Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Detection of chiral sum frequency generation vibrational spectra of proteins and peptides at interfaces in situ.

ABSTRACT: In this work, we demonstrate the feasibility to collect off-electronic resonance chiral sum frequency generation (SFG) vibrational spectra from interfacial proteins and peptides at the solid/liquid interface in situ. It is difficult to directly detect a chiral SFG vibrational spectrum from interfacial fibrinogen molecules. By adopting an interference enhancement method, such a chiral SFG vibrational spectrum can be deduced from interference spectra between the normal achiral spectrum and the chiral spectrum. We found that the chiral SFG vibrational spectrum of interfacial fibrinogen was mainly contributed by the beta-sheet structure. For a beta-sheet peptide tachyplesin I, which may be quite ordered at the solid/liquid interface, chiral SFG vibrational spectra can be collected directly. We believe that these chiral signals are mainly contributed by electric dipole contributions, which can dominate the chiroptical responses of uniaxial systems. For the first time, to our knowledge, this work indicates that the off-electronic resonance SFG technique is sensitive enough to collect chiral SFG vibrational spectra of interfacial proteins and peptides, providing more structural information to elucidate interfacial protein and peptide structures.

SUBMITTER: Wang J

PROVIDER: S-EPMC555967 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Chiral sum frequency generation for in situ probing proton exchange in antiparallel β-sheets at interfaces.

Project description:Studying hydrogen/deuterium (H/D) exchange in proteins can provide valuable insight on protein structure and dynamics. Several techniques are available for probing H/D exchange in the bulk solution, including NMR, mass spectroscopy, and Fourier transform infrared spectroscopy. However, probing H/D exchange at interfaces is challenging because it requires surface-selective methods. Here, we introduce the combination of in situ chiral sum frequency generation (cSFG) spectroscopy and ab initio simulations of cSFG spectra as a powerful methodology to probe the dynamics of H/D exchange at interfaces. This method is applied to characterize H/D exchange in the antiparallel β-sheet peptide LK7β. We report here for the first time that the rate of D-to-H exchange is about 1 order of magnitude faster than H-to-D exchange in the antiparallel structure at the air/water interface, which is consistent with the existing knowledge that O-H/D dissociation in water is the rate-limiting step, and breaking the O-D bond is slower than breaking the O-H bond. The reported analysis also provides fundamental understanding of several vibrational modes and their couplings in peptide backbones that have been difficult to characterize by conventional methods, including Fermi resonances of various combinations of peptide vibrational modes such as amide I and amide II, C-N stretch, and N-H/N-D bending. These results demonstrate cSFG as a sensitive technique for probing the kinetics of H/D exchange in proteins at interfaces, with high signal-to-noise N-H/N-D stretch bands that are free of background from the water O-H/O-D stretch.

| S-EPMC9208335 | biostudies-literature

Chiral Inversion of Amino Acids in Antiparallel β-Sheets at Interfaces Probed by Vibrational Sum Frequency Generation Spectroscopy.

Project description:A parallel study of protein variants with all (l-), all (d-), or mixed (l-)/(d-) amino acids can be used to assess how backbone architecture versus side chain identity determines protein structure. Here, we investigate the secondary structure and side chain orientation dynamics of the antiparallel β-sheet peptide LK7β (Ac-Leu-Lys-Leu-Lys-Leu-Lys-Leu-NH2) composed of all (l-), all (d-), or alternating (l-Leu)/(d-Lys) amino acids. Using interface-selective vibrational sum frequency generation spectroscopy (VSFG), we observe that the alternating (l-)/(d-) peptide lacks a resonant C-H stretching mode compared to the (l-) and (d-) variants and does not form antiparallel β-sheets. We rationalize our observations on the basis of density functional theory calculations and molecular dynamics (MD) simulations of LK7β at the air-water interface. Irrespective of the handedness of the amino acids, leucine side chains prefer to orient toward the hydrophobic air phase while lysine side chains prefer the hydrophilic water phase. These preferences dictate the backbone configuration of LK7β and thereby the folding of the peptide. Our MD simulations show that the preferred side chain orientations can force the backbone of a single strand of (l-) LK7β at the air-water interface to adopt β-sheet Ramachandran angles. However, denaturation of the β-sheets at pH = 2 results in a negligible chiral VSFG amide I response. The combined computational and experimental results lend critical support to the theory that a chiral VSFG response requires macroscopic chirality, such as in β-sheets. Our results can guide expectations about the VSFG optical responses of proteins and should improve understanding of how amino acid chirality modulates the structure and function of natural and de novo proteins at biological interfaces.

| S-EPMC9059514 | biostudies-literature

In situ sum-frequency vibrational spectroscopy of electrochemical interfaces with surface plasmon resonance.

