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
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The Spread of SARS-CoV-2 Omicron Variant in CALABRIA: A Spatio-Temporal Report of Viral Genome Evolution
Cla Veneziano,Nadia Marascio,Carmela De Marco,Barbara Quaresima,Flavia Biamonte,Enrico Maria Trecarichi,Gianluca Santamaria,Angela Quirino,Daniele Torella,Aldo Quattrone,Giovanni Matera,Carlo Torti,Caterina De Filippo,Francesco Costanzo,Giuseppe Viglietto +14 more
TL;DR: In this article , the authors investigated the evolution of SARS-CoV-2 spread in Calabria, Southern Italy, in 2022, and found that BA.1 disappeared in April 2018, but not in the rest of Italy; recombinant BA.2 appeared later than in other Italian regions.
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SARS-CoV-2 Protein S Fusion Peptide Is Capable of Wrapping Negatively-Charged Phospholipids
TL;DR: In this paper , all-atom molecular dynamics was used to analyse the binding of SARS-CoV-2 fusion peptide to specific phospholipids in model membranes composed of only one phospholine plus cholesterol in the presence of either Na+ or Ca2+.
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Host Cell Membrane Capture by the SARS-CoV-2 Spike Protein Fusion Intermediate
TL;DR: In this paper , the authors constructed a full-length model of the SARS-CoV-2 FI by extrapolating from known pre-and post-fusion structures and showed that the FI was remarkably flexible and executed giant bending and extensional fluctuations due to three hinges in the Cterminal base.
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S2 Subunit of SARS-CoV-2 Spike Protein Induces Domain Fusion in Natural Pulmonary Surfactant Monolayers
TL;DR: Using combined bio-physicochemical assays and atomic force microscopy imaging, it was found that the S2 subunit inhibited the biophysical properties of the surfactant and induced microdomain fusion in the Surfactant monolayer.
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Computational methods to study enveloped viral entry.
TL;DR: A review of recent progress in the field can be found in this paper, with an emphasis on the insight that has been gained using a mixture of coarse-grained and atomic-resolution molecular dynamics simulations.
References
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Scikit-learn: Machine Learning in Python
Fabian Pedregosa,Gaël Varoquaux,Alexandre Gramfort,Vincent Michel,Bertrand Thirion,Olivier Grisel,Mathieu Blondel,Peter Prettenhofer,Ron Weiss,Vincent Dubourg,Jake Vanderplas,Alexandre Passos,David Cournapeau,Matthieu Brucher,Matthieu Perrot,Edouard Duchesnay +15 more
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VMD: Visual molecular dynamics
TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.
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Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China
Chaolin Huang,Yeming Wang,Xingwang Li,Lili Ren,Jianping Zhao,Yi Hu,Li Zhang,Guohui Fan,Jiuyang Xu,Xiaoying Gu,Zhenshun Cheng,Ting Yu,Jia'an Xia,Yuan Wei,Wenjuan Wu,Xuelei Xie,Wen Yin,Li Hui,Min Liu,Yan Xiao,Hong Gao,Li Guo,Jungang Xie,Guang-Fa Wang,Rongmeng Jiang,Zhancheng Gao,Qi Jin,Jianwei Wang,Bin Cao +28 more
TL;DR: The epidemiological, clinical, laboratory, and radiological characteristics and treatment and clinical outcomes of patients with laboratory-confirmed 2019-nCoV infection in Wuhan, China, were reported.
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Comparison of simple potential functions for simulating liquid water
TL;DR: In this article, the authors compared the Bernal Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P potential functions for liquid water in the NPT ensemble at 25°C and 1 atm.
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Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems
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