The folding landscape of the Trp-cage miniprotein : effects of perturbations on the structural and thermodynamic ensembles

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Authors
English, Charles A.
Issue Date
2014-12
Type
Electronic thesis
Thesis
Language
ENG
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Physics
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Abstract
According to the protein folding funnel theory, proteins reach their folded state by navigating a free energy landscape and must overcome any barriers and avoid any traps that may exist. However, the factors that influence the characteristics of the landscape remain poorly characterized. In this thesis, two variants of the Trp-cage mini-protein are simulated using replica-exchange molecular dynamics in order to explore the effects of changes to the protein sequence, such as charge states and mutations, to the protein folding funnel landscape. The effects of different charge states as well as stabilizing mutations on the folding energy landscape are explored. It is found that stabilizing mutations could prevent the Trp-cage from denaturing at high pressures while the addition of charges radically alters the kinetics and significantly lengthens the equilibration time of the simulations.
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December 2014
School of Science
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Rensselaer Polytechnic Institute, Troy, NY
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