Quantitation of the global secondary structure of globular proteins by FTIR spectroscopy: Comparison with X-ray crystallographic structure.

Fourier transform infrared spectroscopy (FTIR) is potentially a powerful tool for determining the global secondary structure of proteins in solution, providing the spectra are analyzed using a statistically and theoretically justified methodology. We have performed FTIR experiments on 14 globular proteins and two synthetic polypeptides whose X-ray crystal structures are known to exhibit varying types and amounts of secondary structures. Calculation of the component structural elements of the vibrational bands was accomplished using nonlinear regression analysis, by fitting both the amide I and amide II bands of the Fourier self-deconvoluted spectra, the second-derivative spectra, and the original spectra. The methodology was theoretically justified by comparing (via nonlinear regression analysis) the global secondary structure determined after deconvolving into component bands the vibrational amide I envelopes with the calculated structure determined by first principles from Ramachandran analysis of the X-ray crystallographic structure of 14 proteins from the Brookhaven protein data bank. Justification of the nonlinear regression analysis model with respect to experimental and instrumental considerations was achieved by the decomposition of all the bands of benzene and an aqueous solution of ammonium acetate into component bands while floating the Gaussian/Lorentzian character of the line shapes. The results for benzene yield all pure Lorentzian line shapes with no Gaussian character while the ammonium acetate spectra yielded all Gaussian line shapes with no Lorentzian character. In addition, all-protein spectra yielded pure Gaussian line shapes with no Lorentzian character. Finally, the model was statistically justified by recognizing random deviation patterns in the regression analysis from all fits and by the extra sum of squares F-test which uses the degrees of freedom and the root mean square values as a tool to determine the optimum number of component bands required for the nonlinear regression analysis. Results from this study demonstrate that the globular secondary structure calculated from the amide I envelope for these 14 proteins from FTIR is in excellent agreement with the values calculated from the X-ray crystallographic data using three-dimensional Ramachandran analysis, providing that the proper contribution from GLN and ASN side chains to the 1667 and 1650 cm(-1) component bands has been taken into account. The standard deviation of the regression analysis for the per cent helix, extended, turn and irregular conformations was found to be 3.49%, 2.07%, 3.59% and 3.20%, respectively.

Reproducibility of the nonlinear regression fit to the FTIR spectra of lysozyme.

Controversy exists concerning the influence of experimental artifacts on the number of component FTIR vibrational bands which may be resolved from the amide I and II envelopes of proteins in water. Whether these bands represent unique populations of vibrating protein groups in a particular global 2 degrees structure or whether the bands are due to instrumental and environmental fluctuations has been addressed, T.F. Kumosinski and J.J. Unruh, Talanta, 43 (1996) 199-219. The repeatability of the methodology and the apparent uniqueness of the nonlinear regression fits are addressed in this study. We obtained a series of the spectra of lysozyme, and carried-out nonlinear regression analysis of each spectrum. Coefficients of variation (COV) were calculated for the wavenumber and area values of assigned component peaks obtained. Low COVs obtained attest to the precision of the methodology and the apparent uniqueness of the nonlinear regression fits. This methodology for acquisition and analysis of protein FTIR spectra yields results with good precision.

Solid-phase clean-up and thin-layer chromatographic detection of veterinary aminoglycosides.

Chemical methods are needed to confirm the presence of antibiotics detected by microbial inhibition assays in fluids and tissues of farm animals. We have optimized the conditions for the isolation of hygromycin B with a copolymeric bonded solid-phase silica column followed by thin-layer chromatography (TLC) separation and detection of its fluorescence derivative after reaction with fluorescamine. The detection limit of the drug was 50 ng. Serum and plasma samples fortified with hygromycin B were acidified and passed through the copolymerized solid-phase columns previously conditioned with phosphate buffer. Hygromycin B was trapped in the columns and eluted with diethylamine-methanol and analyzed by TLC using acetone-ethanol-ammonium hydroxide as the developing solvent. Hygromycin B bands were derivatized at acidic pH with fluorescamine and visualized under ultraviolet light. Hygromycin B added to bovine plasma was detectable at 25, 50, 100, 250 and 500 ng/ml (ppb). Hygromycin B added to swine serum was detected at 50 ng/ml. However, the serum had to be deproteinized with trichloroacetic acid or acetonitrile prior to solid-phase extraction to gain accurate values. Neomycin and gentamicin (100 ng/ml aqueous solutions) could also be isolated with copolymeric solid-phase columns at a level of 50 ng. Gentamicin, neomycin, gentamicin, spectinomycin, hygromycin B and streptomycin could be separated by TLC, allowing multiresidue detection of these aminoglycosides. The respective RF values of 0.64, 0.56, 0.52, 0.33 and 0.20 indicate the separation of these five compounds. This procedure provides a rapid and sensitive method for the semi-quantitative estimation of aminoglycosides.

