The effect of disulfide bonds on protein folding,unfolding, and misfolding investigated by FT–Raman spectroscopy

Disulfide bond is relevant to many protein folding/unfolding functions and conformational diseases. To elucidate the effects of disulfide bonds on protein folding, unfolding, and misfolding, we performed Fourier transform–Raman measurements on serial chemical‐induced denaturations of bovine serum albumin (BSA). By directly monitoring Raman stretching at S–S (~507 cm⁻¹), S–H (~2566 cm⁻¹), amide I (1655 cm⁻¹ for α‐helix; 1667 cm⁻¹ for β‐sheet structure), and amide III (>1300 cm⁻¹ for α‐helix; 1246 cm⁻¹ for β‐sheet structure), the status of disulfide bonds and secondary structure of BSA at different states were elucidated. Both disulfide bonds and secondary structure (mostly in α‐helix) of BSA appeared relatively stable even when the protein was unfolded by urea solution. However, disulfide bonds were completely reduced and protein secondary structure changed from α‐helix to a relatively β‐sheet dominant when the protein was modified by the mixed solution of urea and dithiothreitol (urea/DTT). Adhering to these structural changes, the protein proceeded to different degrees of polymerization. BSA would aggregate into a high molecular mass (over 700 kDa) of protein ensemble when it was exposed to the mixed urea/DTT solution. An irreversible change in S–S/S–H conversion and secondary structure was responsible for protein misfolding. We demonstrate here that Fourier transform–Raman directly probe S–S/S–H conversion and secondary structural change of BSA at different states, and these results clearly indicate that disulfide bonds and secondary structure of BSA serve as concrete frameworks to stabilize protein structure. As the frameworks collapse, the protein undergoes an irreversible structural change and results in protein misfolding. Copyright © 2016 John Wiley & Sons, Ltd.     

Spectroscopic analysis of a dye–mineral composite–a Raman and FT‐IR study

In this investigation, we address the question of how organic thioindigo binds to inorganic palygorskite to form a pigment similar to Maya Blue. We also address how such binding, if it occurs, might be affected by varying the proportion of dye relative to that of the mineral, and by varying the length of heating time used in preparation of the pigment. In addition to samples of palygorskite and thioindigo both alone, four synthetic pigment samples were prepared; two samples of 8 wt.% dye, one heated at 170 °C for 3 h and one at 170 °C for 9 h, and two samples of 16 wt.% dye, one heated at 170 °C for 3 h and one at 170 °C for 9 h. All samples were examined using Fourier transform‐infrared (FT‐IR) and FT‐Raman spectroscopy. For the pigment samples, FT‐IR peaks at 1627 cm⁻¹ are attributed to a downshifted CO stretching mode of thioindigo due to dye–clay interaction. This interpretation is corroborated by FT‐Raman CO peaks with 14 cm⁻¹ shifts to lower wavenumber for the pigment relative to thioindigo alone. Additional Raman scattering between 550 cm⁻¹ and 650 cm⁻¹ also suggests dye–clay interaction through metal–oxygen bonding. We are thus led to the possibility of mostly hydrogen bonding between silanol and carbonyl at lower dye concentration, with a predominance of metal–oxygen bonding at higher dye concentration. Copyright © 2008 John Wiley & Sons, Ltd.     

Two‐dimensional correlation Raman spectroscopy for characterizing protein structure and dynamics

Since the initial introduction of the basic concept almost twenty years ago, two‐dimensional correlation spectroscopy (2DCoS) has become a popular analytical tool applicable to a broad range of science problems. Vibrational spectroscopy remains the major area of 2DCoS applications where infrared spectroscopy is the most popular technique followed by Raman and Near Infrared spectroscopies. An increasing number of publications over the past few years have established Raman 2DCoS as a powerful problem solving technique in protein studies. In this review we provide a critical survey of recent protein studies using the 2DCoS Raman approach. We also analyze common misconceptions and potential pitfalls in the interpretation of 2D correlation data. Over the past decade, there have been a number of publications pointing to artifacts associated with visualization and interpretation of 2D correlation maps. We demonstrate here how some of the ‘artifacts’ of the 2DCoS approach in ‐ reality turn into the strength of the method. Copyright © 2009 John Wiley & Sons, Ltd.     

