Ab initio-based exciton model of amide I vibrations in peptides: Definition, conformational dependence, and transferability

Abstract

Various aspects of the ab initio-based parametrization of an exciton model of amide I vibrations in peptides are discussed. Adopting "glycine dipeptide" (Ac-Gly-NHCH3) as a simple building-block model that describes the vibrational interaction between two peptide units, we perform comprehensive quantum-chemical calculations to investigate the effect and importance of the level of theory, the choice of local coordinates, and the localization method. A solvent continuum model description turns out important to obtain planar CONH peptide units when a full geometry optimization (which is necessary to obtain the correct frequencies) is performed. To study the conformational dependence of the amide I vibrations, we calculate (phi,psi) maps of the local-mode frequencies and couplings. Performing conformational averages of the (phi,psi) maps with respect to the most important peptide conformational states in solution (alpha, beta, P(II), and C5), we discuss the relation between these measurable quantities and the corresponding conformation of the peptide. Finally, the transferability of these maps to dipeptides with hydrophilic and hydrophobic side chains as well as to tripeptides with charged end groups is investigated.

Optimization of Model Parameters for Describing the Amide I Spectrum of a Large Set of Proteins

“…These maps display the overall characteristic form of maps published in previous studies 24,[58][59][60] by construction.…”

“…24,[58][59][60] The shift of the intrinsic frequency is then described using two maps parametrized with respect to the dihedral angles, which are used to evaluate the influence of the local conformation before and after the oscillator…”

“…68 The coupling between covalently bonded neighbors in the polypeptide chain is therefore often described using parametrized values from ab initio coupling maps for dipeptides. 24,60,67,[69][70][71][72][73][74] Here, spline interpolation in the DFT/ B3LYP map of Stock and co-workers was used. 73 Computational Details…”

“…Gorbunov et al 59 have, however, published shift maps both for dipeptides in solvent and gas phase environment that show very different magnitudes of shift, but are very similar in shape. In a solvated large protein, the local environment is not well represented by either case, but should be somewhere in between.…”

Two-dimensional vibrational lineshapes of amide III, II, I and A bands in a helical peptide

“…They also calculated the amide I couplings between non-neighboring amide units using the transition dipole coupling mechanism (TDC). Neighboring amide I maps have subsequently been developed [23,18] based on normal mode calculations of GLDP at higher computational levels (MP2 and DFT) by employing the Hessian reconstruction. Non-neighboring couplings were calculated by the interaction of vibration-induced partial charges determined by normal mode analysis of NMA [18].…”