Spectroscopic characterization of selected beta- sheet hairpin models

Simplified and enhanced VCD analysis of cyclic peptides guided by artificial intelligence

Cyclic peptides are privileged structures in medicinal chemistry; however, their solution-state structure characterization is difficult. Vibrational circular dichroism (VCD) spectroscopy is a powerful alternative to NMR, but requires challenging calculations. We present a VCD approach guided by a genetic algorithm, which is simple, more effective, and has a higher conformer resolution.

Conformational preferences induced by cyclization in orbitides: a vibrational CD study

Orbitides are bioactive head-to-tail natural cyclic peptides from plant species. Their bioactivity is intrinsically related to the main conformations adopted in solution, whose correct characterization represents an important bottleneck for...

Assignment of absolute stereostructures through quantum mechanics electronic and vibrational circular dichroism calculations

Elucidation of absolute configuration of chiral molecules including structurally complex natural products remains a challenging problem in organic chemistry. A reliable method for assigning the absolute stereostructure is to combine the experimental circular dichroism (CD) techniques such as electronic and vibrational CD (ECD and VCD), with quantum mechanics (QM) ECD and VCD calculations. The traditional QM methods as well as their continuing developments make them more applicable with accuracy. Taking some chiral natural products with diverse conformations as examples, this review describes the basic concepts and new developments of QM approaches for ECD and VCD calculations in solution and solid states.

Design of monomeric water-soluble β-hairpin and β-sheet peptides

Since the first report in 1993 (JACS 115, 5887-5888) of a peptide able to form a monomeric β-hairpin structure in aqueous solution, the design of peptides forming either β-hairpins (two-stranded antiparallel β-sheets) or three-stranded antiparallel β-sheets has become a field of growing interest and activity. These studies have yielded great insights into the principles governing the stability and folding of β-hairpins and antiparallel β-sheets. This chapter provides an overview of the reported β-hairpin/β-sheet peptides focussed on the applied design criteria, reviews briefly the factors contributing to β-hairpin/β-sheet stability, and describes a protocol for the de novo design of β-sheet-forming peptides based on them. Guidelines to select appropriate turn and strand residues and to avoid self-association are provided. The methods employed to check the success of new designed peptides are also summarized. Since NMR is the best technique to that end, NOEs and chemical shifts characteristic of β-hairpins and three-stranded antiparallel β-sheets are given.

Two-Dimensional Infrared (2DIR) Spectroscopy of the Peptide Beta3s Folding

Probing underlying free energy landscape, pathways, and mechanism is the key for understanding protein folding in theory and experiment. Recently time-resolved two-dimensional infrared (2DIR) with femtosecond laser pulses, has emerged as a promising tool for investigating the protein folding dynamics on faster timescales than possible by NMR. We have employed molecular dynamics simulations to compute 2DIR spectra of the folding process of a peptide, Beta3s. Simulated non-chiral and chiral 2DIR signals illustrate the variation of the spectra as the peptide conformation evolves along the free energy landscape. Chiral spectra show stronger changes than the non-chiral signals because cross peaks caused by the formation of the β-sheet are clearly resolved. Chirality-induced 2DIR may be used to detect the folding of β-sheet proteins with high spectral and temporal resolution.

VCD spectroscopic properties of the beta-hairpin forming miniprotein CLN025 in various solvents

Electronic and vibrational circular dichroism are often used to determine the secondary structure of proteins, because each secondary structure has a unique spectrum. Little is known about the vibrational circular dichroic spectroscopic features of the beta-hairpin. In this study, the VCD spectral features of a decapeptide, YYDPETGTWY (CLN025), which forms a stable beta-hairpin that is stabilized by intramolecular weakly polar interactions and hydrogen bonds were determined. Molecular dynamics simulations and ECD spectropolarimetry were used to confirm that CLN025 adopts a beta-hairpin in water, TFE, MeOH, and DMSO and to examine differences in the secondary structure, hydrogen bonds, and weakly polar interactions. CLN025 was synthesized by microwave-assisted solid phase peptide synthesis with N(alpha)-Fmoc protected amino acids. The VCD spectra displayed a (-,+,-) pattern with bands at 1640 to 1656 cm(-1), 1667 to 1687 cm(-1), and 1679 to 1686 cm(-1) formed by the overlap of a lower frequency negative couplet and a higher frequency positive couplet. A maximum IR absorbance was observed at 1647 to 1663 cm(-1) with component bands at 1630 cm(-1), 1646 cm(-1), 1658 cm(-1), and 1675 to 1680 cm(-1) that are indicative of the beta-sheet, random meander, either random meander or loop and turn, respectively. These results are similar to the results of others, who examined the VCD spectra of beta-hairpins formed by (D)Pro-Xxx turns and indicated that observed pattern is typical of beta-hairpins.

