Redox-dependent changes in beta-sheet and loop structures of Cu,Zn superoxide dismutase in solution observed by infrared spectroscopy

Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c

Amide I difference spectroscopy is widely used to investigate protein function and structure changes. In this article, we show that the common approach of assigning features in amide I difference signals to distinct secondary structure elements in many cases may not be justified. Evidence comes from Fourier transform infrared (FTIR) and 2D-IR spectroelectrochemistry of the protein cytochrome c in the amide I range, in combination with computational spectroscopy based on molecular dynamics (MD) simulations. This combination reveals that each secondary structure unit, such as an alpha-helix or a beta-sheet, exhibits broad overlapping contributions, usually spanning a large part of the amide I region, which in the case of difference absorption experiments (such as in FTIR spectroelectrochemistry) may lead to intensity-compensating and even sign-changing contributions. We use cytochrome c as the test case, as this small electron-transferring redox-active protein contains different kinds of secondary structure units. Upon switching its redox-state, the protein exhibits a different charge distribution while largely retaining its structural scaffold. Our theoretical analysis suggests that the change in charge distribution contributes to the spectral changes and that structural changes are small. However, in order to confidently interpret FTIR amide I difference signals in cytochrome c and proteins in general, MD simulations in combination with additional experimental approaches such as isotope labeling, the insertion of infrared labels to selectively probe local structural elements will be required. In case these data are not available, a critical assessment of previous interpretations of protein amide I 1D- and 2D-IR difference spectroscopy data is warranted.

Purification and Characterization of Superoxide Dismutases from Sea Buckthorn and Chestnut Rose

Superoxide dismutases (SODs) were purified from sea buckthorn and chestnut rose by ammonium sulfate precipitation and anion-exchange chromatography, and the detection methods of water-soluble tetrazolium-1 (WST-1), nitrobluetetrazolium (NBT) and pyrogallol autoxidation (PA) for SOD activity were compared. WST-1 method was selected due to its coefficient of variation (CV) <6% in this study. Two SODs exhibited similar characteristics. Their molecular mass and isoelectric point were about 30 kDa and 4.8 to 5.0 estimated by electrophoresis, and the K_m was 0.05 to 0.08 mmol/L, respectively. Dynamic light scattering analysis suggested their hydrodynamic radius distributes from 60 to 1500 nm. The activity of two SODs was unchanged at <80 °C or pH 2 to 9 or in simulated human gastric fluid. Their circular dichroism spectra suggested a main β-sheet structure, the fluorescence spectra reflected that the tryptophan residues of two SODs is partially exposed, these structures were rather stable at pH 2 to 9 or 50 to 90 °C. PRACTICAL APPLICATION: Superoxide dismutase (SOD) is an important antioxidant enzyme. SODs from sea buckthorn and chestnut rose were stable at high temperature or low pH or simulated gastric fluid. This result can provide a new approach for the potential application of SOD in the food and pharmaceutical fields.

Extracting Infrared Spectra of Protein Secondary Structures Using a Library of Protein Spectra and the Ramachandran Plot

Infrared (IR) spectra from 1200 to 1800 cm(-1) of the pure α-helix and β-sheet secondary structures have been extracted using a covariant least-squares procedure which relates a library of 40 infrared (IR) solution protein spectra from the work of Dong, Carpenter, and Caughey and amino acid fractions of the proteins based on assignments by STRIDE (secondary structure identification) of Eisenhaber and Argos. The excitonic splitting of the β-sheet structures is determined for this library of solution proteins. The method is extended to find a set of spectral basis functions that analyze IR spectra of protein samples for α-helix and β-sheet content. A rigorous error analysis including covariance, the correlations between the input library spectra, was used to justify the results and avoid less meaningful results. The utility of the results on α-helix and β-sheet regions is demonstrated by detecting protein changes due to cancer in imaging Fourier transform IR (FTIR) spectra of liver tissue slices. This work ends with a method to extract IR spectra of less prominent torsional angle distributions.

