Vibrational circular dichroism and IR spectral analysis as a test of theoretical conformational modeling for a cyclic hexapeptide

Abstract

A model cyclohexapeptide, cyclo-(Phe-(D)Pro-Gly-Arg-Gly-Asp) was synthesized and its IR and VCD spectra were used as a test of density functional theory (DFT) level predictions of spectral intensities for a peptide with a nonrepeating but partially constricted conformation. Peptide structure and flexibility was estimated by molecular dynamics (MD) simulations and the spectra were simulated using full quantum mechanical (QM) approaches for the complete peptide and for simplified models with truncated side chains. After simulated annealing, the backbone conformation of the ring structure is relatively stable, consisting of a normal beta-turn and a tight loop (no H-bond) which does not vary over short trajectories. Only in quite long MD runs at high temperatures do other conformations appear. MD simulations were carried out for the cyclic peptide in water and in TFE, which match experimental solvents, as well as with and without protonation of the Asp carboxyl group. DFT spectral simulations were made using the annealed structure and were extended to include basis set variation, to determine an optimal computational approach, and solvent simulation with a polarized continuum model (PCM). Stepwise full DFT simulation of spectra was done for various sequences with the same backbone geometry but based on (1) solely Gly residues, (2) Ala substitution except Gly and Pro, and (3) complete sequences with side chains. Additionally, a selection of structures was used to compute IR and VCD spectra with the optimal method to determine structural variation effects. The side chains, especially the Asp-COOH and Arg-NH(2) transitions, had an impact on the computed amide frequencies, IR intensities and VCD pattern. Since experimentally these groups would have little chirality, due to conformational variation, they do not impact the observed VCD spectra. Correcting for frequency shifts, the Ala model for the cyclopeptide gives the clearest representation of the amide VCD. The experimental sign pattern for the amide I' band in D(2)O and also the sharper, more intense amide I VCD band in TFE was seen to some degree in one conformer with Type II' turns, but the data favor a mix of structures.

Vibrational circular-dichroism spectroscopy of homologous cyclic peptides designed to fold into β helices of opposite chirality

“…A complementary technique, vibrational CD ͑VCD͒, uses circularly polarized IR light and provides spectra with detailed "fingerprints" analogous to standard IR spectra. VCD measurements in the amide I and II regions have been widely used to study conformations of small peptides, including small cyclic peptides and turns [28][29][30][31][32] that resemble the peptides analyzed in this work. These measurements can be challenging because VCD bands tend to be weaker than IR absorbance bands by a factor of 10 4 -10 5 ; however, the vibrational transitions probed by VCD are typically more localized to specific chromophores or normal modes and are sensitive to dipole coupling of nearby residues.…”

“…Calculations at the level appropriate for assignments and interpretation of VCD spectra of medium and large peptides are computationally demanding. 29 Even predictions for two-amino-acid ␤ turns vary depending on method, basis set, and choice of solvent model. 31 Therefore, in this work we aim to explore how reference data from model peptides having well-defined conformations can be used to assist in empirical interpretation of results for larger, complex, and heterogeneous peptides.…”

The role of central ion in chiral recognition by taking phenylalanine as an example

“…Therefore, chiral separation and analysis is an important topic in chemistry and biochemistry. A number of approaches have been utilized for chiral analysis, including spectropolarimetry [2] , circular dichroism [3] , high performance liquid chromatography [4] , gas chromatography [5] , capillary electrophoresis [6] . Mass spectrometry (MS) provides a unique method by virtue of high sensitivity, speed, direct stoichiometry information and moreover the ability to study intrinsic properties of the chiral effect by isolating the interacting molecules in the gas phase [7] .…”

VCD studies on cyclic peptides assembled from L‐α‐amino acids and a trans‐2‐aminocyclopentane‐ or trans‐2‐aminocyclohexane carboxylic acid

“…Vibrational circular dichroism (VCD) has become a well‐known area of chiroptical spectroscopy over the past decades23, 24. A wealth of vibrational transitions commonly occurs in the IR spectrum that are associated with a VCD band with a particular sign and intensity.…”

“…In the field of polypeptides and proteins, VCD spectroscopy can be applied for revealing the presence of protein periodic secondary structures such as α‐helix and β‐structure and evaluating their relative contribution26. VCD spectral characteristics of β‐turns in linear and disulfide‐cyclized tetrapeptides and longer natural and model sequences have been studied24, 27, 28. Lovas and coworkers studied the VCD spectra of disulfide bridged Ac‐cyclo‐(Cys‐Xxx‐Yyy‐Cys)‐NH 2 cyclic peptides, where Xxx and Yyy are amino acids, which were previously found to occur in different types of β‐turns preferentially28.…”