Proteins atomic 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). 

In soluble globular proteins, hydrophilic amino acids tend to be on the exterior of the molecule whereas hydrophobic amino acids are packed in the interior [13]. To quantitatively describe the location of an amino acid in relation to the protein surface, different measures of solvent exposure have been developed. In the present context, the solvent exposure is modeled by the number s of protein atoms that are within a sphere of radius R centered at the position of atom c of amino acid a [5]. If the amino acid is buried in the protein interior, s is large because the surrounding volume is (almost) completely filled by protein atoms. On the other hand, if the amino acid is exposed, part of the volume is occupied by solvent molecules, which results in a smaller s (see Table 11.1 and Figure 11.3). Again, relative frequencies fac(s) and fc(s) are derived from the database and the net potential for solvent exposure is then... 

If the packing density (p) between redox cofactors is known (i.e., the fractional volume of the medium between the cofactors that is within the van der Waals radius of protein atoms), the value of p can be adjusted to reflect a higher or lower effective barrier to electron tunneling to improve the rate estimate [8] ... 

Laskowski RA. Thornton JM. Humblet C. et al. X-SITE use of empirically derived atomic packing preferences to identify favorable interaction regions in the binding sites of proteins. J Mol Biol 1996 259 175-201. 

Voronoi Volumes and the Atomic Packing at Protein-Protein Interfaces... 

The Voronoi volume calculation was also carried out for protein atoms at protein-DNA interfaces in 28 high-resolution structures of protein-DNA complexes by Nadassy et al. (1999). The coordinate files also contain water positions, and volume calculations were performed in the presence of these water molecules. Fifty-seven percent of the interface protein atoms could be included and the V/Vq ratios were found to spread over a narrow range of 0.97-1.04, with a mean of 1.01 (Fig. 5, bottom). Thus, the atomic packing is very similar to that found for protein-protein interfaces. Omitting water molecules from the calculations yielded a broader range (0.94-1.1) and many fewer buried interface atoms. Thus, water molecules once more play a key role in fostering efficient packing at protein-nucleic acid interfaces. 

Atomic packing densities in compact protein molecules higher than that in water... 

The atoms pack closely at the interior of proteins however, there are cavities inside the molecules allowing motion,... 

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