The conformational analysis of peptides using Fourier transform IR spectroscopy

Biophysical studies of the development of amyloid fibrils from a peptide fragment of cold shock protein B

The peptide CspB-1, which represents residues 1-22 of the cold shock protein CspB from Bacillus subtilis, has been shown to form amyloid fibrils when solutions containing this peptide in aqueous (50%) acetonitrile are diluted in water [M. Gross et al. (1999) Protein Science 8, 1350-1357] We established conditions in which reproducible kinetic steps associated with the formation of these fibrils can be observed. Studies combining these conditions with a range of biophysical methods reveal that a variety of distinct events occurs during the process that results in amyloid fibrils. A CD spectrum indicative of beta structure is observed within 1 min of the solvent shift, and its intensity increases on a longer timescale in at least two kinetic phases. The characteristic wavelength shift of the amyloid-binding dye Congo Red is established within 30 min of the initiation of the aggregation process and corresponds to one of the phases observed by CD and to changes in the Fourier transform-infrared spectrum indicative of beta structure. Short fibrillar structures begin to be visible under the electron microscope after these events, and longer, well-defined amyloid fibrils are established on a timescale of hours. NMR spectroscopy shows that there are no significant changes in the concentration of monomeric species in solution during the events leading to fibril formation, but that soluble aggregates too large to be visible in NMR spectra are present throughout the process. A model for amyloid formation by this peptide is presented which is consistent with these kinetic data and with published work on a variety of disease-related systems. These findings support the concept that the ability to form amyloid fibrils is a generic property of polypeptide chains, and that the mechanism of their formation is similar for different peptides and proteins.

A FTIR spectroscopy evidence of the interactions between wheat germ agglutinin and N-acetylglucosamine residues

Wheat germ agglutinin (WGA), a lectin binding a N-acetyl-D-neuraminic acid (NeuNAc) and/or N-acetyl-D-glucosamine (GlcNAc) group, was studied by Fourier transform infrared (FTIR) spectroscopy. Deconvolution of the FTIR spectrum of WGA alone indicated the presence of few alpha-helices and beta-sheets, in contrast to many other lectins. These results agree with previous WGA crystal data. The WGA conformational changes, induced by GlcNAc-bearing liposomes or GlcNAc oligomers, were studied by infrared differential spectroscopy. The GlcNAc binding to WGA resulted in a decrease of turns and alpha-helices and a concomitant appearance of beta-sheets, inducing more or less peptidic N-H deuteration.

A holistic approach to protein secondary structure characterization using amide I band Raman spectroscopy

We have developed a holistic protein structure estimation technique using amide I band Raman spectroscopy. This technique combines the superposition of reference spectra for pure secondary structure elements with simultaneous aromatic, fluorescence, and solvent background subtraction, and is applicable to solution, suspension, and solid protein samples. A key component of this technique was the calculation of the reference spectra for ordered helix, unordered helix, and sheet, turns, and unordered structures from a series of well-characterized reference proteins. We accurately account for the overlap between the amide I and non-amide I regions and allow for different scattering efficiencies for different secondary structures. For hydrated samples, we allowed for the possibility that bound water spectra differ from the bulk water spectra. Our computed reference spectra compare well with previous experimental and theoretical results in the literature. We have demonstrated the use of these reference spectra for the estimation of secondary structures of proteins in solution, suspension, and dry solid forms. The agreement between our structure estimates and the corresponding determinations from X-ray crystallography is good.

Fast events in protein folding: the time evolution of primary processes

Most experimental studies on the dynamics of protein folding have been confined to timescales of 1 ms and longer. Yet it is obvious that many phenomena that are obligatory elements of the folding process occur on much faster timescales. For example, it is also now clear that the formation of secondary and tertiary structures can occur on nanosecond and microsecond times, respectively. Although fast events are essential to, and sometimes dominate, the overall folding process, with a few exceptions their experimental study has become possible only recently with the development of appropriate techniques. This review discusses new approaches that are capable of initiating and monitoring the fast events in protein folding with temporal resolution down to picoseconds. The first important results from those techniques, which have been obtained for the folding of some globular proteins and polypeptide models, are also discussed.

