Quantifying Interactions of Nucleobase Atoms with Model Compounds for the Peptide Backbone and Glutamine and Asparagine Side Chains in Water.

Alkylureas display hydrocarbon and amide groups, the primary functional groups of proteins. To obtain the thermodynamic information that is needed to analyze interactions of amides and proteins with nucleobases and nucleic acids, we quantify preferential interactions of alkylureas with nucleobases differing in the amount and composition of water-accessible surface area (ASA) by solubility assays. Using an established additive ASA-based analysis, we interpret these thermodynamic results to determine interactions of each alkylurea with five types of nucleobase unified atoms (carbonyl spO, amino spN, ring spN, methyl spC, and ring spC). All alkylureas interact favorably with nucleobase spC and spC atoms; these interactions become more favorable with an increasing level of alkylation of urea. Interactions with nucleobase spO are most favorable for urea, less favorable for methylurea and ethylurea, and unfavorable for dialkylated ureas. Contributions to overall alkylurea-nucleobase interactions from interactions with each nucleobase atom type are proportional to the ASA of that atom type with proportionality constant (interaction strength) α, as observed previously for urea. Trends in α-values for interactions of alkylureas with nucleobase atom types parallel those for corresponding amide compound atom types, offset because nucleobase α-values are more favorable. Comparisons between ethylated and methylated ureas show interactions of amide compound spC with nucleobase spC, spC, spN, and spN atoms are favorable while amide spC-nucleobase spO interactions are unfavorable. Strongly favorable interactions of urea with nucleobase spO but weakly favorable interactions with nucleobase spN indicate that amide spN-nucleobase spO and nucleobase spN-amide spO hydrogen bonding (NH···O═C) interactions are favorable while amide spN-nucleobase spN interactions are unfavorable. These favorable amide-nucleobase hydrogen bonding interactions are prevalent in specific protein-nucleotide complexes.