The Effects of Pulsed Electric Field On The Interaction Between SARS-Cov-2 And Human ACE2: Y505 Is A Key Target

Abstract A novel coronavirus has rapidly spread to almost every country in the world, causing over 233 million confirmed cases of coronavirus disease 2019 (COVID-19) and over 209,761,242 deaths by late September 2021. Binding the receptor binding domain (RBD) to the host cell surface receptor protein, angiotensin converter enzyme (ACE2), is a key step in virus infection. In this study, we applied a pulsed electric field to the RBD/ACE2 complex based on molecular dynamics simulation and demonstrated that the electric field affects the structure and binding affinity of the complex. Additionally, residue Y505 is the crucial medium for the effects of electric field on the complex. Overall, these results may help apply an external electric field to virus suppression.

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Critical Sequence Hot-spots for Binding of nCOV-2019 to ACE2 as Evaluated by Molecular Simulations

10.1101/2020.06.27.175448 ◽

2020 ◽

Author(s):

Mahdi Ghorbani ◽

Bernard R. Brooks ◽

Jeffery B. Klauda

Keyword(s):

Md Simulations ◽

Host Cells ◽

Cell Surface Receptor ◽

Receptor Protein ◽

Structural Mechanism ◽

The World ◽

Surface Receptor ◽

Escape Mutants ◽

The Stability ◽

Novel Coronavirus

AbstractThe novel coronavirus (nCOV-2019) outbreak has put the world on edge, causing millions of cases and hundreds of thousands of deaths all around the world, as of June 2020, let alone the societal and economic impacts of the crisis. The spike protein of nCOV-2019 resides on the virion’s surface mediating coronavirus entry into host cells by binding its receptor binding domain (RBD) to the host cell surface receptor protein, angiotensin converter enzyme (ACE2). Our goal is to provide a detailed structural mechanism of how nCOV-2019 recognizes and establishes contacts with ACE2 and its difference with an earlier coronavirus SARS-COV in 2002 via extensive molecular dynamics (MD) simulations. Numerous mutations have been identified in the RBD of nCOV-2019 strains isolated from humans in different parts of the world. In this study, we investigated the effect of these mutations as well as other Ala-scanning mutations on the stability of RBD/ACE2 complex. It is found that most of the naturally-occurring mutations to the RBD either strengthen or have the same binding affinity to ACE2 as the wild-type nCOV-2019. This may have implications for high human-to-human transmission of coronavirus in regions where these mutations have been found as well as any vaccine design endeavors since these mutations could act as antibody escape mutants. Furthermore, in-silico Ala-scanning and long-timescale MD simulations, highlight the crucial role of the residues at the interface of RBD and ACE2 that may be used as potential pharmacophores for any drug development endeavors. From an evolutional perspective, this study also identifies how the virus has evolved from its predecessor SARS-COV and how it could further evolve to become more infectious.

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SARS-CoV-2 Spike Glycoprotein Receptor Binding Domain is Subject to Negative Selection with Predicted Positive Selection Mutations

10.1101/2020.05.04.077842 ◽

2020 ◽

Cited By ~ 3

Author(s):

You Li ◽

Ye Wang ◽

Yaping Qiu ◽

Zhen Gong ◽

Lei Deng ◽

...

Keyword(s):

Negative Selection ◽

Hot Spot ◽

Cell Surface Receptor ◽

The Public ◽

Downstream Effects ◽

Surface Receptor ◽

Host Cell Surface ◽

Novel Coronavirus ◽

Virus Strains ◽

Transmission Ability

AbstractCOVID-19 is a highly contagious disease caused by a novel coronavirus SARS-CoV-2. The interaction between SARS-CoV-2 spike protein and the host cell surface receptor ACE2 is responsible for mediating SARS-CoV-2 infection. By analyzing the spike-hACE2 interacting surface, we predicted many hot spot residues that make major contributions to the binding affinity. Mutations on most of these residues are likely to be deleterious, leading to less infectious virus strains that may suffer from negative selection. Meanwhile, several residues with mostly advantageous mutations have been predicted. It is more probable that mutations on these residues increase the transmission ability of the virus by enhancing spike-hACE2 interaction. So far, only a limited number of mutations has been reported in this region. However, the list of hot spot residues with predicted downstream effects from this study can still serve as a tracking list for SARS-CoV-2 evolution studies. Coincidentally, one advantageous mutation, p.476G>S, started to surge in the last couple of weeks based on the data submitted to the public domain, indicating that virus strains with increased transmission ability may have already spread.

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Identification of the Cellular Receptor of Clostridium spiroforme Toxin

Infection and Immunity ◽

10.1128/iai.06378-11 ◽

2012 ◽

Vol 80 (4) ◽

pp. 1418-1423 ◽

Cited By ~ 43

Author(s):

Panagiotis Papatheodorou ◽

Claudia Wilczek ◽

Thilo Nölke ◽

Gregor Guttenberg ◽

Daniel Hornuss ◽

...

