Assessing the reliability of density functional methods in the conformational study of polypeptides: the treatment of intraresidue nonbonding interactions.
The role of intraresidue interactions in determining the conformational behavior of polypeptides is analyzed by means of density functional and post-Hartree-Fock computations on the alanine dipeptide analog and other model compounds. Our computations show that the accuracy of current density functionals is sufficient for H-bond, electrostatic, inductive, and short-range repulsive interactions, whereas medium-range attractions between electron-rich atoms and/or bonds are underestimated. This leads, in turn, to an underestimation of the stability of helical structures w.r.t. extended or folded conformers involving H-bonds. Those results could pave the route for devising local ad hoc corrections able to significantly improve structural and dynamic predictions for polypeptides issuing from DFT computations.
Improta
Roberto
R
Dipartimento di Chimica, Università Federico II, Complesso Universitario Monte S. Angelo, Via Cintia, I-80126 Napoli, Italy.
Barone
Vincenzo
V
D000409:Alanine / Q000737:chemistry*; D000465:Algorithms; D004151:Dipeptides / Q000737:chemistry*; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D013816:Thermodynamics
D004151:Dipeptides; D010455:Peptides; D000409:Alanine