Secondary structural studies of bovine caseins: structure and temperature dependence of beta-casein phosphopeptide (1-25) as analyzed by circular dichroism, FTIR spectroscopy, and analytical ultracentrifugation.

The defining structural feature of all of the caseins is their common phosphorylation sequence. In milk, these phosphoserine residues combine with inorganic calcium and phosphate to form colloidal complexes. In addition, nutritional benefits have been ascribed to the phosphopeptides from casein. To obtain a molecular basis for the functional, chemical, and biochemical properties of these casein peptides, the secondary structure of the phosphopeptide of bovine beta-casein (1-25) was reexamined using Fourier transform infrared (FTIR) and circular dichroism (CD) spectroscopies. Both methods predict secondary structures for the peptide which include polyproline II elements as well as beta-extended sheet and turn-like elements. These structural elements were highly stable from 5 degrees to 70 degrees C. Reexamination of previously published 1H NMR data using chemical shift indices suggests structures in accord with the CD and FTIR data. Dephosphorylation showed little or no secondary structural changes, as monitored by CD and FTIR, but the modified peptide demonstrated pronounced self-association. The polymers formed were not highly temperature sensitive, but were pressure sensitive as judged by analytical ultracentrifugation at selected rotor speeds. Molecular dynamics (MD) simulations demonstrated relatively large volume changes for the dephosphorylated peptide, in accord with the pressure dependent aggregation observed in the analytical ultracentrifuge data. In contrast the native peptide in MD remained relatively rigid. The physical properties of the peptide suggest how phosphorylation can alter its biochemical and physiological properties.

Changes in the secondary structure of bovine casein by Fourier transform infrared spectroscopy: effects of calcium and temperature.

Bovine casein submicelles and reformed micelles, produced by addition of Ca2+, were examined by Fourier transform infrared spectroscopy at 15 and 37 degrees C in aqueous salt solutions of K+ and Na+. Previous measurements of caseins, made in D2O and in the solid form, can now be made in a more realistic environment of H2O. When analyzed in detail, data obtained by Fourier transform infrared spectroscopy have the potential to show subtle changes in secondary structural elements that are associated with changes in protein environment. Electrostatic binding of Ca2+ to casein resulted in a redistribution of the components of the infrared spectra. Addition of Ca2+ in salt solutions of K+ and Na+ led to apparent decreases in large loop or helical structures at 37 degrees C with concomitant increases in the percentage of structures having greater bond energy, such as turns and extended helical structures. At 15 degrees C, Na+ and K+ have differential effects on the Ca(2+)-casein complexes. All of these observations are in accordance with the important role of serine phosphate side chains as sites for Ca2+ binding in caseins and the swelling of the casein structure upon incorporation into reformed micelles at 37 degrees C. This new open, hydrated structure is buttressed by a change in backbone as evidenced by a shift in absorbance to higher wave numbers (greater bond energies) as colloidal micelles are reformed.

Secondary structure of bovine alphaS2-casein: theoretical and experimental approaches.

Circular dichroism and Fourier transform infrared spectroscopy of bovine alphaS2-casein both report a 24 to 32% content of alpha-helix. A consensus of sequence based predictions for alpha-helix suggests a Lys77-Gln91 helix within the sequence (Ser61-Arg125). This motif is repeated at (Ser143-Leu207), and this region contains a longer Thr145-Leu177 predicted alpha-helix. A short, seven-member alpha-helix may also organize the N-terminal peptide that precedes the first phosphoserine [-Srp-]3 cluster. As was found for other caseins studied by these spectroscopic methods, a high degree of extended beta-sheet (approximately 30%) and turns (25 to 30%) are predicted for alphaS2-casein.

Molten globule structures in milk proteins: implications for potential new structure-function relationships.

Recent advances in the field of protein chemistry have significantly enhanced our understanding of the possible intermediates that may occur during protein folding and unfolding. In particular, studies on alpha-lactalbumin have led to the theory that the molten globule state may be a possible intermediate in the folding of many proteins. The molten globule state is characterized by a somewhat compact structure, a higher degree of hydration and side chain flexibility, a significant amount of native secondary structure but little tertiary folds, and the ability to react with chaperones. Purified alpha(s1)- and kappa-caseins share many of these same properties; these caseins may thus occur naturally in a molten globule-like state with defined, persistent structures. The caseins appear to have defined secondary structures and to proceed to quaternary structures without tertiary folds. This process may be explained, in part, by comparison with the architectural concepts of tensegrity. By taking advantage of this "new view" of protein folding, and applying these concepts to dairy proteins, it may be possible to generate new and useful forms of proteins for the food ingredient market.