Effect of gelation on the chemical stability and conformation of leuprolide

PURPOSE

The purpose of this study was to characterize the conformation, aggregation, and stability of leuprolide on gelation.

METHODS

Infrared spectra (FTIR) of leuprolide solutions and gels were collected in water, propylene glycol (PG), dimethyl sulfoxide (DMSO), and trifluoroethanol (TFE). Leuprolide solution and gel stability data were obtained by SEC and RP-HPLC.

RESULTS

Leuprolide was induced to gel with increasing peptide concentration, introduction of salts, and gentle agitation. Leuprolide dissolved in water (400 mg/ml) demonstrated FTIR spectra consisting of two major bands of equal intensity at 1615 cm(-1) and 1630 cm(-1), similar to inter- and intra-molecular beta-sheet structure in proteins. When samples were gently agitated for 24 hours at 25 degrees C, the formulation was observed to change from a viscous liquid to an opaque gel with a concomitant shift in infrared spectra from the equal intensity bands to mostly 1630 cm(-1), indicating a shift to a preferred beta-sheet structure. Incubation of leuprolide with 20-200 mM salts at 25 degrees C and 37 degrees C also produced gels ranging from clear to cloudy and stringy white precipitates. The gel and precipitate were marked by a shift of the predominant beta-sheet band to 1630 cm(-1) and 1615 cm(-1), respectively. Leuprolide was also observed to gel and/or precipitate in mixtures of water, PG or TFE, but not in DMSO.

CONCLUSIONS

Birefringence was noted in many of the firmer gels. Both solutions and gels demonstrated minimal dimer or trimer formation, with no larger order aggregates detected. The chemical stability profile of gelled leuprolide was similar to that of the non-gelled water formulation by RP-HPLC.

Laser-Raman and FT-IR spectroscopic studies of peptide-analogues of silkmoth chorion protein segments

Silkmoth chorion, the proteinaceous major component of the eggshell, with extraordinary mechanical and physiological properties, consists of a complex set of proteins, which have a tripartite structure: a central, evolutionarily conserved, domain and two more variable 'arms'. Peptide-analogues of silkmoth chorion protein central domain segments have been synthesized. Laser-Raman and infrared spectroscopic studies suggest the preponderance of antiparallel beta-pleated sheet structure for these peptides, both in solution and in the solid state.

Protein structure in KBr pellets by infrared spectroscopy

In this work we analyzed the secondary structure of 13 globular proteins in KBr pellet through Fourier transform infrared spectroscopy (FTIR). The quantification was based in singular value decomposition (SVD) theory, a pattern recognition method. The results show better correlation for alpha helix (0.90) and beta sheet (0.84) in amide I band, similar to the results obtained for proteins in solution. These results show that the protein secondary structure is conserved in solid state, in opposition to the results observed by FTIR using resolution enhancement techniques. The SVD analysis also show that in KBr pellets the protein secondary structures have absorbances in different wavenumbers when compared to those in solution. In this way, the use of KBr pellet and the pattern recognition method can be an ideal method to analyze protein secondary structure by FTIR.

A new attenuated total reflectance Fourier transform infrared spectroscopy method for the study of proteins in solution

An attenuated total reflectance Fourier transform infrared method has been developed that allows collection of spectra from proteins in solution. This method eliminates any structural perturbations induced by the internal reflection element (IRE), and thus the spectra reflect the solution conformation of the protein. A key feature of the method is subtraction of the signal from any protein adsorbed to the IRE. The advantages of this method include the small amount of sample required and the high sampling rate. Attenuated total reflectance (ATR)-Fourier transform infrared spectroscopy (FTIR) is more versatile than transmission FTIR because it is possible to collect spectra of nontransparent samples, to use samples of very low protein concentration (< or = 0.3 mg/ml), and to study proteins in the presence of strongly absorbing solutes (such as denaturants). The experimental procedures and data processing routines developed were evaluated by collecting spectra from a set of 13 proteins and evaluating their accuracy with a partial least-squares analysis. The relative mean and standard deviation errors for the basis set analysis were 6.3% for alpha-helix, 5.9% for beta-sheet/extended structure, and 4.4% for turn, which are similar to values from comparable analyses of transmission FTIR spectra. In addition, a detailed comparison between this solution ATR method and the hydrated thin-film ATR technique is presented.

