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 sp²O, amino sp³N, ring sp²N, methyl sp³C, and ring sp²C). All alkylureas interact favorably with nucleobase sp²C and sp³C atoms; these interactions become more favorable with an increasing level of alkylation of urea. Interactions with nucleobase sp²O 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 sp³C with nucleobase sp²C, sp³C, sp²N, and sp³N atoms are favorable while amide sp³C–nucleobase sp²O interactions are unfavorable. Strongly favorable interactions of urea with nucleobase sp²O but weakly favorable interactions with nucleobase sp³N indicate that amide sp²N–nucleobase sp²O and nucleobase sp³N–amide sp²O hydrogen bonding (NH···OC) interactions are favorable while amide sp²N–nucleobase sp³N interactions are unfavorable. These favorable amide–nucleobase hydrogen bonding interactions are prevalent in specific protein–nucleotide complexes

Experimental Atom-by-Atom Dissection of Amide–Amide and Amide–Hydrocarbon Interactions in H₂O

Quantitative information about amide interactions in water is needed to understand their contributions to protein folding and amide effects on aqueous processes and to compare with computer simulations. Here we quantify interactions of urea, alkylated ureas, and other amides by osmometry and amide–aromatic hydrocarbon interactions by solubility. Analysis of these data yields strengths of interaction of ureas and naphthalene with amide sp²O, amide sp²N, aliphatic sp³C, and amide and aromatic sp²C unified atoms in water. Interactions of amide sp²O with urea and naphthalene are favorable, while amide sp²O–alkylurea interactions are unfavorable, becoming more unfavorable with increasing alkylation. Hence, amide sp²O–amide sp²N interactions (proposed n−σ* hydrogen bond) and amide sp²O–aromatic sp²C (proposed n−π*) interactions are favorable in water, while amide sp²O–sp³C interactions are unfavorable. Interactions of all ureas with sp³C and amide sp²N are favorable and increase in strength with increasing alkylation, indicating favorable sp³C–amide sp²N and sp³C–sp³C interactions. Naphthalene results show that aromatic sp²C–amide sp²N interactions in water are unfavorable while sp²C–sp³C interactions are favorable. These results allow interactions of amide and hydrocarbon moieties and effects of urea and alkylureas on aqueous processes to be predicted or interpreted in terms of structural information. We predict strengths of favorable urea–benzene and <i>N</i>-methylacetamide interactions from experimental information to compare with simulations and indicate how amounts of hydrocarbon and amide surfaces buried in protein folding and other biopolymer processes and transition states can be determined from analysis of urea and diethylurea effects on equilibrium and rate constants