Protein-Nucleic Acid Recognition: Statistical Analysis Of Atomic Interactions And Influence Of Dna Structure

We analyzed structural features of 11,038 direct atomic contacts (either
electrostatic, H-bonds, hydrophobic, or other van der Waals interactions)
extracted from 139 protein-DNA and 49 protein-RNA nonhomologous complexes from
the Protein Data Bank (PDB). Globally, H-bonds are the most frequent interactions
(approximately 50%), followed by van der Waals, hydrophobic, and electrostatic
interactions. From the protein viewpoint, hydrophilic amino acids are
over-represented in the interaction databases: Positively charged amino acids
mainly contact nucleic acid phosphate groups but can also interact with base
edges. From the nucleotide point of view, DNA and RNA behave differently: Most
protein-DNA interactions involve phosphate atoms, while protein-RNA interactions
involve more frequently base edge and ribose atoms. The increased participation
of DNA phosphate involves H-bonds rather than salt bridges. A statistical
analysis was performed to find the occurrence of amino acid-nucleotide pairs most
different from chance. These pairs were analyzed individually. Finally, we
studied the conformation of DNA in the interaction sites. Despite the prevalence
of B-DNA in the database, our results suggest that A-DNA is favored in the
interaction sites.