Impact of four (13)C-proline isotope labels on the infrared spectra of ribonuclease T1

Ribonuclease T1 was biosynthesized, with all four prolines (13)C-labeled in the peptide C[double bond]O bond, using a proline auxotrophic yeast strain of Saccharomyces cerevisiae. The (13)C- and (12)C-proline isotopomers of ribonuclease T1 were investigated by infrared spectroscopy in the thermally unfolded and natively folded state at 80 and 20 degrees C, respectively. In the thermally unfolded state, both proteins established almost indistinguishable spectral features in the secondary structure sensitive amide I region. In contrast, the spectra measured at 20 degrees C revealed substantial qualitative and quantitative differences, though parallel analysis by circular dichroism suggested identical native folds for both isotopomers. Major spectral differences in the infrared spectra were detected at 1626 and 1679 cm(-1), which are diagnostic marker bands for antiparallel beta-sheets in ribonuclease T1 and at 1645 cm(-1), a region that is characteristic for the infrared absorption of irregular structures. Starting with the known three-dimensional structure of ribonuclease T1, the observed effects of the isotope labeling are discussed on the basis of transition dipole coupling between the (12)C[double bond]O and (13)C[double bond]O groups. The experimental results were confirmed by transition dipole coupling calculations of the amide I manifold of the labeled and unlabeled variant.     

A study of alpha-helix hydration in polypeptides, proteins, and viruses using vibrational raman optical activity

A vibrational Raman optical activity (ROA) study, supplemented by protein X-ray crystal structure data, of alpha-helices in polypeptides, proteins, and viruses has suggested that ROA bands in the extended amide III spectral region may be used to distinguish between two types of right-handed alpha-helix. One type, associated with a positive ROA band at approximately 1300 cm(-1), dominates in hydrophobic environments and appears to be unhydrated; the other, associated with a positive ROA band at approximately 1340 cm(-1), dominates in hydrophilic environments and appears to be hydrated. Evidence is presented to support the hypothesis that unhydrated alpha-helix corresponds to the canonical conformation alpha(c) and hydrated alpha-helix to a more open conformation alpha(o) stabilized by hydrogen bonding of a water molecule or a hydrophilic side chain to the peptide carbonyl. Alpha-helical poly(L-lysine) and poly(L-ornithine) in aqueous solution and poly(L-alanine) in dichloracetic acid display both bands, but alpha-helical poly(l-glutamic acid) in aqueous solution and poly(gamma-benzyl L-glutamate) in CHCl(3) display only the approximately 1340 cm(-1) band and so may exist purely as alpha(o) due to enhanced stabilization of this conformation by particular side chain characteristics. The ROA spectrum of poly(beta-benzyl L-aspartate) in CHCl(3) reveals that it exists in a single left-handed alpha-helical state more analogous to alpha(o) than to alpha(c).     

In situ Detection of Amide A Bands of Proteins in Water by Raman Ratio Spectrum

The amide A band of protein is sensitive to the hydrogen bands of amide groups of proteins. However, it is hard to distinguish the amide A band of aqueous protein in situ directly, since it overlaps with O-H stretching vibration of water. In this work, we presented a new analytical method of Raman ratio spectrum, which can extract the amide A band of proteins in water. To obtain the Raman ratio spectrum, the Raman spectrum of aqueous protein was divided by that of pure water. A mathematical simulation was employed to examine whether Raman ratio spectrum is effective. Two kinds of protein, lysozyme and α-chymotrypsin were employed. The amide A bands of them in water were extracted from Raman ratio spectra. Additionally, the process of thermal denaturation of lysozyme was detected from Raman ratio spectrum. These results demonstrated the Raman ratio spectra could be employed to study the amide A modes of proteins in water.     

Protonless NMR experiments for sequence-specific assignment of backbone nuclei in unfolded proteins

Natively unfolded proteins are increasingly recognized to play important physiological roles. These proteins do not crystallize, so NMR is the only technique able to provide structural and dynamic information. However, in unfolded proteins, the proton chemical shift dispersion is poor, causing severe problems in resonance assignment. We designed a novel strategy based on two protonless experiments, a CBCACON-IPAP and a novel COCON-IPAP, that permits a straightforward and unequivocal backbone heteronuclear assignment of the natively unfolded protein alpha-synuclein.     

