Ab initio geometry determinations of proteins: 1: crambin

Abstract

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 phi, psi-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 degrees for N-C(alpha)-C' and 0.013 and 0.017 Angstrom, respectively, for N-C(alpha) and C(alpha)-C'. In the case of N-C(alpha)-C' the rms deviations are small compared to the observed range of values, which is from <108 degrees to >118 degrees, confirming a definite conformational dependence of peptide backbone structural parameters on phi and psi. 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 deviation is 0.6 Angstrom for the heavy atom framework and 0.4 Angstrom for the backbone chain. The phenomenon of helix compression is confirmed that is found in elongated helical chains compared to isolated residues or smaller oligomers.