Determination of protein secondary structure using factor analysis of infrared spectra

Predictions of protein secondary structures using factor analysis on Fourier transform infrared spectra: effect of Fourier self-deconvolution of the amide I and amide II bands

Fourier self-deconvolution (FSD) was performed on protein amide I and II Fourier transform infrared (FTIR) spectra to test if the resultant increased band shape variation would lead to improvements in protein secondary structure prediction with our factor analysis based restricted multiple regression (RMR) methods. FTIR spectra of 23 proteins dissolved in H2O were measured and normalized to a constant amide I peak absorbance. The deconvolved spectra were renormalized by area so that the deconvolved spectra sets had the same area as before. Principal component analysis of the deconvolved spectra sets was carried out, which was followed by a selective multiple linear regression (RMR) analysis of the principal component loadings with regard to the fractional components (FC) of secondary structure. As compared to analyses based on the original spectra set, helix and sheet predictions were not noticeably improved by FSD; but, if a very large number of component spectra (16) were retained in the pool to select which loadings to be used in the RMR optimization, better predictions of turn and "other" resulted. The prediction quality varied depending on the deconvolution parameters used.

Conformational changes in the extrinsic manganese stabilizing protein can occur upon binding to the photosystem II reaction center: an isotope editing and FT-IR study

Photosystem II catalyzes the light-driven oxidation of water and reduction of plastoquinone in oxygenic photosynthesis. The manganese stabilizing protein (MSP) of photosystem II is an extrinsic subunit that plays an important role in catalytic activity. This subunit can be extracted and re-bound to the photosystem II reaction center. Extraction is associated with decreased stability of manganese binding by the enzyme and by loss in high rates of oxygen evolution activity; reconstitution reverses these phenomena. Since little is known about the assembly of complex membrane proteins, we have employed isotope editing and vibrational spectroscopy to obtain information about any changes in secondary structure that occur in MSP upon functional reconstitution to photosystem II. The spectroscopic data obtained are consistent with substantial changes in conformation when MSP binds to photosystem II; approximately 30-40% of the peptide backbone undergoes a change in secondary structure. These conclusions were reached by comparing different aliquots, before and after binding, of the same 13[C]MSP sample. Analysis of amide I band line shapes through Fourier deconvolution and nonlinear regression suggests that binding of MSP to photosystem II is associated with a decrease in random structure and an increase in beta-sheet content. We conclude that binding of MSP to the reaction center can induce folding of MSP. Our results also indicate that, in solution, MSP can sample a variety of conformational states, which differ in hydrogen bonding of the peptide backbone.

Infrared absorbances of protein side chains

The spectral parameters of amino acid residue side chain and peptide bond absorptions in the region 1800-1440 cm-1 have been obtained by using an inverse matrix method applied to the infrared spectra of 42 amino acids, dipeptides, and higher peptides in aqueous solution. In addition the pH-dependent extinction coefficients of the amino acid and peptide COO-/NH3+ end groups were derived. It is shown that the secondary structure prediction accuracy of proteins by multivariate data analysis methods increases slightly, if the side chain absorbances of the residues asparagine, glutamine, aspartic acid, glutamic acid, arginine, tyrosine, and lysine are subtracted from the amide I and amide II region.

Role of an extrinsic 33 kilodalton protein of photosystem II in the turnover of the reaction center-binding protein D1 during photoinhibition

