Molecular orbital calculations on the conformation of polypeptides and proteins: VII. Refined calculations on the alanyl residue

Abstract

Our previous quantum-mechanical calculations on the stable conformations of the alanyl residue have been refined by the use of minimization and statistical procedures. A refined conformational energy map has been constructed by allowing variations in the values of the side-chain rotational angle χ 1. For the principal regions of stability a supplementary minimization of φ, Ψ and χ 1 enables a precise positioning of the energy minima. A probability map has also been constructed, clearly indicating that some conformations corresponding to energy minima nevertheless have a low probability of occurrence. In particular, the computations indicate a much greater probability for the seven-membered hydrogen bonded H′-7 ( C 7 eq ) form of the model dipeptide studied than for its seven-membered hydrogen bonded H-7 ( C 7 ax form, in spite of comparable energies. A comparison between the theoretical predictions and the observed conformations of 144 alanyl residues in eight globular proteins shows a satisfactory agreement. Such is also the case for a similar comparison for the valyl, leucyl and isoleucyl residues. The distribution of the electronic charges and the values of the dipole moments are presented for the most stable conformations of the alanyl residue.