Raman spectra and normal vibrations of dipeptides. II. Glycyl-L-proline

Evaluation of IR and Raman spectroscopic markers of human collagens: Insides for indicating colorectal carcinogenesis

Vibrational spectroscopic methods are widely used in the molecular diagnostics of carcinogenesis. Collagen, a component of connective tissue, plays a special role as a biochemical marker of pathological changes in tissues. The vibrational bands of collagens are very promising to distinguish between normal colon tissue, benign and malignant colon polyps. Differences in these bands indicate changes in the amount, structure, conformation and the ratio between the individual structural forms (subtypes) of this protein. The screening of specific collagen markers of colorectal carcinogenesis was carried out based on the FTIR and Raman (λ_ex 785 nm) spectra of colon tissue samples and purified human collagens. It was found that individual types of human collagens showed significant differences in their vibrational spectra, and specific spectral markers were found for them. These collagen bands were assigned to specific vibrations in the polypeptide backbone, amino acid side chains and carbohydrate moieties. The corresponding spectral regions for colon tissues and colon polyps were investigated for the contribution of collagen vibrations. Mentioned spectral differences in collagen spectroscopic markers could be of interest for early ex vivo diagnosis of colorectal carcinoma if combine vibrational spectroscopy and colonoscopy.

High-temperature Raman spectra of dipeptide α-L-aspartyl-L-alanine crystal

Crystals of dipeptide α-L-aspartyl-L-alanine (α-Asp-Ala), C₇H₁₂N₂O₅, were studied under high-temperature conditions through vibrational spectroscopy (IR and Raman) and thermal analysis (Differential Scanning Calorimetry - DSC). From the analysis of the results, it is possible to conclude that: (i) the studied material undergoes a reversible order-disorder phase transition at 373 K on heating, where several changes were observed in the vibrational spectra, especially with vibrational modes of the units that participate directly of the hydrogen bonds; (ii) the phase transition undergone by the α-Asp-Ala crystal (about 373 K) involves changes in hydrogen bonds, possibly the rupture of at least one of them, and change in the conformation of the molecules in the unit cell.

Surface-enhanced Raman difference between bombesin and its modified analogues on the colloidal and electrochemically roughen silver surfaces

In this article, surface-enhanced Raman scattering (SERS) spectra of bombesin (BN) and its six modified analogues ([D-Phe(12)]BN, [Tyr(4)]BN, [Tyr(4),D-Phe(12)]BN, [D-Phe(12),Leu(14)]BN, [Leu(13)-(R)-Leu(14)]BN, and [Lys(3)]BN) on a colloidal silver surface are reported and compared with SERS spectra of these species immobilized onto an ellectrochemically roughen silver electrode. Changes in enhancement and wavenumber of proper bands upon adsorption on different silver surfaces are consistent with BN and its analogues adsorption primarily through Trp(8). Slightly different adsorption states of these molecules are observed depending upon natural amino acids substitution. For example, the indole ring in all the peptides interacts with silver nanoparticles in a edge-on orientation. It is additionally coordinated to the silver through the N(1)--H bond for all the peptides, except [Phe(12)]BN. This is in contrary to the results obtained for the silver roughen electrode that show direct but not strong N(1)--H/Ag interaction for all peptides except [D-Phe(12),Leu(14)]BN and [Leu(13)-(R)-Leu(14)]BN. For BN only C==O is not involved in the chemical coordination with the colloidal surface. [Lys(3)]BN and BN also adsorb with the C--N bond of NH(2) group normal and horizontal, respectively, to the colloidal surface, whereas C--NH(2) in other peptides is tilted to this surface. Also, the Trp(8) --CH(2)-- moiety of only [Tyr(4)]BN, [Lys(3)]BN, and [Tyr(4),D-Phe(12)]BN coordinates to Ag, whereas the Phe(12) ring of [Phe(12)]BN, [Tyr(4),D-Phe(12)]BN, and [D-Phe(12),Leu(14)]BN assists in the peptides binding only on the colloidal silver.

Application of Fourier transform Raman spectroscopy for prediction of bitterness of peptides

The potential application of Fourier transform (FT) Raman spectroscopy to predict the bitterness of peptides was investigated. FT-Raman spectra were measured for the amino acid Phe and 9 synthetic di-, tri-, and tetra peptides composed of Phe, Gly, and Pro. Partial least squares regression (PLS)-1 analysis was applied to correlate the FT-Raman spectra with bitterness intensity values (R(caf) and log 1/T) reported in the literature. Using full cross-validation, Model 1 based on the single spectral data set for the nine peptides yielded a high correlation coefficient for calibration (R = 0.99), but a low correlation coefficient for prediction (R = 0.56). Two models were constructed using the data sets including replicate spectra for the calibrations and were validated using full cross-validation. Using leave-one-sample-set-out calibrations, Model 2, which was developed with the data for the peptides as well as Phe, yielded a low correlation coefficient (R = 0.533) for the prediction of the bitterness, while Model 3 developed with only the peptide data provided better correlation coefficients (R = 0.807 and 0.724 for R(caf) and log 1/T values, respectively). The correlation coefficients for prediction were 0.975 (R(caf) values) and 0.874 (log 1/T values) for Model 4, which was developed using subtracted spectral data (spectra of peptides with higher R(caf) values minus spectra of peptides with lower R(caf) values). Examination of the PLS regression coefficients at wavenumbers most highly correlated with bitterness revealed the importance of hydrophobicity and peptide length on bitterness. This study indicates the potential of FT-Raman spectroscopy as a useful tool for predicting bitterness of peptides and amino acids.

