scholarly journals Assessing the extent of the structural and dynamic modulation of membrane lipids due to pore forming toxins: insights from molecular dynamics simulations

Soft Matter ◽  
2020 ◽  
Vol 16 (20) ◽  
pp. 4840-4857 ◽  
Author(s):  
Vadhana Varadarajan ◽  
Rajat Desikan ◽  
K. G. Ayappa
Keyword(s):  
Molecular Dynamics ◽  
Plasma Membrane ◽  
Molecular Dynamics Simulations ◽  
Bacterial Infections ◽  
Membrane Lipids ◽  
Dynamic Modulation ◽  
Structure And Dynamics ◽  
Transmembrane Pores ◽  
Dynamics Simulations

Pore forming toxins released during bacterial infections form transmembrane pores disrupting the structure and dynamics of lipids in the plasma membrane.

scholarly journals How does temperature affect the dynamics of SARS-CoV-2 M proteins? Insights from Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Soumya Lipsa Rath ◽  
Madhusmita Tripathy ◽  
Nabanita Mandal
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Membrane Lipids ◽  
Membrane System ◽  
Host Cells ◽  
Coarse Grained ◽  
M Protein ◽  
Effect Of Temperature ◽  
M Proteins ◽  
Dynamics Simulations

Enveloped viruses, in general, have several transmembrane proteins and glycoproteins, which assist the virus in entry and attachment onto the host cells. These proteins also play a significant role in determining the shape and size of the newly formed virus particles. The lipid membrane and the embedded proteins affect each other in non-trivial ways during the course of the viral life cycle. Unravelling the nature of the protein-protein and protein-lipid interactions, under various environmental and physiological conditions, could therefore prove to be crucial in development of therapeutics. Here, we study the M protein of SARS-CoV-2 to understand the effect of temperature on the properties of the protein-membrane system. The membrane embedded dimeric M proteins were studied using atomistic and coarse-grained molecular dynamics simulations at temperatures ranging between 10 and 50 ˚C. While temperature induced fluctuations should be monotonic, we observe a steady rise in the protein dynamics up to 40 ˚C, beyond which it surprisingly reverts back to the low temperature behaviour. Detailed investigation reveals disordering of the membrane lipids in the presence of the protein, which induces additional curvature around the transmembrane region. Coarse-grained simulations indicate temperature dependent aggregation of M protein dimers. Our study clearly indicates that the dynamics of membrane lipids and integral M protein of SARS-CoV-2 enables it to better associate and aggregate only at a certain temperature range (i.e., ~30 to 40 ˚C). This can have important implications in the protein aggregation and subsequent viral budding/fission processes.   

scholarly journals Membrane potential and dynamics in a ternary lipid mixture: insights from molecular dynamics simulations

2018 ◽  
Vol 20 (23) ◽  
pp. 15841-15851 ◽  
Author(s):  
Xubo Lin ◽  
Vinay Nair ◽  
Yong Zhou ◽  
Alemayehu A. Gorfe
Keyword(s):  
Molecular Dynamics ◽  
Membrane Potential ◽  
Molecular Dynamics Simulations ◽  
Transmembrane Potential ◽  
Lipid Mixture ◽  
Structure And Dynamics ◽  
Head Groups ◽  
Acyl Chains ◽  
Dynamics Simulations

Transmembrane potential modulates the structure and dynamics of lipid head-groups and acyl chains.

Structure and dynamics of gold nanoparticles decorated with chitosan–gentamicin conjugates: ReaxFF molecular dynamics simulations to disclose drug delivery

2019 ◽  
Vol 21 (24) ◽  
pp. 13099-13108 ◽  
Author(s):  
Susanna Monti ◽  
Jiya Jose ◽  
Athira Sahajan ◽  
Nandakumar Kalarikkal ◽  
Sabu Thomas
Keyword(s):  
Drug Delivery ◽  
Molecular Dynamics ◽  
Gold Nanoparticles ◽  
Molecular Dynamics Simulations ◽  
Atomic Scale ◽  
Functionalized Gold Nanoparticles ◽  
Structure And Dynamics ◽  
Antibiotic Drug ◽  
Dynamics Simulations

Functionalized gold nanoparticles for antibiotic drug delivery: from the nanoscale to the atomic scale.

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