Ultraviolet resonance Raman spectroscopy of a β‐sheet peptide: a model for membrane protein folding

The partitioning of a hydrophobic hexapeptide, N‐acetyl‐tryptophan‐pentaleucine (AcWL5), into self‐associated β‐sheets within a vesicle membrane was studied as a model for integral membrane protein folding and insertion via vibrational and electronic spectroscopy. Ultraviolet resonance Raman spectroscopy allows selective examination of the structures of amino acid side chains and the peptide backbone and provides information about local environment and molecular conformation. The secondary structure of AcWL5 within a vesicle membrane was investigated using 207.5‐nm excitation and found to consist of β‐sheets, in agreement with previous studies. The β‐sheet peptide shows enhanced Raman scattering cross‐sections for all amide modes as well as extensive hydrogen‐bonding networks. Tryptophan vibrational structure was probed using 230‐nm excitation. Increases in Raman cross‐sections of tryptophan modes W1, W3, W7, W10, W16, W17, and W18 of membrane‐incorporated AcWL5 are primarily attributed to greater resonance enhancement with the B_b electronic transition. The W17 mode, however, undergoes a much greater enhancement than is expected for a simple resonance effect, and this observation is discussed in terms of hydrogen bonding of the indole ring in a hydrophobic environment. The observed tryptophan mode frequencies and intensities overall support a hydrophobic environment for the indole ring within a vesicle, and these results have implications for the location of tryptophan in membrane protein systems. Copyright © 2009 John Wiley & Sons, Ltd.     

Tip‐enhanced Raman spectroscopy – an interlaboratory reproducibility and comparison study

Since its first experimental realization, tip‐enhanced Raman spectroscopy (TERS) has emerged as a potentially powerful nanochemical analysis tool. However, questions about the comparability and reproducibility of TERS data have emerged. This interlaboratory comparison study addresses these issues by bringing together different TERS groups to perform TERS measurements on nominally identical samples. Based on the spectra obtained, the absolute and relative peak positions, number of bands, peak intensity ratios, and comparability to reference Raman and surface‐enhanced Raman spectroscopy (SERS) data are discussed. Our general findings are that all research groups obtained similar spectral patterns, irrespective of the setup or tip that was used. The TERS (and SERS) spectra consistently showed fewer bands than the conventional Raman spectrum. When comparing these three methods, the spectral pattern match and substance identification is readily possible. Absolute and relative peak positions of the three major signals of thiophenol scattered by 19 and 9 cm⁻¹, respectively, which can probably be attributed to different spectrometer calibrations. However, within the same group (but between different tips), the signals only scattered by 3 cm⁻¹ on average. This study demonstrated the suitability of TERS as an analytical tool and brings TERS a big step forward to becoming a routine technique. Copyright © 2014 John Wiley & Sons, Ltd.     

Density functional and experimental studies on the FT‐IR and FT‐Raman spectra and structure of benzoic acid and 3,5‐dichloro salicylic acid

FT‐IR and FT‐Raman spectra of benzoic acid (BA) and 3,5‐dichloro salicylic acid (SA) have been recorded in the regions of 4000–400 and 4000–50 cm⁻¹ respectively. The spectra were interpreted with the aid of normal coordinate analysis following the full structure optimizations and force field calculations based on density functional theory (DFT) using standard B3LYP6‐31G** method and basis set combinations. The DFT force field transformed to natural internal coordinates was corrected by a well‐established set of scale factors that were found to be transferable to the title compounds. The infrared and Raman spectra were also predicted from the calculated intensities. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. Copyright © 2008 John Wiley & Sons, Ltd.     

FT‐IR,FT‐Raman and DFT calculations of the salicylanilide derivate 4‐chloro‐2‐(4‐bromophenylcarbamoyl)phenyl acetate

FT‐IR and FT‐Raman spectra of 4‐chloro‐2‐(4‐bromophenylcarbamoyl)phenyl acetate were recorded and analyzed. The vibrational wavenumbers and corresponding vibrational assignments were examined theoretically using the Gaussian03 set of quantum chemistry codes. The red shift of the NH stretching wavenumber in the infrared (IR) spectrum from the computed wavenumber indicates the weakening of the NH bond resulting in proton transfer to the neighbouring oxygen atom. The simultaneous IR and Raman activations of the CO stretching mode give the charge transfer interaction through a π‐conjugated path. Optimized geometrical parameters of the title compound are in agreement with similar reported structures. From the optimized structure, it is clear that the hydrogen bonding decreases the double bond character of CO bond and increases the double bond character of the C N bonds. The first hyperpolarizability, predicted infrared intensities and Raman activities are reported. The calculated first hyperpolarizability is comparable with the reported values of similar derivatives and is an attractive object for future studies of non‐linear optics. The assignments of the normal modes are done by potential energy distribution (PED) calculations. Copyright © 2009 John Wiley & Sons, Ltd.     