A density functional theory study of vibrational coupling in the amide I band of beta-sheet models

We report the first molecular orbital/density functional theory (DFT) calculations on the vibrational frequencies involved in the amide I band of completely geometrically optimized models for beta-sheet peptides based upon (up to 16) glycine residues. These calculations use the B3LYP/D95** level of DFT. The primary means of vibrational coupling occurs through H bond, rather than through space, interactions, which is consistent with a previous report on alpha-helical polyalanines and H-bonding chains of both formamides and 4-pyridones. We decoupled the C=O stretching vibrations using selected 14C substitutions to probe the coupling mechanism and to determine "natural" frequencies for individual 14C=Os. The intermolecular H-bonding interactions affect the geometries of the amide groups. Those near the center of H-bonding chains have long C=O bonds. The C=O bond lengths correlate with these "natural" frequencies, The frequencies obtained from the DFT calculations are generally more coupled, and the most intense are more red shifted than those calculated by transition dipole coupling (TDC). TDC inverts the order of the shifted frequencies compared to DFT in several cases.

Structural malleability of plasticins: Preorganized conformations in solution and relevance for antimicrobial activity

Plasticins (23 long-residue glycine-leucine-rich dermaseptin-related peptides produced by the skin of South American hylids) have very similar amino acid sequences, hydrophobicities, and amphipathicities, but differ in their membrane-damaging properties and structurations (i.e. destabilized helix states, beta-hairpin, beta-sheet, and disordered states) at anionic and zwitterionic membrane interfaces. Structural malleability of plasticins in aqueous solutions together with parameters that may govern their ability to fold within beta-hairpin like structures were analyzed through circular dichroism and FTIR spectroscopic studies completed by molecular dynamics simulations in polar mimetic media. The goal of this study was to probe to which extent pre-existent peptide conformations, i.e. intrinsic "conformational landscape", may be responsible for variability in bioactive conformation and antimicrobial/hemolytic mechanisms of action of these peptides in relation with their various membrane disturbing properties. All plasticins present a turn region that does not always result in folding into a beta-hairpin shaped conformation. Residue at position 8 plays a major role in initiating the folding, while position 12 is not critical. Conformational stability has no major impact on antimicrobial efficacy. However, preformed beta-hairpin in solution may act as a conformational lock that prevents switch to alpha-helical structure. This lock lowers the antimicrobial efficiency and explains subtle differences in potencies of the most active antimicrobial plasticins.

Simulation of Infrared Spectra for β-Hairpin Peptides Stabilized by an Aib-Gly Turn Sequence: Correlation between Conformational Fluctuation and Vibrational Coupling

Vibrational spectra of a 12-residue beta-hairpin peptide, RYVEVBGKKILQ (HBG), stabilized by an Aib-Gly turn sequence (B = Aib) were investigated theoretically using a combination of molecular dynamics (MD) and density functional theory (DFT) calculations. Selected conformations of HBG were extracted from a classical MD trajectory and used for spectral simulations. DFT calculations, based on the Cartesian coordinate spectral property transfer protocol, were carried out for peptide structures in which all residues are replaced with Ala, except for the Aib and Gly residues, but the backbone (phi, psi, omega) structure of the original configuration is retained. The simulations provide a basis for interpretation of the HBG amide I infrared spectra in terms of structural variables such as detailed secondary structure and thermal conformational fluctuation as well as vibrational coupling as indicated by spectra of 13C isotope-labeled variants. The characteristic amide I band shape of such small beta-hairpin peptides appears to arise from the structure of the short antiparallel beta-sheet strands. The role of structural parameter fluctuation in vibrational coupling is evaluated by comparison of DFT-derived amide coupling constants for selected configurations and from transition dipole coupling calculations of coupling parameters between (13)C isotopically labeled residues for a MD-derived ensemble of configurations. Calculated results were compared with the experimentally obtained spectra for several (13)C isotope-labeled peptides of this sequence.

Dependence of folding dynamics and structural stability on the location of a hydrophobic pair in beta-hairpins

We study the dependence of folding time, nucleation site, and stability of a model beta-hairpin on the location of a cross-strand hydrophobic pair, using a coarse-grained off-lattice model with the aid of Monte Carlo simulations. Our simulations have produced 6500 independent folding trajectories dynamically, forming the basis for extensive statistical analysis. Four folding pathways, zipping-out, middle-out, zipping-in, and reptation, have been closely monitored and discussed in all seven sequences studied. A hydrophobic pair placed near the beta-turn or in the middle section effectively speed up folding; a hydrophobic pair placed close to the terminal ends or next to the beta-turn encourages stability of the entire chain.

