Standard atomic volumes in double-stranded DNA and packing in protein-DNA interfaces

Standard volumes for atoms in double-stranded B-DNA are derived using high resolution crystal structures from the Nucleic Acid Database (NDB) and comp ared with corresponding values derived from crystal structures of small org anic compounds in the Cambridge Structural Database (CSD). Two different me thods are used to compute these volumes: the classical Voronoi method, whic h does not depend on the size of atoms, and the related Radical Planes meth od which does. Results show that atomic groups buried in the interior of do uble-stranded DNA are, on average, more tightly packed than in related smal l molecules in the CSD. The packing efficiency of DNA atoms at the interfac es of 25 high resolution protein-DNA complexes is determined by computing t he ratios between the volumes of interfacial DNA atoms and the correspondin g standard volumes. These ratios are found to be close to unity, indicating that the DNA atoms at protein-DNA interfaces are as closely packed as in c rystals of B-DNA. Analogous volume ratios, computed for buried protein atom s, are also near unity, confirming our earlier conclusions that the packing efficiency of these atoms is similar to that in the protein interior. In a ddition, we examine the number, volume and solvent occupation of cavities l ocated at the protein-DNA interfaces and compared them with those in the pr otein interior. Cavities are found to be ubiquitous in the interfaces as we ll as inside the protein moieties. The frequency of solvent occupation of c avities is however higher in the interfaces, indicating that those are more hydrated than protein interiors. Lastly, we compare our results with those obtained using two different measures of shape complementarity of the anal ysed interfaces, and find that the correlation between our volume ratios an d these measures, as well as between the measures themselves, is weak. Our results indicate that a tightly packed environment made up of DNA, protein and solvent atoms plays a significant role in protein-DNA recognition.