Formation of stable polypeptide monolayers at interfaces: controlling molecular conformation and orientation

The molecular self-organization and structural properties of peptide assemblies at different interfaces, using either amphipathic or hydrophobic polypeptide helices, is described. The two peptides under investigation form stable monolayers on the water surface under the conservation of their molecular conformation, as studied by circular dichroism and polarization-modulation Fourier transform infrared (FTIR) spectroscopy. Using surface plasmon resonance and reflection-absorption FTIR, we show that such molecular layers can be transferred unaltered to solid substrates. Most importantly, the molecular orientation of the hydrophobic helices on solid supports such as gold can be controlled by choosing a particular procedure for the layer formation. The helices were oriented parallel to the interface in Langmuir-Blodgett monolayers, and perpendicular to the interface in self-assembled monolayers. Our reflection-absorption FTIR measurements have delivered for the first time direct experimental evidence for the molecular conformation and orientation of pure peptide monolayers. Suitable reference spectra of polypeptides with defined conformation and orientation are necessary to use this technique for the determination of the molecular orientation of peptides in monomolecular films. We have solved the problem for alpha-helical polypeptides by using bacteriorhodopsin as a reference in combination with synthetic alpha-helices of defined interfacial orientation. The present study shows the possibility of constructing immobilized peptide monolayers with predefined macroscopic properties and molecular structure by choosing the proper polypeptide amino acid sequence, the technique used for layer formation, and the supporting surface properties.

Fast events in protein folding: relaxation dynamics of secondary and tertiary structure in native apomyoglobin

We report the fast relaxation dynamics of "native" apomyoglobin (pH 5.3) following a 10-ns, laser-induced temperature jump. The structural dynamics are probed using time-resolved infrared spectroscopy. The infrared kinetics monitored within the amide I absorbance of the polypeptide backbone exhibit two distinct relaxation phases which have different spectral signatures and occur on very different time scales (nu = 1633 cm(-1),tau = 48 ns; nu = 1650 cm(-1),tau = 132 micros). We assign these two spectral components to discrete substructures in the protein: helical structure that is solvated (1633 cm(-1)) and native helix that is protected from solvation by interhelix tertiary interactions (1650 cm(-1)). Folding rate coefficients inferred from the observed relaxations at 60 degrees C are k(f)(solvated) = (7 to 20) x 10(6) s(-1) and k(f)(native) = 3.6 x 10(3) s(-1), respectively. The faster rate is interpreted as the intrinsic rate of solvated helix formation, whereas the slower rate is interpreted as the rate of formation of tertiary contacts that determine a native helix. Thus, at 60 degrees C helix formation precedes the formation of tertiary structure by over three orders of magnitude in this protein. Furthermore, the distinct thermodynamics and kinetics observed for the apomyoglobin substructures suggest that they fold independently, or quasi-independently. The observation of inhomogeneous folding for apomyoglobin is remarkable, given the relatively small size and structural simplicity of this protein.

