Packing density, protein structural

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). 

Van der Waals Forces. Van der Waals interactions are of two types one attractive and one repulsive. Attractive van der Waals forces involve interactions among induced dipoles that arise from fluctuations in the electron charge densities of neighboring nonbonded atoms. Such interactions amount to 0.1-0.2 kcal/mol despite their small size, the large number of such interactions that occur when molecules come close together makes such interactions quite significant. Van der Waals forces favor close packing in folded protein structures. 

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. 

After direct high-resolution structural measurements on proteins became practicable, interest in crystalline amino acids decreased, but became renewed in attempts to simulate the distribution of electronic charge density in biopolymers using amino acids and simple peptides as model systems, to derive some transferable parameters and potentials [2-15]. Another research direction involved these systems and their packing patterns to mimic selected folds and interaction patterns of biopolymers. Typical molecular conformations and patterns of hydrogen bonds and packing in the structures of crystalline amino acids have been reviewed [16-19]. Similar analyses were performed for small peptides [18, 20-22]. 

The contribution of van der Waals interactions to the stability of protein structures is most clearly indicated by the packing density of... 

First, it has been estimated that more the medium between the two redox centers is highly packed with atoms, more electron tunneling will be fast and probable. However, from the intramolecular electron transfer and structure deposited in the protein Data bank, Page et al. (1999) found the packing density is statistically identical whether... 

In the 75 protein-protein complexes of Lo Conte et al. (1999), 96% of the interfaces have V/Vq in the range 0.97-1.06. Thus, the packing of atoms buried at protein-protein interfaces is very similar to that of the protein interior. In 36 complexes with X-ray structures at a resolution of 2.5 A and better, the V/Vq ratios calculated in the presence of water molecules were distributed over a narrow range of 0.97-1.03 (Fig. 5, top). Therefore, their interfaces are packed like the protein core, except that water, which is almost entirely excluded from the protein core, makes an important contribution to the packing at protein-protein interfaces. There is one exception to this rule in the sample analyzed by Lo Conte et al. (1999) the complex between cytochrome peroxidase and cytochrome c [PDB code, Iccp (Pelletier and Kraut, 1992)]. Its interface is small and has only a few buried atoms and a large volume ratio (1.07). In contrast, the 19 protease-inhibitor and the 19 antigen-antibody complexes of this sample have mean V/Vq ratios of 1.00 and 1.01, respectively. Thus, unlike 5c and the gap index, the volume ratio indicates that these two types of interfaces are close-packed and shows no difference in their packing density, at least for their buried atoms. 

Richards, F. M. (1974). The interpretation of protein structures Total volume, group volume distributions and packing density./. Mol. Biol. 82, 1-14. 

The crystal structures of protein-DNA complexes reveal the presence of several ordered water molecules at protein-DNA interfaces. Such water molecules may reside in the solvation shells of the protein before their binding to DNA, and they may serve to fill all the gaps arising from imperfect matches of protein and DNA surfaces to maintain a suitable packing density for the system, or they may act as mediators of the protein-DNA recognition process. Some water molecules are also found in the interior cavities of such macromolecules. 

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