Protein packing density

The secondary and tertiary structures of myoglobin and ribonuclease A illustrate the importance of packing in tertiary structures. Secondary structures pack closely to one another and also intercalate with (insert between) extended polypeptide chains. If the sum of the van der Waals volumes of a protein s constituent amino acids is divided by the volume occupied by the protein, packing densities of 0.72 to 0.77 are typically obtained. This means that, even with close packing, approximately 25% of the total volume of a protein is not occupied by protein atoms. Nearly all of this space is in the form of very small cavities. Cavities the size of water molecules or larger do occasionally occur, but they make up only a small fraction of the total protein volume. It is likely that such cavities provide flexibility for proteins and facilitate conformation changes and a wide range of protein dynamics (discussed later). 

Fig. 3.6. Schematic indication of the degree of chain motional restriction in the various shells of lipid surrounding cytochrome oxidase in dimyristoyl phosphatidylcholine complexes. The vertical scale corresponds to the normalized linesplittings in the ESR spectra of the 14-PCSL spin label (Knowles et al., 1979). T is a shared second shell which exists only in regions of high protein packing density (low lipid/protein ratios), where the perturbations from two adjacent proteins overlap (Marsh et al., 1978).

Natural biological membranes consist of lipid bilayers, which typically comprise a complex mixture of phospholipids and sterol, along with embedded or surface associated proteins. The sterol cholesterol is an important component of animal cell membranes, which may consist of up to 50 mol% cholesterol. As cholesterol can significantly modify the bilayer physical properties, such as acyl-chain orientational order, model membranes containing cholesterol have been studied extensively. Spectroscopic and diffraction experiments reveal that cholesterol in a lipid-crystalline bilayer increases the orientational order of the lipid acyl-chains without substantially restricting the mobility of the lipid molecules. Cholesterol thickens a liquid-crystalline bilayer and increases the packing density of lipid acyl-chains in the plane of the bilayer in a way that has been referred to as a condensing effect. 

There are several indications that a crystalline solid is the most appropriate state to model the protein interior (Chothia, 1984). The very fact that protein structures can be determined to high resolution by X-ray diffraction is indicative of the crystalline nature of the protein. Additionally, the packing density and volume properties of amino acid residues in proteins are characteristic of amino acid crystals (Richards, 1974, 1977). In spite of the apparent crystallinity of the protein interior, most model compound studies have investigated either the transfer of compounds from an organic liquid into water (see, for example, Nozaki and Tanford, 1971 Gill et al., 1976 Fauch-ere and Pliska, 1983), or the association of solute molecules in aqueous solution (see, for example, Schellman, 1955 Klotz and Franzen, 1962 Susi et al., 1964 Gill and Noll, 1972). Both these approaches tacitly assume a liquidlike protein interior. 

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