Vibrational CD of the amide II band in some model polypeptides and proteins

A Computational Protocol for Vibrational Circular Dichroism Spectra of Cyclic Oligopeptides

Cyclic peptides are a promising class of compounds for next-generation antibiotics as they may provide new ways of limiting antibiotic resistance development. Although their cyclic structure will introduce some rigidity, their conformational space is large and they usually have multiple chiral centers that give rise to a wide range of possible stereoisomers. Chiroptical spectroscopies such as vibrational circular dichroism (VCD) are used to assign stereochemistry and discriminate enantiomers of chiral molecules, often in combination with electronic structure methods. The reliable determination of the absolute configuration of cyclic peptides will require robust computational methods than can identify all significant conformers and their relative population and reliably assign their stereochemistry from their chiroptical spectra by comparison with ab initio calculated spectra. We here present a computational protocol for the accurate calculation of the VCD spectra of a series of flexible cyclic oligopeptides. The protocol builds on the Conformer-Rotamer Ensemble Sampling Tool (CREST) developed by Grimme and co-workers ( Phys. Chem. Chem. Phys. 2020, 22, 7169-7192 and J. Chem. Theory. Comput. 2019, 15, 2847-2862) in combination with postoptimizations using B3LYP and moderately sized basis sets. Our recommended computational protocol for the computation of VCD spectra of cyclic oligopeptides consists of three steps: (1) conformational sampling with CREST and tight-binding density functional theory (xTB); (2) energy ranking based on single-point energy calculations as well as geometry optimization and VCD calculations of conformers that are within 2.5 kcal/mol of the most stable conformer using B3LYP/6-31+G*/CPCM; and (3) VCD spectra generation based on Boltzmann weighting with Gibbs free energies. Our protocol provides a feasible basis for generating VCD spectra also for larger cyclic peptides of biological/pharmaceutical interest and can thus be used to investigate promising compounds for next-generation antibiotics.

Evaluation of formation and proportion of secondary structure in γ-polyglutamic acid by terahertz time-domain spectroscopy

The study of secondary structure is essential for understanding peptides and proteins. Here, we measured the terahertz (THz) spectra of γ-polyglutamic acid (γ-PGA) dominated by α-helix and random coil (RC) respectively. The α-helix has two absorption peaks in the THz region, but no absorption peak is observed in the RC conformation. We believe this is because the hydrogen bonding effect leads to a higher orientation in the helix-dominated γ-PGA. At lower pH, the absorption intensity of γ-PGA increases with the induction time. Similar changes were obtained in the Fourier infrared spectroscopy (FTIR). Through the correlation analysis of THz and IR spectroscopy, it is found that the characteristic peak at 1.2 THz can be used as a sensitive indicator of the intermediate conformation of the α-helical structure. In addition, the transformation of α-helix-RC conformation is related to the peak intensity at 1.99 THz (R² = 0.991), which preliminarily indicates that terahertz time-domain spectroscopy (THz-TDS) has the potential to become a new effective method for characterizing and evaluating secondary structure.

Site-specific structure of Aβ(25-35) peptide: isotope-assisted vibrational circular dichroism study

We investigated the site-specific local structure of an amyloid peptide, NH(2)-GSNKGAIIGLM-COOH [Aβ(25-35)], one of the active fragments of amyloid β peptide that is known to be responsible for Alzheimer's disease, in the fibrillar aggregated state. Isotope-assisted infrared vibrational circular dichroism (VCD) and absorption (VA) spectroscopy were used for the parent Aβ(25-35) peptide, along with doubly (13)C labeled peptides at the carbonyl groups of residues 29 (Gly) and 30 (Ala) [Aβ(25-35:(13)C-29/30)] and at the carbonyl groups of residues 33 (Gly) and 34 (Leu) [Aβ(25-35:(13)C-33/34)]. The present results confirm that Aβ(25-35) peptide fibrils adopt a β-sheet structure and isotopic dilution experiments suggest a parallel β-sheet structure. The isotopic shifts suggest that the microenvironment of residues 29 (Gly) and 30 (Ala) could be different from that of residues 33 (Gly) and 34 (Leu). An unusual enhancement for the amide II' VCD intensities of Aβ(25-35:(13)C-29/30) and Aβ(25-35:(13)C-33/34) peptide fibrils, considered to originate from inter-strand coupling, was found for the first time. The structural information reported in this manuscript has important implications in understanding the role of this peptide in the development of Alzheimer's disease.

