & Molecular Biology

3Drefine: an interactive web server for efficient protein structure refinement

Debswapna Bhattacharya et al.

NUCLEIC ACIDS RESEARCH (2016)

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Article Biochemical Research Methods

The anisotropic network model web server at 2015 (ANM 2.0)

Eran Eyal et al.

BIOINFORMATICS (2015)

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Article Chemistry, Physical

A Stochastic Algorithm for the Isobaric-Isothermal Ensemble with Ewald Summations for All Long Range Forces

Michele Di Pierro et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

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Article Pharmacology & Pharmacy

Avidity and positive allosteric modulation/cooperativity act hand in hand to increase the residence time of bivalent receptor ligands

Georges Vauquelin et al.

FUNDAMENTAL & CLINICAL PHARMACOLOGY (2014)

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Article Chemistry, Physical

Stability Mechanisms of Laccase Isoforms using a Modified FoldX Protocol Applicable to Widely Different Proteins

Niels J. Christensen et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

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Article Chemistry, Multidisciplinary

Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories

Panagiotis I. Koukos et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2013)

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Article Biochemistry & Molecular Biology

BeAtMuSiC: prediction of changes in protein-protein binding affinity on mutations

Yves Dehouck et al.

NUCLEIC ACIDS RESEARCH (2013)

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Article Chemistry, Medicinal

Accurate Stabilities of Laccase Mutants Predicted with a Modified FoldX Protocol

Niels J. Christensen et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)

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Article Chemistry, Physical

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone φ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

Robert B. Best et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

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Article Biochemical Research Methods

A graphical interface for the FoldX forcefield

Joost Van Durme et al.

BIOINFORMATICS (2011)

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Review Biophysics

Global Dynamics of Proteins: Bridging Between Structure and Function

Ivet Bahar et al.

ANNUAL REVIEW OF BIOPHYSICS, VOL 39 (2010)

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Article Biochemistry & Molecular Biology

WIWS: a protein structure bioinformatics Web service collection

M. L. Hekkelman et al.

NUCLEIC ACIDS RESEARCH (2010)

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Article Biochemical Research Methods

Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0

Yves Dehouck et al.

BIOINFORMATICS (2009)

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Article Biochemistry & Molecular Biology

Improved prediction of protein side-chain conformations with SCWRL4

Georgii G. Krivov et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)

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Article Biochemistry & Molecular Biology

The stability effects of protein mutations appear to be universally distributed

Nobuhiko Tokuriki et al.

JOURNAL OF MOLECULAR BIOLOGY (2007)

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Article Biochemistry & Molecular Biology

ArchPRED: a template based loop structure prediction server

Narcis Fernandez-Fuentes et al.

NUCLEIC ACIDS RESEARCH (2006)

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Review Chemistry, Multidisciplinary

Scalable molecular dynamics with NAMD

JC Phillips et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)

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Article Biochemistry & Molecular Biology

The FoldX web server: an online force field

J Schymkowitz et al.

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