Experimentally determined strengths of favorable and unfavorable interactions of amide atoms involved in protein self-assembly in water
Xian Cheng, Irina A. Shkel, Kevin O’Connor, M. Thomas Record
Abstract
Significance Quantitative information about strengths of amide nitrogen−amide oxygen hydrogen bonds and π-system and hydrophobic interactions involving amide-context sp 2 and/or sp 3 carbons is needed to assess their contributions to specificity and stability of protein folds and assemblies in water, as well as to predict or interpret how urea and other amides interact with proteins and affect protein processes. Here we obtain this information from thermodynamic measurements of interactions between amide compounds in water and an analysis that determines intrinsic strengths of atom−atom interactions, relative to water and per unit area of each atom type present. These findings allow prediction or interpretation of effects of any amide on protein processes from structure, and may be useful to analyze protein interfaces.