UV raman examination of alpha-helical peptide water hydrogen bonding

UV resonance Raman spectra (UVRS) of an alpha-helical, 21 residue, mainly Ala peptide (AP) in the dehydrated solid state were compared to those in aqueous solution at different temperatures. The UVRS amide band frequencies of a dehydrated solid alpha-helix peptide show frequency shifts compared to those in aqueous solution due to the loss of amide backbone hydrogen bonding to water; the amide II and amide III bands of the solid alpha-helix downshift, while the amide I band upshifts. The shifts are identical in direction but smaller than those that occur for alpha-helices in aqueous solution as the temperature increases; water hydrogen bonding strengths decrease as the temperature increases. The UV Raman amide band frequency shifts can be used to monitor alpha-helix hydrogen bonding.     

Vibrational Raman optical activity characterization of poly(l-proline) II helix in alanine oligopeptides

A vibrational Raman optical activity (ROA) study of a series of alanine peptides in aqueous solution is presented. The seven-alanine peptide Acetyl-OOAAAAAAAOO-Amide (OAO), recently shown by NMR and UVCD to adopt a predominantly poly(l-proline II) (PPII) helical conformation in aqueous solution, gave an ROA spectrum very similar to that of disordered poly(l-glutamic acid) which has long been considered to adopt the PPII conformation, both being dominated by a strong positive extended amide III ROA band at approximately 1319 cm-1 together with weak positive amide I ROA intensity at approximately 1675 cm-1. A series of alanine peptides Ala2-Ala6 studied in their cationic states in aqueous solution at low pH displayed ROA spectra which steadily evolved toward that of OAO with increasing chain length. As well as confirming that alanine peptides can support the PPII conformation in aqueous solution, our results also confirm the previous ROA band assignments for PPII structure, thereby reinforcing the foundation for ongoing ROA studies of unfolded and partially folded proteins.     

UV near-resonance Raman spectroscopic study of 1,1'-bi-2-naphthol solutions

The normal and UV near-resonance Raman (UVRR) spectra of 1,1'-bi-2-naphthol (BN) in basic solution were measured and analyzed. Density functional theory (DFT) calculations were carried out to study the ground state geometry structure, vibrational frequencies nu, off-resonance Raman intensities I, and depolarization ratios rho of 1,1'-bi-2-naphtholate dianion (BN(2-)). On the basis of the calculated and experimental results of nu, I, and rho, the observed Raman bands were assigned in detail. The 1612 cm(-1) Raman band of BN in basic solution was found dramatically enhanced in the UV resonance Raman spectrum in comparison with the normal Raman spectrum. Analyzing the depolarization ratios of the 1366 and 1612 cm(-1) bands in the RR spectra manifests that both the symmetric and antisymmetric parts of transition polarizabilities contribute to the 1366 cm(-1) band, but that only the symmetric part contributes to the 1612 cm(-1) band.     

The effects of stretching on wool fibres as monitored by FT-Raman spectroscopy

FT-Raman spectroscopy coupled with amide I band deconvolution was used to monitor the conformational changes of the peptide backbone of sulphite pre-treated wool fibres during stretching. The spectral changes observed are consistent with the transition of -helical to β-pleated sheet structure. These changes, which are most rapid during the early stages of stretching, can be related to protein secondary structure at both the crystalline and molecular levels. Analysis of the amide III region of the spectra reveals that a very small amount of additional disorder is imparted to the peptide backbone as a result of stretching. The consistency in the widths at half-height of the amide I band components implies that stretching does not significantly change the distribution of peptide chain conformations. From the Raman analysis of cells isolated from the stretched fibres, it is evident that conformational changes occur in both the cuticle and cortex. The most evident change, however, is in the cortical cells.     

Two-dimensional Raman and Raman optical activity correlation analysis of the alpha-helix-to-disordered transition in poly(L-glutamic acid)

Rich and complex Raman scattering and Raman optical activity (ROA) spectra have been measured monitoring the pH induced alpha-helix-to-disordered conformational transition in poly(L-glutamic acid). Two-dimensional (2D) correlation techniques have been applied to facilitate a comprehensive analysis of these two complementary spectral sets. Synchronous contour plots have identified band assignments of alpha-helical and disordered conformations, and have revealed bands characteristic of changes in the protonation state of the polypeptide. Asynchronous plots, on the other hand, have probed the relative sequential orders of intensity changes indicating a decrease in intensity of alpha-helical bands in the backbone skeletal stretch region, followed by a subsequent decrease in intensity in the extended amide III and amide I regions, underlying the appearance of disordered structure, including poly(L-proline) II (PPII) helix. The application of a 2D correlation 'moving' window has also disclosed two distinct phases during helix unfolding in the alpha-helix-to-disordered transition, occurring at approximately pH 4.9 and approximately pH 5.2, possibly a result of the difference in helical stability between the end and central regions of the alpha-helix. This paper demonstrates the potential value of combining 2D Raman, 2D ROA and moving window correlation techniques for the detailed investigation of complex and subtle changes of secondary structure during the unfolding mechanisms of polypeptides and proteins.     

