Protein idealized shapes

Figure 2-7 Some idealized shapes that a 34.5 kDa protein molecule of 300 amino acids might assume.

Freely suspended liquid droplets are characterized by their shape determined by surface tension leading to ideally spherical shape and smooth surface at the subnanometer scale. These properties suggest liquid droplets as optical resonators with extremely high quality factors, limited by material absorption. Liquid microdroplets have found a wide range of applications for cavity-enhanced spectroscopy and in analytical chemistry, where small volumes and a container-free environment is required for example for protein crystallization investigations. This chapter reviews the basic physics and technical implementations of light-matter interactions in liquid-droplet optical cavities. 

Altered thermodynamic activity of proteins in solution arises when unreactive (or inert) macromolecules are added to a solution and occupy more than a few percent of total solution volume. Terms such as unreactive , "background, or inert are used to emphasize that the added protein need not exhibit and direct binding interaction with the protein of interest. Instead, the consequences have more to do with molecular crowding, and approximate theoretical models show that this effect depends on the shapes and sizes of the macromolecules. Thus, biological fluids are anything but ideal or dilute solutions. 

Let us now examine the assumptions underljdng the Oncley treatment. First, thermodynamically V is defined as the increment of the volume of the solution per unit mass of the solute added and therefore is not identical with Fsp of the solute. These two quantities may be equal in magnitude if and only if the system is an ideal solution, that is, there is no solute-solvent interaction whatsoever present. To eliminate one unknown Fsp in Eq. (14) by introducing F we have at the same time added another uncertain term w into the equation. Thus this treatment offers at most a rough estimate of the shape of proteins for a chosen model, a prolate or an oblate ellipsoid. Furthermore the estimated p value corresponds only to the hydrated particle, which is slightly different from that of the unhydrated particle unless the bound water is so distributed throughout the protein molecule that it does not change its axial ratio because of hydration. 

Studies of lipid mobility have shown that the molecules close to membrane proteins are more disordered than those lipids further removed. In a lipid bilayer with variation in lateral disorder, the proteins should therefore be expected to go into positions of highest disorder. Thus, there is a driving force for proteins to locate in the "holes" in the bilayer structure, which are surroimded by maximally curved membrane. There is also a lateral packing pressure to adopt the protein according to the average hydrocarbon chain direction. Ideally, the proteins filling the "hole" of the lipid bilayer should be wedge-shaped (see Fig. 5.7). 

The above-mentioned Human rhinovirus (the cause of common colds) represents an ideal model system for this purpose because it exists in a large variety of different so-called serotypes. All of them have the same microscopic shape, i.e. they are almost spherical with 30 nm diameter, but they differ in the chemical structure of the proteins constituting the respective re-... 

---