Increased accuracy of vibrational circular dichroism calculations for isotopically labeled helical peptides.

Vibrational circular dichroism (VCD) spectra have been computed with qualitatively correct sign patterns for α-helical peptides using various methods, ranging from empirical models to ab initio quantum mechanical computations. However, some details, such as deuteration effects and isotope substitution shifts and sign patterns for the resultant amide I' band shape, have remained a predictive challenge. Fully optimized computations for a 25-residue Ala-rich peptide, including implicit solvent corrections and explicit side chains that experimentally stabilize these model helical peptides in water, have been carried out using density functional theory (DFT).

Monitoring peptide tyrosine nitration by spectroscopic methods.

Oxidative stress can lead to various derivatives of the tyrosine residue in peptides and proteins. A typical product is 3-nitro-L-tyrosine residue (Nit), which can affect protein behavior during neurodegenerative processes, such as those associated with Alzheimer's and Parkinson's diseases. Surface enhanced Raman spectroscopy (SERS) is a technique with potential for detecting peptides and their metabolic products at very low concentrations.

Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques.

Peptides and proteins are naturally chiral molecular systems so that sensing their structure and conformation with chirality-based spectral methods is an obvious and long-used diagnostic application. Extending chiroptical techniques to measurement of vibrational transitions, in the form of vibrational circular dichroism (VCD) and Raman optical activity (ROA), expands the number and types of excitations available that might provide structural insight and can provide an alternate and, in some cases, a more distinctive conformational probe. Since the dominant repeating structural element in peptides is the locally achiral amide group, VCD senses the polymeric structure through amide coupling, which is directly dependent on secondary structure.

Enhanced Sensitivity to Local Dynamics in Peptides by Use of Temperature-Jump IR Spectroscopy and Isotope Labeling.

Site-specific isotopic labeling of molecules is a widely used approach in IR spectroscopy to resolve local contributions to vibrational modes. The induced frequency shift of the corresponding IR band depends on the substituted masses, as well as on hydrogen bonding and vibrational coupling. The impact of these different factors was analyzed with a designed three-stranded β-sheet peptide and by use of selected C isotope substitutions at multiple positions in the peptide backbone.

β-Type Amyloidlike Fibrils of Poly-l-glutamic Acid Convert into Long, Highly Ordered Helices upon Dissolution in Dimethyl Sulfoxide.

Replacing water with dimethyl sulfoxide (DMSO) completely reshapes the free-energy landscapes of solvated proteins. In DMSO, a powerful hydrogen-bond (HB) acceptor, formation of HBs between backbone NH groups and solvent is favored over HBs involving protein's carbonyl groups. This entails a profound structural disruption of globular proteins and proteinaceous aggregates (e.

Isotopically Site-Selected Dynamics of a Three-Stranded β-Sheet Peptide Detected with Temperature-Jump Infrared-Spectroscopy.

Infrared detected temperature-jump (T-jump) spectroscopy and site-specific isotopic labeling were applied to study a model three-stranded β-sheet peptide with the goal of individually probing the dynamics of strand and turn structural elements. This peptide had two Pro-Gly (pG) turn sequences to stabilize the two component hairpins, which were labeled with C═O on each of the Gly residues to resolve them spectroscopically. Labeling the second turn on the amide preceding the Pro (Xxx-Pro amide) provided an alternate turn label as a control.

Vibrational Circular Dichroism Sheds New Light on the Competitive Effects of Crowding and β-Synuclein on the Fibrillation Process of α-Synuclein.

The effects of crowding, using the crowding agent Ficoll 70, and the presence of β-synuclein on the fibrillation process of α-synuclein were studied by spectroscopic techniques, transmission electron microscopy, and thioflavin T assays. This combined approach, in which all techniques were applied to the same original sample, generated an unprecedented understanding of the effects of these modifying agents on the morphological properties of the fibrils. Separately, crowding gives rise to shorter mutually aligned fibrils, while β-synuclein leads to branched, short fibrils.

Instrumentation for Vibrational Circular Dichroism Spectroscopy: Method Comparison and Newer Developments.

Vibrational circular dichroism (VCD) is a widely used standard method for determination of absolute stereochemistry, and somewhat less so for biomolecule characterization and following dynamic processes. Over the last few decades, different VCD instrument designs have developed for various purposes, and reliable commercial instrumentation is now available. This review will briefly survey historical and currently used instrument designs and describe some aspects of more recently reported developments.

Theory of Molecular Vibrational Zeeman Effects as Measured with Circular Dichroism.

We present a general theory that enables the first nonempirical computation of molecular vibrational Zeeman effects as are detectable with magnetic vibrational circular dichroism spectroscopy (MVCD). In this method, the second derivatives of the molecular magnetic moment appear to be essential to determine the observable MVCD intensities. Using a quasiharmonic approximation, computations based on our method allowed a band-to-band comparison of simulated to measured spectra.