Conformational changes of arginine kinase induced by photochemical release of nucleotides from caged nucleotides--an infrared difference-spectroscopy investigation

The conformations of arginine kinase (AK) in AK x Mg x ADP, AK x Mg x ATP, AK x Mg x ADP x NO3-, AK x Mg x ADP x Arg and AK x Mg x ADP x NO3- x Arg complexes were investigated by measuring their reaction-induced infrared difference spectra (RIDS). The photochemical release of ATP from ATP[Et(PhNO2)] and of ADP from ADP[Et(PhNO2)] produced distinct RIDS of AK complexes, suggesting that binding of ADP and ATP promoted different structural alterations of the enzyme active-site. Small infrared changes in the amide-I region were observed, indicating that about 5-10 amino acid residues were involved in the nucleotide-binding site. These infrared changes were due to the structural alteration of the peptide backbone caused by the nucleotide-binding and to the coupling effects between the nucleotide-binding site and the other substrate (Arg or NO3-)-binding site. ATP binding to AK (as well as ADP-binding to AK in the presence of NO3-) induced protonation of a carboxylate group of Asp or Glu, as evidenced by the appearance of the 1733-cm(-1) band, which was not observed with the AK x Mg x ADP, AK x Mg x ADP x Arg and AK x Mg x ADP x NO3- x Arg complexes. The RIDS of the AK x Mg x ADP x NO3- x Arg complex showed new infrared bands at 1622 cm(-1) (negative) and at 1613 cm(-1) (positive), which were not seen in the RIDS of other complexes (without NO3- or/and Arg). In the transition-state-analog complex of AK, no protonation of the carboxylate residue (Asp or Glu) was observed, and the binding site of NO3- or the gamma-phosphate group of nucleotide was altered.

Synthesis and FTIR conformational studies of peptides from the basic region of c-Jun: a critical analysis on the basis of CD and NMR data

The peptide (35 residues) corresponding to the basic subdomain (bSD) of c-Jun (residues 252-281) and its fragments NP (N-terminal peptide, 1-19) and CP (C-terminal peptide, 16-35) were synthesized in stepwise solid-phase using the tert-butyloxycarbonyl/benzyl strategy. In a previous paper, we have shown that during its binding to the DNA site CRE (cAMP-responsive element) the bSD structure was converted into alpha-helix from an initial random coil conformation [Krebs, D., Dahmani, B., El Antri, S., Monnot, M., Convert, O., Mauffret, O., Troalen, F. & Fermandjian, S. Eur. J. Biochem. 231, 370-380 (1995)]. Our results suggested both a high flexibility and a helical potential in bSD, these two properties seeming crucial for the accommodation of the basic subdomain of c-Jun to its specific DNA targets. In this work, we assessed the conformational variability of bSD through the study of the secondary structures of its NP and CP fragments in trifluoroethanol (TFE)/2H2O mixtures, using Fourier transform infrared (FTIR) spectroscopy. The IR results were critically analyzed in light of our previously reported circular dichroism (CD) and NMR data [Krebs, D., Dahmani, B., Monnot, M., Mauffret, O., Troalen, F. & Fermandjian, S. Eur. J. Biochem, 235, 699-712 (1996)]. Upon addition of TFE, the relative areas of the seven components of the amide I. band (1700-1620 cm-1) reflected the conversion of a large amount of random coil conformation into alpha-helix for the two fragments and bSD. This effect was accompanied by more subtle variations of the less populated structures, in agreement with the results of CD and NMR experiments. The IR results stipulated the conservation of the parent bSD secondary structures in both fragments; however, NP and CP peptides did not display similar random-to-alpha-helix stabilization pattern upon additions of TFE to aqueous solutions. The profile from CD signal at 222 nm was found sigmoidal for NP and almost linear for CP, while that corresponding to the parent peptide bSD was just in between those of its fragments. Thus, the present study confirms the high flexibility and helix propensity of the c-Jun basic subdomain and suggests that the N- and C-terminal parts of the peptide do not follow the same random-to-helix conversion profile during their complexation with DNA.