The reaction center-binding protein D1 of photosystem II (PS II) undergoes rapid turnover under light stress conditions. In the present study, we investigated the role of the extrinsic 33 kDa protein (OEC33) in the early stages of D1 turnover. D1 degradation was measured after strong illumination (1000-5000 microE m-2 S-1) of spinach manganese-depleted, PSII-enriched membrane and core samples in the presence and absence of the OEC33 under aerobic conditions at room temperature. PSII samples lacking the OEC33 were prepared by standard biochemical treatments with Tris or CaCl2/NH2OH while samples retaining the OEC33 were prepared with NH2OH or NaCl/NH2OH. The degradation of D1, monitored by SDS/urea-polyacrylamide gel electrophoresis and Western blotting using specific antibodies against D1, proceeds to a greater extent in NH2OH-treated samples than in Tris-treated samples over a 60 min illumination period. Under the same conditions, significantly more aggregation of D1 occurs in the Tris-treated samples than in the NH2OH-treated samples. The lower level of D1 degradation in Tris-treated samples is not due to secondary proteolysis, as judged from the time course for degradation at 25 degrees C or the degradation pattern at 4 degrees C. Similarly, for NaCl/NH2OH-treated samples, D1 degradation is greater and D1 aggregation less than in CaCl2/NH2OH-treated samples. The effect of the presence of the OEC33 on D1 degradation and aggregation is confirmed by reconstitution experiments in which the isolated OEC33 is restored back to Tris-treated samples. During very strong illumination, significant loss of CP43 also occurs in Tris-treated but not in NH2OH-treated samples. Structural analysis of PS II core complexes by Fourier transform infrared (FT-IR) spectroscopy revealed very little change in the protein secondary structure after 10 min illumination of NH2OH-treated samples while a large 10% decrease of alpha-helix content occurs in Tris-treated samples. On the basis of these results, we suggest that either (1) the OEC33 stabilizes the structural integrity of PS II such that it prevents the photodamaged D1 protein from aggregating with nearby polypeptides and thereby facilitating degradation or (2) the OEC33 specifically stabilizes CP43, a putative D1-specific protease, which normally promotes the efficient degradation of D1.

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.

Vibrational circular dichroism spectra of proteins in the amide III region: measurement and correlation of bandshape to secondary structure

Vibrational circular dichroism (VCD) spectra have been measured for 23 globular proteins dissolved in H2O/phosphate buffer over the 1400 to 1100 cm(-1) region which encompasses the amide III mode. Spectral responses characteristic of the dominant secondary structure type were found as broad features at approximately 1300 cm(-1), with the extreme forms having positive VCD for highly helical proteins and negative VCD for highly sheet-containing proteins. Quantitative correlation with secondary structure was carried out using previously developed factor analysis and restricted multiple regression (FA/RMR) techniques. Since the absorbance intensity of the amide III mode is difficult to determine due to overlap with other transitions, an alternative, absolute intensity-independent, simple structural analysis method was used. A linear regression was developed between the fractional components of secondary structure for the protein set and the overlap integrals of the normalized spectra from the set with that of a selected protein. The results of this simple method are quite comparable to those of the FA/ RMR approach for analysis with amide III VCD. On the other hand, test calculations with the new method when used with electronic CD spectra are not as good as FA/RMR due to its more intensity-dependent relationship with secondary structure.

Qualitative and quantitative analysis of the secondary structure of cytochrome C Langmuir-Blodgett films

A qualitative and quantitative analysis of the conformation of Langmuir-Blodgett (LB) dried films of cytochrome C on silicon wafers was performed by Fourier transform ir (FTIR) spectroscopy. A deconvolution procedure was applied to the amide I band analysis, in order to determine the percentage of the different secondary structures. Qualitative analysis was performed by examining difference spectra. Films obtained by spreading protein solutions at pH 7.4 and 1, dried at 25 and 100 degrees C, on silicon wafers were also examined in order to detect spectral components associated with denatured protein domains, and to compare them with cytochrome C LB films. FTIR spectroscopy showed that the following important changes characterise LB film spectra: (a) the alpha-helix component is higher (its percentage is 57 and 54%) than the one estimated in dried film obtained by spreading the solutions at pH 7.4 on a silicon substrate (43%), (b) there is an increase in the intensity of bands attributed to protonated carboxy group bands, involved and not involved in the formation of hydrogen bonds, and a decrease in those attributed to deprotonated carboxy groups, (c) the intensity of several bands attributed to aromatic amino acids and aliphatic chains increases, and (d) bands due to O-H stretching vibrations of crystallization water are present. These conformational changes could be induced by protein-protein interaction caused by the close packing of molecules that occurs during LB film formation; it cannot be excluded that they may be accompanied by partial changes in the tertiary structure of the protein. A preferential orientation of protein molecules in LB films is also a possibility.