Substituent effect on structure and surface activity of N‐methylpyridinium salts studied by FT‐IR,FT‐RS,SERS and DFT calculations

The substituent effect on structure and surface activity of mono‐ and disubstituted N‐methylpyridinium salts was investigated by means of Raman, infrared and surface‐enhanced Raman spectroscopy (SERS). The significant differences observed in Raman and infrared spectra have been correlated with marker bands assigned to in‐plane and out‐of‐plane vibrations, respectively. This vibrational analysis, complemented by quantum chemical calculations (B3LYP/6‐311++G(d,p)) was a basis for investigation of the surface activity of the studied compounds. Significant differences in their SERS spectra related to the enhancement mechanism and adsorbate orientation have been observed and analyzed. Copyright © 2012 John Wiley & Sons, Ltd.     

The analysis of pH‐dependent protonated conformers of 1‐hydroxyethylidene‐1,1‐diphosphonic acid by means of FT‐Raman spectroscopy,multivariate curve resolution and DFT modelling

1‐Hydroxyethylidene‐1,1‐diphosphonic acid (HEDP) solutions in the pH range 0.98–13.00 were analysed using FT‐Raman spectroscopy and ³¹P and ²³Na NMR spectroscopy. Vibrational bands for different protonated species were observed in the Raman spectra, whereas only a single NMR signal that shifted with pH was observed for all samples over the entire pH range. No significant shift in the ²³Na NMR signal was observed, confirming that formation of Na⁺(aq) complexes did not take place; hence, no interference with the different protonated forms of HEDP occurred. Vibrational bands were assigned using density functional theory(DFT)‐calculated spectra of the most likely conformers in solution. Multivariate curve resolution was performed on the Raman spectra in the region containing the PO stretching vibrations to determine the number of protonated species formed over the entire pH range. Chemometric analysis compares very favourably with the experimental species distribution diagram which was generated using the reported log K_H values. Copyright © 2009 John Wiley & Sons, Ltd.     

FT‐Raman spectroscopic study of thoracic aortic wall subjected to uniaxial stress

The combination of Fourier transform‐Raman spectroscopy and uniaxial tensile tests (in MTS Synergie 100 testing machine) was used to investigate microstructural changes in the secondary protein structure of the aortic wall under different levels of stress. The spectroscopic analysis clearly shows differing tension thresholds for material excised in two directions: circumferential and longitudinal. This is confirmed by the results of macroscopic mechanical analyses. The application of strain does not lead to any noticeable change in the bandwidths of the Raman bands. The stress‐controlled Raman band analysis shows that the modes at 938 cm⁻¹ assigned as C_α C of the α‐helix, 1660 cm⁻¹ amide I (the unordered structure of elastin) and 1668 cm⁻¹ amide I (the collagen triple helix) undergo wavenumber shifting, but the bands at 1004 cm⁻¹ assigned to the phenyl ring breathing mode and 2940 cm⁻¹ to the ν (CH₃) and ν (CH₂) modes are not affected during the elastic behaviour. A clear correlation between Raman band shifting and the level of mechanical stress has been established. Elastin alone participates in the transmission of low stresses in the circumferential direction, whereas both elastin and collagen take part in the transmission of physiological and higher stresses. Copyright © 2009 John Wiley & Sons, Ltd.     

Nanomechanics of single keratin fibres: A Raman study of the α‐helix →β‐sheet transition and the effect of water

The use of micro‐Raman spectroscopy, through chemical‐bond, nano‐scale probes, allows the changes in conformations (α‐helix →β‐sheet), chain orientation, breakage of disulfide bonds (20%) and the increase of intra‐ and inter‐chain distances during the application of stress to be distinguished. The combination of micro‐Raman spectroscopy and a Universal Fibre Tester allows a quantitative measurement of the extension of chemical bonds in the peptide chain during loading. The nano‐structural transformations of keratin during strain of human hair in a dry environment (40–60% relative humidity) and saturated with water have been studied. Water permits the sliding of the chains and decreases the bond energy of the hair. Spectral analyses and 2D correlation are two coherent and independent methods to follow the structural nano‐mechanical (Raman) and micro‐mechanical (strain/stress) analyses, and confirm the validity of the experimental results, tools and principles used, as well as the agreement with the structural model of keratin fibres described by Chapman and Hearle. Copyright © 2006 John Wiley & Sons, Ltd.     

