Using 2D-IR Spectroscopy to Measure the Structure, Dynamics, and Intermolecular Interactions of Proteins in H₂O

Accounts of Chemical Research, Journal Year: 2024, Volume and Issue: 57(5), P. 685 - 692

Published: Feb. 16, 2024

ConspectusInfrared (IR) spectroscopy probes molecular structure at the level of chemical bond or functional group. In case proteins, most informative band in IR spectrum is amide I band, which arises predominantly from C═O stretching vibration peptide link. The folding proteins into secondary and tertiary structures leads to vibrational coupling between units, generating specific spectral signatures that provide a fingerprint macromolecular conformation. Ultrafast two-dimensional (2D-IR) allows protein be spread over second frequency dimension way mirrors 2D-NMR methods. This means 2D-IR produces map exquisitely sensitive dynamics so provides detailed insights cannot matched by absorption spectroscopy. As result, has emerged as powerful tool for probing broad range time length scales solution phase room temperature. However, coincides with an bending water (δHOH), natural biological solvent. To circumvent this problem, studies are routinely performed D2O solutions because H/D substitution shifts solvent mode (δDOD) lower frequency, revealing band. While effective, method raises fundamental questions regarding impact change mass on structural solvation removal energetic resonance solute.In Account, series applying study H2O-rich solvents reviewed. A comparison protein-containing fluids used demonstrate basis approach before applications presented. These measurements biophysics recent machine learning gain insight protein–drug binding complex mixtures. An outlook presented, considering potential contribute our understanding behavior under near-physiological conditions, along evaluation obstacles still need overcome.

Language: Английский

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pH‐Gated Switch of LCST‐UCST Phase Transition of Hydrogels

Advanced Functional Materials, Journal Year: 2024, Volume and Issue: unknown

Published: May 14, 2024

Abstract Temperature‐responsive hydrogels including lower critical solution temperature (LCST)‐ and upper (UCST)‐type are attractive in various fields. However, the swift switch between LCST UCST stimuli‐responsive behaviors remains intriguing challenging. Here is reported a kind of hydrogel with pH‐gated response behaviors. This achieved using hydrogen bonding carboxylic acid groups poly(acrylic acid‐ co ‐acrylamide) hydroxyl hydroxypropyl cellulose (HPC). The ‐acrylamide)‐HPC (PACA‐HPC) exhibit reversible LCST‐UCST phase transition behavior. When transparent PACA‐HPC placed an bath, COO − get protonated, rapidly forming bonds HPC to render light‐scattering state making opaque. Furthermore, opaque exhibits behavior at 20–45 °C. PCAC‐HPC alkaline environment, hydrogen‐bonded complexes gradually dissociate as COOH deprotonated form homogeneous state. 20–45° C. Therefore, shown strategy fabricate tunable responses. With this switchable LCST/UCST responsive behaviors, demonstrated its applications smart windows information encryption.

Language: Английский

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Dissecting the hydrogen bond network of water: Charge transfer and nuclear quantum effects

Science, Journal Year: 2024, Volume and Issue: 386(6726)

Published: Oct. 24, 2024

The molecular structure of water is dynamic, with intermolecular hydrogen (H) bond interactions being modified by both electronic charge transfer and nuclear quantum effects (NQEs). Electronic NQEs potentially change under acidic or basic conditions, but such details have not been measured. In this work, we developed correlated vibrational spectroscopy, a symmetry-based method that separates interacting from noninteracting molecules in self- cross-correlation spectra, giving access to previously inaccessible information. We found hydroxide (OH − ) donated ~8% more negative the H network water, hydronium (H 3 O + accepted ~4% less water. Deuterium oxide (D 2 O) had ~9% bonds compared O), solutions displayed dominant than ones.

Language: Английский

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Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(11)

Published: March 7, 2024

Water is known to play an important role in collagen self-assembly, but it still largely unclear how water–collagen interactions influence the assembly process and determine fibril network properties. Here, we use H 2 O/D O isotope effect on hydrogen-bond strength water investigate of hydration self-assembly. We dissolve D compare growth kinetics structure assemblies formed these isotopomers. Surprisingly, occurs ten times faster than O, self-assembles into much thinner fibrils, that form a more inhomogeneous softer network, with fourfold reduction elastic modulus when compared O. Combining spectroscopic measurements atomistic simulations, show less hydrated This partial dehydration lowers enthalpic penalty for removal reorganization at collagen–water interface, increasing self-assembly rate number nucleation centers, leading fibrils network. Coarse-grained simulations acceleration initial can be reproduced by enhancement electrostatic interactions. These results acts as mediator between monomers, modulating their so optimize and, thus, final believe isotopically proteins valuable method protein structural dynamics