Bioinspired interactions studied by vibrational circular dichroism

Vibrational circular dichroism (VCD) spectra are reliable indicators of the spatial structure of chiral molecules. The specific and characteristic feature of vibrational spectroscopy, and therefore also of VCD, where the energy of some vibrational modes is predominantly focused to a specific part of the molecule, enables monitoring both the structure of the molecule dissolved in different solvents and under different physicochemical conditions and molecular interactions. This minireview deals with recent contributions covering structural information on the bioinspired interactions obtained by means of VCD, especially in the following areas: interaction of DNA with biomolecules and biogenic metals, guanine tetramers and quadruplexes, biointeractions of bile pigments, and polypeptide and protein interactions with other biomolecules.

Structures of plant viruses from vibrational circular dichroism

Vibrational circular dichroism (VCD) spectra in the amide I and II regions have been measured for viruses for the first time. VCD spectra were recorded for films prepared from aqueous buffer solutions and also for solutions using D2O buffers at pH 8. Investigations of four filamentous plant viruses, Tobacco mosaic virus (TMV), Papaya mosaic virus, Narcissus mosaic virus (NMV) and Potato virus X (PVX), as well as a deletion mutant of PVX, are described in this paper. The film VCD spectra of the viruses clearly revealed helical structures in the virus coat proteins; the nucleic acid bases present in the single-stranded RNA could also be characterized. In contrast, the solution VCD spectra showed the characteristic VCD bands for α-helical structures in the coat proteins but not for RNA. Both sets of results clearly indicated that the coat protein conformations are dominated by helical structures, in agreement with earlier reports. VCD results also indicated that the coat protein structures in PVX and NMV are similar to each other and somewhat different from that of TMV. The present study demonstrates the feasibility of measuring VCD spectra for viruses and extracting structural information from these spectra.

Isotope-labeled vibrational circular dichroism studies of calmodulin and its interactions with ligands

In this work we have studied ligand-induced secondary structure changes in the small calcium regulatory protein calmodulin (CaM) using vibrational circular dichroism (VCD) spectroscopy. We find that, due to its chiral sensitivity, VCD spectroscopy has increased ability over IR spectroscopy to detect changes in the structure and flexibility of secondary structure elements upon ligand binding. Moreover, we demonstrate that the uniform isotope labeling of CaM with (13)C shifts its amide I' VCD band by about approximately 43 cm(-1) to lower wavenumbers, which opens up a spectral window to simultaneously visualize a bound target protein. Therefore this study also provides the first example of how isotope labeling enables protein-protein interactions to be studied by VCD with good separation of the signals for both isotope-labeled and unlabeled proteins.

A study of the conformations of valinomycin in solution phase

Vibrational absorption and vibrational circular dichroism (VCD) spectra of valinomycin are measured, in different solvents, in the ester and amide carbonyl stretching regions. The influence of cations, namely Li(+), Na(+), K(+), and Cs(+), in methanol-d(4) solvent is also investigated. Ab initio quantum mechanical calculations using density functional theory and 6-31G* basis set are used to predict the absorption and VCD spectra. A bracelet-type structure for valinomycin that reproduces the experimental absorption and VCD spectra in inert solvents is identified. For the structure of valinomycin in polar solvents, a propeller-type structure was optimized, but further investigations are required to confirm this structure. A symmetric octahedral environment for the ester carbonyl groups in the valinomycin-K(+) complex is supported by the experimental VCD spectra. The results obtained in the present study demonstrate that even for large macrocyclic peptides, such as valinomycin, VCD can be used as an independent structural tool for the study of conformations in solution.