Observation of persistent α‐helical content and discrete types of backbone disorder during a molten globule to ordered peptide transition via deep‐UV resonance Raman spectroscopy

The molten globule (MG) state can aid in the folding of a protein to a functional structure and is loosely defined as an increase in structural disorder with conservation of the ensemble secondary structure content. Simultaneous observation of persistent secondary structure content with increased disorder has remained experimentally problematic. As a consequence, modeling how the MG state remains stable and how it facilitates proper folding remains difficult due to a lack of amenable spectroscopic techniques to characterize this class of partially unfolded proteins. Previously, deep‐UV resonance Raman (dUVRR) spectroscopy has proven useful in the resolution of global and local structural fluctuations in the secondary structure of proteins. In this work, dUVRR was employed to study the MG to ordered transition of a model four‐helix bundle protein, HP7. Both the average ensemble secondary structure and types of local disorder were monitored, without perturbation of the solvent, pH, or temperature. The MG to ordered transition is induced by stepwise coordination of two heme molecules. Persistent dUVRR spectral features in the amide III region at 1295–1301 and 1335–1338 cm⁻¹ confirm previous observations that HP7 remains predominantly helical in the MG versus the fully ordered state. Additionally, these spectra represent the first demonstration of conserved helical content in a MG protein. With successive heme binding, significant losses are observed in the spectral intensity of the amide III₃ and S regions (1230–1260 and 1390 cm⁻¹, respectively), which are known to be sensitive to local disorder. These observations indicate that there is a decrease in the structural populations able to explore various extended conformations with successive heme binding events. DUVRR spectra indicate that the first heme coordination between two helical segments diminishes exploration of more elongated backbone structural conformations in the inter‐helical regions. A second heme coordination by the remaining two helices further restricts protein motion. Copyright © 2013 John Wiley & Sons, Ltd.     

The interaction of iron and metal‐free meso‐tetra (4‐sulfonatophenyl) porphines with CVD graphene: a comparative Raman spectroscopy study

In this work, a non‐covalent interaction of iron and metal‐free meso‐tetra (4‐sulfonatophenyl) porphines (FeTPPS and TPPS, respectively) with high‐quality single‐layer graphene is studied by Raman spectroscopy. Such a kind of graphene functionalization is promising for a development of novel optoelectronic devices and sensors. Our results show that the central metal atom of porphyrin macrocycle, iron particularly, plays an important role in the integrity of FeTPPS on graphene surface; however, the predicted Raman enhancement is not significant. The interaction of metal‐free TPPS with graphene leads to the deprotonation of TPPS molecules and higher Raman enhancement values. Moreover, initially deprotonated TPPS solutions after the adsorption onto the graphene surface demonstrate the appearance of new Raman bands and significantly enhanced Raman signals. We propose that a strong interaction between deprotonated TPPS and graphene is realized through pyrrole and desulfonated phenyl rings of closely located planar TPPS molecules on the graphene surface. The results show that both the protonation of porphyrin macrocycle and the existence of central metal atom are crucial for a formation of nanocomposites with defined electronic properties. Copyright © 2014 John Wiley & Sons, Ltd.     

Molecular structure and vibrational spectra of 3 (or 4 or 6)‐methyl‐5‐nitro‐2‐pyridinethiones: FT‐IR,FT‐Raman and DFT quantum chemical calculations

IR and Raman spectra (RS) of polycrystalline 3‐(or 4 or 6)‐methyl‐5‐nitro‐2‐pyridinethione have been measured and analyzed by means of density functional theory (DFT) quantum chemical calculations. The B3LYP/6‐311G(2d,2p) approach has been applied for both the thiol and thione tautomers due to the possibility of the formation of these two thiole forms. Molecular structures of these compounds have been optimized starting from different molecular geometries of the thiol group and thione group. Two conformations of the 2‐mercaptopyridine, trans and cis, have been taken into account. It was shown that the studied compounds appear in the solid state in the thione form. The effect of the hydrogen‐bond formation in the studied compounds has been considered. Copyright © 2008 John Wiley & Sons, Ltd.     

Raman spectroscopy of proteins: a review

In this work, 26 proteins of different structure, function and properties are investigated by Raman spectroscopy with 488, 532 and 1064 nm laser lines. The excitation lines were chosen in NIR and Vis range as the most common and to show the difference due to normal and resonance effect, sometimes accompanied by the fluorescence. The selected proteins were divided, according to the Structural Classification of Proteins, into four classes according to their secondary structure, i.e. α‐helical (α), β‐sheet (β), mixed structures (α/β, α + β, s) and others. For all compounds, FT‐Raman and two Vis spectra are presented along with the detailed band assignment. To the best of our knowledge, this is the first review showing the potential of Raman spectroscopy for the measurement and analysis of such a large collection of individual proteins. This work can serve as a comprehensive vibrational spectra library, based on our and previous Raman measurements. Copyright © 2013 John Wiley & Sons, Ltd.     