Peptide bond vibrational coupling

Neutral trialanine (Ala3), which is geometrically constrained to have its peptide bond at Phi and Psi angles of alpha-helix and PPII-like conformers, are studied at the B3LYP/6-31+G(d,p) level of theory to examine vibrational interactions between adjacent peptide units. Delocalization of the amide I, amide II, and amide III3 vibrations are analyzed by calculating their potential energy distributions (PED). The vibrational coupling strengths are estimated from the frequency shifts between the amide vibrations of Ala3 and the local amide bond vibrations of isotopically substituted Ala3 derivatives. Our calculations show the absence of vibrational coupling of the amide I and amide II bands in the PPII conformations. In contrast, the alpha-helical conformation shows strong coupling between the amide I vibrations due to the favorable orientation of the C=O bonds and the strong transitional dipole coupling. The amide III3 vibration shows weak coupling in both the alpha-helix and PPII conformations; this band can be treated as a local independent vibration. Our calculated results in general agree with our previous experimental UV Raman studies of a 21-residue mainly alanine-based peptide (AP).     

Site-specific vibrational dynamics of the CD3zeta membrane peptide using heterodyned two-dimensional infrared photon echo spectroscopy

Heterodyned two-dimensional infrared (2D IR) spectroscopy has been used to study the amide I vibrational dynamics of a 27-residue peptide in lipid vesicles that encompasses the transmembrane domain of the T-cell receptor CD3zeta. Using 1-(13)C[Double Bond](18)O isotope labeling, the amide I mode of the 49-Leucine residue was spectroscopically isolated and the homogeneous and inhomogeneous linewidths of this mode were measured by fitting the 2D IR spectrum collected with a photon echo pulse sequence. The pure dephasing and inhomogeneous linewidths are 2 and 32 cm(-1), respectively. The population relaxation time of the amide I band was measured with a transient grating, and it contributes 9 cm(-1) to the linewidth. Comparison of the 49-Leucine amide I mode and the amide I band of the entire CD3zeta peptide reveals that the vibrational dynamics are not uniform along the length of the peptide. Possible origins for the large amount of inhomogeneity present at the 49-Leucine site are discussed.     

Alpha-synuclein misfolding and neurodegenerative diseases

Alpha-synuclein is an abundant presynaptic brain protein, misfolding, aggregation and fibrillation of which are implicated as critical factors in several neurodegenerative diseases. The list of the well-known synucleinopathies includes such devastating disorders as Parkinson's disease, Lewy body variant of Alzheimer's disease, diffuse Lewy body disease, dementia with Lewy bodies, multiple system atrophy, and neurodegeneration with brain iron accumulation type I. The precise functions of alpha-synuclein remain elusive, but there are evidence indicating its involvement in regulation vesicular release and/or turnover and synaptic function in the central nervous system. It might play a role in neuronal plasticity responses, bind fatty acids, regulate certain enzymes, transporters, and neurotransmitter vesicles, be involved in neuronal survival and even can act as a molecular chaperone. Structurally, alpha-synuclein is an illustrative member of the rapidly growing family of natively unfolded (or intrinsically disordered) proteins and considerable knowledge has been accumulated about its structural properties and conformational behavior. The molecular mechanisms underlying misfolding, aggregation and fibrillation of alpha-synuclein and the role of various environmental and genetic factors in stimulation and inhibition of these processes are relatively well understood. Here, the main structural features of alpha-synuclein, its functions, and involvement in various human diseases are summarized providing a foundation for better understanding of the biochemistry, biophysics and neuropathology of alpha-synuclein aggregation.     

A new perspective on beta-sheet structures using vibrational Raman optical activity: from poly(L-lysine) to the prion protein

The vibrational Raman optical activity (ROA) spectrum of a polypeptide in a model beta-sheet conformation, that of poly(l-lysine), was measured for the first time, and the alpha-helix --> beta-sheet transition monitored as a function of temperature in H(2)O and D(2)O. Although no significant population of a disordered backbone state was detected at intermediate temperatures, some side chain bands not present in either the alpha-helix or beta-sheet state were observed. The observation of ROA bands in the extended amide III region assigned to beta-turns suggests that, under our experimental conditions, beta-sheet poly(L-lysine) contains up-and-down antiparallel beta-sheets based on the hairpin motif. The ROA spectrum of beta-sheet poly(L-lysine) was compared with ROA data on a number of native proteins containing different types of beta-sheet. Amide I and amide II ROA band patterns observed in beta-sheet poly(L-lysine) are different from those observed in typical beta-sheet proteins and may be characteristic of an extended flat multistranded beta-sheet, which is unlike the more irregular and twisted beta-sheet found in most proteins. However, a reduced isoform of the truncated ovine prion protein PrP(94-233) that is rich in beta-sheet shows amide I and amide II ROA bands similar to those of beta-sheet poly(L-lysine), which suggests that the C-terminal domain of the prion protein is able to support unusually flat beta-sheets. A principal component analysis (PCA) that identifies protein structural types from ROA band patterns provides a useful representation of the structural relationships among the polypeptide and protein states considered in the study.     