NMR analysis of aromatic interactions in designed peptide beta-hairpins

Designed octapeptide beta-hairpins containing a central (D)Pro-Gly segment have been used as a scaffold to place the aromatic residues Tyr and Trp at various positions on the antiparallel beta-strands. Using a set of five peptide hairpins, aromatic interactions have been probed across antiparallel beta-sheets, in the non-hydrogen bonding position (Ac-L-Y-V-(D)P-G-L-Y/W-V-OMe: peptides 1 and 2), diagonally across the strands (Boc-Y/W-L-V-(D)P-G-W-L-V-OMe: peptides 3 and 6), and along the strands at positions i and i + 2 (Boc-L-L-V-(D)P-G-Y-L-W-OMe: peptide 4). Two peptides served as controls (Boc-L-L-V-(D)P-G-Y-W-V-OMe: peptide 5; Boc-L-Y-V-(D)P-G-L-L-V-OMe: peptide 7) for aromatic interactions. All studies have been carried out using solution NMR methods in CDCl(3) + 10% DMSO-d(6) and have been additionally examined in CD(3)OH for peptides 1 and 2. Inter-ring proton-proton nuclear Overhauser effects (NOEs) and upfield shifted aromatic proton resonances have provided firm evidence for specific aromatic interactions. Calculated NMR structures for peptides 1 and 2, containing aromatic pairs at facing non-hydrogen bonded positions, revealed that T-shaped arrangements of the interacting pairs of rings are favored, with ring current effects leading to extremely upfield chemical shifts and temperature dependences for specific aromatic protons. Anomalous far-UV CD spectra appeared to be a characteristic feature in peptides where the two aromatic residues are spatially proximal. The observation of the close approach of aromatic rings in organic solvents suggests that interactions of an electrostatic nature may be favored. This situation may be compared to the case of aqueous solutions, where clustering of aromatic residues is driven by solvophobic (hydrophobic) forces.

Role of hydrophobic interactions and salt-bridges in β-hairpin folding

Beta-hairpins are the simplest form of beta-sheets which, due to the presence of long-range interactions, can be considered as tertiary structures. Molecular dynamics simulation is a powerful tool that can unravel whole pathways of protein folding/unfolding at atomic resolution. We have performed several molecular dynamics simulations, to a total of over 250 ns, of a beta-hairpin peptide in water using GROMACS. We show that hydrophobic interactions are necessary for initiating the folding of the peptide. Once formed, the peptide is stabilized by hydrogen bonds and disruption of hydrophobic interactions in the folded peptide does not denature the structure. In the absence of hydrophobic interactions, the peptide fails to fold. However, the introduction of a salt-bridge compensates for the loss of hydrophobic interactions to a certain extent.

Simulation Studies of Amide I IR Absorption and Two-Dimensional IR Spectra of β Hairpins in Liquid Water

Amide I IR absorption and two-dimensional (2D) IR photon echo spectra of a model beta hairpin in aqueous solution are theoretically studied and simulated by combining semiempirical quantum chemistry calculations and molecular dynamics simulation methods. The instantaneous normal-mode analysis of the beta hairpin in solution is performed to obtain the density of states and the inverse participation ratios of the one-exciton states. The motional and exchange narrowing processes are taken into account by employing the time-correlation function theory for the linear and nonlinear response functions. Numerically simulated IR absorption and 2D spectra are then found to be determined largely by the amide I normal modes delocalized on the peptides in the two strands. The site-specific isotope-labeling effects on the IR and 2D IR spectra are discussed. The simulation results for the ideal (A17) beta hairpin are directly compared with those of the realistic 16-residue (GB1) beta hairpin from an immunoglobulin G-binding protein. It was found that the characteristic features in IR and 2D spectra of both the ideal (A17) beta hairpin and the GB1 beta hairpin are the same. The simulated IR spectrum of the GB1 beta hairpin is found to be in good agreement with experiment, which demonstrates that the present computational method is quantitatively reliable.

Empirical solvent correction for multiple amide group vibrational modes

Previously proposed solvent correction to the amide I peptide vibration was extended so that it can be applied to a general solvated chromophore. The combined molecular and quantum mechanics (MMQM) method is based on a linear dependence of harmonic force field and intensity tensor components of the solute on solvent electrostatic field. For N-methylacetamide, realistic solvent frequency and intensity changes as well as inhomogeneous band widths were obtained for amide A, I, II , and III modes. A rather anomalous basis set size dependence was observed for the amide A and I vibrations, when bigger basis lead to narrowing of spectral bands and lesser molecular sensibility to the environment. For a model alpha-helical peptide, a W-shape of the vibrational circular dichroism signal observed in deuterated solvent for the amide I band was reproduced correctly, unlike with previous vacuum models.