Obtaining information about protein secondary structures in aqueous solution using Fourier transform IR spectroscopy

Fourier transform IR (FTIR) spectroscopy is a nondestructive technique for structural characterization of proteins and polypeptides. The IR spectral data of polymers are usually interpreted in terms of the vibrations of a structural repeat. The repeat units in proteins give rise to nine characteristic IR absorption bands (amides A, B and I-VII). Amide I bands (1,700-1,600 cm(-1)) are the most prominent and sensitive vibrational bands of the protein backbone, and they relate to protein secondary structural components. In this protocol, we have detailed the principles that underlie the determination of protein secondary structure by FTIR spectroscopy, as well as the basic steps involved in protein sample preparation, instrument operation, FTIR spectra collection and spectra analysis in order to estimate protein secondary-structural components in aqueous (both H2O and deuterium oxide (D2O)) solution using algorithms, such as second-derivative, deconvolution and curve fitting. Small amounts of high-purity (>95%) proteins at high concentrations (>3 mg ml(-1)) are needed in this protocol; typically, the procedure can be completed in 1-2 d.

A primary role for disulfide formation in the productive folding of prokaryotic Cu,Zn-superoxide dismutase

Enzymatic activation of Cu,Zn-superoxide dismutase (SOD1) requires not only binding of a catalytic copper ion but also formation of an intramolecular disulfide bond. Indeed, the disulfide bond is completely conserved among all species possessing SOD1; however, it remains obscure how disulfide formation controls the enzymatic activity of SOD1. Here, we show that disulfide formation is a primary event in the folding process of prokaryotic SOD1 (SodC) localized to the periplasmic space. Escherichia coli SodC was found to attain β-sheet structure upon formation of the disulfide bond, whereas disulfide-reduced SodC assumed little secondary structure even in the presence of copper and zinc ions. Moreover, reduction of the disulfide bond made SodC highly susceptible to proteolytic degradation. We thus propose that the thiol-disulfide status in SodC controls the intracellular stability of this antioxidant enzyme and that the oxidizing environment of the periplasm is required for the enzymatic activation of SodC.

Equilibrium titrations of acid-induced unfolding–refolding and salt-induced molten globule of cytochrome c by FT-IR spectroscopy

Despite extensive investigations on the acid-unfolded and acid/salt-induced molten globule(-like) states of cytochrome c using variety of techniques, structural features of the acid-unfolded state in terms of residual secondary structures and the structural transition between the acid-unfolded and acid/salt-refolded states have not been fully characterized beyond the circular dichroism (CD) spectroscopy. It is unusual that secondary structure(s) of the unfolded state leading to the molten globule state, an important protein folding intermediate, as determined by CD was not fully corroborated by independent experimental method(s). In this study, we carried out an equilibrium titration of acid-induced unfolding and subsequent acid- and salt-induced refolding of cytochrome c using Fourier transform infrared spectroscopy. The spectral profiles of the equilibrium titration reveal new structural details about the acid-unfolded state and the structural transition associated with the acid/salt-refolded molten globule(-like) states of cytochrome c.

Structural Changes of ?-Lactoglobulin during Thermal Unfolding and Refolding ? An FT-IR and Circular Dichroism Study

We have quantitatively characterized by FT-IR spectroscopy the contents of secondary structure of beta-lactoglobulin during thermal unfolding and subsequent refolding. Our data clearly indicate that considerable amount of secondary structure, particularly beta-sheet, still remained intact even at 90 degrees C. Noticeable changes in secondary structure of beta-lactoglobulin were observed only above 70 degrees C. The refolded protein regained, within limits of experimental error, all of the secondary structure lost during thermal unfolding. The data also indicate that the refolding mechanism operating at pH 7.0 and 2.0 are the same. Identical secondary structure of native and refolded beta-lactoglobulin was also indicated by far-UV circular dichroic spectra of the two forms of protein. Near UV circular dichroic spectra of the same two forms showed considerable differences indicating less tertiary structure of refolded beta-lactoglobulin. The combined CD and FT-IR data indicated that refolded form of beta-lactoglobulin could be characterized as a molten globule state as it had native-like secondary structure and compromised tertiary structure.