Differentiation of beta-sheet-forming structures: ab initio-based simulations of IR absorption and vibrational CD for model peptide and protein beta-sheets

Ab initio quantum mechanical computations of force fields (FF) and atomic polar and axial tensors (APT and AAT) were carried out for triamide strands Ac-A-A-NH-CH(3) clustered into single-, double-, and triple-strand beta-sheet-like conformations. Models with phi, psi, and omega angles constrained to values appropriate for planar antiparallel and parallel as well as coiled antiparallel (two-stranded) and twisted antiparallel and parallel sheets were computed. The FF, APT, and AAT values were transferred to corresponding larger oligopeptide beta-sheet structures of up to five strands of eight residues each, and their respective IR and vibrational circular dichroism (VCD) spectra were simulated. The antiparallel planar models in a multiple-stranded assembly give a unique IR amide I spectrum with a high-intensity, low-frequency component, but they have very weak negative amide I VCD, both reflecting experimental patterns seen in aggregated structures. Parallel and twisted beta-sheet structures do not develop a highly split amide I, their IR spectra all being similar. A twist in the antiparallel beta-sheet structure leads to a significant increase in VCD intensity, while the parallel structure was not as dramatically affected by the twist. The overall predicted VCD intensity is quite weak but predominantly negative (amide I) for all conformations. This intrinsically weak VCD can explain the high variation seen experimentally in beta-forming peptides and proteins. An even larger variation was predicted in the amide II VCD, which had added complications due to non-hydrogen-bonded residues on the edges of the model sheets.

Peptoid oligomers with alpha-chiral, aromatic side chains: effects of chain length on secondary structure

Oligomeric N-substituted glycines or "peptoids" with alpha-chiral, aromatic side chains can adopt stable helices in organic or aqueous solution, despite their lack of backbone chirality and their inability to form intrachain hydrogen bonds. Helical ordering appears to be stabilized by avoidance of steric clash as well as by electrostatic repulsion between backbone carbonyls and pi clouds of aromatic rings in the side chains. Interestingly, these peptoid helices exhibit intense circular dichroism (CD) spectra that closely resemble those of peptide alpha-helices. Here, we have utilized CD to systematically study the effects of oligomer length, concentration, and temperature on the chiral secondary structure of organosoluble peptoid homooligomers ranging from 3 to 20 (R)-N-(1-phenylethyl)glycine (Nrpe) monomers in length. We find that a striking evolution in CD spectral features occurs for Nrpe oligomers between 4 and 12 residues in length, which we attribute to a chain length-dependent population of alternate structured conformers having cis versus trans amide bonds. No significant changes are observed in CD spectra of oligomers between 13 and 20 monomers in length, suggesting a minimal chain length of about 13 residues for the formation of stable poly(Nrpe) helices. Moreover, no dependence of circular dichroism on concentration is observed for an Nrpe hexamer, providing evidence that these helices remain monomeric in solution. In light of these new data, we discuss chain length-related factors that stabilize organosoluble peptoid helices of this class, which are important for the design of helical, biomimetic peptoids sharing this structural motif.