Molecular understanding of the UCST-type phase separation behavior of a stereocontrolled poly(N-isopropylacrylamide) in bis(2-methoxyethyl) ether

The upper critical solution temperature (UCST)-type phase separation of an isotactic-rich poly( N-isopropylacrylamide) (PNiPA) in bis(2-methoxyethyl) ether (diglyme) has been investigated by turbidity measurement and infrared (IR) spectroscopy. The IR spectra of stereocontrolled PNiPAs in various solvents have clearly indicated that the amide I bands do not directly reflect the tacticity of the polymer. The relative intensity of the amide I bands changes depending upon the molecular environment around the amide groups of PNiPA, which is influenced by the tacticity. During the UCST-type phase separation of the isotactic-rich PNiPA in diglyme, the amide I band at around 1625 cm (-1) changes. To link the IR spectral change with the molecular information, quantum chemical calculations have been carried out for NiPA n-mers ( n = 1-4) with an isotactic stereosequence. The result has suggested that the amide I band at around 1625 cm (-1) arises from a helical structure formed by the isotactic stereosequences in the PNiPA main chain with the aid of intramolecular CO...H-N hydrogen bonding. The experimental IR spectra have revealed that the helical structures are unfolded as the temperature rises. The folding and unfolding of the isotactic sequences in the main chain may induce the thermal change in the solubility of the isotactic rich PNiPA in diglyme, resulting in the UCST-type phase separation of the solution.     

Tertiary contact formation in alpha-synuclein probed by electron transfer

To explore tertiary contact formation in alpha-synuclein, a natively unfolded protein implicated in Parkinson's disease, we have measured the rates of reaction between a powerful electron donor, the tryptophan (W) triplet excited state, and an acceptor, 3-nitro-tyrosine (Y(NO2)) in six different variants, probing loop sizes between 15 and 132 residues. Electron transfer rates decrease with loop size with the fastest contact time of 140 ns for the N-terminal pair and the slowest of 1.2 mus for the N- to C-terminal pair. Diffusion coefficients ranging from approximately 2 x 10-6 to approximately 10-5 cm2 s-1 were extracted from simultaneous fits of the W to Y(NO2) electron (triplet excited state) and energy transfer (singlet excited state) kinetics.     

Effect of water on the formamide-intercalation of kaolinite

The molecular structures of low defect kaolinite completely intercalated with formamide and formamide-water mixtures have been determined using a combination of X-ray diffraction, thermoanalytical techniques, DRIFT and Raman spectroscopy. Expansion of the kaolinite to 10.09 A was observed with subtle differences whether the kaolinite was expanded with formamide or formamide-water mixtures. Thermal analysis showed that greater amounts of formamide could be intercalated into the kaolinite in the presence of water. New infrared bands were observed for the formamide intercalated kaolinites at 3648, 3630 and 3606 cm(-1). These bands are attributed to the hydroxyl stretching frequencies of the inner surface hydroxyls hydrogen bonded to formamide with water, formamide and interlamellar water. Bands were observed at similar positions in the Raman spectrum. At liquid nitrogen temperature, the 3630 cm(-1) Raman band separated into two bands at 3633 and 3625 cm(-1). DRIFT spectra showed the hydroxyl deformation mode at 905 cm(-1). Changes in the molecular structure of the formamide are observed through both the NH stretching vibrations and the amide 1 and 2 bands. Upon intercalation of kaolinite with formamide, bands are observed at 3460, 3344, 3248 and 3167 cm(-1) attributed to the NH stretching vibration of the NH involved with hydrogen bonded to the oxygens of the kaolinite siloxane surface. In the DRIFT spectra of the formamide intercalated kaolinites bands are observed at 1700 and 1671 cm(-1) and are attributed to the amide 1 and amide 2 vibrations.     

