Predictions of protein backbone bond distances and angles from first principles

Abstract

Using φ(NC α) ψ(C αC′) conformational geometry maps of N-acetyl- N′-methylalanine amide obtained from ab initio calculations, a simple procedure has been developed that allows one to model the backbone bond distances and angles of proteins as functions of the φ and ψ torsional angles. For bond angles, comparisons with protein crystal structures can be made, and calculated conformational variations in bond distances (several hundredths of an Å) are more precise than the current resolution of experimental techniques. For the important backbone parameter NC αC′, the accuracy of the calculations is found to be comparable with that of high resolution protein crystallography. Further improvements are possible by applying empirical corrections. For example, the dipeptide derived modeled values of N C αC′ are consistently ≈ 2–3 ° above the values found in helical regions of oligopeptides and proteins. The procedure promises to be useful in many practical applications, for example in peptide and protein modeling and in the refinement of protein crystal data.