Part I: surface-enhanced Raman spectroscopy investigation of amino acids and their homodipeptides adsorbed on colloidal silver

Surface-enhanced Raman scattering spectra (SERS) were measured for various amino acids: L-methionine (Met), L-cysteine (Cys), Lglycine (Gly), L-leucine (Leu), L-phenylalanine (Phe), and L-proline (Pro) and their homodipeptides (Met-Met, Cys-Cys, Gly-Gly, LeuLeu, Phe-Phe, and Pro-Pro) in silver colloidal solutions. The geometry and orientation of the amino acids or dipeptides on the silver surface, and their specific interaction with the surface, were deducted by detailed spectral analysis of the SERS spectra. This analysis has allowed us to propose the particular surface geometry of amino acids or dipeptides and also implied that C-C bonds were almost parallel to the surface, as evidenced by the absence of marker bands in the skeletal C-C stretching region of the spectra. Additionally, using "time-dependent" SERS measurements we solved an existing controversy regarding the binding specificity of Gly-Gly on the silver surface.

Part II: surface-enhanced Raman spectroscopy investigation of methionine containing heterodipeptides adsorbed on colloidal silver

Surface-enhanced Raman scattering (SERS) spectra of methionine (Met) containing dipeptides: Met-X and X-Met, where X is: L-glycine (Gly), L-leucine (Leu), L-proline (Pro), and L-phenylalanine (Phe) are reported. Using pre-aggregated Ag colloid we obtained high-quality SERS spectra of these compounds spontaneously adsorbed on colloidal silver. Additionally, we measured Raman spectra (RS) of these heterodipeptides in a solid state as well as in acidic and basic solutions. The RS and SERS spectra of Met-X and X-Met presented in this work appear to be different. One of the most prominent and common features in the SERS spectra of all these dipeptides is a band in the 660-690 cm(-1) range that is due to the C-S stretching, v(CS), vibration of Met. This suggests that all the abovementioned compounds adsorb on the silver surface through a thioether atom. On the other hand, the SERS spectra of X-Met show clearly that not only the S atom but also the carboxylate group interact with the colloid surface as manifested by the enhancement of bands in the 920-930 and 1380-1396 cm(-1) regions. These bands are ascribed to the v(C-COO(-)) and v(sym)(COO(-)) vibrations, respectively. Additionally, a SERS spectrum of Phe-Met indicates that the interaction of the thioether atom, amine group, and aromatic side chain with the silver surface is favorable and may dictate the orientation and conformation of adsorbed peptide.

Vibrational neutron spectroscopy of collagen and model polypeptides

A pulsed source neutron spectrometer has been used to measure vibrational spectra (20-4000 cm-1) of dry and hydrated type I collagen fibers, and of two model polypeptides, polyproline II and (prolyl-prolyl-glycine)10, at temperatures of 30 and 120 K. the collagen spectra provide the first high resolution neutron views of the proton-dominated modes of a protein over a wide energy range from the low frequency phonon region to the rich spectrum of localized high frequency modes. Several bands show a level of fine structure approaching that of optical data. The principal features of the spectra are assigned. A difference spectrum is obtained for protein associated water, which displays an acoustic peak similar to pure ice and a librational band shifted to lower frequency by the influence of the protein. Hydrogen-weighted densities of states are extracted for collagen and the model polypeptides, and compared with published calculations. Proton mean-square displacements are calculated from Debye-Waller factors measured in parallel quasi-elastic neutron-scattering experiments. Combined with the collagen density of states function, these yield an effective mass of 14.5 a.m.u. for the low frequency harmonic oscillators, indicating that the extended atom approximation, which simplifies analyses of low frequency protein dynamics, is appropriate.

Effect of Urey-Bradley-Shimanouchi force field on the harmonic dynamics of proteins

A normal mode analysis of bovine pancreatic trypsin inhibitor is carried out by using a Urey-Bradley-Shimanouchi potential energy function. The density of vibrational states, the magnitudes, and time scales of the atomic fluctuations are compared with experimental and theoretical results obtained by the more commonly used potential energy functions. The atomic fluctuations of Lys-15 are subject to extensive considerations as this residue is buried in the trypsin specificity pocket. It is found that Arg-17 is likely to be of importance in order to understand the way BPTI binds on trypsin.

Raman spectroscopy and normal vibrations of peptides. Characteristic normal modes of a type-II beta turn

Raman and infrared spectra have been recorded on the peptide Gly-LPro-Gly-Gly in its zwitterionic form and on its protected homolog Z-Gly-LPro-Gly-Gly-OMe (Z = N-benzyloxycarbonyl and OMe = methyl ester). Both peptides adopt a type-II beta-turn conformation into appropriate solvents, that is in dimethylsulfoxide and chloroform respectively. A normal coordinate treatment has been performed on Gly-LPro-Gly-Gly using a modified Urey-Bradley force field and the characteristic normal modes of vibrations. Their corresponding frequencies have been extracted from experimental investigations.