"Sweet" Martini 3 - Guidelines for a transferable sugar model in Martini 3

Punt, Mats (2021) "Sweet" Martini 3 - Guidelines for a transferable sugar model in Martini 3. Master's Research Project 1, Biomolecular Sciences.

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Abstract

Carbohydrates (saccharides) play a key role in a large number of biological processes. Precise experimental determination of structure-function relationships of carbohydrate systems through NMR or cryo-EM methods remains problematic. Molecular dynamics (MD) approaches, by use of force fields like Martini, can bridge this gap and help to study complex carbohydrate systems in detail. The original extension of the Martini force field to carbohydrates, released over ten years ago, succesfully reproduced complex properties of saccharides such as the transition between different cellulose allomorphs, the mechanical properties of bacterial peptidoglycan and beta-cyclodextrin mediated cholesterol extraction. However, reports of unphysical aggregation behaviour in i.e. proteins and carbohydrates, colloquially referred to as the "sticky effect", raised questions on the accuracy of carbohydrate interactions in Martini 2. With the recent release of the Martini 3 force field, the underlying interaction matrix has been completely reparameterized, including more interaction levels and size dependent cross-interactions. In this work we propose mapping guidelines for carbohydrates in Martini 3, based on an extensive top down approach. Retaining the building block principle of Martini, we improve on the Martini 2 carbohydrates with a more specific representation of chemical variety and glycosidic linkages and define clear mapping guidelines that can be applied to any carbohydrate of interest.

Item Type:	Thesis (Master's Research Project 1)
Supervisor name:	Marrink, S.J.
Degree programme:	Biomolecular Sciences
Thesis type:	Master's Research Project 1
Language:	English
Date Deposited:	02 Aug 2021 09:45
Last Modified:	02 Aug 2021 09:45
URI:	https://fse.studenttheses.ub.rug.nl/id/eprint/25488

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