Understanding ice recrystallisation inhibitors via molecular dynamics simulations
Ice recrystallisation (IR), i.e. the growth and ripening of small ice crystals into larger ones is a spontaneously driven process and occurs during the freeze-thaw cycle of a substance containing water molecules. In the field of cryobiology, IR is of particular concern as the growth or larger ice crystals exposes biological samples to potential cryoinjuries. Current strategies for mitigating IR damage is to use cryoprotectants (CPAs), but these are far from ideal needing high concentrations, are time-consuming to remove post-thaw, and have potential cytotoxicity associated with them. Ice recrystallisation inhibitors (IRIs) prevent further crystal ripening and could be a viable alternative to CPAs. Nature has already provided some of the blueprints in creating IRI molecules in the form of antifreeze (glyco) proteins (AF(G)Ps) but whilst extremely successful at IRI activity within the host organism, these are unfortunately not transferable for in vitro, or indeed in vivo use. Thus there is currently active research to find (bio)mimetic alternatives. Our experimental collaborators at the University of Warwick, led by Prof. Gibson, have shown that the PVA polymer, a small cyclic peptide, and the amino acid alanine are all able to confer IRI activity. Despite this remarkable progress in finding (bio)mimetic alternatives, there is still a major gap in understanding exactly how they prevent IR. This is clearly a blindspot which needs to be addressed. The bulk of this thesis is therefore dedicated to finding how PVA, cyclic peptide and alanine exhibit IRI activity at the molecular level, using molecular dynamics simulations. Our aim is to understand why certain molecules are IRI active, as well as assess whether there is an overarching design rule which governs their macroscopic behaviour. Our simulations are unique as they explicitly consider the interaction of an inhibitor at the interface of a dynamically growing ice crystal. We consider the role of conformation, functional groups and thermodynamic driving forces on IRI activity. This approach provides new insights into the IRI mechanism of small (bio)mimetic molecules which challenge several longheld assumptions about the probable mode of inhibition. The work therefore represents a novel contribution to the field and will help in inform the rational design of next-generation IRIs.
http://webcat.warwick.ac.uk/record=b3926291
https://wrap.warwick.ac.uk/178886/
https://wrap.warwick.ac.uk/178886/1/WRAP_Theses_Bachtiger_2023.pdf