Binding mode of SARS-CoV-2 fusion peptide to human cellular membrane.
TLDR
In this article, the authors used an array of molecular dynamics simulations that take advantage of the highly mobile membrane mimetic model to investigate the interaction of the SARS-CoV2 FP with a lipid bilayer representing mammalian cellular membranes at an atomic level and to characterize the membrane-bound form of the peptide.About:
This article is published in Biophysical Journal.The article was published on 2021-03-04 and is currently open access. It has received 28 citations till now. The article focuses on the topics: Host cell membrane & Lipid bilayer fusion.read more
Citations
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Ca2+-dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide.
TL;DR: In this article, the authors predicted the preferred positions of Ca2+ binding to the SARS-CoV-2-FP, the role of ca2+ ions in mediating peptide-membrane interactions, and the preferred mode of insertion of the Ca2-bound SARS CoV2-2FP, and consequent effects on the lipid bilayer from extensive atomistic molecular dynamics simulations and trajectory analyses.
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Could metabolomics drive the fate of COVID-19 pandemic? A narrative review on lights and shadows.
Michele Mussap,Vassilios Fanos +1 more
TL;DR: In this paper, a limited number of metabolomics-and lipidomics-based clinical studies in COVID-19 patients have been published and are discussed in this review, where remarkable alterations in the lipid and amino acid metabolism depict the molecular phenotype of subjects infected by SARS-CoV-2.
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Binding of SARS-CoV-2 Fusion Peptide to Host Endosome and Plasma Membrane.
TL;DR: In this paper, the SARS-CoV-2 virus fuses its viral envelope with cellular membranes of its human host and forms an anchor strong enough to withstand the mechanical force during membrane fusion.
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Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion.
TL;DR: In this paper, an all-atom model with simplified energetics was used to perform thousands of simulations in which the protein transitions between the prefusion and post-fusion conformations.
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COVID-19 and Neurodegenerative Diseases: Prion-Like Spread and Long-Term Consequences.
TL;DR: It is hypothesized that people with neurodegenerative diseases, Parkinson's disease, and aged people are at higher risk of getting the COVID-19 than normal adults and that the risk of having the infection increases with dementia and that infected people with severe symptoms could develop dementia as a long-term consequence.
References
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CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.
Kenno Vanommeslaeghe,Elizabeth Hatcher,Chayan Acharya,Sibsankar Kundu,Shijun Zhong,Jihyun Shim,Eva Darian,Olgun Guvench,Pedro E. M. Lopes,Igor Vorobyov,Alexander D. MacKerell +10 more
TL;DR: An extension of the CHARMM force field to drug‐like molecules is presented, making it possible to perform “all‐CHARMM” simulations on drug‐target interactions thereby extending the utility ofCHARMM force fields to medicinally relevant systems.
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CHARMM-GUI: a web-based graphical user interface for CHARMM.
TL;DR: The CHARMM-GUI as mentioned in this paper is a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM.
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Constant pressure molecular dynamics algorithms
TL;DR: In this paper, a modularly invariant equations of motion are derived that generate the isothermal-isobaric ensemble as their phase space averages, and the resulting methods are tested on two problems, a particle in a one-dimensional periodic potential and a spherical model of C60 in the solid/fluid phase.
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Constant pressure molecular dynamics simulation: The Langevin piston method
TL;DR: In this paper, a new method for performing molecular dynamics simulations under constant pressure is presented, which is based on the extended system formalism introduced by Andersen, the deterministic equations of motion for the piston degree of freedom are replaced by a Langevin equation; a suitable choice of collision frequency then eliminates the unphysical "ringing" of the volume associated with the piston mass.
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Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus.
TL;DR: These analyses provide insights into the receptor usage, cell entry, host cell infectivity and animal origin of 2019-nCoV and may help epidemic surveillance and preventive measures against 2019- nCoV.