Simulations of oligopeptide vibrational CD: effects of isotopic labeling

Simulated ir absorption and vibrational CD (VCD) spectra of four alanine-based octapeptides, each having its main chain constrained to a different secondary structure conformation, were analyzed and compared with experimental results for several different peptides. The octapeptide simulations were based on transfer of property tensors from a series of ab initio calculations for a short L-alanine based segment containing 3 peptide bonds with relative straight phi, psi angles fixed to those appropriate for alpha-helix, 3(10)-helix, ProII-like helix, and beta-sheet-like strand. The tripeptide force field (FF) and atomic polar tensors were obtained with density functional theory techniques at the BPW91/6-31G** level and the atomic axial tensor at the mixed BPW91/6-31G**/HF/6-31G level. Allowing for frequency correction due to the FF limitations, the octapeptide results obtained are qualitatively consistent with experimental observations for ir and VCD spectra of polypeptides and oligopeptides in established conformations. In all cases, the correct VCD sign patterns for the amide I and II bands were predicted, but the intensities did have some variation from the experimental patterns. Predicted VCD changes upon deuteration of either the peptide or side-chains as well as for (13)C isotopic labeling of the amide C=O at specific sites in the peptide chain were computed for analysis of experimental observations. A combination of theoretical modeling with experimental data for labeled compounds leads both to enhanced resolution of component transitions and added conformational applicability of the VCD spectra.

Vibrational circular dichroism spectra of proteins in the amide III region: measurement and correlation of bandshape to secondary structure

Vibrational circular dichroism (VCD) spectra have been measured for 23 globular proteins dissolved in H2O/phosphate buffer over the 1400 to 1100 cm(-1) region which encompasses the amide III mode. Spectral responses characteristic of the dominant secondary structure type were found as broad features at approximately 1300 cm(-1), with the extreme forms having positive VCD for highly helical proteins and negative VCD for highly sheet-containing proteins. Quantitative correlation with secondary structure was carried out using previously developed factor analysis and restricted multiple regression (FA/RMR) techniques. Since the absorbance intensity of the amide III mode is difficult to determine due to overlap with other transitions, an alternative, absolute intensity-independent, simple structural analysis method was used. A linear regression was developed between the fractional components of secondary structure for the protein set and the overlap integrals of the normalized spectra from the set with that of a selected protein. The results of this simple method are quite comparable to those of the FA/ RMR approach for analysis with amide III VCD. On the other hand, test calculations with the new method when used with electronic CD spectra are not as good as FA/RMR due to its more intensity-dependent relationship with secondary structure.

Comparison of and limits of accuracy for statistical analyses of vibrational and electronic circular dichroism spectra in terms of correlations to and predictions of protein secondary structure

This work provides a systematic comparison of vibrational CD (VCD) and electronic CD (ECD) methods for spectral prediction of secondary structure. The VCD and ECD data are simplified to a small set of spectral parameters using the principal component method of factor analysis (PC/FA). Regression fits of these parameters are made to the X-ray-determined fractional components (FC) of secondary structure. Predictive capability is determined by computing structures for proteins sequentially left out of the regression. All possible combinations of PC/FA spectral parameters (coefficients) were used to form a full set of restricted multiple regressions with the FC values, both independently for each spectral data set as well as for the two VCD sets and all the data grouped together. The complete search over all possible combinations of spectral parameters for different types of spectral data is a new feature of this study, and the focus on prediction is the strength of this approach. The PC/FA method was found to be stable in detail to expansion of the training set. Coupling amide II to amide I' parameters reduced the standard deviations of the VCD regression relationships, and combining VCD and ECD data led to the best fits. Prediction results had a minimum error when dependent on relatively few spectral coefficients. Such a limited dependence on spectral variation is the key finding of this work, which has ramifications for previous studies as well as suggests future directions for spectral analysis of structure. The best ECD prediction for helix and sheet uses only one parameter, the coefficient of the first subspectrum. With VCD, the best predictions sample coefficients of both the amide I' and II bands, but error is optimized using only a few coefficients. In this respect, ECD is more accurate than VCD for alpha-helix, and the combined VCD (amide I' + II) predicts the beta-sheet component better than does ECD. Combining VCD and ECD data sets yields exceptionally good predictions by utilizing the strengths of each. However, the residual error, its distribution, and, most importantly, the lack of dependence of the method on many of the significant components derived from the spectra leads to the conclusion that the heterogeneity of protein structure is a fundamental limitation to the use of such spectral analysis methods. The underutilization of these data for prediction of secondary structure suggests spectral data could predict a more detailed descriptor.

