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

Proc Natl Acad Sci U S A. 2020 Nov 3;117(44):27339-27345. doi: 10.1073/pnas.2012481117. Epub 2020 Oct 21.


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 sp2O-sp2C (lone pair-π, presumably n-π*), sp2C-sp2C (π-π and/or hydrophobic), sp2O-sp2N (hydrogen bonding) and sp3C-sp2C (CH-π and/or hydrophobic). Interactions of sp3C with itself (hydrophobic) and with sp2N are modestly favorable, while sp2N interactions with sp2N and with amide/aromatic sp2C are modestly unfavorable. Amide sp2O-sp2O interactions and sp2O-sp3C interactions are more unfavorable, indicating the preference of amide sp2O to interact with water. These intrinsic interaction strengths are used to predict interactions of amides with proteins and chemical effects of amides (including urea, N-ethylpyrrolidone [NEP], and polyvinylpyrrolidone [PVP]) on protein stability.

Keywords: additivity; amide atom interactions; aqueous interactions; preferential interactions; thermodynamics.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amides / chemistry*
  • Hydrogen Bonding
  • Hydrophobic and Hydrophilic Interactions
  • Models, Theoretical
  • Nitrogen / chemistry
  • Oxygen / chemistry
  • Protein Stability
  • Proteins / chemistry*
  • Thermodynamics
  • Water / chemistry*


  • Amides
  • Proteins
  • Water
  • Nitrogen
  • Oxygen