Amino close packing

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). 

The pH range over which an enzyme undergoes changes in activity can provide a clue to the type of amino acid residue involved (see Table 3-1). A change in activity near pH 7.0, for example, often reflects titration of a His residue. The effects of pH must be interpreted with some caution, however. In the closely packed environment of a protein, the pKa of amino acid... 

The crystal structure of the N-terminal 80 residues of tropomyosin (Brown et al., 2001) contains its first alanine cluster and displays two specific consequences of this motif for the main-chain geometry of the coiled-coil. One is that the coiled-coil in this segment becomes locally narrow, to 8.0 A diameter, as would be expected from alanine s small size. This feature is directly related to the stability of the coiled-coil in a 10 A wide dimeric coiled-coil, a pair of core alanines from the opposite helices would generally leave unfilled spaces in the interior these spaces become smaller as the main chains of the helices approach each other and the core becomes more close-packed. Recent studies of model coiled-coils with identical amino acid compositions, but different arrangements,... 

The (110) surfaces of Au [24], Pt [25] and Ir [26] display (2 x 1) LEED patterns, which are described by missing row reconstructions, in which every other closed-packed atomic row along [110] is missing. The driving force in this case seems to be the formation of (111) microfacets with their lower surface energy [22]. The resulting ID channels have been used as a template for assembling molecular wires , e.g. of the amino acid cysteine [27]. 

The bonds that maintain the tertiary structure of proteins are shown in Figure 19.11. The importance of these bonds becomes clear when we realize that it is the tertiary structure of the protein that defines its biological function. Most of the time, nonpolar amino acids are buried, closely packed, in the interior of a globular protein, out of contact with water. Polar and charged amino acids lie on the surfaces of globular proteins. Globular proteins are extremely compact. The tertiary... 

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