Structure and conformational behavior of biopolymers by density functional calculations employing periodic boundary conditions. I. The case of polyglycine, polyalanine, and poly-alpha-aminoisobutyric acid in vacuo.
Fully quantum mechanical calculations exploiting periodic boundary conditions (PBC) have been applied to the study of four different regular structures (alpha- and 3(10)-helix, fully extended and repeated gamma-turns) of the infinite polypeptides of glycine, alanine, and alpha-aminoisobutyric acid (Aib) in vacuo. alpha-Helix is predicted to be the most stable conformer for polyalanine and polyglycine, being stabilized over the 3(10)-helix mainly by more favorable dipole-dipole interactions. Contrary to previous suggestions, steric effects and hydrogen-bond strengths are comparable for both helix structures. 3(10)-Helix is preferred for poly-Aib, since in this case alpha-helix is strongly distorted due to unfavorable intrachain repulsions. Extended structures and repeated gamma-turns are much less stable than helix structures for all of the polypeptides examined, mainly due to the absence of favorable long-range interactions. The optimized geometries are in good agreement with the available experimental data and reveal a remarkable dependence on the nature of the residue forming the polypeptides; at the same time the electronic and structural parameters of each residue strongly depend on the secondary structure of the polypeptides.
Improta
R
R
Dipartimento di Chimica, Università Federico II, Complesso Universitario Monte S. Angelo, Via Cintia, I-80126 Napoli, Italy.
Barone
V
V
Kudin
K N
KN
Scuseria
G E
GE
D000621:Aminoisobutyric Acids / Q000737:chemistry*; D004151:Dipeptides / Q000737:chemistry; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011789:Quantum Theory; D014618:Vacuum
D000621:Aminoisobutyric Acids; D004151:Dipeptides; D010455:Peptides; C100049:2-aminoisobutyric acid; C019529:polyalanine; C011080:polyglycine