Raman spectra and structure of a 25mer HCV RNA

We have employed Raman spectroscopy to investigate the conformation of an (Hepatitis C virus) HCV RNA 25mer (1–25 nucleotides) in solution. The principal findings of this study are (1) the A‐form secondary structure involving C3′‐ endo/anti ribofuranose pucker is predominant; (2) some uridine and guanosine nucleoside residues adopt the C2′‐ endo/anti and C3′‐ endo/syn conformations, respectively, which appear in looped nucleotide sequences; and (3) six out of nine guanine residues are base‐paired probably forming a stem. These results are interpreted as formation of a hairpin whose secondary structure is consistent with that proposed on the basis of phylogenetic comparisons with other viral RNAs. Copyright © 2009 John Wiley & Sons, Ltd.     

Raman spectroscopy of 3‐(pent‐1‐enyl) methyl ether and selected deuterium‐labelled analogues

The Raman spectra of 3‐(pent‐1‐enyl) methyl ether (3‐methoxypent‐1‐ene) and four deuterium‐labelled analogues are reported and discussed. Correlations between specific structural features and the associated Raman bands are developed, with a view to enhancing the analytical application of Raman spectroscopy in investigating materials containing an alkenyl group. Particular attention is given to developing means of distinguishing the methyl group attached to the carbon skeleton from that of the methoxy group, to maximize the analytical utility of the signals associated with ν(sp² CH), ν(sp² CH₂) and ν(CC) stretching vibrations, and to interpreting in more detail certain δ(sp² CH) and δ(sp² CH₂) vibrations of the atoms of the double bond. These results establish a definitive spectroscopic protocol for differentiating a methoxy group from a methyl substituent attached directly to a carbon atom in unsaturated ethers. Copyright © 2007 John Wiley & Sons, Ltd.     

Characterisation of structural changes in collagen with Raman spectroscopy

Raman spectroscopy can detect conformational changes in collagen structures and these findings are reviewed in this article. More specifically, some progressive diseases are mainly caused by alterations of collagen molecules but what is occurring at the biochemical level of this complex molecule usually remains unclear. While it may be true that a number of analytical techniques can analyze collagen, most of them have a series of limitations that limit their applicability to a wide range of samples. To understand in more detail the progression of a disease due to changes in the collagen structure, a technique that can detect subtle alterations at the biochemical level is needed. Raman spectroscopy is a label-free and noninvasive technique that can easily pick up on any conformational changes reflected primarily at the lipids, amides and proline and hydroxyproline regions. This review is the first compilation of studies of conformational changes in collagen molecules, providing help to understand changes in collagen biochemistry that can be of relevance to the human wound healing, ageing and pathologies.     

Identification and spectra–structure determination of soil minerals: Raman study supported by IR spectroscopy and X‐ray powder diffraction

Raman and IR spectroscopy were used for the characterization of several minerals in morphologically similar vertisol sequences from Kiževak (Serbia). It helped us to establish the surface layer transition going from calcic vertisols (containing gypsum and calcite) to calcimagnesic vertisols (containing aragonite, magnesium‐calcite and dolomite) derived from peridotite and serpentinite. The observed band positions are found to be solely characteristic for each carbonate mineral and are used to discuss the main structural features of carbonates and sulfates present in the studied soil. It was found that the dolomite, calcite and aragonite concretions are present in the deepest layer of the soil, whereas the gypsum is found in the topsoil. The identification was confirmed of the carbonates having calcite and aragonite structure, and the representative from the sulfate group (gypsum) was confirmed by X‐ray powder diffraction. Copyright © 2009 John Wiley & Sons, Ltd.     

Silica‐overcoated substrates for detection of proteins by surface‐enhanced Raman spectroscopy

Ag film over nanosphere (AgFON) substrates for surface‐enhanced Raman spectroscopy (SERS) are shown to be ineffective for the detection of proteins in phosphate buffer solution (PBS) because of the decomposition of the substrate resulting in a total loss of SERS activity. However, modification of these substrates with SiO₂ overlayers overcomes this problem. The SiO₂ overlayers are produced by filtered arc deposition (FAD) and are characterised by atomic force microscopy (AFM). Their porosity is examined using Raman spectroscopy and the detection of cytochrome c and bovine serum albumin in PBS is successfully demonstrated. These findings show promise for the detection of proteins in biologically relevant conditions using Ag‐based SERS substrates. Copyright © 2008 John Wiley & Sons, Ltd.