Ab Initio Geometry Determinations of Proteins. 1. Crambin

The geometry of crambin, a protein with 46 residues, was determined by ab initio HF/4-21G geometry optimization. The results are compared with the crystal structure of the compound and with HF/4-21G φ,ψ-conformational geometry maps calculated for the model dipeptide N-acetyl-N‘-methylalaninamide. Root-mean-square (rms) deviations between calculated and crystallographic backbone structural parameters are 1.5° for N−C(α)−C‘ and 0.013 and 0.017 A, respectively, for N−C(α) and C(α)−C‘. In the case of N−C(α)−C‘ the rms deviations are small compared to the observed range of values, which is from 118°, confirming a definite conformational dependence of peptide backbone structural parameters on φ and ψ. In contrast, the deviations in bond lengths are of the same magnitude as the overall variations. The considerable nonplanarity of the peptide units found in the crystal structure is well reproduced by the calculations. When the calculated and crystal structures are superimposed, the rms positional deviat...