Structural insights into the Middle East respiratory syndrome coronavirus 4a protein and its dsRNA binding mechanism

Batool, Maria; Shah, Masaud; Patra, Mahesh Chandra; Yesudhas, Dhanusha; Choi, Sangdun

doi:10.1038/s41598-017-11736-6

Cited by 27 publications

(25 citation statements)

References 73 publications

(64 reference statements)

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“…which shows the high structural similarity. 4,8,9 Experimental binding affinity measurements using Surface Plasmon Resonance (SPR) have shown that nCOV-3 fold higher affinity than SARS-COV binding to ACE2. 7 Based on the sequence similarity between RBD of nCOV-2019 and SARS-COV and also the tight binding between RBD of nCOV-2019 and ACE2, it is most probable that nCOV-2019 uses this receptor on human cells to gain entry into the body.…”

Section: Introductionmentioning

confidence: 99%

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

Ghorbani

Brooks

Klauda

2020

Preprint

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The 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 naturallyoccurring 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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Section: Introductionmentioning

confidence: 99%

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

Ghorbani

Brooks

Klauda

2020

Preprint

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“…These data, along with the genetic link observed in yeast, suggest that ORF4a and SIRT1 may have a functional connection without direct binding and that there is an additional node of regulation between the two proteins, which is under investigation. This work adds SIRT1 to the list of host factors that mediate MERS-CoV replication such as stress granule formation and host innate immune machinery ( 9 – 12 ). The magnitude of inhibition when those factors are affected is ∼1 log, demonstrating that, as seen in SIRT1, host machinery interacts with various virus replication steps to potentially hinder replication.…”

Section: Discussionmentioning

confidence: 99%

“…One such protein, produced by MERS-CoV, is ORF4a. This accessory protein has been shown in vitro to bind double-stranded RNA and to disrupt the innate immune sensing pathways of RIG-I and MDA5 to suppress the interferon response ( 7 – 9 ). Additionally, ORF4a has been found to inhibit the PKR and stress granule response in cells ( 10 – 12 ), further interfering with cellular function to promote viral infection.…”

Section: Introductionmentioning

confidence: 99%

A Yeast Suppressor Screen Used To Identify Mammalian SIRT1 as a Proviral Factor for Middle East Respiratory Syndrome Coronavirus Replication

Weston

Matthews

Lent

et al. 2019

J Virol

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Viral proteins must intimately interact with the host cell machinery during virus replication. Here, we used the yeast Saccharomyces cerevisiae as a system to identify novel functional interactions between viral proteins and eukaryotic cells. Our work demonstrates that when the Middle East respiratory syndrome coronavirus (MERS-CoV) ORF4a accessory gene is expressed in yeast it causes a slow-growth phenotype. ORF4a has been characterized as an interferon antagonist in mammalian cells, and yet yeast lack an interferon system, suggesting further interactions between ORF4a and eukaryotic cells. Using the slow-growth phenotype as a reporter of ORF4a function, we utilized the yeast knockout library collection to perform a suppressor screen where we identified the YDL042C/SIR2 yeast gene as a suppressor of ORF4a function. The mammalian homologue of SIR2 is SIRT1, an NAD-dependent histone deacetylase. We found that when SIRT1 was inhibited by either chemical or genetic manipulation, there was reduced MERS-CoV replication, suggesting that SIRT1 is a proviral factor for MERS-CoV. Moreover, ORF4a inhibited SIRT1-mediated modulation of NF-B signaling, demonstrating a functional link between ORF4a and SIRT1 in mammalian cells. Overall, the data presented here demonstrate the utility of yeast studies for identifying genetic interactions between viral proteins and eukaryotic cells. We also demonstrate for the first time that SIRT1 is a proviral factor for MERS-CoV replication and that ORF4a has a role in modulating its activity in cells. IMPORTANCE Middle East respiratory syndrome coronavirus (MERS-CoV) initially emerged in 2012 and has since been responsible for over 2,300 infections, with a case fatality ratio of approximately 35%. We have used the highly characterized model system of Saccharomyces cerevisiae to investigate novel functional interactions between viral proteins and eukaryotic cells that may provide new avenues for antiviral intervention. We identify a functional link between the MERS-CoV ORF4a proteins and the YDL042C/SIR2 yeast gene. The mammalian homologue of SIR2 is SIRT1, an NAD-dependent histone deacetylase. We demonstrate for the first time that SIRT1 is a proviral factor for MERS-CoV replication and that ORF4a has a role in modulating its activity in mammalian cells.

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“…66 ORF4a's protein can mask viral dsRNA to play a role in immune evasion, including type 1 IFN and protein kinase R-mediated antiviral stress responses. 67 MERS-CoV NSP13 is a full-length coronavirus helicase that contains multiple domains, including an N-terminal Cys/His rich domain with three zinc atoms, a beta-barrel domain and a C-terminal superfamily (SF) 1 helicase (SF1) core with two RecA-like subdomains. This protein might interfere with the nonsensemediated mRNA decay pathway to avoid degradation of viral RNA.…”

Section: Epidemiological Analysis and Symptoms Of Sars Mers And Cormentioning

confidence: 99%

Overview of lethal human coronaviruses

Chen

Tian

et al. 2020

Sig Transduct Target Ther

251

236

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Coronavirus infections of multiple origins have spread to date worldwide, causing severe respiratory diseases. Seven coronaviruses that infect humans have been identified: HCoV-229E, HCoV-OC43, HCoV-NL63, HCoV-HKU1, SARS-CoV, MERS-CoV, and SARS-CoV-2. Among them, SARS-CoV and MERS-CoV caused outbreaks in 2002 and 2012, respectively. SARS-CoV-2 (COVID-19) is the most recently discovered. It has created a severe worldwide outbreak beginning in late 2019, leading to date to over 4 million cases globally. Viruses are genetically simple, yet highly diverse. However, the recent outbreaks of SARS-CoV and MERS-CoV, and the ongoing outbreak of SARS-CoV-2, indicate that there remains a long way to go to identify and develop specific therapeutic treatments. Only after gaining a better understanding of their pathogenic mechanisms can we minimize viral pandemics. This paper mainly focuses on SARS-CoV, MERS-CoV, and SARS-CoV-2. Here, recent studies are summarized and reviewed, with a focus on virus-host interactions, vaccine-based and drug-targeted therapies, and the development of new approaches for clinical diagnosis and treatment.

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Structural insights into the Middle East respiratory syndrome coronavirus 4a protein and its dsRNA binding mechanism

Cited by 27 publications

References 73 publications

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

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

A Yeast Suppressor Screen Used To Identify Mammalian SIRT1 as a Proviral Factor for Middle East Respiratory Syndrome Coronavirus Replication

Overview of lethal human coronaviruses

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