Coherent third-order spectroscopic probes of molecular chirality

The third-order optical response of a system of coupled localized anharmonic vibrations is studied using a Green's function solution of the nonlinear exciton equations for bosonized excitons, which are treated as interacting quasiparticles. The explicit calculation of two-exciton states is avoided and the scattering of quasiparticles provides the mechanism of optical nonlinearities. To first-order in the optical wave vector we find several rotationally invariant tensor components for isotropic ensembles which are induced by chirality. The nonlocal nonlinear susceptibility tensor is calculated for infinitely large periodic structures in momentum space, where the problem size reduces to the exciton interaction radius. Applications are made to alpha and 3(10) helical infinite peptides.

Solvent Effects on IR and VCD Spectra of Helical Peptides: DFT-Based Static Spectral Simulations with Explicit Water

Simulations of IR and VCD spectra are carried out for model alpha-helical, 3(10)-helical, and 3(1)-helical (polyProII-like) oligopeptides, with up to 21 amide groups, and including explicit consideration of effects of directly hydrogen-bonded solvent (water). Parameters used were obtained from ab initio density functional theory (DFT) computations of force field, atomic polar and axial tensors for oligopeptides of 5 to 7 amides, whose structures were constrained in (phi,psi) to target the secondary structure type but otherwise fully optimized. By comparison with experimental data as well as with calculations for identical but isolated (gas phase) peptides, the computed effects of an inner shell of aqueous solvent on the vibrational spectra of helical oligopeptides are illustrated. The interaction with solvent causes significant frequency shifts of the amide bands, but only minor changes in the characteristic IR intensity distributions and splittings and the VCD band shapes. Better agreement with experimental band shapes is achieved for the alpha-helical amide I' (N-deuterated) VCD by inclusion of explicit solvent in the calculations. Some improvements are also observed in theoretical VCD predictions for 13C labeled alpha-helical peptides when solvated models are used. However, the qualitative isotopic splitting patterns are preserved and just shifted in frequency due to consistent, solvent independent interamide coupling constants. The critical match of experiment and theory for relative positions of transitions in peptides with specifically separated 13C=O labels, including and neglecting solvent, confirms the stability of the coupling interactions. Despite these solvation effects, the calculated VCD band shape of the amide I mode is shown to be a reliable conformational probe, since it remains basically insensitive to frequency shifts caused by environment. Thus theoretical VCD simulations, even vacuum calculations, are shown to provide useful spectral predictions for solution-phase peptides.

Ab Initio Modeling of Amide I Coupling in Antiparallel β-Sheets and the Effect of 13C Isotopic Labeling on Infrared Spectra

Isotopic substitution with 13C on the amide C=O has become an important means of determining localized structural information about peptide conformations with vibrational spectroscopy. Various approaches to the modeling of the interactions between labeled amide sites, specifically for antiparallel two-stranded, beta-forming peptides, were investigated, including different force fields [dipole-dipole interaction vs density functional theory (DFT) treatments], basis sets, and sizes of model peptides used for ab initio calculations, as well as employing models of solvation. For these beta-sheet systems the effect of the relative positions of the 13C isotopic labels in each strand on their infrared spectra was investigated. The results suggest that the interaction between labeled amide groups in different strands can be used as an indicator of local beta-structure formation, because coupling between close-lying C=O groups on opposing chains leads to the largest frequency shifts, yet some alternate placements can lead to intensity enhancements. The basic character of the coupling interaction between labeled modes on opposing strands is independent of changes in peptide length, water solvent environment, twisting of the sheet structure, and basis set used in the calculations, although the absolute frequencies and detailed coupling magnitudes change under each of these perturbations. In particular, two strands of three amides each contain the basic interactions needed to simulate larger sheets, with the only exception that the C=O groups forming H-bonded rings at the termini can yield different coupling values than central ones of the same structure. Spectral frequencies and intensities were modeled ab initio by DFT primarily at the BPW91/6-31G** level for pairs of three, four, and six amide strands. Comparison to predictions of a classical coupled oscillator model show qualitative but not quantitative agreement with these DFT results.

