Experimentally determined strengths of favorable and unfavorable interactions of amide atoms involved in protein self-assembly in water.

Folding and other protein self-assembly processes are driven by favorable interactions between O, N, and C unified atoms of the polypeptide backbone and side chains. These processes are perturbed by solutes that interact with these atoms differently than water does. Amide NH···O=C hydrogen bonding and various π-system interactions have been better characterized structurally or by simulations than experimentally in water, and unfavorable interactions are relatively uncharacterized. To address this situation, we previously quantified interactions of alkyl ureas with amide and aromatic compounds, relative to interactions with water. Analysis yielded strengths of interaction of each alkylurea with unit areas of different hybridization states of unified O, N, and C atoms of amide and aromatic compounds. Here, by osmometry, we quantify interactions of 10 pairs of amides selected to complete this dataset. An analysis yields intrinsic strengths of six favorable and four unfavorable atom-atom interactions, expressed per unit area of each atom and relative to interactions with water. The most favorable interactions are spO-spC (lone pair-π, presumably -π*), spC-spC (π-π and/or hydrophobic), spO-spN (hydrogen bonding) and spC-spC (CH-π and/or hydrophobic). Interactions of spC with itself (hydrophobic) and with spN are modestly favorable, while spN interactions with spN and with amide/aromatic spC are modestly unfavorable. Amide spO-spO interactions and spO-spC interactions are more unfavorable, indicating the preference of amide spO to interact with water. These intrinsic interaction strengths are used to predict interactions of amides with proteins and chemical effects of amides (including urea, -ethylpyrrolidone [NEP], and polyvinylpyrrolidone [PVP]) on protein stability.