chapter  4
Nanoscale Imaging and Modeling
Pages 22

As we saw in the previous chapter, organization of the genome into the information-dense, yet accessible DNA molecule is critical to life, for which in Chapter 1 we used the working definition of “an entropy partitioning system.” This chapter examines some of the structures that cells use to spatially partition their internal structures such as tubulin, structures that cells uses to maintain their boundaries such as the cell membrane, as well as structures that allow cells to maintain their spatial distribution among other cells such as collagen. 4.1 The Structures of Entropy PartitioningIn this chapter, we use atomic force microscopy as lens through which we can study nanoscopic structures such as collagen

fibrils, microtubules, and liposomes. These three were selected as model systems because they may be regarded as quasi-static mechanical structures that are responsible for maintaining spatial relationships among cells and subcellular components. All three of them are produced by metabolic processes and are thus relied upon by living systems to maintain a spatial organization among individual cells (collagen), material gradients (polymerized tubulin), or entropy and concentration gradients (cell membranes). Thus, the information inherent in the spatial position and orientation of all of the molecular subunits (amino acids and phospholipids) of each of these three structures is inherent to allowing a living system to maintain a large entropy gradient, DS via relatively little information content, I, implying a large a, which as we argued in Section 1.4.1 is preferable for survival.Of particular interest is the relationship between the tertiary structure of individual proteins and their mechanical properties. 4.1.1 CollagenCollagen, the most ubiquitous protein in mammals (Ricard-Blum, 2011), appears to have been “searching” genomic space looking for a structure that is capable of binding to itself in either a triple helix with cleaved N and C termini, or in afibrillar structures. With at least 38 genes in the human genome (Myllyharju and Kivirikko, 2001; Baronas-Lowell et al., 2003), and its prevalence on a global mass basis, its central role in maintaining multicellular life cannot be understated. More recently, its role in maintaining the structural organization of “lower” organisms such as hydra (Dansky and Johnson, 1986; Shimizu et al., 2008) and cyanobacteria (Layton et al., 2008; Price, 2013; Price and Anandan, 2013) as well as other prokaryotes (Caswell et al., 2008) has been of interest. The precise singular path (if in fact there is one) by which these prokaryotes came to contain and express collagens is not known, and the pathways by which their expression is regulated is far from well understood. However, one could imagine constructing a cost-benefit function for the expression of collagen (or any other protein for that matter), using the theories of Darwin and Dawkins

as guiding principles (Zeiger and Layton, 2008). Some of collagen’s roles are highlighted in Table 4.1. For a more exhaustive list of collagen’s multifaceted roles, see Layton (2003a). Table 4.1 A few key mechanical/structural proteins and their locations and roles within cells Protein Location Tissue RoleActin cytoskeleton all cells except nematode sperm compression bearingtension bearingCollagen type I extracellular bone, ligament, cornea, nerve, skin maintenance of tensile force; maintenance of compressive force if

calcifiedCollagen type II extracellular cartilage maintenance of compressive forceElastin extracellular arteries, lungs, skin, bladder, cartilage long-range force interactionsLamin nucleus all dna binding; nuclear pore interactionsSpectrin sub-cellular membrane erythrocytes shear bearingTubulin nucleus, axons all, esp neurons compression bearing, transportTo maintain multicellularity, an extracellular matrix (ECM) structure such as cellulose and collagen (Fig. 4.1) is necessary. Without an ECM, whose primary role is to maintain spatial organization among cells, other physical pathways, including chemical, electrical, and thermal networks among and between cells of a given organism or colony, would not be maintained and the organism would quickly disintegrate.As we have seen in the preceding chapter, there are also a great number of roles for structural mechanics within individual cells and indeed within individual nuclei. Revealing the molecular events of cell growth is critical to obtaining a deeper understanding

of tissue and organ development, injury response, and for tissue engineering applications. Central to this is the need to understand the mechanical interactions between the cytoskeleton and the cell membrane and how these interactions affect the overall growth mechanics of cells. We will visit this topic in detail in Chapter 5.