Language: Английский

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Role of Heavy Water in the Synthesis and Nanocatalytic Activity of Gold Nanoparticles

ACS Nanoscience Au, Journal Year: 2025, Volume and Issue: 5(1), P. 52 - 59

Published: Jan. 7, 2025

Heavy water (D2O) has found extensive application as a moderator in nuclear reactors. Additionally, it serves substitute for regular (H2O) biological or spectroscopic experiments, providing deuterium source and addressing challenges related to solvent opacity contrast. This is particularly relevant experiments involving neutron scattering, infrared absorption, magnetic resonance. However, replacing H2O with D2O not always straightforward harmless substitution can instead have unintended chemical consequences. In this study, we highlight the significant impact of deuteration on two common gold nanoparticle syntheses-borohydride reduction ascorbic acid reduction-by comparing reactions mixtures thereof. The resulting colloids exhibit differences size spectral characteristics, their effectiveness nanocatalysts widely used 4-nitrophenol benchmark reaction adversely affected by presence during both particle synthesis catalytic medium. Ultimately, these results underscore critical awareness often overlooked scientists engineers: despite its widespread sometimes indispensable use analytical spectroscopy, cellular imaging, biophysics, organic chemistry, cannot truly replace without significantly altering environment reaction.

Language: Английский

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High-speed cryo-microscopy reveals that ice-nucleating proteins of Pseudomonas syringae trigger freezing at hydrophobic interfaces

Science Advances, Journal Year: 2024, Volume and Issue: 10(27)

Published: July 3, 2024

Ice-nucleating proteins (INpro) trigger the freezing of supercooled water droplets relevant to atmospheric, biological, and technological applications. The high ice nucleation activity INpro isolated from bacteria

Language: Английский

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Experimental two-dimensional infrared spectra of methyl thiocyanate in water and organic solvents

The Journal of Chemical Physics, Journal Year: 2024, Volume and Issue: 160(11)

Published: March 15, 2024

Thiocyanates, nitriles, and azides represent a versatile set of vibrational probes to measure the structure dynamics in biological systems. The are minimally perturbative, nitrile stretching mode appears an otherwise uncongested spectral region, spectra report on local environment around probe. Nitrile frequencies lineshapes, however, difficult interpret, theoretical models that connect environments with often necessary. However, development both more accurate intuitive remains challenge for community. present work provides experimentally consistent collection experimental measurements, including IR absorption ultrafast two-dimensional infrared (2D IR) spectra, serve as benchmark future models. Specifically, we catalog methyl thiocyanate (MeSCN) fourteen different solvents, non-polar, polar, protic solvents. Absorption indicate π-interactions may be responsible line shape differences observed between aromatic aliphatic alcohols. We also demonstrate recent Kamlet-Taft formulation describes center frequency MeSCN. Furthermore, cryogenic lead insights into peak asymmetry aprotic 2D measured solvents hydrogen bonding static inhomogeneity. expect these insights, along publicly available dataset, will useful continue advancing capable quantitatively describing relation environments, shapes, probes.

Language: Английский

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Contrast and Contrast Variation in Neutron, X-ray, and Light Scattering

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 151 - 181

Published: Jan. 1, 2025

Language: Английский

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Probing DNA melting behaviour under vibrational strong coupling

QRB Discovery, Journal Year: 2025, Volume and Issue: 6

Published: Jan. 1, 2025

Abstract Manipulating matter by strong coupling to the vacuum field has attracted intensive interests over last decade. In particular, vibrational (VSC) shown great potential for modifying ground state properties in solution chemistry and biochemical processes. this work, effect of VSC water on melting behaviour ds-DNA, an important biophysical process, is explored. Several experimental conditions, including concentration cavity profile, environment, as well thermal annealing treatment, were tested. No significant was observed ds-DNA sequence used. This demonstrates yet again robustness outside perturbations. Our work also provides a general protocol probe effects biological systems inside microfluid Fabry–Perot cavities should be beneficial better understand harness phenomenon.

Language: Английский

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Observation of Solvent Enantio-Isotope Effect in Asymmetric Ring-Opening of Cyclic Diaryliodoniums with Selenocyanate

Chemical Science, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

The deuterium isotope effect of D 2 O enhanced the enantioselectivity in an aqueous emulsion reaction, enabling Cu/PyBox-catalyzed highly chemo- and enantioselective ring-opening cyclic diaryliodoniums with KSeCN.

Language: Английский

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