Predominant torsional forms adopted by dipeptide conformers in solution: parameters for molecular recognition

The present paper describes the predominant conformational forms adopted by dipeptides in aqueous solution. More than 50 dipeptides were subjected to conformational analysis using SYBYL Random Search. The resultant collections of conformers for individual dipeptides, for small groups with related side chain residues and for large groups of about 50 dipeptides were visualized graphically and analysed using a novel three‐dimensional pseudo‐Ramachandran plot. The distribution of conformers, weighted according to the percentage of each in the total conformer pool, was found to be restricted to nine main combinations of backbone psi (ψ) and phi (ϕ) torsion angles. The preferred ψ values were in sectors A7 (+150° to ±180°), A10 (+60° to +90°) and A4 (−60° to −90°), and these were combined with preferred ϕ values in sectors B12 (−150° to ±180°), B9 (−60° to −90°) and B2 (+30° to +60°). These combinations of ψ and ϕ values are distinct from those found in common secondary structures of proteins. These results show that although dipeptides can each adopt many conformations in solution, each possesses a profile of common conformers that is quantifiable. A similarly weighted distribution of dipeptide conformers according to distance between amino‐terminal nitrogen and carboxyl‐terminal carbon shows how the preferred combinations of backbone torsional angles result in particular N – C geometries for the conformers. This approach gives insight into the important conformational parameters of dipeptides that provide the basis for their molecular recognition as substrates by widely distributed peptide transporters. It offers a basis for the rational design of peptide‐based bioactive compounds able to exploit these transporters for targeting and delivery. Copyright © 2000 European Peptide Society and John Wiley & Sons, Ltd.