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The exploration of the thermodynamics of SNARE complex stability and the automatization of the generation of hybrid topologies

Karnebeek, Benjan (2020) The exploration of the thermodynamics of SNARE complex stability and the automatization of the generation of hybrid topologies. Research Project 1, Biomolecular Sciences.

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Abstract

SNAREs are multimeric protein complexes consisting of four chains, they can enable membrane fusion thus allowing for vesicle trafficking between organelles of a cell. Recently four key residues were discovered by Malmersjö et al. that retard vesicle fusion when phosphorylated or mutated to glutamate but improve vesicle fusion when mutated to alanine. Here the mutations and phosphorylation of the residues is simulated using thermodynamic integration. This reveals that the mutations and phosphorylation affect the free energy of folding of the SNARE complex thus either stabilizing (for mutations to alanine) or destabilizing (for mutations to glutamate or phosphorylation) the complex, thus either promoting or inhibiting SNARE mediation vesicle fusion. In addition a modified version of pmx program called martini-pmx was made. This version can also make hybrid topologies compatible with the Martini 3.0 force field.

Item Type: Thesis (Research Project 1)
Supervisor name: Marrink, S.J. and Vries, A.H. de and Patmanidis, I.
Degree programme: Biomolecular Sciences
Thesis type: Research Project 1
Language: English
Date Deposited: 13 Jul 2020 13:48
Last Modified: 13 Jul 2020 13:48
URI: http://fse.studenttheses.ub.rug.nl/id/eprint/22605

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