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

Desikan, Rajat ; Behera, Amit ; Maiti, Prabal K. ; Ayappa, K. Ganapathy (2021) Using multiscale molecular dynamics simulations to obtain insights into pore forming toxin mechanisms Methods in Enzymology, 649 . pp. 461-502. ISSN 0076-6879

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

Related URL: http://dx.doi.org/10.1016/bs.mie.2021.01.021

Abstract

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:Article
Source:Copyright of this article belongs to Elsevier Science.
ID Code:123937
Deposited On:25 Oct 2021 11:49
Last Modified:25 Oct 2021 11:49

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