Amide-I characteristics of helical β-peptides by linear infrared measurement and computations

Chasing weakly-bound biological water in aqueous environment near the peptide backbone by ultrafast 2D infrared spectroscopy

There has been a long-standing debate as to how many hydrogen bonds a peptide backbone amide can form in aqueous solution. Hydrogen-bonding structural dynamics of N-ethylpropionamide (a β-peptide model) in water was examined using infrared (IR) spectroscopy. Two amide-I sub bands arise mainly from amide C=O group that forms strong H-bonds with solvent water molecules (SHB state), and minorly from that involving one weak H-bond with water (WHB state). This picture is supported by molecular dynamics simulations and ab-initio calculations. Further, thermodynamics and kinetics of the SHB and WHB species were examined mainly by chemical-exchange two-dimensional IR spectroscopy, yielding an activation energy for the SHB-to-WHB exchange of 13.25 ± 0.52 kJ mol‒1, which occurs in half picosecond at room temperature. Our results provided experimental evidence of an unstable water molecule near peptide backbone, allowing us to gain more insights into the dynamics of the protein backbone hydration.

Structural dynamics and vibrational feature of N-Acetyl-d-glucosamine in aqueous solution

Molecular dynamics simulations and DFT calculations were performed for the demonstration of the structural dynamics and vibrational feature of N-Acetyl-d-glucosamine (NAG) in solution phase. The interactions between NAG and solvent molecules were evaluated through spatial distribution function and radial distribution function, and the preferred conformations of NAG in aqueous solution were revealed by cluster analysis. Results from normal mode analysis show that the solvent induced structural fluctuation of NAG could be reflected in the vibrational feature of specific chromophores, thus we can evaluate the molecular structure with the help of its vibrational signature based on the built correlation between molecular structure and vibrational frequencies of specific groups.

Specific and non-specific interactions between metal cations and zwitterionic alanine tripeptide in saline solutions reported by the symmetric carboxylate stretching and amide-II vibrations

The "specific" interaction between metal cations (Na⁺, Ca²⁺, Mg²⁺, and Zn²⁺) and the charged COO^- group, and the "non-specific" interaction between these cations and the peptide backbone of a zwitterionic trialanine (Ala3) in aqueous solutions were examined in detail, using linear infrared (IR) absorptions of the COO^- symmetric stretching and the amide-II (mainly the C-N stretching) modes as IR probes. Different IR spectral changes in peak positions and intensities of the two IR probes clearly demonstrate their sensitivities to nearby cation distributions in distance and population. Quantum chemistry calculations and molecular dynamics simulations were used to describe the cation-peptide interaction picture. These combined results suggest that Na⁺ and Ca²⁺ tend to bind to the COO^- group in the bidentate form, while Mg²⁺ and Zn²⁺ tend to bind to the COO^- group in the pseudo-bridging form. The results also show that while all three divalent cations indirectly interact with the peptide backbone with large population, Ca²⁺ and Mg²⁺ can be sometimes distributed very close to the backbone. Such a non-specific cation interaction can be moderately sensed by the C-N stretching of the amide-II mode when cations approach the polar amide C[double bond, length as m-dash]O group, and is also influenced by the NH₃⁺ charge group located at the N-terminus. The results suggest that the experimentally observed complication of the Hofmeister cation series shall be understood as a combined specific and non-specific cation-peptide interactions.

Application of a transparent window vibrational probe (azido probe) to the structural dynamics of model dipeptides and amyloid β-peptide

