AB-INITIO CONFORMATIONAL-ANALYSIS OF THE MODEL TRIPEPTIDE N-FORMYL-L-ALANYL-L-ALANINE AMIDE

The ab initio conformational energy minima of the model tripeptide N-f ormyl-L-alanyl-L-alanine amide (ALA-ALA) were determined by ab initio RHF/4-21G and RHF/6-31G gradient geometry refinement. For the current investigation, 11 664 RHF/4-21G structures were optimized, representi ng grid points in the four-dimensional (phi(1), psi(1), phi(2), psi(2) ) conformational space, which were constructed in 40 degrees increment s along the outer torsions phi(1) and psi(2) and in 30 degrees increme nts along the inner torsions psi(1) and phi(2) of ALA-ALA. Two new ene rgy minima, previously not reported, are described. The positions of t he RHF/6-31G energy minima in phi,psi-space can differ significantly from the corresponding RHF/4-21G locations, and both sets are not clus tered in the centers but on the fringes of the most populated regions of phi,psi-space in protein crystal structures. Thus, the torsion angl es of the ab initio energy minima are not those of the typical substru ctures of proteins: the most stable helices are not alpha(R), and the torsion angles of the most stable bend forms are not those most freque ntly encountered in protein bends. Limitations of the dipeptide approx imation are explored, illustrating how the conformational energies of an amino acid residue depend on the state of its neighbor.