Stretching the Definition of a Lipid Bilayer: Elasticity's Role in Protein and Lipid Organization

The Central Dogma forms the foundation of molecular biology couched in polymer language; all the key players are there — DNA, RNA, protein — or so it would seem. Yet one class of biologically synthesized molecules, crucial for life, is often over looked: lipids. These amphiphilic molecules exhibit a number of strange properties, integral to the cells ability to separate self from non-self in a chemically diverse environment. Lipids self-assemble into two-dimensional bi-layered fluids with aspect ratios of a thousand to one or more, capable of self-healing and bending into extraordinarily complex shapes. Within the cell, membranes allow for numerous chemically-distinct compartments, essential for metabolism, protein assembly, genome management, and cell division. With literally hundreds of different kinds of lipids and proteins interacting on a given membrane, we have much to learn about how membranes regulate the flow of materials into and out of cells. Clearly, molecular level detail is integral to our understanding of these systems, however, on the mesoscopic level membranes exhibit certain mechanical effects that serve to organize lipids and proteins, the study of which forms the bulk of this dissertation. We start by building an elastic model of bilayers, where embedded proteins deform the surrounding membrane and incur a free energy cost. This allows the mechanical attributes of the bilayer to influence the conformation of embedded proteins. We explore this connection in the context of mechanosensation in bacteria, as well as developing methods that allow bilayer mechanics to comment on the structure of classically voltage-gated ion channels. In addition to affecting conformational preferences, these same deformations have a finite length-scale that results in interactions between embedded proteins. Depending on the protein shape, these interactions can be attractive or repulsive, may exert torques on proteins, provide for a mechanism of shape-specific oligomerization, and importantly allow proteins to utilize the bilayer as a generic communicator of conformational information. The effects of these elastic interactions are discussed in the context of mean protein spacing, dimerization, conformational cooperativity, and likely pathways to multi-mer protein assembly, with the bacterial mechanosensitive channel MscL as a structural example. In subsequent chapters, bilayer elasticity is used to shed light on the large-scale organization of lipids themselves. Biological membranes likely have multiple fluid, lipid phases, where sequestration of saturated lipids and cholesterol form lipid domains. We found that formation of domains above a certain critical size induces morphological transitions to a ‘dimpled’ phase which turns on repulsive, elastic interactions that serve to spatially organize domains as well as severely inhibit domain coalescence. This provides a mechanism for the maintenance of lipid lateral heterogeneity on relatively short length-scales and long time scales. We further observed discrete transitions to a ‘budded’ domain morphology and developed a set of interpretive energetic transition rules between flat, dimpled and budded domains. We demonstrate that these morphologies and their attendant transitions lead to a unique form of domain-size-dependent transport in membranes. Further, we employ the mechanics of vesicles to model osmoregulation via channel proteins, and in the setting of conserved surface area and volume to develop a theoretical and experimental framework to study membrane adhesion in the context of the homophilic protein binding.