Structure and thermal stability of photosystem II reaction centers studied by infrared spectroscopy

The secondary structure of photosystem II reaction centers isolated from pea has been deduced from quantitative analysis of the component bands of the infrared amide I spectral region, determined by FTIR spectroscopy. The analysis shows the isolated complex to consist of 40% alpha-helix, 10% beta-sheet, 14% beta-strands (or extended chains), 17% turns, 15% loops, and 3% nonordered segments. These structural protein elements were determined for samples in H2O, in D2O, and in dried films. The isolated reaction center, composed of proteins D1,D2,cytochrome b559, and PsbI, has been predicted to contain a total of 13 transmembrane alpha-helices, which conveys a percentage of this type of structure congruent with the structural determination deduced from FTIR spectra. The process of thermal destabilization of the reaction centers has also been studied by FTIR spectroscopy, showing a clear main conformational transition at 42 degrees C, which indicates a high thermal sensitivity of the secondary structure of this protein complex. Such thermal instability may correlate with the well-described high sensitivity of photosystem II to damage and may relate to the process of rapid protein degradation that photosystem II suffers during photoinhibition of plants.

Secondary structures comparison of aquaporin-1 and bacteriorhodopsin: a Fourier transform infrared spectroscopy study of two-dimensional membrane crystals

Aquaporins are integral membrane proteins found in diverse animal and plant tissues that mediate the permeability of plasma membranes to water molecules. Projection maps of two-dimensional crystals of aquaporin-1 (AQP1) reconstituted in lipid membranes suggested the presence of six to eight transmembrane helices in the protein. However, data from other sequence and spectroscopic analyses indicate that this protein may adopt a porin-like beta-barrel fold. In this paper, we use Fourier transform infrared spectroscopy to characterize the secondary structure of highly purified native and proteolyzed AQP1 reconstituted in membrane crystalline arrays and compare it to bacteriorhodopsin. For this analysis the fractional secondary structure contents have been determined by using several different algorithms. In addition, a neural network-based evaluation of the Fourier transform infrared spectra in terms of numbers of secondary structure segments and their interconnections [sij] has been performed. The following conclusions were reached: 1) AQP1 is a highly helical protein (42-48% alpha-helix) with little or no beta-sheet content. 2) The alpha-helices have a transmembrane orientation, but are more tilted (21 degrees or 27 degrees, depending on the considered refractive index) than the bacteriorhodopsin helices. 3) The helices in AQP1 undergo limited hydrogen/deuterium exchange and thus are not readily accessible to solvent. Our data support the AQP1 structural model derived from sequence prediction and epitope insertion experiments: AQP1 is a protein with at least six closely associated alpha-helices that span the lipid membrane.

Prediction of secondary structures of proteins using the sequence and spectroscopical data

An algorithm is presented which modifies the parameter of given methods of prediction of secondary protein structures by comparing the predictions with the frequency of secondary structures derived from infrared spectra in a way that the predictions align to the given data. Depending on the prediction method and accuracy of the given secondary structures a 1-6% increase in accuracy can be reached. The algorithm compares the difference between the predicted and real frequency of a given secondary structure in the protein and modifies accordingly the parameter used in the prediction method in order to give a new, more accurate prediction. A correlation between the accuracy of the prediction and increasing correctness between the prediction and infrared data was found using a set of 39 proteins.

