Biologically Inspired Structures in Confined Systems

Abstract

Biological structures, whether they are those of a single cellular bacterium or a specialised filtration cell found in a human liver, usually exist in a state of confinement. This confinement can be transient, such as a transit though a protein complex, or permanent, such as the confining effect of an extracellular matrix on an enclosed membrane. There is growing evidence that spatial confinement of biological systems contribute not just to shape and size of a particular structure but also affects the formation, behaviour, evolution, and eventual death of organelles, individual cells, and even tissues. This thesis considers two model examples of confinement that exists in nature. The first is a giant unilamellar vesicle (GUV) composed of DOPC and encapsulated in an agarose hydrogel. The lipid vesicles are encapsulated in agarose in an attempt to mirror various extracellular matrices or the cell wall that surround most cell membranes in nature. The agarose density is varied to understand the effect of confinement and changing the adhesion between the model membrane and ECM. These model membranes were perturbed using osmotic shocks to impose varying volume loss on the vesicles. The in-vitro experiments are corroborated with simulations using a modified limited memory Broyden-Fletcher-Goldfarb-Shanno (LBFGS) energy minimisation algorithm applied to a simulated lipid vesicle. In this investigation, four key parameters are varied, volume, area, external potential and spontaneous curvature. Volume, area, and external potential are identified prior to the in-vitro experiments whilst spontaneous curvature is applied as a result of complex geometries found in-vitro. The second model of confinement is the transit of a human immunodeficiency virus (HIV-1) capsid through the nuclear pore complex, a supramolecular protein complex embedded in the nuclear envelope. Using a similar version of the L-BFGS as the investigation into confined vesicles, the transit of various capsid structures is simulated as it moves through a pore filled with a biomolecular condensate.