Amides as models to study the hydration of proteins and peptides — spectroscopic and theoretical approach on hydration in various temperatures

Carbonyl stretching band in amides as Lorentz oscillator. Insights into anharmonicity and local environment in the liquid phase from NIR and MIR spectra of N-methylformamide and di-N,N-methylformamide

We investigated the anharmonicity and intermolecular interactions of N-methylformamide (NMF) and di-N,N-methylformamide (DMF) in the neat liquid phase with particular interest in the amide bands. The vibrational spectra, complex refractive index, and complex electric permittivity were determined in in the mid- (MIR) and near-infrared (NIR) regions (11,500-560 cm-1; 870-17857 nm). Dispersion analysis was based on the Classical Damped Harmonic Oscillator (CDHO) and simultaneous modelling of the real and imaginary components of the spectra. This data delivered insights into the vibrational energy dissipation and self-association in liquid amides. Identification of the MIR and NIR bands was based on anharmonic GVPT2//B3LYP/6-311++G(d,p) calculations. DMF and NMF follow distinct self-association, evidenced in the MIR fingerprint by the two components of the νCO, the analog of the Amide I band. These conclusions are supported by the structural information derived from the NIR spectra. Furthermore, the contribution of overtones and combination bands in the MIR spectra of amides was examined. The conclusions on molecular interactions and structural dynamics of NMF and DMF contribute to a deeper understanding of the effects of changes in the local environment of the amide group.

Weakly Hydrated Solute of Mixed Hydrophobic-Hydrophilic Nature

Infrared (IR) spectroscopy is a commonly used and invaluable tool in studies of solvation phenomena in aqueous solutions. Concurrently, density functional theory calculations and ab initio molecular dynamics simulations deliver the solvation shell picture at the molecular detail level. The mentioned techniques allowed us to gain insights into the structure and energy of the hydrogen bonding network of water molecules around methylsulfonylmethane (MSM). In the hydration sphere of MSM, there are two types of populations of water molecules: a significant share of water molecules weakly bonded to the sulfone group and a smaller share of water molecules strongly bonded to each other around the methyl groups of MSM. The very weak hydrogen bond of water molecules with the hydrophilic group causes the extended network of water hydrogen bonds to be not "anchored" on the sulfone group, and consequently, the MSM hydration shell is labile.

Effect of the N-Alkyl Side Chain on the Amide-Water Interactions

Amide-water interactions influence the structure and functions of amide-based systems, such as proteins and homopolymers. In particular, the N-alkylation of the amide unit appears to play a critical role in defining the interactions of the amide group. Previous studies have linked the thermal behavior of amide-based polymers to the nature of their N-alkyl side chain. However, the connection between the chemical structure of the N-alkyl and the hydration of the amide remains elusive. In this study, the solvation structure and dynamics of amides, having differing N-alkyl groups, are investigated using a combination of linear and nonlinear infrared spectroscopies and computational methods. Interestingly, the dynamics of the amide local environment do not slow down as the N-alkyl side chain becomes bulkier, but rather speeds up. Computational calculations confirm the hydration dynamics and assign the effect to smaller amplitude and faster rotations of the bulkier group. It is also observed experimentally that the hydrogen-bond making and breaking between water and the amide carbonyl do not directly relate to the size of the N-alkyl side chain. The bulkier N-isopropyl substituent presents significantly slower chemical exchange dynamics than smaller chains (ethyl and methyl), but the two small groups do not present a major difference. The hydrogen-bond making and breaking disparities and similarities among groups are well modeled by the theory demonstrating that the N-alkyl group affects the amide hydration structure and dynamics via a steric effect. In summary, the results presented here show that the size of the N-substituted alkyl group significantly influences the hydration dynamics of amides and stress the importance of considering this effect on much larger systems, such as polymers.

Mechanism of Osmolyte Stabilization-Destabilization of Proteins: Experimental Evidence

In this work, we investigated the influence of stabilizing (N,N,N-trimethylglycine) and destabilizing (urea) osmolytes on the hydration spheres of biomacromolecules in folded forms (trpzip-1 peptide and hen egg white lysozyme—hewl) and unfolded protein models (glycine—GLY and N-methylglycine—NMG) by means of infrared spectroscopy. GLY and NMG were clearly limited as minimal models for unfolded proteins and should be treated with caution. We isolated the spectral share of water changed simultaneously by the biomacromolecule/model molecule and the osmolyte, which allowed us to provide unambiguous experimental arguments for the mechanism of stabilization/destabilization of proteins by osmolytes. In the case of both types of osmolytes, the decisive factor determining the equilibrium folded/unfolded state of protein was the enthalpy effect exerted on the hydration spheres of proteins in both forms. In the case of stabilizing osmolytes, enthalpy was also favored by entropy, as the unfolded state of a protein was more entropically destabilized than the folded state.