Effect of temperature on the secondary structure of beta-lactoglobulin at pH 6.7, as determined by CD and IR spectroscopy: a test of the molten globule hypothesis

Previous CD measurements of changes in the conformation of beta-lactoglobulin at neutral pH as a function of temperature indicated the formation of a molten globule state above approx. 70 degrees C. New CD measurements are reported at temperatures up to 80 degrees C with an instrument on the Daresbury synchrotron radiation source which gives spectra of good signal-to-noise ratio down to 170 nm. IR spectra were recorded up to 94.8 degrees C with a ZnSe circle cell and a single simplified model of the substructure of the amide I' band was used to give the fractional contents of beta-sheet structure unambiguously and independently of the CD spectroscopy. The results of both techniques, however, were in agreement in showing a progressive loss of beta-sheet structure with increasing temperature, beginning below the denaturation temperature. Nevertheless, the CD spectroscopy showed a fairly abrupt loss of virtually all the helical conformation at approx. 65 degrees C. Comparison of the present results with other studies on the molten globule formed at acid pH in the lipocalin family suggests that above 65 degrees C a partly unfolded state is formed, possibly by destabilization of the intermolecular beta-strand I and the loss of the main helix, but it is not a classical molten globule transition.

Effects of temperature and SDS on the structure of beta-glycosidase from the thermophilic archaeon Sulfolobus solfataricus

The effects of temperature and SDS on the three-dimensional organization and secondary structure of beta-glycosidase from the thermophilic archaeon Sulfolobus solfataricus were investigated by CD, IR spectroscopy and differential scanning calorimetry. CD spectra in the near UV region showed that the detergent caused a remarkable change in the protein tertiary structure, and far-UV CD analysis revealed only a slight effect on secondary structure. Infrared spectroscopy showed that low concentrations of the detergent (up to 0.02%) induced slight changes in the enzyme secondary structure, whereas high concentrations caused the alpha-helix content to increase at high temperatures and prevented protein aggregation.

Determination of secondary structure of normal fibrin from human peripheral blood

The secondary structure of human fibrin from normal donors and from bovine and suilline plasma was studied by Fourier transform ir spectroscopy and a quantitative analysis of its secondary structure was suggested. For this purpose, a previously experimented spectrum deconvolution procedure based on the use of the Conjugate Gradient Minimisation Algorithm with the addition of suitable constraints was applied to the analysis of conformation-sensitive amide bands. This procedure was applied to amide I and III analysis of bovine and suilline fibrin, obtained industrially, and to amide III analysis of human fibrin clots. The analysis of both amide I and III in the first case was useful in order to test the reliability of the method. We found bovine, suilline, and human fibrin to contain about 30% alpha-helix (amide I and III components at 1653 cm-1, and 1312 and 1284 cm-1, respectively), 40% beta-sheets (amide I and III components at 1625 and 1231 cm-1, respectively) and 30% turns (amide I and III components at 1696, 1680, 1675 cm-1, and 1249 cm-1, respectively). The precision of the quantitative determination depends on the amount of these structures in the protein. Particularly, the coefficient of variation is < 10% for percentage values of amide I and III components > 15 and 5%, respectively. The good agreement of our quantitative data, obtained separately by amide I and amide III analysis, and consistent with a previous fibrinogen (from commercial sources) study that reports only information about fibrin beta-sheet content obtained by factor analysis, leads us to believe that the amounts of secondary structures found (alpha-helix, beta-sheets, and turns) are accurate.

Protein structural segments and their interconnections derived from optical spectra. Thermal unfolding of ribonuclease T1 as an example

A novel descriptor for protein structure is examined here that goes beyond predictions of the average fractional components (FC) of a few conformational types and represents the number and interconnection of segments of continuous, well-defined secondary structural elements such as alpha-helices and beta-sheets. This matrix descriptor can be predicted from optical spectra using neural network methods. The new matrix plus traditional FC descriptors can be quickly and generally obtained to provide a level of detail not previously derived from optical spectra and a discrimination between proteins that might otherwise be viewed as being very similar using just the FC descriptor. As an example of its potential utilization, this matrix descriptor approach was applied to an analysis of both the native state and the reversible thermal denaturation of ribonuclease T1 in H2O. Analyses of the FTIR spectral data indicate initial loss of the major helical segment at 50-55 degrees C but with little accompanying change in the number of sheet segments or the sheet FC values. Circular dichroism (CD) and vibrational CD data are also used to support this interpretation based on FC changes with temperature. Parallel analysis of the corresponding data for this protein in D2O demonstrates that the method is sensitive to the match between the degree of H-D exchange used to prepare samples for the unknown and the reference data set.