Keyword(s):

Host Cell ◽

Cell Receptor ◽

Cell Surface Receptor ◽

Target Cells ◽

Content Type ◽

Recombinant Production ◽

Host Cell Receptor ◽

Surface Receptor ◽

Microscopic Studies ◽

Host Cell Surface

ABSTRACTClostridium spiroformeproduces the binary actin-ADP-ribosylating toxin CST (C. spiroformetoxin), which has been proposed to be responsible for diarrhea, enterocolitis, and eventually death, especially in rabbits. Here we report on the recombinant production of the enzyme component (CSTa) and the binding component (CSTb) ofC. spiroformetoxin inBacillus megaterium. By using the recombinant toxin components, we show that CST enters target cells via the lipolysis-stimulated lipoprotein receptor (LSR), which has been recently identified as the host cell receptor of the binary toxinsClostridium difficiletransferase (CDT) andClostridium perfringensiota toxin. Microscopic studies revealed that CST, but not the relatedClostridium botulinumC2 toxin, colocalized with LSR during toxin uptake and traffic to endosomal compartments. Our findings indicate that CST shares LSR withC. difficileCDT andC. perfringensiota toxin as a host cell surface receptor.

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The Cell-Specific Phenotype of the Polymorphic vacA Midregion Is Independent of the Appearance of the Cell Surface Receptor Protein Tyrosine Phosphatase β

Infection and Immunity ◽

10.1128/iai.74.1.49-55.2006 ◽

2006 ◽

Vol 74 (1) ◽

pp. 49-55 ◽

Cited By ~ 15

Author(s):

David A. G. Skibinski ◽

Christophe Genisset ◽

Silvia Barone ◽

John L. Telford

Keyword(s):

Cell Surface ◽

Cell Lines ◽

Protein Tyrosine Phosphatase ◽

Tyrosine Phosphatase ◽

Cell Surface Receptor ◽

Receptor Protein ◽

Protein Tyrosine ◽

Amino Acid Region ◽

Receptor Protein Tyrosine Phosphatase ◽

Surface Receptor

ABSTRACT There are two alleles, m1 and m2, of the midregion of the vacuolating cytotoxin gene (vacA) of Helicobacter pylori which code for toxins with different cell specificities. Here we describe the construction of five chimeric strains in which regions of vacA were exchanged between the two genotypes. By analyzing the toxicity of these strains for HeLa and RK13 cells we have confirmed that a 148-amino-acid region determines the phenotypic differences between the two forms of the protein and that this entire region is important for cytotoxicity. Furthermore, we have used our chimeric strains to investigate whether variations in the midregion of VacA have an effect on phorbol 12-myristate 13-acetate (PMA)-induced VacA sensitivity in HL-60 cells. The PMA-induced VacA sensitivity of HL-60 cells has been previously associated with the appearance of the cell surface receptor protein tyrosine phosphatase beta (RPTPβ). Our data indicate that both the m1 and m2 forms of VacA are able to utilize RPTPβ, and the cell-specific phenotype of the midregion is independent of the presence of RPTPβ. It appears that another as-yet-unidentified receptor exists in HL-60 cells that accounts for the m2 phenotype in this cell line. Also, by studying the effect of PMA on levels of RPTPβ in other cell lines and toxicity of VacA in these cell lines we have shown that RPTPβ does not play a major role in the vacuolation of HeLa cells.

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Receptor Binding Domain (RBD) Structural Susceptibility in the SARS-CoV-2 Virus Spike Protein Exposed to a Pulsed Electric Field

Journal of Nuclear Physics Material Sciences Radiation and Applications ◽

10.15415/jnp.2021.82023 ◽

2021 ◽

Vol 8 (2) ◽

pp. 177-182

Author(s):

D. Osorio-González ◽

V. J. Muñiz-Orozco ◽

C. P. González ◽

M. Fuentes-Acosta ◽

J. Mulia-Rodríguez ◽

...

Keyword(s):

Electric Field ◽

Receptor Binding ◽

Conformational Changes ◽

In Silico Analysis ◽

Pulsed Electric Field ◽

Binding Domain ◽

Chemical Components ◽

Receptor Binding Domain ◽

Viral Inhibition ◽

Starting Point

SARS-CoV-2 is responsible for causing the Coronavirus disease 2019 (COVID-19) pandemic, which has so far infected more than thirty million people and caused almost a million deaths. For this reason, it has been a priority to stop the transmission of the outbreak through preventive measures, such as surface disinfection, and to establish bases for the design of an effective disinfection technique without chemical components. In this study, we performed in silico analysis to identify the conformational alterations of the SARS-CoV-2 Spike Receptor Binding Domain (RBD) caused by the effect of a pulsed electric field at two different intensities. We found that both stimuli, especially the one with the highest angular frequency and amplitude, modified the electrical charge distribution in the RBD surface and the number of hydrogen bonds. Moreover, the secondary structure was significantly affected, with a decrease of the structured regions, particularly the regions with residues involved in recognizing and interacting with the receptor ACE2. Since many regions suffered conformational changes, we calculated RMSF and ΔRMSF to identify the regions and residues with larger fluctuations and higher flexibility. We found that regions conformed by 353-372, 453-464, and 470-490 amino acid residues fluctuate the most, where the first is considered a therapeutic target, and the last has alreadybeen characterized for its flexibility. Our results indicate that a pulsed electric field can cause loss of stability in the Spike-RBD, and we were able to identify the vulnerable sites to be used as a starting point for the development of viral inhibition or inactivation mechanisms.