The azido asymmetric stretching motion is widely used for the elucidation of the intrinsic conformational preference and folding mechanism of protein since it has strong vibrational absorbance in the spectral transparent windows. However, the possible secondary structural disturbance induced by the insertion of azido group in the side chain of polypeptides should be carefully evaluated. Here, DFT calculation and enhanced sampling method were employed for model dipeptides with or without azido substitution, and the outcome results show that the lower potential energy basins of isolated model dipeptides are consistent with the preferred structural distributions of model dipeptides in aqueous solution. The azido asymmetric stretching frequency shows its sensitivity to the backbone configurations just like amide-I vibration does, and the azido vibration exhibits great potential as a structural reporter in the transparent window. For the evaluation of the application of azido group in biologically related system, the structural dynamics of Aβ_37-42 and N₃-Aβ_37-42 fragments and the self-assemble process of their protofiliments in aqueous solution were demonstrated. The outcome results show that the structural fluctuations of Aβ_37-42 and its protofilament in aqueous solution are quite similar with or without azido substitution, and the dewetting transitions of Aβ_37-42 and N₃-Aβ_37-42 β-sheet layers are both complete within 30 ns and assemble into stable protofilaments. Therefore, the azido asymmetric vibrational motion is a minimally invasive structural probe and would not introduce much disturbance to the structural dynamics of polypeptides.

Intensified C≡C Stretching Vibrator and Its Potential Role in Monitoring Ultrafast Energy Transfer in 2D Carbon Material by Nonlinear Vibrational Spectroscopy

In this work, an intensity-enhanced C≡C stretching infrared (IR) absorption is observed in hexakis[(trimethylsilyl)ethynyl]benzene (HTEB), whose IR transition dipole magnitude becomes comparable to that of a typical C═O stretch, and the enhancement is believed to be due to a joint effect of π-π conjugation and hyperconjugation associated with a terminal trimethylsilyl group. Using dynamical time-dependent two-dimensional infrared (2D IR) spectroscopy, a picosecond intramolecular energy redistribution process is observed between two nondegenerate C≡C stretching modes, whose symmetry breaking is attributed to a noncovalent halogen-bonding interaction between HTEB and solvent CH₂Cl₂. The rigid structure of HTEB and limited structural dynamics are also inferred from the insignificant initial spectral diffusion value extracted from the 2D IR spectra. This work provides the first nonlinear infrared investigation of the conventionally weak C≡C stretch. The methods outlined are particularly important for detailed understanding of the structure-related processes such as vibrational energy transfer in novel C≡C species containing materials such as graphdiyne.

Direct Anionic Effect on Water Structure and Indirect Anionic Effect on Peptide Backbone Hydration State Revealed by Thin-Layer Infrared Spectroscopy

In this work, the anionic effect on water structure and on the peptide backbone and water interaction was investigated directly in aqueous solution using thin-layer transmission infrared spectroscopy. The chaotropic anions were found to weaken the water hydrogen-bonding strength and red shift the HOH bending frequency, while the kosmotropic anions were found to strengthen the water hydrogen-bonding network and blue shift the HOH bending frequency. The kosmotropes, especially F^-, blue shift the vibrational frequencies of both amide II and amide III bands of N-methylacetamide (NMA), indicating NMA is in the "salting-in" state; while the chaotropes (Cl^-, NO₃^-, Br^-, I^-, and SCN^-) red shift the frequencies of the two normal modes, indicating NMA is in the "salting-out" state. Furthermore, the changes of the vibrational frequencies of the HOH bending, amide II and III bands were found to generally follow the Hofmeister anionic series. Our results suggest that hydrated anion influences the peptide backbone mainly through the N-H group, but a weak and indirect effect through the amide C═O group also contributes. Thus, these amide modes can be used as vibrational measures of anionic influences on peptide backbone's hydration state. Our work also suggests that deuteration of the amide unit decreases the sensitivity of the amide II and III vibrational modes in this regard.

Electrostatic frequency maps for amide-I mode of β-peptide: Comparison of molecular mechanics force field and DFT calculations

The spectroscopy of amide-I vibrations has been widely utilized for the understanding of dynamical structure of polypeptides. For the modeling of amide-I spectra, two frequency maps were built for β-peptide analogue (N-ethylpropionamide, NEPA) in a number of solvents within different schemes (molecular mechanics force field based, GM map; DFT calculation based, GD map), respectively. The electrostatic potentials on the amide unit that originated from solvents and peptide backbone were correlated to the amide-I frequency shift from gas phase to solution phase during map parameterization. GM map is easier to construct with negligible computational cost since the frequency calculations for the samples are purely based on force field, while GD map utilizes sophisticated DFT calculations on the representative solute-solvent clusters and brings insight into the electronic structures of solvated NEPA and its chemical environments. The results show that the maps' predicted amide-I frequencies present solvation environmental sensitivities and exhibit their specific characters with respect to the map protocols, and the obtained vibrational parameters are in satisfactory agreement with experimental amide-I spectra of NEPA in solution phase. Although different theoretical schemes based maps have their advantages and disadvantages, the present maps show their potentials in interpreting the amide-I spectra for β-peptides, respectively.