Infrared and circular dichroism spectroscopic characterisation of secondary structure components of a water treatment coagulant protein extracted from Moringa oleifera seeds

The secondary structure of a water treatment coagulant protein extracted from Moringa oleifera (MO) seeds has been investigated by Fourier transform infrared spectroscopy (FTIR) in the dried state, and by circular dichroism (CD) spectroscopy. The FTIR and CD spectra indicate that the secondary structure of the protein is dominated by alpha-helix. The FTIR spectrum recorded two distinct and strong absorption bands at 1656 cm(-1) and 1542 cm(-1), in the usual range of absorption of helices of proteins. The CD spectrum showed the shape of mainly alpha-helical secondary structure (estimated to be 58+/-4%) characteristic of negative ellipticity bands near 222 nm and 208 nm and a positive band at 192 nm. The beta-sheet structure composition was estimated to be 10+/-3% whereas unordered structures were around 33%. Changes in solution pH affected the protein secondary structure significantly only at pH values above 10, as indicated by CD spectra, whereas ionic strength had minimal effect. CD data also showed that sodium dodecyl sulphate (SDS) interacts with the coagulant protein and modifies the protein conformation. The surfactant-induced conformational change of the coagulant protein was confirmed by quenching of tryptophan fluorescence of the protein.     

Raman micro-spectroscopic analysis of cultured HCT116 colon cancer cells in the presence of roscovitine

Raman micro-spectroscopic analysis of cultured HCT116 colon cancer cells in the presence of roscovitine, [seliciclib, 2-(1-ethyl-2-hydroxy-ethylamino)-6-benzylamino-9-isopropylpurine], a promising drug candidate in cancer therapy, has been performed for the first time. The aim of this study was to investigate modulations in colon cancer cells induced by roscovitine. Raman spectra of the cultured HCT116 colon cancer cells treated with roscovitine at different concentrations (0, 5, 10, 25 and 50 μM) were recorded in the range 400-1850 cm(-1). It was shown that the second derivative profile of the experimental spectrum gives valuable information about the wavenumbers and band widths of the vibrational modes of cell components, and it eliminates the appearance of false peaks arising from incorrect baseline corrections. In samples containing roscovitine, significant spectral changes were observed in the intensities of characteristic protein and DNA bands, which indicate roscovitine-induced apoptosis. Roscovitine-induced apoptosis was also assessed by flow cytometry analysis, and analysis of propidium iodide staining. We observed some modifications in amide I and III bands, which arise from alterations in the secondary structure of cell proteins caused by the presence of roscovitine.     

Surface-enhanced Raman spectroscopic studies of coactivator-associated arginine methyltransferase 1

We report, for the first time, the surface-enhanced Raman spectra of an important enzyme, coactivator-associated arginine methyltransferase 1 (CARM1), involved in various biological activities such as tumor suppressor function and stem cell differentiation. We have employed surface-enhanced Raman scattering (SERS) to obtain insight into the structural details of CARM1 by adsorbing it to silver (Ag) nanoparticles. The enzyme retains its activity even after its adsorption onto Ag nanoparticles. We observe strong SERS modes arising from amide vibrations and aromatic ring amino acids. The SERS spectra revealed amide I bands at 1637 cm(-1) and 1666 cm(-1), which arise as a result of the alpha helix of the protein and the polypeptide backbone vibration of a random coil, respectively. In order to confirm the amide vibrations, we have performed SERS on deuterated CARM1, which exhibits a clear red shift in amide band positions. The SERS spectra may provide useful information, which could be harnessed to study the functional interactions of CARM1 with small molecule modulators.     

UV Raman demonstrates that alpha-helical polyalanine peptides melt to polyproline II conformations

We examined the 204-nm UV Raman spectra of the peptide XAO, which was previously found by Shi et al.'s NMR study to occur in aqueous solution in a polyproline II (PPII) conformation. The UV Raman spectra of XAO are essentially identical to the spectra of small peptides such as ala(5) and to the large 21-residue predominantly Ala peptide, AP. We conclude that the non-alpha-helical conformations of these peptides are dominantly PPII. Thus, AP, which is highly alpha-helical at room temperature, melts to a PPII conformation. There is no indication of any population of intermediate disordered conformations. We continued our development of methods to relate the Ramachandran Psi-angle to the amide III band frequency. We describe a new method to estimate the Ramachandran Psi-angular distributions from amide III band line shapes measured in 204-nm UV Raman spectra. We used this method to compare the Psi-distributions in XAO, ala(5), the non-alpha-helical state of AP, and acid-denatured apomyoglobin. In addition, we estimated the Psi-angle distributions of peptide bonds which occur in non-alpha-helix and non-beta-sheet conformations in a small library of proteins.