Amide isomerization pathways II: Tracing geometrical prerequisites of acid-catalyzed amide <i>cis</i> – <i>trans</i> isomerization in globular proteins

Abstract

Although the ribosome primarily synthesizes peptide bonds in a trans conformation, native proteins contain cis amide bonds despite the high activation energy required for spontaneous cis–trans isomerization. We recently proposed a non-enzyme-catalyzed reaction pathway in which a nearby Asp/Glu carboxyl side chain, assisted by one or more water molecules, facilitates the O-protonation of the amide bond, whose proton is subsequently transferred to Namide, eliminating the energy barrier for C–N bond rotation and enabling isomerization. In this study, we performed molecular dynamics simulations on cyclase FamC1, a protein containing a cis peptide bond adjacent to an Asp side chain. Our analysis identified favorable orientations of the carboxyl side chain and surrounding water molecules, satisfying the geometric criteria for the key steps of the isomerization mechanism. Statistical analysis of PDB structures revealed that a carboxyl group is frequently found near Xxx–nonPro peptide bonds, supporting the feasibility of this cis–trans isomerization pathway.