Direct observation of protein structural transitions through entire amyloid aggregation processes in water using 2D-IR spectroscopy

Chun, So Yeon; Son, Myung Kook; Park, Chae Ri; Lim, Chaiho; Kim, Hugh I.; Kwak, Kyungwon; Cho, Minhaeng

doi:10.1039/d1sc06047c

Cited by 23 publications

(29 citation statements)

References 65 publications

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“…Second, Raman spectroscopy itself is sufficiently sensitive to detect secondary structural elements of proteins via the analysis of the amide I band profile. Third, compared to infrared (IR) spectroscopy and microscopy, which is not suitable for the study of protein structures in ordinary water due to the spectral overlap between H 2 O bending and the amide I band, 29 Raman microspectroscopy takes advantage of the fact that H 2 O bending has a low Raman intensity, thus avoiding the need to use D 2 O. 30 Fourth, in addition to the characterization of the amide I bands, the O-D stretching band of HOD in isotopically dilute solutions provides information about the local water structure 31,32 inside and outside the droplet.…”

Section: Introductionmentioning

confidence: 99%

Micro-Raman spectroscopic analysis of liquid–liquid phase separation

Choi

Chun

Kwak

et al. 2023

Phys. Chem. Chem. Phys.

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Section: Introductionmentioning

confidence: 99%

Micro-Raman spectroscopic analysis of liquid–liquid phase separation

Choi

Chun

Kwak

et al. 2023

Phys. Chem. Chem. Phys.

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“…3D-IR-DOSY is a powerful analytical tool, opening up novel applications of 2D-IR to study supramolecular complexes, self-assembly protein fibers, and amyloids. Since recent work has demonstrated the potential of 2D-IR as a biomedical and diagnostic tool, [22,[29][30][31] this new method might also contribute to further develop 2D-IR for biomedical investigations. Performing 3D-IR-DOSY experiments with IR-compatible microfluidics [32] should make the sample injection in such experiments comparatively simple.…”

Section: Femtosecond 3d-ir-dosymentioning

confidence: 99%

Infrared Diffusion‐Ordered Spectroscopy Reveals Molecular Size and Structure**

et al. 2022

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Inspired by ideas from NMR, we have developed Infrared Diffusion-Ordered Spectroscopy (IR-DOSY), which simultaneously characterizes molecular structure and size. We rely on the fact that the diffusion coefficient of a molecule is determined by its size through the Stokes-Einstein relation, and achieve sensitivity to the diffusion coefficient by creating a concentration gradient and tracking its equilibration in an IR-frequency resolved manner. Analogous to NMR-DOSY, a two-dimensional IR-DOSY spectrum has IR frequency along one axis and diffusion coefficient (or equivalently, size) along the other, so the chemical structure and the size of a compound are characterized simultaneously. In an IR-DOSY spectrum of a mixture, molecules with different sizes are nicely separated into distinct sets of IR peaks. Extending this idea to higher dimensions, we also perform 3D-IR-DOSY, in which we combine the conformation sensitivity of femtosecond multi-dimensional IR spectroscopy with size sensitivity.

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“…A recent study focused on the length scale, showing that the presence of a protein surface perturbs the structural ordering of hydration layer water molecules and characterizes their distinct dynamical behavior . There are also studies highlighting the function of water molecules in mediating peptide–peptide interactions in amyloid aggregation/fibril elongation. − …”

Section: Introductionmentioning

confidence: 99%

Exploring the Heterogeneous Dynamical Environment at the Interface of Aβ₄₂ Peptide in Aqueous Ionic Liquid Solution

et al. 2023

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In this study, we have investigated the heterogeneous dynamical environment around an ensemble of full-length amyloid-β (Aβ 42 ) peptide monomers in binary aqueous solution containing the ionic liquid (IL) 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM][BF 4 ] as a co-solvent. Atomistic molecular dynamics (MD) simulations have been employed with the aim of understanding the effect of the IL on the distribution of water molecules and IL components around distinct segments of the peptide. As compared to pure aqueous medium, locally heterogeneous restricted water motions at the interface have been spotted in the presence of the IL. Our calculations revealed faster diffusion of water molecules hydrating hydrophilic segments (Nterm and turn) as opposed to that around hydrophobic segments (hp1, hp2, and C-term). The extent of non-uniform restriction on the center-of-mass motions as well as the reorientation of water molecules and IL ions have been similarly affected in the binary IL−water solution. The effects of IL on the formation of hydrogen bond networks have been evident from the longer hydrogen bond relaxation time scales of peptide−water, with only a small fraction of peptide−anion hydrogen bonds contributing to the structural relaxation. Due to the size and shape factors, the increasingly sluggish dynamics of the IL components in the solvation shell can be attributed to a longer time scale for the onset of maximum dynamic heterogeneity. Interestingly, the water molecules around the polar segments of the peptide take longer to attain dynamic heterogeneity, which intensifies in the presence of IL. These calculations clearly suggest that electrostatic interaction plays a crucial role in water-mediated peptide−IL interaction, thereby shielding the surface from hydrophobic collapse and preventing possible further growth of the monomers into fibrils at higher peptide concentrations.

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Direct observation of protein structural transitions through entire amyloid aggregation processes in water using 2D-IR spectroscopy

Abstract: Amyloid proteins that undergo self-assembly to form insoluble fibrillar aggregates have attracted much attention due to their role in biological and pathological significance in amyloidosis. This study aims to understand...

Cited by 23 publications

References 65 publications

Micro-Raman spectroscopic analysis of liquid–liquid phase separation

Micro-Raman spectroscopic analysis of liquid–liquid phase separation

Infrared Diffusion‐Ordered Spectroscopy Reveals Molecular Size and Structure**

Exploring the Heterogeneous Dynamical Environment at the Interface of Aβ₄₂ Peptide in Aqueous Ionic Liquid Solution

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Direct observation of protein structural transitions through entire amyloid aggregation processes in water using 2D-IR spectroscopy

Abstract: Amyloid proteins that undergo self-assembly to form insoluble fibrillar aggregates have attracted much attention due to their role in biological and pathological significance in amyloidosis. This study aims to understand...

Cited by 23 publications

References 65 publications

Micro-Raman spectroscopic analysis of liquid–liquid phase separation

Micro-Raman spectroscopic analysis of liquid–liquid phase separation

Infrared Diffusion‐Ordered Spectroscopy Reveals Molecular Size and Structure**

Exploring the Heterogeneous Dynamical Environment at the Interface of Aβ42 Peptide in Aqueous Ionic Liquid Solution

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Exploring the Heterogeneous Dynamical Environment at the Interface of Aβ₄₂ Peptide in Aqueous Ionic Liquid Solution