Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins.
BACKGROUND
There is no consensus in the literature about how the deepest portions of protein structures are packed. Using an improved Voronoi procedure, we calculate reference packing densities for different regions in the protein interior. Furthermore, we want to clarify where cavities are located.


RESULTS
Sets of reference packing densities are provided for regions in proteins that differ in their distance to the surface and to internal cavities, supplementing previous data. Packing in the protein interior is tight but generally inhomogeneous. There are about 4.4 cavities per 100 amino acids in protein structures, they occur in all regions, most frequently in a depth of 2.5-3.6 A underneath the Connolly surface. However, the deepest protein regions have a lower mean packing density than circumjacent regions, because more contacts to cavities occur in the core.
Calculation software and detailed packing data are available on request.
Berlin Center of Genome Based Bioinformatics (BCB), Humboldt University, Institute of Biochemistry at the Charite, Monbijoustr. 2, 10117 Berlin, Germany.
Kristian
K
Rother
Robert
R
Preissner
Andrean
A
Goede
Cornelius
C
Frömmel
D000595:Amino Acid Sequence; D016880:Anisotropy; D001665:Binding Sites; D022081:Cell Surface Extensions; D030562:Databases, Protein; D004735:Energy Transfer; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000145:classification*
D011506:Proteins