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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Effect of the Graphene Nanosheet on Functions of the Spike Protein in Open and Closed States: Comparison between SARS-CoV-2 Wild Type and the Omicron Variant
TL;DR: In this paper , the effect of the SARS-CoV-2 variant on the nanomaterial-spike protein interaction was investigated by molecular simulations, where the authors took the graphene nanosheet (GN) as the model and investigated its interaction with the spike protein in both wild type (WT) and Omicron.
Posted ContentDOI
Large fluctuations of the fusion intermediate help SARS-CoV-2 capture host cell membranes
TL;DR: In this paper, the authors constructed a full-length model of the CoV-2 FI by extrapolating from known pre-and post-fusion structures and showed that the FI is a remarkably flexible mechanical assembly executing large orientational and extensional fluctuations due to three hinges in the C-terminal base.
Posted ContentDOI
Binding of SARS-CoV-2 fusion peptide to host membranes
TL;DR: In this article, the authors use molecular dynamics simulations to study the two core functions of the SARS-CoV-2 peptide: to attach quickly to cellular membranes and to form an anchor strong enough to withstand the mechanical force during membrane fusion.
Journal ArticleDOI
Towards de novo design of transmembrane α-helical assemblies using structural modelling and molecular dynamics simulation.
Ai Niitsu,Yuji Sugita +1 more
TL;DR: In this paper , two major approaches to designing transmembrane α-helical assemblies, consensus and de novo design, are described and discussed. And the possibility to introduce all-atom molecular dynamics simulations after the existing static modelling and screening of design decoys as an additional step for refinement of the design, which considers membrane protein folding dynamics and interactions with explicit membranes.
Journal ArticleDOI
Effect of Disulfide Bridge on the Binding of SARS-CoV-2 Fusion Peptide to Cell Membrane: A Coarse-Grained Study
Hujun Shen,Zhenhua Wu +1 more
TL;DR: This work indicates that the stable helical structure is crucial for binding the SARS-CoV-2 FP to cell membranes, and the helical stability of FP should have a significant influence on the FP–membrane binding.
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
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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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