A Complete Set of NMR Chemical Shifts and Spin−Spin Coupling Constants forl-Alanyl-l-alanine Zwitterion and Analysis of Its Conformational Behavior

Abstract

With the aid of labeling with stable isotopes ((15)N and (13)C) a complete set of chemical shifts and indirect spin-spin coupling constants was obtained for the zwitterionic form of L-alanyl-L-alanine in aqueous solution. Different sensitivities of the NMR parameters to the molecular geometry were discussed on the basis of comparison with ab initio (DFT) calculated values. An adiabatic two-dimensional vibrational wave function was constructed and used for determination of the main chain torsion angle dispersions and conformational averaging of the NMR shifts and coupling constants. The quantum description of the conformational dynamics based on the density functional theory and a polarizable continuum solvent model agrees reasonably with classical molecular dynamics simulations using explicit solvent. The results consistently evidence the presence of a single form in the aqueous solution with equilibrium main chain torsion angle values (psi = 147 degrees, varphi = -153 degrees), close to that one found previously in an X-ray study. Under normal temperature the torsion angles can vary by about 10 degrees around their equilibrium values, which leads, however, to minor corrections of the NMR parameters only. The main chain heavy atom chemical shifts and spin-spin coupling constants involving the alpha-carbon and hydrogen atoms appear to be most useful for the peptide structural predictions.

l-Alanyl-l-alanine Conformational Changes Induced by pH As Monitored by the Raman Optical Activity Spectra

“…The present results and reasonable agreement between the simulated and experimental ROA and Raman spectra (cf. Figures 3-5) spectra are consistent with the previous works on AAZW 10,12,13,16,27,54 and support the dominance of one backbone conformer in the solution. Attempts to vary the lowestenergy conformation in Table 1 did not bring a convincing improvement of the spectra and are not shown.…”

“…17 Torsional angles and relative energies of the lowest-energy conformations included in this study are summarized in Table 1. As discussed previously for AA, 27 N-acetylalanine-N′-methylamide, 19 and similar dipeptides, 9 conformations of these small molecules significantly differ from canonical peptide secondary structures. The zwitterion AAZW adopts only one conformer in solution.…”

“…26 Details of the synthesis are given elsewhere. 27 Unlabeled L-Ala-L-Ala was purchased from Sigma-Aldrich and used without further purification. Zwitterionic forms for the measurement were obtained by dissolving the peptide in deionized water (pH 6.5, 2.1 mol/L).…”

Comparison of Quantitative Conformer Analyses by Nuclear Magnetic Resonance and Raman Optical Activity Spectra for Model Dipeptides

“…19 The DFT-predicted equilibrium geometries are in a reasonable agreement with the average angles found by the molecular dynamics (MD) computations. The MD angular distributions (Figure 4) for the Pro-Gly and Pro-Ala peptides exhibit similar ψ and main chain torsion angles properties as in the Ala-Ala molecule, 43 which again suggests a limited influence of the side chains on the backbone conformation in this case. The computationally more demanding Amoeba force field was attempted only for the Ala-Pro peptide (bottom of Figure 4); in this case it produced average geometries and dispersion very similar to that obtained by the Amber force field.…”

“…42,43 Indeed, the enthalpies corresponding to the cis-trans isomerization extracted from the NMR data (Table 2) are well below the computational error. 19 The DFT-predicted equilibrium geometries are in a reasonable agreement with the average angles found by the molecular dynamics (MD) computations.…”