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Using multiscale molecular dynamics simulations to obtain insights into pore forming toxin mechanisms

Desikan, R and Behera, A and Maiti, PK and Ayappa, KG (2021) Using multiscale molecular dynamics simulations to obtain insights into pore forming toxin mechanisms. [Book Chapter]

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Official URL: https://doi.org/10.1016/bs.mie.2021.01.021


Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the molecular insights gleaned from these techniques on the pore forming pathways of PFTs. In addition to all-atom simulations which are widely used, coarse-grained MARTINI models and structure-based models have also been used to study PFTs. Here, the emphasis is on methods and techniques involved while setting up, monitoring, and evaluating properties from MD simulations of PFTs in a membrane environment. We draw from several case studies to illustrate how MD simulations have provided molecular insights into protein–protein and protein–lipid interactions, lipid dynamics, conformational transitions and structures of both the oligomeric intermediates and assembled pore structures.

Item Type: Book Chapter
Publication: Methods in Enzymology
Publisher: Academic Press Inc.
Additional Information: The copyright for this article belongs to the Academic Press Inc.
Keywords: All-atom; Coarse-grained; Lipid bilayer; MARTINI; Membrane protein; Molecular dynamics simulation; Pore forming toxin; Structure-based model
Department/Centre: Division of Interdisciplinary Sciences > Centre for Biosystems Science and Engineering
Division of Mechanical Sciences > Chemical Engineering
Division of Physical & Mathematical Sciences > Physics
Date Deposited: 25 Oct 2023 12:44
Last Modified: 25 Oct 2023 12:44
URI: https://eprints.iisc.ac.in/id/eprint/82784

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