The disordered- and ordered-state structures of κ-carrageenan : an X-ray scattering, molecular dynamics, and density-functional theory study : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Physics at Massey University, Palmerston North, New Zealand
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Date
2022
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Massey University
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Abstract
κ-carrageenan is a biopolymer extracted from marine algae. It exists in aqueous solution,
at high temperatures and/or low salt concentrations as a ‘disordered-state’,
and at low temperatures and in the presence of certain salts as an ‘ordered-state’.
The transition between disordered- and ordered-states involves molecular structural
changes, which are essential to its interesting viscoelastic properties that are routinely
exploited in a plethora of applications. Despite this, the molecular conformations of the
disordered- and ordered-states, as well as the details of the transitional pathway connecting
them, remain a source of contention. While decades of research have amassed a
vast trove of information on the disorder-order transition, an atomistic understanding
of the structure in solution has remained elusive. This study takes advantages of recent
advances in computational capabilities in order to simulate κ-carrageenan solutions
on length scales of ∼10 nm over μs time scales, and thus develop atomistic models
of the disordered- and ordered-states. Both models are used to calculate wide-angle
X-ray scattering profiles, and these are subsequently validated by comparison to data
obtained at a synchrotron facility. The models will be further explored using density functional
theory to calculate their expected optical rotation behaviour, which finds
that the formation of double-helices from single chains is able to explain the increase
in optical rotation measured experimentally when transitioning from the disordered to
ordered-state. Structural analysis of both experimentally-verified models find the
disordered-state to have a significant amount of residual helical secondary-structure,
whereas the ordered-state is mostly double-helical. Crucially, simulations show that
the ordered-state arises spontaneously from the so-called disordered-state at a rate
dependant on salt concentration, without prior uni-molecular changes. The findings
of this research are the most detailed model of the disorder-order transition to-date,
and demonstrate that the existing paradigm of a ‘coil-to-helix’ transition is in need of
revision.
Description
Listed in 2023 Dean's List of Exceptional Theses
Keywords
Biopolymers, Structure, Marine algae, Order-disorder models, X-rays, Scattering, Density functionals, Dean's List of Exceptional Theses