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Hydroxyzine inhibits SARS-CoV-2 Spike protein binding to ACE2 in a qualitative in vitro assay

10.1101/2021.01.04.424792 ◽

2021 ◽

Author(s):

Maria Dolores Rivas ◽

Jose Maria Rafael Saponi-Cortes ◽

Jose Zamorano

Keyword(s):

Public Health Problem ◽

In Vitro Assay ◽

Host Cells ◽

Cell Surface Receptor ◽

Spike Protein ◽

Major Public Health Problem ◽

Receptor Binding Domain ◽

Vitro Assay ◽

Surface Receptor

AbstractCOVID-19 currently represents a major public health problem. Multiple efforts are being performed to control this disease. Vaccinations are already in progress. However, no effective treatments have been found so far. The disease is caused by the SARS-CoV-2 coronavirus that through the Spike protein interacts with its cell surface receptor ACE2 to enter into the host cells. Therefore, compounds able to block this interaction may help to stop disease progression. In this study, we have analyzed the effect of compounds reported to interact and modify the activity of ACE2 on the binding of the Spike protein. Among the compounds tested, we found that hydroxyzine could inhibit the binding of the receptor-binding domain of Spike protein to ACE2 in a qualitative in vitro assay. This finding supports the reported clinical data showing the benefits of hydroxyzine on COVID-19 patients, raising the need for further investigation into its effectiveness in the treatment of COVID-19 given its well-characterized medical properties and affordable cost.

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The Bacteriophage T7 Virion Undergoes Extensive Structural Remodeling During Infection

Science ◽

10.1126/science.1231887 ◽

2013 ◽

Vol 339 (6119) ◽

pp. 576-579 ◽

Cited By ~ 134

Author(s):

Bo Hu ◽

William Margolin ◽

Ian J. Molineux ◽

Jun Liu

Keyword(s):

Conformational Changes ◽

Molecular Mechanisms ◽

Electron Tomography ◽

Cell Surface Receptor ◽

Dna Ejection ◽

Phage Tail ◽

Cryo Electron Tomography ◽

Surface Receptor ◽

Host Cell Surface ◽

Tail Fibers

Adsorption and genome ejection are fundamental to the bacteriophage life cycle, yet their molecular mechanisms are not well understood. We used cryo–electron tomography to capture T7 virions at successive stages of infection ofEscherichia coliminicells at ~4-nm resolution. The six phage tail fibers were folded against the capsid, extending and orienting symmetrically only after productive adsorption to the host cell surface. Receptor binding by the tail triggered conformational changes resulting in the insertion of an extended tail, which functions as the DNA ejection conduit into the cell cytoplasm. After ejection, the extended phage tail collapsed or disassembled, which allowed resealing of the infected cell membrane. These structural studies provide a detailed series of intermediates during phage infection.

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Structure and Mechanism of a Coreceptor for Infection by a Pathogenic Feline Retrovirus

Journal of Virology ◽

10.1128/jvi.77.4.2717-2729.2003 ◽

2003 ◽

Vol 77 (4) ◽

pp. 2717-2729 ◽

Cited By ~ 31

Author(s):

Anna L. Barnett ◽

David L. Wensel ◽

Weihua Li ◽

Deborah Fass ◽

James M. Cunningham

Keyword(s):

Virus Entry ◽

Leukemia Virus ◽

Competitive Inhibitor ◽

Feline Leukemia Virus ◽

Cell Surface Receptor ◽

Receptor Binding Domain ◽

Couple Interaction ◽

X Ray ◽

X Ray Crystallography ◽

Surface Receptor

ABSTRACT Infection of T lymphocytes by the cytopathic retrovirus feline leukemia virus subgroup T (FeLV-T) requires FeLIX, a cellular coreceptor that is encoded by an endogenous provirus and closely resembles the receptor-binding domain (RBD) of feline leukemia virus subgroup B (FeLV-B). We determined the structure of FeLV-B RBD, which has FeLIX activity, to a 2.5-Å resolution by X-ray crystallography. The structure of the receptor-specific subdomain of this glycoprotein differs dramatically from that of Friend murine leukemia virus (Fr-MLV), which binds a different cell surface receptor. Remarkably, we find that Fr-MLV RBD also activates FeLV-T infection of cells expressing the Fr-MLV receptor and that FeLV-B RBD is a competitive inhibitor of infection under these conditions. These studies suggest that FeLV-T infection relies on the following property of mammalian leukemia virus RBDs: the ability to couple interaction with one of a variety of receptors to the activation of a conserved membrane fusion mechanism. A comparison of the FeLV-B and Fr-MLV RBD structures illustrates how receptor-specific regions are linked to conserved elements critical for postbinding events in virus entry.

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