Long Distance Charge Redistribution Upon Cu,Zn-Superoxide Dismutase Reduction

Cu,Zn-superoxide dismutase (Cu,Zn-SOD) is a ubiquitous enzyme with an essential role in antioxidant defense. To better understand structural factors at the origin of the highly efficient superoxide dismutation mechanism, we analyzed the consequence of copper reduction on the electronic properties of the backbone and individual amino acids by using electrochemistry coupled to Fourier transform infrared spectroscopy. Comparison of data recorded with bovine erythrocyte and recombinant chloroplastic Cu,Zn-SOD from Lycopersicon esculentum, expressed as a functional tetramer in Escherichia coli and (14)N- or fully (15)N-labeled, demonstrated that the infrared changes were dominated by reorganizations of peptide bonds and histidine copper ligands. Two main infrared modes of histidine side chain, markers of metal coordination, were identified by using Cu- and Zn-methylimidazole models: the nu(C(4)C(5))at 1605-1594 cm(-1) or approximately 1586 cm(-1) for Ntau or Npi coordination, and the nu(C(5)Ntau) at approximately 1113-1088 cm(-1). These modes, also identified in Cu,Zn-SOD by using (15)N labeling, showed that the electronic properties of the histidine Ntau ligands of copper are mostly affected upon copper reduction. A striking conclusion of this work is that peptide groups from loops and beta-sheet largely participate in charge redistribution upon copper reduction, and in contrast, electronic properties of polar and charged amino acids of the superoxide access channel remain unaffected. This is notably shown for the strictly conserved Arg-143 by site-directed mutagenesis on chloroplastic Cu,Zn-SOD. Charge compensation by the peptide backbone and preserved electronic properties of the superoxide access channel and docking site upon copper reduction may be the determinant factors for the high reaction kinetics of superoxide with both reduced and oxidized Cu,Zn-SOD.

Fourier transform IR and Fourier transform Raman spectroscopy studies of metallothionein-III: amide I band assignments and secondary structural comparison with metallothioneins-I and -II

The secondary structures of porcine brain Cu(4)Zn(3)-metallothionein (MT)-III and Cd(5)Zn(2)MT-I, Cd(5)Zn(2)MT-II, and Zn(7)MT-I from rabbit livers in the solid state are investigated by Fourier transform IR spectroscopy (FTIR) and Fourier transform Raman spectroscopy (FT-Raman). The Cu(4)Zn(3)MT-III contains 26-28% beta-turns and half-turns, 13-14% 3(10)-helices, 47-49% random coils, and 11-12% beta-extended chains. The structural comparison of porcine brain Cu(4)Zn(3)MT-III with rabbit liver Cd(5)Zn(2)MT-I (II) and Zn(7)MT-I shows that the contents of the random coil structure are obviously increased. The results indicate that the insert of an acidic hexapeptide in the alpha domain of Cu(4)Zn(3)MT-III possibly forms an alpha helix. However, because the bands assigned to the alpha-helix and random coil structures are overlapped in the spectra, the content of random coil structures in Cu(4)Zn(3)MT-III is therefore higher than those in Cd(5)Zn(2)MT-I, Cd(5)Zn(2)MT-II, and Zn(7)MT-I.

Thermal-induced changes in the secondary conformation of superoxide dismutase containing different metal ions

The thermal stability of three superoxide dismutases (SODs) with different metal ions (Mn, Cu/Zn, Fe) in the solid state was studied by a Fourier transform infrared (FT-IR) microspectroscopy combined with thermal analyzer. The IR spectra showed a maximum peak at 1652 cm(-1) for all the native SODs in the amide I band, suggesting a predominant random coil with less alpha-helix structures. By heating each sample, a shoulder at 1631 cm(-1) in the amide I band gradually appeared from 45 degrees C for Fe SOD and from 50 degrees C for Mn SOD but another shoulder at 1639 cm(-1) appeared from 50 degrees C for Cu/Zn SOD. The peak at 1631 cm(-1) is due to the intermolecular beta-sheet structure, but the peak at 1639 cm(-1) corresponds to the major intramolecular beta-sheet with less random coil structure. This reveals that in the first heating process the transformation from random coil/alpha-helix structure to beta-sheet structure initiated from around 45-50 degrees C. There was about 16-22% compositional change resulting from that transformation. However, both additional shoulders stood there and did not restore to their original spectra even with cooling to room temperature, suggesting the denaturation and irreversible properties of the solid SODs after heating. The thermal-dependent denaturation and irreversibility of Mn SOD, Cu/Zn SOD and Fe SOD were clearly evidenced by the increase in intramolecular and intermolecular beta-sheet structure.

