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

Area of Science:

• Structural Biology
• Biophysics
• Computational Chemistry

Background:

• Understanding atomic packing in biological macromolecules is crucial for deciphering molecular interactions.
• Standard atomic volumes provide a baseline for assessing packing density in various molecular contexts.

Purpose of the Study:

• To derive standard atomic volumes for double-stranded B-DNA using high-resolution crystal structures.
• To compare DNA atomic packing with that of small organic molecules.
• To investigate the packing efficiency of DNA and protein atoms at protein-DNA interfaces.

Main Methods:

• Utilized crystal structures from the Nucleic Acid Database (NDB) and Cambridge Structural Database (CSD).
• Employed classical Voronoi and Radical Planes methods for atomic volume computation.
• Calculated volume ratios to assess packing efficiency at protein-DNA interfaces.

Main Results:

• Buried atomic groups in double-stranded DNA are more tightly packed than in small organic molecules.
• DNA atoms at protein-DNA interfaces exhibit packing density comparable to B-DNA crystals.
• Protein atoms at interfaces show packing similar to the protein interior.
• Protein-DNA interfaces are more hydrated than protein interiors, with more solvent-occupied cavities.

Conclusions:

• Tightly packed environments involving DNA, protein, and solvent are significant in protein-DNA recognition.
• Shape complementarity measures show weak correlation with atomic packing density.
• The study provides insights into the structural basis of protein-DNA interactions.