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Modelling the kinetics of amyloid fibril nucleation

Cabriolu, Raffaela (2012) Modelling the kinetics of amyloid fibril nucleation. PhD thesis, University of Leeds.

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Abstract

A kinetic theory has been developed within the framework of preexisting nucleation theory and applied, for the first time, to investigate the one-step formation of amyloid fibrils. Atomistic Nucleation Theory (ANT) for fibrils, in particular, has been successfully applied to model real peptides and proteins, in order to investigate at the molecular level the nucleation of amyloid fibrils from a homogeneous solution. Kinetic parameters predicted by the theory, such as the nucleation rates, have been compared successfully to the results of experiments. The present theoretical study has shown that variations in solubility are the primary origin of the changes in the nucleation rates between a protein and its point-mutations. The same ANT approach allows the analysis of the fibril size distribution, whose results, once again, are consistent with experimental observations. In the last stage of the investigation, computer simulations have been carried out to test selected assumptions underlying the theory. For the first time, the nucleation of strongly anisotropic systems has been investigated using kinetic Monte Carlo (KMC) simulations. Novel and unexpected features, never discussed before in either experiments or simulations studies, have been revealed by the simulations. Although obtained within the study of amyloid fibrils nucleation, these last results are of general validity, providing useful insight on the nucleation of all systems whose molecules interact via strongly anisotropic forces.

Item Type: Thesis (PhD)
ISBN: 978-0-85731-263-1
Academic Units: The University of Leeds > Faculty of Maths and Physical Sciences (Leeds) > School of Physics and Astronomy (Leeds)
Identification Number/EthosID: uk.bl.ethos.566329
Depositing User: Repository Administrator
Date Deposited: 08 Feb 2013 10:36
Last Modified: 07 Mar 2014 11:24
URI: http://etheses.whiterose.ac.uk/id/eprint/3349

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