Evaluation of the secondary structure of vaccinia-virus thymidine kinase by circular-dichroism spectroscopy of overlapping synthetic peptides

A new approach is reported that includes multiple-peptide synthesis and CD spectroscopy of overlapping peptides to evaluate the secondary structure of the vaccinia-virus thymidine kinase (TK). We divided the sequence of the vaccinia-virus TK into 82 peptides of 15 residues that overlapped by 13 residues and covered the complete sequence of vaccinia-virus TK. All peptides were synthesized by solid-phase multiple-peptide synthesis by means of the Fmoc/tert-butyl strategy. Subsequently, the secondary structure of each peptide was studied by means of CD spectroscopy in a mixture of 30% trifluoroethanol and sodium phosphate, pH 7. Secondary-structure evaluation led to determination of a vaccinia-virus-TK secondary-structure pattern. Consecutive peptides with alpha-helical content mainly showed CD spectra with increasing and decreasing Cotton effects typical of alpha-helices. This phenomenon was used to localize the helices on the sequence. In contrast, only single CD spectra with clear beta-sheet conformation, or CD spectra of mixed secondary-structure content were observed for beta-sheets. Therefore, the exact localization of beta-sheet-containing residues was deduced by comparison with isofunctional sequence-dissimilar proteins. We identified seven alpha-helices and six beta-sheet-containing regions, which we used for a secondary-structure model of the vaccinia-virus TK protein.

Intramolecular disulfide bonds enhance the antimicrobial and lytic activities of protegrins at physiological sodium chloride concentrations

Protegrins are 2-kDa antimicrobial peptides that contain 16-18 amino acid residues and two intramolecular disulfide bonds. We studied the contribution of these disulfide bonds to the bactericidal activity of protegrins in physiological concentrations of NaCl by comparing protegrin PG-1 with variants that lacked one or both cysteine disulfides. Whereas the bactericidal and liposome-lytic properties of protegrin PG-1 were enhanced by adding 100 mM NaCl to the phosphate-buffered medium, NaCl addition strongly inhibited the effects of its linearized, disulfide-free variant, [A6, A8, A13, A15]protegrin-1. Whereas protegrin PG-1 manifested beta-sheet structure by CD (circular dichroism) and ATR-FTIR (attenuated-total-reflectance-Fourier-transform-infrared) spectroscopy in buffer or membrane-mimetic environments, [A6, A8, A13, A15]protegrin-1 manifested disordered structure in phosphate buffer and alpha-helical characteristics in membrane-mimetic environments. Both single-disulfide protegrin variants, [A8, A13]protegrin-1 and [A6, A15]protegrin-1, assumed beta-sheet conformations with liposomes that simulated bacterial membranes, and both retained substantial bactericidal activity when 100 mM NaCl was present. These findings demonstrate that the intramolecular disulfide bonds of protegrins are required for their antiparallel beta-sheet conformation in membrane-mimetic environments and for their potent antimicrobial activity in media containing NaCl concentrations comparable to those found in serum and extracellular fluids.

Progress towards understanding beta-sheet structure

This review is focused on recent advances in our understanding of beta-sheet structure. It is intended to supplement previous surveys describing the early characterization and study of beta-sheet structure. The first two sections of this review provide a brief introduction to beta-sheet structure referencing the prior comprehensive reviews in this area as well as integrating new concepts. The next part outlines the typical problems encountered in solution studies on beta-sheet structures. The most useful spectroscopic and biophysical techniques used to characterize beta-sheet structures are described in the fourth section. Current hypotheses regarding the folding of predominantly beta-sheet proteins are discussed in some detail in the fifth segment. The efforts of a number of laboratories to utilize peptides or peptidomimetics to serve as small beta-sheet model systems are reviewed in the penultimate section. Finally, the efforts of a number of research groups focusing on the de novo design of beta-sheet-based proteins are outlined.

FTIR study of the thermal denaturation of horseradish and cytochrome c peroxidases in D2O