Entrapping intermediates of thermal aggregation in alpha-helical proteins with low concentration of guanidine hydrochloride

Aggregation of proteins is a problem with serious medical implications and economic importance. To develop strategies for preventing aggregation, the mechanism(s) and pathways by which proteins aggregate must be characterized. In this study, the thermally induced aggregation processes of three alpha-helix proteins (myoglobin, cytochrome c, and lysozyme) in the presence and absence of 1.0 m guanidine hydrochloride (GdnHCl) were investigated by means of infrared spectroscopy. In the absence of GdnHCl, intensities of the alpha-helix bands (approximately 1656 cm(-1)) decrease as a function of temperature at above 50 degrees C. With myoglobin and cytochrome c, the loss of helix bands was accompanied by the appearance of two new bands at 1694 and 1623 cm(-1), indicative of the formation of intermolecular beta-sheet aggregates. For lysozyme, bands indicative of intermolecular beta-sheet aggregates did not appear in any significant intensity. In the presence of 1.0 m GdnHCl, two major intermediate states rich in 3(10)-helix (represented by the band at 1663 cm(-1)) and beta-turn structure (represented by the band at 1667 cm(-1)), respectively, were observed. These findings demonstrated that IR spectroscopic studies of protein aggregation using a combination of thermal and chemical denaturing factors could provide a means to populate and characterize aggregation intermediates.

Secondary structure dependent on metal ions of copper,zinc superoxide dismutase investigated by Fourier transform IR spectroscopy

Copper, zinc superoxide dismutase (Cu2Zn2-SOD) from bovine erythrocyte and its metal ion free derivatives, E2Zn2-SOD, Cu2E2-SOD, and E2E2-SOD (E: empty) were prepared and their secondary structures were investigated by Fourier transform ir spectroscopy. In 20 mM deuterated phosphate buffer (pD 7.5) solution at room temperature, the native Cu2Zn2-SOD contains about 34% beta-strand, 17% beta-turn, and 49% unordered structures, which is similar to the content determined by x-ray crystal structural analysis. The metal ion free derivatives decrease the component of beta-strand and increase the unordered structure component in trend. Especially in the cases of zinc-free derivatives, Cu2E2-SOD and E2E2-SOD, about 24% beta-strand, 20% beta-turn, and 57% unordered structures are obtained. The result indicates that the zinc ion plays an important role in determining the secondary structure of copper,zinc superoxide dismutase.

Infrared and circular dichroism spectroscopic characterization of structural differences between beta-lactoglobulin A and B

Structural differences between two genetic variants of bovine beta-lactoglobulins (type A and B) in aqueous solutions were characterized using Fourier transform infrared and circular dichroism spectroscopies. To probe differences in structural dynamics, the effects hydrogen-deuterium exchange were also compared for the two proteins. The infrared spectra recorded in H2O solution for the two proteins were nearly identical in the conformationlly sensitive amide I region. The only exceptions were small differences at the band ascribed to a high-wavenumber beta-sheet component near 1693 cm-1 and the band assigned to turns at 1684 cm-1. In contrast, when the proteins were prepared in D2O solution, marked spectral differences were observed at all regions ascribed to beta-sheet and turn structures. These differences are consistent with the structural differences of the two variants at amino acid residues 64 and 118, which are located at a turn and a beta-sheet structure, respectively, as revealed by X-ray crystallographic studies [Monaco et al. (1987) J. Mol. Biol. 197, 695-706]. The circular dichroism spectra for the two proteins were essentially identical, both before and after hydrogen-deuterium exchange. Therefore, hydrogen-deuterium exchange did not alter the proteins' secondary structure. The enhancement of the amide I spectral difference upon hydrogen-deuterium exchange was ascribed to the differences in the structural mobility of the two proteins. Since the rate of exchange was greater for variant A, it was concluded that this variant has greater structural mobility than variant B. These findings indicate that the combination of infrared spectroscopy and hydrogen-deuterium exchange has great potential in characterization of even subtle structural differences in proteins induced by naturally occurring point mutations and/or site-directed mutagenesis.