Signatures of β-sheet secondary structures in linear and two-dimensional infrared spectroscopy

Using idealized models for parallel and antiparallel beta sheets, we calculate the linear and two-dimensional infrared spectra of the amide I vibration as a function of size and secondary structure. The model assumes transition-dipole coupling between the amide I oscillators in the sheet and accounts for the anharmonic nature of these oscillators. Using analytical and numerical methods, we show that the nature of the one-quantum vibrational eigenstates, which govern the linear spectrum, is, to a large extent, determined by the symmetry of the system and the relative magnitude of interstrand interactions. We also find that the eigenstates, in particular their trends with system size, depend sensitively on the secondary structure of the sheet. While in practice these differences may be difficult to distinguish in congested linear spectra, we demonstrate that they give rise to promising markers for secondary structure in the two-dimensional spectra. In particular, distinct differences occur between the spectra of parallel and antiparallel beta sheets and between beta hairpins and extended beta sheets.

Absolute configuration determination of chiral molecules in the solution state using vibrational circular dichroism

Advances in the measurement, calculation, and application of vibrational circular dichroism (VCD) for the determination of absolute configuration are described. The purpose of the review is to provide an up-to-date perspective on the capability of VCD to solve problems of absolute stereochemistry for chiral molecules primarily in the solution state. The scope of the article covers the experimental methods needed for the accurate measurement of VCD spectra and the theoretical steps required to systematically deduce absolute configuration. Determination of absolute configuration of a molecule by VCD requires knowledge of its conformation or conformational distribution, and hence VCD analysis necessarily provides solution-state conformation information, in many cases available by no other method, as an additional benefit. Comparisons of the advantages and limitations of VCD relative to other available chiroptical methods of analysis are also presented.

Optical spectroscopic investigations of model beta-sheet hairpins in aqueous solution

In this contribution we report optical spectroscopic data on a series of designed beta hairpins previously shown by NMR to contain a substantial population of beta-sheet structure. These models contain a designed hydrophobic cluster and a (D)Pro-Gly sequence to promote formation of a turn geometry. FTIR, electronic and vibrational CD (ECD and VCD) spectra for these small peptides are comparable to expected bandshapes for peptides of high beta-sheet content. The (D)Pro-Gly sequence provides a better turn motif than Asn-Gly as measured by its beta-sheet spectral characteristics. IR and VCD spectra are in qualitative agreement with theoretical simulations based on transfer of parameters from ab initio quantum mechanical force field and intensity computations for the turn and strands. These calculations provide assignments for some distinguishing modes in both IR and VCD spectra. Increased sheet structure can be induced in these hairpins by use of mixed solvent conditions. Thermal denaturation studies reveal that these hairpins undergo very broad unfolding transitions. Guanidine hydrochloride unfolding transitions for the selected hairpin models are similarly broad. However, the "end-states" of temperature and chaotropic denaturation are spectroscopically differentiable.

Ab initio quantum mechanical models of peptide helices and their vibrational spectra

Structural parameters for standard peptide helices (alpha, 3(10), 3(1) left-handed) were fully ab initio optimized for Ac-(L-Ala)(9)-NHMe and for Ac-(L-Pro)(9)-NHMe (poly-L-proline-PLP I and PLP II-forms), in order to better understand the relative stability and minimum energy geometries of these conformers and the dependence of the ir absorption and vibrational CD (VCD) spectra on detailed variation in these conformations. Only the 3(10)-helical Ala-based conformation was stable in vacuum for this decaamide structure, but both Pro-based conformers minimized successfully. Inclusion of solvent effects, by use of the conductor-like screening solvent model (COSMO), enabled ab initio optimizations [at the DFT/B3LYP/SV(P) level] without any constraints for the alpha- and 3(10)-helical Ala-based peptides as well as the two Pro-based peptides. The geometries obtained compare well with peptide chain torsion angles and hydrogen-bond distances found for these secondary structure types in x-ray structures of peptides and proteins. For the simulation of VCD spectra, force field and intensity response tensors were obtained ab initio for the complete Ala-based peptides in vacuum, but constrained to the COSMO optimized torsional angles, due to limitations of the solvent model. Resultant spectral patterns reproduce well many aspects of the experimental spectra and capture the differences observed for these various helical types.

Protein and peptide secondary structure and conformational determination with vibrational circular dichroism

Vibrational circular dichroism (VCD) provides alternative views of protein and peptide conformation with advantages over electronic (UV) CD (ECD) or IR spectroscopy. VCD is sensitive to short-range order, allowing it to discriminate beta-sheet and various helices as well as disordered structure. Quantitative secondary structure analyses use protein VCD bandshapes, but are best combined with ECD and IR for balance. Much recent work has focused on empirical and theoretical VCD analyses of peptides, with detailed prediction of helix, sheet and hairpin spectra and site-specific application of isotopic substitution for structure and folding.