General Applicable Frequency Map for the Amide-I Mode in β-Peptides

In this work, a general applicable amide-I vibrational frequency map (GA map) for β-peptides in a number of common solvents was constructed, based on a peptide derivative, N-ethylpropionamide (NEPA). The map utilizes force fields at the ab initio computational level to accurately describe molecular structure and solute-solvent interactions, and also force fields at the molecular mechanics level to take into account long-range solute-solvent interactions. The results indicate that the GA map works reasonably for mapping the vibrational frequencies of the amide-I local-modes for β-peptides, holding promises for understanding the complicated infrared spectra of the amide-I mode in β-polypeptides.

Solvent induced conformational fluctuation of alanine dipeptide studied by using vibrational probes

The solvation effect on the three dimensional structure and the vibrational feature of alanine dipeptide (ALAD) was evaluated by applying the implicit solvents from polarizable continuum solvent model (PCM) through ab initio calculations, by using molecular dynamic (MD) simulations with explicit solvents, and by combining these two approaches. The implicit solvent induced potential energy fluctuations of ALAD in CHCl3, DMSO and H2O are revealed by means of ab initio calculations, and a global view of conformational and solvation environmental dependence of amide I frequencies is achieved. The results from MD simulations with explicit solvents show that ALAD trends to form PPII, αL, αR, and C5 in water, PPII and C5 in DMSO, and C5 in CHCl3, ordered by population, and the demonstration of the solvated structure, the solute-solvent interaction and hydrogen bonding is therefore enhanced. Representative ALAD-solvent clusters were sampled from MD trajectories and undergone ab initio calculations. The explicit solvents reveal the hydrogen bonding between ALAD and solvents, and the correlation between amide I frequencies and the CO bond length is built. The implicit solvents applied to the ALAD-solvent clusters further compensate the solvation effect from the bulk, and thus enlarge the degree of structural distortion and the amide I frequency red shift. The combination of explicit solvent in the first hydration shell and implicit solvent in the bulk is helpful for our understanding about the conformational fluctuation of solvated polypeptides through vibrational probes.

Dissecting amide-I vibration in β-peptide helices

The vibrational properties of the amide-I modes of β-peptides in five helical conformations (8-helix, 10-helix, 12-helix, 14-helix, and 10/12-helix) from tetramer to heptamer were examined by ab initio calculations. The normal modes have been first decoupled into local modes, whose transition energies are found to be intrinsically sensitive to peptide structure and intramolecular hydrogen bonding interactions. By further removing the intramolecular hydrogen bonding interactions, pure local modes are obtained, whose transition energies still exhibit some conformational dependence in 8-helix and 10/12 hybrid helix, but not much in homogeneous 10-, 12-, and 14-helical conformations. This suggests that a set of nearly degenerated pure local-mode transitions can be specified when excitonic modeling the amide-I vibration in latter cases. The work provides important benchmark measurements for understanding the complexity of the amide-I absorption spectra of β-polypeptides.

Site-specific infrared probes of proteins

Infrared spectroscopy has played an instrumental role in the study of a wide variety of biological questions. However, in many cases, it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and environmental information in a site-specific manner. To overcome this limitation, investigators have dedicated many recent efforts to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural or environmental properties. In this review, we highlight recent advancements in this rapidly growing research area.

Ultrafast vibrational and structural dynamics of dimeric cyclopentadienyliron dicarbonyl examined by infrared spectroscopy

Equilibrium and ultrafast structural dynamics of a classic transition metal carbonyl compound were revealed by linear and nonlinear infrared methods.

Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed "maps," which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala)5-Lys-H(+) in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly (13)C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and (13)C(18)O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm(-1) for both frequencies and couplings, having larger errors only for the frequencies of terminal amides.