Sequence-dependent aggregation-prone conformations of islet amyloid polypeptide.

Amyloid proteins, which aggregate to form highly ordered structures, play a crucial role in various disease pathologies. Despite many previous studies on amyloid fibrils, which are an end product of protein aggregation, the structural characteristics of amyloid proteins in the early stage of aggregation and their related aggregation mechanism still remain elusive. The role of the amino acid sequence in the aggregation-prone structures of amyloid proteins at such a stage is not understood. Here, we have studied the sequence-dependent structural characteristics of islet amyloid polypeptide based on atomistic simulations and spectroscopic experiments. We show that the amino acid sequence determines non-bonded interactions that play a leading role in the formation of aggregation-prone conformations. Specifically, a single point mutation critically changes the population of aggregation-prone conformations, resulting in a change of the aggregation mechanism. Our simulation results were supported by experimental results suggesting that mutation affects the kinetics of aggregation and the structural characteristics of amyloid aggregates. Our study provides an insight into the role of sequence-dependent aggregation-prone conformations in the underlying mechanisms of amyloid aggregation.

Scattering Elimination of Heterodyne-Detected Two-Dimensional Infrared Spectra Using Choppers and Shutters.

Obtaining high-quality 2D IR spectra of heterogeneous samples such as perovskite films or metal-organic framework powder is hampered by severe light scattering. In the pump-probe (PP) method, this problem can be circumvented by phase cycling. However, in the heterodyned photon echo (HPE) method, phase cycling does not function as effectively as the PP method. This study demonstrates that the scattering problem can be solved mechanically by introducing another chopper and two shutters into the existing 2D IR setup without moving any translation stages to introduce a phase shift in the HPE method. For a perovskite film having a very rough surface, containing a small amount of residual dimethylformamide, and having a maximum absorbance of ∼0.0004 in the C═O stretch region, this advanced experimental method is tested and proven to be highly effective.

Interconverting Hydrogen-Bonding and Weak n → π* Interactions in Aqueous Solution: A Direct Spectroscopic Evidence.

Molecular structure and function depend on myriad noncovalent interactions. However, the weak and transient nature of noncovalent interactions in solution makes them challenging to study. Information on weak interactions is typically derived from theory and indirect structural data. Solvent fluctuations, not revealed by structure analysis, further complicate the study of these interactions. Using 2D infrared spectroscopy, we show that the strong hydrogen bond and the weak n → π* interaction coexist and interconvert in aqueous solution. We found that the kinetics of these interconverting interactions becomes faster with increasing water content. This experimental observation provides a new perspective on the existence of weak noncovalent interactions in aqueous solution.

Synergistic Configuration of Diols as Brønsted Bases.

As viscous hydroxylic organic compounds, diols are of interest for their functional molecular conformation, which is based on inter- and intramolecular hydrogen (H)-bonds. By utilising steady-state electronic and vibrational spectroscopy, time-resolved fluorescence spectroscopy, and computational analyses, we report the association of the hydroxyl groups of diols via intra- or intermolecular H-bonds to enhance their reactivity as a base. Whereas the formation of an intermolecularly H-bonded dimer is requisite for diols of weak intramolecular H-bond to extract a proton from a model strong photoacid, a well-configured single diol molecule with an optimised intramolecular H-bond is revealed to serve as an effective Brønsted base with increased basicity. This observation highlights the collective role of H-bonding in acid-base reactions, and provides mechanistic backgrounds to understand the reactivity of polyols in the acid-catalysed dehydration for the synthesis of cyclic ethers at the molecular level.

Two-Dimensional Infrared Spectroscopy Reveals Cosolvent-Composition-Dependent Crossover in Intermolecular Hydrogen-Bond Dynamics.

Cosolvents have versatile composition-dependent applications in chemistry and biology. The simultaneous presence of hydrophobic and hydrophilic groups in dimethyl sulfoxide (DMSO), an industrially important amphiphilic cosolvent, when combined with the unique properties of water, plays key roles in the diverse fields of pharmacology, cryoprotection, and cell biology. Moreover, molecules dissolved in aqueous DMSO exhibit an anomalous concentration-dependent nonmonotonic behavior in stability and activity near a critical DMSO mole fraction of 0.15. An experimental identification of the origin of this anomaly can lead to newer chemical and biological applications. We report a direct spectroscopic observation of the anomalous behavior using ultrafast two-dimensional infrared spectroscopy experiments. Our results demonstrate the cosolvent-concentration-dependent nonmonotonicity arises from nonidentical mechanisms in ultrafast hydrogen-bond-exchange dynamics of water above and below the critical cosolvent concentration. Comparison of experimental and theoretical results provides a molecular-level mechanistic understanding: a distinct difference in the stabilization of the solute through dynamic solute-solvent interactions is the key to the anomalous behavior.

Phase-Resolved Heterodyne-Detected Transient Grating Enhances the Capabilities of 2D IR Echo Spectroscopy.

2D IR echo spectroscopy, with high sensitivity and femtosecond time resolution, enables us to understand structure and ultrafast dynamics of molecular systems. Application of this experimental technique on weakly absorbing samples, however, had been limited by the precise and unambiguous phase determination of the echo signals. In this study, we propose a new experimental scheme that significantly increases the phase stability of the involved IR pulses. We have demonstrated that the incorporation of phase-resolved heterodyne-detected transient grating (PR-HDTG) spectroscopy greatly enhances the capabilities of 2D IR spectroscopy. The new experimental scheme has been used to obtain 2D IR spectra on weakly absorbing azide ions (N3-) in H2O (absorbance ∼0.025), free of phase ambiguity even at large waiting times. We report the estimated spectral diffusion time scale (1.056 ps) of azide ions in aqueous solution from the 2D IR spectra and the vibrational lifetime (750 ± 3 fs) and the reorientation time (1108 ± 24 fs) from the PR-HDTG spectra.

Cosolvent Effects on Solute-Solvent Hydrogen-Bond Dynamics: Ultrafast 2D IR Investigations.

Cosolvents strongly influence the solute-solvent interactions of biomolecules in aqueous environments and have profound effects on the stability and activity of several proteins and enzymes. Experimental studies have previously reported on the hydrogen-bond dynamics of water molecules in the presence of a cosolvent, but understanding the effects from a solute's perspective could provide greater insight into protein stability. Because carbonyl groups are abundant in biomolecules, the current study used 2D IR spectroscopy and molecular dynamics simulations to compare the hydrogen-bond dynamics of the solute's carbonyl group in aqueous solution, with and without the presence of DMSO as a cosolvent. 2D IR spectroscopy was used to quantitatively estimate the time scales of the hydrogen-bond dynamics of the carbonyl group in neat water and 1:1 DMSO/water solution. The 2D IR results show spectral signatures of a chemical exchange process: The presence of the cosolvent was found to lower the hydrogen-bond exchange rate by a factor of 5. The measured exchange rates were 7.50 × 10(11) and 1.48 × 10(11) s(-1) in neat water and 1:1 DMSO/water, respectively. Molecular dynamics simulations predict a significantly shorter carbonyl hydrogen-bond lifetime in neat water than in 1:1 DMSO/water and provide molecular insights into the exchange mechanism. The binding of the cosolvent to the solute was found to be accompanied by the release of hydrogen-bonded water molecules to the bulk. The widely different hydrogen-bond lifetimes and exchange rates with and without DMSO indicate a significant change in the ultrafast hydrogen-bond dynamics in the presence of a cosolvent, which, in turn, might play an important role in the stability and activity of biomolecules.