Mini review: Instrumentation for vibrational circular dichroism spectroscopy, still a role for dispersive instruments.

Vibrational circular dichroism (VCD) has become a standard method for determination of absolute stereochemistry, particularly now that reliable commercial instrumentation has become available. These instruments use a now well-documented Fourier transform infrared-based approach to measure VCD that has virtually displaced initial dispersive infrared-based designs. Nonetheless, many papers have appeared reporting dispersive VCD data, especially for biopolymers.

Role of Aromatic Cross-Links in Structure and Dynamics of Model Three-Stranded β-Sheet Peptides.

A series of closely related peptide sequences that form triple-strand structures was designed with a variation of cross-strand aromatic interactions and spectroscopically studied as models for β-sheet formation and stabilities. Structures of the three-strand models were determined with NMR methods and temperature-dependent equilibrium studies performed using circular dichroism and Fourier transform infrared spectroscopies. Our equilibrium data show that the presence of a direct cross-strand aromatic contact in an otherwise folded peptide does not automatically result in an increased thermal stability and can even distort the structure.

Sensing site-specific structural characteristics and chirality using vibrational circular dichroism of isotope labeled peptides.

Isotope labeling has a long history in chemistry as a tool for probing structure, offering enhanced sensitivity, or enabling site selection with a wide range of spectroscopic tools. Chirality sensitive methods such as electronic circular dichroism are global structural tools and have intrinsically low resolution. Consequently, they are generally insensitive to modifications to enhance site selectivity.

Engineering a Novel Porin OmpGF Via Strand Replacement from Computational Analysis of Sequence Motif.

β-Barrelmembrane proteins (βMPs) form barrel-shaped pores in the outer membrane of Gram-negative bacteria, mitochondria, and chloroplasts. Because of the robustness of their barrel structures, βMPs have great potential as nanosensors for single-molecule detection. However, natural βMPs currently employed have inflexible biophysical properties and are limited in their pore geometry, hindering their applications in sensing molecules of different sizes and properties.

Structural Rearrangement from Oligomer to Fibril Detected with FRET in a Designed Amphiphilic Peptide.

β-Sheet conformation is promoted in peptides with amphiphilic design, and stable β-turn formation is favored with the unnatural amino acid d-Pro followed by a flexible residue such as Gly. A 19-residue peptide (B3) was synthesized with alternating hydrophobic and hydrophilic residues connected by symmetrical d-Pro-Gly and Gly-d-Pro turns. B3 forms an oligomeric aggregate, rich in β-sheet conformation, that reversibly transforms into an unordered structure on heating, as evidenced by its temperature-dependent IR spectra.

Reduced and mutant lysozyme refolding with lipid vesicles. Model study of disulfide impact on equilibria and dynamics.

The recovery of secondary structure in disordered, disulfide-reduced hen egg white lysozyme (HEWL) upon interaction with lipid vesicles was studied using circular dichroism (CD), fluorescence and infrared (IR) spectroscopic techniques. Lipid vesicles having negative head groups, such as DMPG, interact with reduced HEWL to induce formation of more helical structure than in native HEWL, but no stable tertiary structure was evident. Changes in tertiary structure, as evidenced by local environment of the tryptophan residues, were monitored by fluorescence.

Collagen-collagen interactions mediated by plant-derived proanthocyanidins: A spectroscopic and atomic force microscopy study.

Unlabelled: Collagen cross-linkings are determinant of biological tissue stability and function. Plant-derived proanthocyanidins (PACs) mimic different hierarchical levels of collagen cross-links by non-enzymatic interactions resulting in the enhancement to the biomechanics and biostability of collagen-rich tissues such as dentin. This study investigated the interaction of PACs from Vitis vinifera grape seed extract with type I collagen in solubilized form and in the demineralized dentin matrix (DDM) by fluorescence spectral analysis; collagen-collagen binding forces in presence of cross-linking solutions by atomic force microscopy (AFM); and spectroscopic analysis of the DDM using attenuated total reflectance Fourier transform-infrared spectroscopy (ATR-FTIR).

Role of Side Chains in β-Sheet Self-Assembly into Peptide Fibrils. IR and VCD Spectroscopic Studies of Glutamic Acid-Containing Peptides.

Poly(glutamic acid) at low pH self-assembles after incubation at higher temperature into fibrils composed of antiparallel sheets that are stacked in a β2-type structure whose amide carbonyls have bifurcated H-bonds involving the side chains from the next sheet. Oligomers of Glu can also form such structures, and isotope labeling has provided insight into their out-of-register antiparallel structure [ Biomacromolecules 2013 , 14 , 3880 - 3891 ]. In this paper we report IR and VCD spectra and transmission electron micrograph (TEM) images for a series of alternately sequenced oligomers, Lys-(Aaa-Glu)5-Lys-NH2, where Aaa was varied over a variety of polar, aliphatic, or aromatic residues.

