A quantum-topological analysis of noncovalent interactions in secondary polyalanine structures

The geometric parameters and relative stability of gamma- and beta-loop conformers of oligomers based on alanine were determined by the Kohn-Sham method (the B3LYP/6-31+G** approximation). The three-dimensional architecture of the beta-folded structure and protein alpha-helix was reproduced using Kohn-Sham calculations with periodic boundary conditions. The Bader quantum-topological molecular structure theory was used to reveal and quantitatively characterize noncovalent interatomic interactions in the secondary structures of model peptides under consideration. Earlier unnoticed additional noncovalent interactions stabilizing the structures under consideration were revealed. In beta-loops, these are C-Ha <-O and Ha <-H interactions, and, in antiparallel beta-folded structures, these are weak C-beta-Ha <-H-C-beta interactions between side chains. Additional weak bonding interaction between C=O groups in position i and H-C-beta groups in position i + 3 was revealed for the protein alpha-helix; this interaction is usually ignored in amino acid folding simulations with the use of classic force fields.