Predicted alpha-helix/beta-sheet secondary structures for the zinc-binding motifs of human papillomavirus E7 and E6 proteins by consensus prediction averaging and spectroscopic studies of E7

The E7 and E6 proteins are the main oncoproteins of human papillomavirus types 16 and 18 (HPV-16 and HPV-18), and possess unknown protein structures. E7 interacts with the cellular tumour-suppressor protein pRB and contains a zinc-binding site with two Cys-Xaa2-Cys motifs spaced 29 or 30 residues apart. E6 interacts with another cellular tumour-suppressor protein p53 and contains two zinc-binding sites, each with two Cys-Xaa2-Cys motifs at a similar spacing of 29 or 30 residues. By using the GOR I/III, Chou-Fasman, SAPIENS and PHD methods, the effectiveness of consensus secondary structure predictions on zinc-finger proteins was first tested with sequences for 160 transcription factors and 72 nuclear hormone receptors. These contain Cys2His2 and Cys2Cys2 zinc-binding regions respectively, and possess known atomic structures. Despite the zinc- and DNA-binding properties of these protein folds, the major alpha-helix structures in both zinc-binding regions were correctly identified. Thus validated, the use of these prediction methods with 47 E7 sequences indicated four well-defined alpha-helix (alpha) and beta-sheet (beta) secondary structure elements in the order beta beta alpha beta in the zinc-binding region of E7 at its C-terminus. The prediction was tested by Fourier transform infrared spectroscopy of recombinant HPV-16 E7 in H2O and 2H2O buffers. Quantitative integration showed that E7 contained similar amounts of alpha-helix and beta-sheet structures, in good agreement with the averaged prediction of alpha-helix and beta-sheet structures in E7 and also with previous circular dichroism studies. Protein fold recognition analyses predicted that the structure of the zinc-binding region in E7 was similar to a beta beta alpha beta motif found in the structure of Protein G. This is consistent with the E7 structure predictions, despite the low sequence similarities with E7. This predicted motif is able to position four Cys residues in proximity to a zinc atom. A model for the zinc-binding motif of E7 was constructed by combining the Protein G coordinates with those for the zinc-binding site in transcription factor TFIIS. Similar analyses for the two zinc-binding motifs in E6 showed that they have different alpha/beta secondary structures from that in E7. When compared with 12 other zinc-binding proteins, these results show that E7 and E6 are predicted to possess novel types of zinc-binding structure.

A Spectroscopic Study of the Structures of Latent, Active and Reactive-Center-Cleaved Type-1 Plasminogen-Activator Inhibitor

Type-1 plasminogen-activator inhibitor (PAI-1) was studied by Fourier-transform infrared spectroscopy, far-ultraviolet CD spectroscopy, and fluorescence-emission spectroscopy, with the aim to obtain structural information about its active form. The spectra of latent, active and reactive-center-cleaved forms of PAI-1 produced by HT-1080 cells were different. While the cleaved and the latent forms were similar with regard to their beta-structure content, comparison of the spectra of these forms with the spectra of active PAI-1 suggested a much higher degree of unordered structure for the active form compared with the latent and reactive-center-cleaved forms than previously assumed. We discuss our results with reference to the known three-dimensional X-ray structures of latent PAI-1, of reactive-center-cleaved serpins, including reactive-center-cleaved PAI-1, and of intact serpins, and with reference to previous results on the differences in the affinity of mAbs for the different PAI-1 forms. We interpret our results in favor of a global rearrangement of secondary structure during latency transition and reactive-center cleavage in PAI-1, not only involving the reactive-center loop and parts of beta-sheets A and C, but also the "rear' side of the molecule, such as helices H and G. Thus, we suggest flexibility in serpin structural elements that were previously regarded as rigid.