Project description:Electrochemical (EC) reactions are crucial in many applications, yet most EC analytical tools lack the sensitivity to access molecular-level information of reactants and products. By combining sum-frequency vibrational spectroscopy and surface plasmon resonance at EC interfaces, we demonstrate the feasibility of measuring in situ and real-time vibrational spectra during EC reactions at noble metal electrodes. Application of the technique to EC reactions at a gold surface helps in understanding how the surface in a basic solution is oxidized and reduced during a cyclic voltammetry cycle. Study of desorption of a thiol self-assembled monolayer from gold through EC reactions in a basic solution shows that the desorbed thiols by reductive reaction remain as an ordered layer near the gold interface, but do diffuse away if they are desorbed oxidatively from gold.

| S-EPMC3910618 | biostudies-literature

Quantifying Double-Layer Potentials at Liquid-Gas Interfaces from Vibrational Sum-Frequency Generation.

Project description:Vibrational sum-frequency generation (SFG) spectroscopy is demonstrated as a fast method to quantify variations of the electric double-layer potential ϕ0 at liquid-gas interfaces. For this, mixed solutions of nonionic tetraethyleneglycol-monodecylether (C10E4) and cationic hexadecyltrimethylammonium bromide (C16TAB) surfactants were investigated using SFG spectroscopy and a thin-film pressure balance (TFPB). Derjaguin-Landau-Verwey-Overbeek analysis of disjoining pressure isotherms obtained with the TFPB technique provides complementary information on ϕ0, which we apply to validate the results from SFG spectroscopy. By using a single ϕ0 value, we can disentangle χ(2) and χ(3) contributions to the O-H stretching modes of interfacial water molecules in the SFG spectra. Having established the latter, we show that unknown double-layer potentials at the liquid-gas interface from solutions with different C16TAB/C10E4 mixing ratios can be obtained from an analysis of SFG spectra and are in excellent agreement with the complementary results from the TFPB technique.

| S-EPMC6354727 | biostudies-literature

In situ molecular level studies on membrane related peptides and proteins in real time using sum frequency generation vibrational spectroscopy.

Project description:Sum frequency generation (SFG) vibrational spectroscopy has been demonstrated to be a powerful technique to study the molecular structures of surfaces and interfaces in different chemical environments. This review summarizes recent SFG studies on hybrid bilayer membranes and substrate-supported lipid monolayers and bilayers, the interaction between peptides/proteins and lipid monolayers/bilayers, and bilayer perturbation induced by peptides/proteins. To demonstrate the ability of SFG to determine the orientations of various secondary structures, studies on the interactions between different peptides/proteins (melittin, G proteins, alamethicin, and tachyplesin I) and lipid bilayers are discussed. Molecular level details revealed by SFG in these studies show that SFG can provide a unique understanding on the interactions between a lipid monolayer/bilayer and peptides/proteins in real time, in situ and without any exogenous labeling.

| S-EPMC2753614 | biostudies-other

Characterization of Parallel β-Sheets at Interfaces by Chiral Sum Frequency Generation Spectroscopy.

Project description:Characterization of protein secondary structures at interfaces is still challenging due to the limitations of surface-selective optical techniques. Here, we address the challenge of characterizing parallel β-sheets by combining chiral sum frequency generation (SFG) spectroscopy and computational modeling. We focus on human islet amyloid polypeptide aggregates and a de novo designed short polypeptide at lipid/water and air/glass interfaces. We find that parallel β-sheets adopt distinct orientations at various interfaces and exhibit characteristic chiroptical responses in the amide I and N-H stretch regions. Theoretical analysis indicates that the characteristic chiroptical responses provide valuable information on the symmetry, orientation, and vibrational couplings of parallel β-sheet at interfaces.

| S-EPMC6022735 | biostudies-literature

Disentangling Sum-Frequency Generation Spectra of the Water Bending Mode at Charged Aqueous Interfaces.

