Interpretation of Synchrotron Radiation Circular Dichroism Spectra of Anionic, Cationic, and Zwitterionic Dialanine Forms

Abstract

Electronic absorption and synchrotron radiation circular dichroism (SRCD) spectra of the anionic, cationic, and zwitterionic forms of L-alanyl-L-alanine (AA) in aqueous solutions were measured and interpreted by molecular dynamics (MD) and ab initio computations. Time-dependent density functional theory (TD DFT) was applied to predict the electronic excited states. The modeling enabled the assessment of the role of molecular conformation, charge, and interaction with the polar environment in the formation of the spectral shapes. Particularly, inclusion of explicit solvent molecules in the computations appeared to be imperative because of the participation of water orbitals in the amide electronic structure. Implicit dielectric continuum solvent models gave inferior results for clusters, especially at low-energy transitions. Because of the dispersion of transition energies, tens of water/AA clusters had to be averaged in order to obtain reasonable spectral shapes with a more realistic inhomogeneous broadening. The modeling explained most of the observed differences, as the anionic and zwitterionic SRCD spectra were similar and significantly different from the cationic spectrum. The greatest deviation between the experimental and theoretical curves observed for the lowest-energy negative anion signal can be explained by the limited precision of the TD DFT method, but also by the complex dynamics of the amine group. The results also indicate that differences in the experimental spectral shapes do not directly correlate with the peptide main-chain conformation. Future peptide and protein conformational studies based on circular dichroic spectroscopy can be reliable only if such effects of molecular dynamics, solvent structure, and polar solvent-solute interactions are taken into account.

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

“…12 Geometries of the peptide with hydrogen-bonded waters were partially optimized in normal mode coordinates. 36,37 Normal modes within -300 and 300 cm -1 were fixed (imaginary frequencies are considered as a negative), while the remaining ones were fully relaxed.…”

“…[4][5][6][7] Additionally, the inhomogeneous band broadening of the Raman and ROA spectral lines of small polar molecules could be recently interpreted in terms of molecular flexibilities. 8,9 As the previous NMR 10 and CD 11,12 studies indicate subtle changes in the L-alanyl-L-alanine (Ala-Ala) geometry upon pH change, in this work, we analyze the variances of the Raman and ROA spectra of the zwitterionic (AAZW), anionic (AA -), and cationic (AA + ) dipeptide ( Figure 1) to relate them to the conformational differences. The 15 N 13 C isotope analogue was synthesized and used for a more reliable assignment of the AAZW vibrational transitions of the backbone modes, whereas the more usual deuteration of the dialanine investigated before 13 enabled classification of the hydrogen stretching vibrations in particular.…”

Charge-Transfer Transitions in the Vacuum-Ultraviolet of Protein Circular Dichroism Spectra

“…Recently, SRCD measurements in combination with ab initio calculations were used to study the influence of solvent molecules on dialanine. 9 The CD spectra of the anionic, cationic, and zwitterionic forms show substantial differences around 210 and 170 nm, the latter information only made accessible by SRCD experiments. Ab initio calculations indicated that the backbone conformation was not the only factor influencing CD spectra but that solvent effects have to be considered.…”

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

“…As mentioned in the introduction, the IR and VCD techniques have not been used for the monitoring of the peptide sign chain conformation so far, but they could resolve the secondary structure of prolinerich peptides. [46][47][48] The ultraviolet techniques are even less local 49 but also sensitive to polyproline secondary structure. 16 However, solid-state and computational studies well-recognized the limited flexibility of this residue a long time ago.…”