Hydration Dynamics of Model Peptides with Different Hydrophobic Character

The multi-scale dynamics of aqueous solutions of the hydrophilic peptide N-acetyl-glycine-methylamide (NAGMA) have been investigated through extended frequency-range depolarized light scattering (EDLS), which enables the broad-band detection of collective polarizability anisotropy fluctuations. The results have been compared to those obtained for N-acetyl-leucinemethylamide (NALMA), an amphiphilic peptide which shares with NAGMA the same polar backbone, but also contains an apolar group. Our study indicates that the two model peptides induce similar effects on the fast translational dynamics of surrounding water. Both systems slow down the mobility of solvating water molecules by a factor 6–8, with respect to the bulk. Moreover, the two peptides cause a comparable far-reaching spatial perturbation extending to more than two hydration layers in diluted conditions. The observed concentration dependence of the hydration number is explained considering the random superposition of different hydration shells, while no indication of solute aggregation phenomena has been found. The results indicate that the effect on the dynamics of water solvating the amphiphilic peptide is dominated by the hydrophilic backbone. The minor impact of the hydrophobic moiety on hydration features is consistent with structural findings derived by Fourier transform infrared (FTIR) measurements, performed in attenuated total reflectance (ATR) configuration. Additionally, we give evidence that, for both systems, the relaxation mode in the GHz frequency range probed by EDLS is related to solute rotational dynamics. The rotation of NALMA occurs at higher timescales, with respect to the rotation of NAGMA; both processes are significantly slower than the structural dynamics of hydration water, suggesting that solute and solvent motions are uncoupled. Finally, our results do not indicate the presence of super-slow water (relaxation times in the order of tens of picoseconds) around the peptides investigated.

DMSO and TMAO-Differences in Interactions in Aqueous Solutions of the K-Peptide

Interactions between a solvent and their co-solute molecules in solutions of peptides are crucial for their stability and structure. The K-peptide is a synthetic fragment of a larger hen egg white lysozyme protein that is believed to be able to aggregate into amyloid structures. In this study, a complex experimental and theoretical approach is applied to study systems comprising the peptide, water, and two co-solutes: trimethylamide N-oxide (TMAO) or dimethyl sulfoxide (DMSO). Information about their interactions in solutions and on the stability of the K-peptide was obtained by FTIR spectroscopy and differential scanning microcalorimetry. The IR spectra of various osmolyte-water-model-peptide complexes were simulated with the DFT method (B3LYP/6-311++G(d,p)). The FTIR results indicate that both solutes are neutral for the K-peptide in solution. Both co-solutes affect the peptide to different degrees, as seen in the shape of its amide I band, and have different influences on its thermal stability. DFT calculations helped simplify the experimental data for easier interpretation.

Seeking Solvation: Exploring the Role of Protein Hydration in Silk Gelation

The mechanism by which arthropods (e.g., spiders and many insects) can produce silk fibres from an aqueous protein (fibroin) solution has remained elusive, despite much scientific investigation. In this work, we used several techniques to explore the role of a hydration shell bound to the fibroin in native silk feedstock (NSF) from Bombyx mori silkworms. Small angle X-ray and dynamic light scattering (SAXS and DLS) revealed a coil size (radius of gyration or hydrodynamic radius) around 12 nm, providing considerable scope for hydration. Aggregation in dilute aqueous solution was observed above 65 °C, matching the gelation temperature of more concentrated solutions and suggesting that the strength of interaction with the solvent (i.e., water) was the dominant factor. Infrared (IR) spectroscopy indicated decreasing hydration as the temperature was raised, with similar changes in hydration following gelation by freezing or heating. It was found that the solubility of fibroin in water or aqueous salt solutions could be described well by a relatively simple thermodynamic model for the stability of the protein hydration shell, which suggests that the affected water is enthalpically favoured but entropically penalised, due to its reduced (vibrational or translational) dynamics. Moreover, while the majority of this investigation used fibroin from B. mori, comparisons with published work on silk proteins from other silkworms and spiders, globular proteins and peptide model systems suggest that our findings may be of much wider significance.