Project description:The origin of the sum-frequency generation (SFG) signal of the water bending mode has been controversially debated in the past decade. Unveiling the origin of the signal is essential, because different assignments lead to different views on the molecular structure of interfacial water. Here, we combine collinear heterodyne-detected SFG spectroscopy at the water-charged lipid interfaces with systematic variation of the salt concentration. The results show that the bending mode response is of a dipolar, rather than a quadrupolar, nature and allows us to disentangle the response of water in the Stern and the diffuse layers. While the diffuse layer response is identical for the oppositely charged surfaces, the Stern layer responses reflect interfacial hydrogen bonding. Our findings thus corroborate that the water bending mode signal is a suitable probe for the structure of interfacial water.

| S-EPMC8279539 | biostudies-literature

Theoretical Sum Frequency Generation Spectroscopy of Peptides.

Project description:Vibrational sum frequency generation (SFG) has become a very promising technique for the study of proteins at interfaces, and it has been applied to important systems such as anti-microbial peptides, ion channel proteins, and human islet amyloid polypeptide. Moreover, so-called "chiral" SFG techniques, which rely on polarization combinations that generate strong signals primarily for chiral molecules, have proven to be particularly discriminatory of protein secondary structure. In this work, we present a theoretical strategy for calculating protein amide I SFG spectra by combining line-shape theory with molecular dynamics simulations. We then apply this method to three model peptides, demonstrating the existence of a significant chiral SFG signal for peptides with chiral centers, and providing a framework for interpreting the results on the basis of the dependence of the SFG signal on the peptide orientation. We also examine the importance of dynamical and coupling effects. Finally, we suggest a simple method for determining a chromophore's orientation relative to the surface using ratios of experimental heterodyne-detected signals with different polarizations, and test this method using theoretical spectra.

| S-EPMC4516311 | biostudies-other

Momentum-dependent sum-frequency vibrational spectroscopy of bonded interface layer at charged water interfaces

Project description:Interface-specific hydrogen (H)–bonding network of water directly controls the energy transfer and chemical reaction pathway at many charged aqueous interfaces, yet to characterize these bonded water layer structures remains a challenge. We now develop a sum-frequency spectroscopic scheme with varying photon momenta as an all-optic solution for retrieving the vibrational spectra of the bonded water layer and the ion diffuse layer and, hence, microscopic structural and charging information about an interface. Application of the method to a model surfactant-water interface reveals a hidden weakly donor H-bonded water species, suggesting an asymmetric hydration-shell structure of fully solvated surfactant headgroups. In another application to a zwitterionic phosphatidylcholine lipid monolayer–water interface, we find a highly polarized bonded water layer structure associating to the phosphatidylcholine headgroup, while the diffuse layer contribution is experimentally proven to be negligible. Our all-optic method offers an in situ microscopic probe of electrochemical and biological interfaces and the route toward future imaging and ultrafast dynamics studies. Momentum-varying optical technique unveils interfacial water structure that controls energy transfer and chemistry at interfaces.

| S-EPMC10096568 | biostudies-literature

Adding a dimension to the infrared spectra of interfaces using heterodyne detected 2D sum-frequency generation (HD 2D SFG) spectroscopy.

Project description:In the last ten years, two-dimensional infrared spectroscopy has become an important technique for studying molecular structures and dynamics. We report the implementation of heterodyne detected two-dimensional sum-frequency generation (HD 2D SFG) spectroscopy, which is the analog of 2D infrared (2D IR) spectroscopy, but is selective to noncentrosymmetric systems such as interfaces. We implement the technique using mid-IR pulse shaping, which enables rapid scanning, phase cycling, and automatic phasing. Absorptive spectra are obtained, that have the highest frequency resolution possible, from which we extract the rephasing and nonrephasing signals that are sometimes preferred. Using this technique, we measure the vibrational mode of CO adsorbed on a polycrystalline Pt surface. The 2D spectrum reveals a significant inhomogenous contribution to the spectral line shape, which is quantified by simulations. This observation indicates that the surface conformation and environment of CO molecules is more complicated than the simple "atop" configuration assumed in previous work. Our method can be straightforwardly incorporated into many existing SFG spectrometers. The technique enables one to quantify inhomogeneity, vibrational couplings, spectral diffusion, chemical exchange, and many other properties analogous to 2D IR spectroscopy, but specifically for interfaces.

| S-EPMC3248474 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data