Liquid NMA: A surprisingly realistic model for hydrogen bonding motifs in proteins

Abstract

The structure of liquid N-methylacetamide is examined using a combination of classical and ab initio molecular dynamics. Polymeric hydrogen bonded (N-H⋯OC) chain motifs having complex topologies emerge as the dominant structural features. Interchain associations, reminiscent of β-sheets in proteins, are also evident and may be stabilized by improper (methyl-donated) hydrogen bonds. Both ab initio and classical simulations lead to a consistent picture of local structure, including the presence of close contacts between oxygen and methyl hydrogen atoms. Liquid NMA, therefore, exhibits a surprisingly complex structure, and possesses two clear bonding motifs relevant to the stability of protein secondary structure. © 2005 Elsevier B.V. All rights reserved.