Fourier transform infrared (FTIR) spectroscopy was employed to examine the thermal denaturation of the Fe(III), Fe(II), and Fe(II)-CO forms of cytochrome c peroxidase and horseradish peroxidase in phosphate buffer at pD 7.0. The amide I' regions of the deconvolved spectra are consistent with predominantly alpha-helical secondary structure around room temperature, but the alpha-helical absorption of the two peroxidases differs significantly; bands assigned to alpha-helical components occur at 1659 and 1649 cm-1 in horseradish peroxidase and at 1652 and 1637 cm-1 in cytochrome c peroxidase. The thermal denaturation mechanisms of the peroxidases also vary. All three forms of cytochrome c peroxidase retain their secondary structure up to 50 degrees C, when bands characteristic of aggregation (1616 and 1684 cm-1) appear in the amide I' region, and above 55 degrees C rapid loss of secondary structure is accompanied by enhanced aggregation. In horseradish peroxidase, on the other hand, the Fe(III) and Fe(II) states exhibit dissimilar denaturation mechanisms. Slow, gradual alteration of secondary structure is observed for Fe(III) horseradish peroxidase on heating, and polypeptide unfolding appears to be complete around 90 degrees C, without aggregation. In Fe(II) and Fe(II)-CO horseradish peroxidase, aggregation bands appear at approximately 55 degrees C, signaling the onset of denaturation. Frequency shifts in the v(CO) bands above room temperature reveal the conformational changes in the heme cavity precede global conformational changes in cytochrome c peroxidase but not in horseradish peroxidase. The reduction in amide II intensities, due to peptide H-D exchange on heating the peroxidases in D2O, indicates the formation above room temperature of partially unfolded states with increased solvent accessibility but intact secondary structures.

Dissection of the basic subdomain of the c-Jun oncoprotein: a structural analysis of two peptide fragments by CD, Fourier-transform infrared and NMR

In a previous paper, we reported on the structural properties of a 35-residue peptide corresponding to a modified basic subdomain (bSD) of the basic zipper protein c-Jun (residues 252-281) as determined by combined use of 1H-NMR, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopies [Krebs, D., Dahmani, B., El Antri, S., Monnot, M., Convert, O,. Mauffret, O., Troalen, F. & Fermandjian, S. (1995) Eur. J. Biochem. 231, 370-380]. The fragments NP and CP (the N-terminal residues 1-19 and C-terminal residues 16-35 of bSD, respectively) proved to be particularly useful for the assignment of the 1H-NMR spectra of the full-length bSD, which has been achieved completely in aqueous solution and partially in trifluoroethanol. Here, we report on the structural properties of NP and CP in aqueous solution and under varying H2O/trifluoroethanol conditions, again using 1H-NMR, CD and FT-IR experiments. Both CD and FT-IR results established that the fragments are weakly structured in aqueous solution. Addition of trifluoroethanol to aqueous solutions of the peptides produced their stabilization into helix, following a profile sigmoidal for NP and nearly linear for CP. Quantitative NOEs, secondary Halpha chemical shifts, NH temperature coefficients and 3JalphaN coupling constants for the peptides in aqueous solutions provided indications for weak helix features (nascent helices) manifested within two sites (continuous dNN NOEs) in both NP and CP. For each peptide, an excellent agreement was observed between experiments and predictions with the AGADIR program for the location of these nascent helices in the sequences. Trifluoroethanol provoked both the alpha-helix stabilization within these sites and the alpha-helix propagation to adjacent amino acid residues. Finally, our results reflected the high flexibility and helix potential of the NP and CP fragments, these two properties seeming crucial for the accommodation of c-Jun to its specific DNA targets. The results demonstrated also the fragmentation's benefits in dissecting a protein or a complex peptide into smaller fragments and analyzing their structure individually.

Orientational order determination by internal reflection infrared spectroscopy

PATIR-FTIR spectroscopy is a powerful technique for the determination of molecular order in thin films such as supported lipid membranes, but it relies on electromagnetic theory which is incomplete and potentially misleading. A complete derivation of the current theory for two, three and four phase system has been reported. The two phase and thin film approximations most commonly used in practice have been shown to represent the thickness-dependent expressions from which they are derived with a high degree of accuracy. However, these expressions are based on the macroscopic behavior of dielectric materials, and may not be accurate when applied to microscopic circumstances. The potential error introduced is qualitatively and quantitatively significant. Further experimental and theoretical work is needed to verify the accuracy of this theory, or to refute and refine it. This effort to do this is warranted by the power and increasing popularity of the technique.