Vibrational optical activity of oligopeptides

Vibrational optical activity (VOA) is a relatively new spectroscopic technique, which has two principal manifestations, ir vibrational CD and vibrational Raman optical activity. Progress in the study of oligopeptides using both of these forms of VOA is reviewed from the perspective of theoretical and instrumental techniques, spectral results, and structural interpretations.

Empirical studies of protein secondary structure by vibrational circular dichroism and related techniques. Alpha-lactalbumin and lysozyme as examples

Vibrational circular dichroism (VCD) has been shown to be sensitive to secondary structure in proteins and peptides and has been used as the basis for quantitative secondary-structure-prediction algorithms. However, the accuracy of these algorithms is not matched by the apparent qualitative sensitivity of the VCD spectra. This report provides examples of the use of VCD to follow structural change spectrally and to clarify the qualitative nature of the structural changes underlying the spectral variation. The VCD spectra and the complementary UV electronic CD (ECD) and FTIR spectra of alpha-lactalbumin (LA) have been studied as a function of pH, denaturation, Ca2+ ion and solvent conditions for several species. Spectral data for lysozyme were compared with those of LA because of their very similar crystal structures. In fact, these proteins in D2O-based pH 7 solution have quite different spectra using these optical techniques. Even for the LA proteins, the human differs from the bovine and goat species. Furthermore, under low pH conditions, where the LAs are in a reversibly denatured, molten globule form, the spectra are more similar, species variation is minimal and the spectral differences from lysozyme are in fact smaller. Our data are consistent with native, pH 7, alpha-lactalbumin having a less well organized structure than lysozyme, possibly in a dynamic sense. Conversely, in the low-pH, molten globule form of LA, tertiary structure is lost which could relax constraints that might distort the helical segments in the native form. The differences between the interpretation of our results and those from X-ray and NMR data may be due to motional sampling of various geometries in LA which all contribute to the spectral signatures seen in optical spectra but whose contributions are washed out in NMR or frozen out in the crystal structure. Part of this flexibility may relate to the rather large 3(10)-helical content in the LA protein structure. Fluctionality may have specific functional effects, perhaps allowing LA to bind better to beta-galactosyl transferase and form the biologically active lactose synthetase complex.

Spectroscopic study of the temperature-dependent conformation of glucoamylase

Vibrational circular dichroism, electronic circular dichroism and infrared absorption with Fourier self-deconvolution have been used for a conformational study of the small form, G2, of glucoamylase, 1,4-alpha-D-glucan glucohydrolase from Aspergillus niger (EC 3.2.1.3) in aqueous solution. From the temperature dependence of spectra measured from 25 degrees C to 60 degrees C it was seen that the helical content is relatively constant to 50 degrees C and then sharply decreases by a factor of more than three by 60 degrees C. This decrease in helix is primarily compensated by a rise in the fraction of beta-sheet; but bend, turn and 'other' components also increase. By comparison of the three techniques, it was determined that the electronic CD analysis was quantitatively in error due to interference by glycosidic residues. The inherent resolution of the vibrational techniques, FTIR and VCD, avoids such interference.

CD of proline-rich polypeptides: application to the study of the repetitive domain of maize glutelin-2

An overview of CD of proline-rich peptides is reported. First, structural characteristics, theoretical CD studies, and the biological relevance of polyproline II structure in such peptides are discussed. Second, a CD study of peptides belonging to the repetitive domain of maize glutelin-2, H-(Val-His-Leu-Pro-Pro-Pro)n-OH (n = 3, 5, 8), is described. This series of peptides displayed the CD features of polyproline II structure in water (5 degrees C, pH 5). Moreover, it was shown that the addition of increasing amounts of the polyanionic molecule heparin forced a displacement of the conformational equilibrium of those peptides toward higher proportions of the polyproline II structure. In contrast, when the temperature is raised such a structure gradually disappears, leading to more disordered conformations.