Site-Specific Dynamics of β-Sheet Peptides with (D) Pro-Gly Turns Probed by Laser-Excited Temperature-Jump Infrared Spectroscopy.

Turn residues and side-chain interactions play an important role for the folding of β-sheets. We investigated the conformational dynamics of a three-stranded β-sheet peptide ((D) P(D) P) and a two-stranded β-hairpin (WVYY-(D) P) by time-resolved temperature-jump (T-jump) infrared spectroscopy. Both peptide sequences contain (D) Pro-Gly residues that favor a tight β-turn.

Dimethyl Sulfoxide Induced Destabilization and Disassembly of Various Structural Variants of Insulin Fibrils Monitored by Vibrational Circular Dichroism.

Dimethyl sulfoxide (DMSO) induced destabilization of insulin fibrils has been previously studied by Fourier transform infrared spectroscopy and interpreted in terms of secondary structural changes. The variation of this process for fibrils with different types of higher-order morphological structures remained unclear. Here, we utilize vibrational circular dichroism (VCD), which has been reported to provide a useful biophysical probe of the supramolecular chirality of amyloid fibrils, to characterize changes in the macroscopic chirality following DMSO-induced disassembly for two types of insulin fibrils formed under different conditions, at different reduced pH values with and without added salt and agitation.

Effect of hydrophobic interactions on the folding mechanism of β-hairpins.

Hydrophobic interactions are essential in stabilizing protein structures. How they affect the folding pathway and kinetics, however, is less clear. We used time-resolved infrared spectroscopy to study the dynamics of hydrophobic interactions of β-hairpin variants of the sequence Trpzip2 (SWTWENGKWTWK-NH2) that is stabilized by two cross-strand Trp-Trp pairs.

Arrangement of fibril side chains studied by molecular dynamics and simulated infrared and vibrational circular dichroism spectra.

Highly ordered assemblies of β-sheet-forming peptide and protein fibrils have been the focus of much attention because of their multiple and partially unknown biological functions, in particular as related to degenerative neuronal disorders. Recently, vibrational circular dichroism (VCD) spectra have been shown to provide a unique means of detection for such extended structures utilizing modes of the peptide main chain backbone. In the case of poly-glutamic acid, surprising VCD responses were also found for side chain modes.

Equilibrium and dynamic spectroscopic studies of the interaction of monomeric β-lactoglobulin with lipid vesicles at low pH.

β-Lactoglobulin (βLG) is a member of the lipocalin protein family that changes structure upon interacting with anionic surfactants and lipid vesicles under higher-pH conditions at which βLG is dimeric. In this study, a β-sheet to α-helix transformation was also observed for monomeric βLG obtained at pH 2.6 when it was mixed with small unilamellar vesicles (SUVs) of zwitterionic lipids, but being mixed with anionic lipids produced little change.

Insight into the packing pattern of β2 fibrils: a model study of glutamic acid rich oligomers with 13C isotopic edited vibrational spectroscopy.

Polyglutamic acid at low pH forms aggregates and self-assembles into a spiral, fibril-like superstructure formed as a β2-type sheet conformation that has a more compact intersheet packing than commonly found. This is stabilized by three-centered bifurcated hydrogen bonding of the amide carbonyl involving the protonated glutamic acid side chain. We report vibrational spectroscopic results and analyses for oligopeptides rich in glutamic acid enhanced with (13)C isotope labeling in a study modeling low pH poly-Glu self-assembly.

Infrared, vibrational circular dichroism, and Raman spectral simulations for β-sheet structures with various isotopic labels, interstrand, and stacking arrangements using density functional theory.

Infrared (IR), Raman, and vibrational circular dichroism (VCD) spectral variations for different β-sheet structures were studied using simulations based on density functional theory (DFT) force field and intensity computations. The DFT vibrational parameters were obtained for β-sheet fragments containing nine-amides and constrained to a variety of conformations and strand arrangements. These were subsequently transferred onto corresponding larger β-sheet models, normally consisting of five strands with ten amides each, for spectral simulations.

Structural analyses of experimental 13C edited amide I' IR and VCD for peptide β-sheet aggregates and fibrils using DFT-based spectral simulations.

In the preceding paper, computational models based on density functional theory (DFT) were presented to characterize the sensitivity of vibrational spectroscopic methods (IR, VCD, and Raman) to structural features of β-sheets. Isotopically edited amide I' IR for peptides labeled with (13)C in multiple different sites provides the most structurally distinct signatures of strand alignment, while VCD is sensitive to the sheet twist and intersheet stacking. In this report, we simulate the IR and VCD spectra for models approximating structures of four β-sheet forming peptides previously experimentally studied using these methods with (13)C isotopic editing.