A correlation between thermal stability and structural features of staphylokinase and selected mutants: a Fourier-transform infrared study

Variants of recombinant staphylokinase (Sak) were investigated by Fourier-transform infrared spectroscopy: Sak (wild type), Sak-M26A, Sak-M26L, and Sak-G34S/R36G/R43H (Sak-B). Estimation of the secondary structure and hydrogen-deuterium exchange experiments revealed the existence of fast-exchanging and strongly solvent-exposed fractions of the helical structures in the two samples Sak and Sak-M26L. These two samples are also thermally less stable with unfolding transition temperatures of 43.7 degrees C (Sak) and 43.5 degrees C (Sak-M26L), respectively. On contrast, Sak-M26A and Sak-G34S/R36G/R43H have a slower hydrogen-deuterium exchange, have a smaller solvent-exposed portion of the helical part, and are more resistant against thermal unfolding; the transition temperatures are 51.7 degrees C and 59.3 degrees C, respectively. The secondary structure analysis was performed by two different approaches, by curve-fitting after band narrowing and by pattern recognition (factor analysis) based upon reference spectra of proteins with known crystal structure. Within the limits of the used methods, we are unable to detect significant differences in the secondary structure of the four variants of Sak. According to the results of the factor analysis, the portions of secondary structure elements were obtained to 16-20% alpha-helix, 28-30% beta-sheet, 23-27% turns, 28-30% irregular (random) and other structure. The sharp differences in the specific plasminogen-activating capacity (Sak, Sak-G34S/R36G/R43H and Sak-M26L are fully active, but Sak-M26A does not form a stable complex with plasminogen) are not reflected in the structural features revealed by the infrared spectra of this study.

Determination of the secondary structure of isomeric forms of human serum albumin by a particular frequency deconvolution procedure applied to Fourier transform IR analysis

A new deconvolution procedure was applied to the analysis of Fourier transform ir spectra of human serum albumin secondary structure in the native state and in states denatured by heat and acid treatment. The deconvolution method is based on the use of the Conjugate Gradient Minimization Algorithm, with the addition of suitable constraints directly obtained by the application to the measured spectrum of the second derivative operator. This method computes central band frequency, bandwidth, and amplitude of the different spectral components of conformation-sensitive amide bands. In the specific case, it was applied to analysis of the amide I band, and the quantitative determination of the different secondary structures (alpha-helix, beta-sheet, beta-turns, and random) was attempted for all the samples examined. The precision of the quantitative determination depends on the amounts of these structures present in the protein. The coefficient of variation is < 10% for values of amide I component > 15%. The accuracy was tested by comparing, by means of linear regression, the results obtained for human serum albumin, hemoglobin, alpha-chymotrypsin, and cytochrome c, using our method, with those obtained by x-ray crystallography and CD; the results obtained by other vibrational spectroscopic approaches were also compared. The fit standard error between x-ray and ir secondary structure values estimated by our method is 2.5% for alpha-helix, 7.16% for beta structures, and 5.1% for other structures (turns and random coils). Quantitative results are given for the secondary structures (alpha-helix, turns, and beta-strands) present in the native state (turns and beta-strands up to now unknown in aqueous solution), together with the percentages of these structures and additional ones (random coils and beta-sheets) formed during denaturization.

Pressure-tuning the conformation of bovine pancreatic trypsin inhibitor studied by Fourier-transform infrared spectroscopy

A hydrostatic pressure of 1.5 GPa induces changes in the secondary structure of bovine pancreatic trypsin inhibitor (BPTI) as revealed by the analysis of the amide I' band with Fourier-transform infrared (FTIR) spectroscopy in the diamond anvil cell. The features of the secondary structure remain distinct at high pressure suggesting that the protein does not unfold. The fitted percentages of the secondary structure elements during compression and decompression strongly suggest that the pressure-induced changes are reversible. The pressure-induced changes in the tyrosine side chain band are also reversible. The results demonstrate that the infrared technique explores different aspects of the behaviour of proteins in comparison with two published molecular dynamics studies performed up to 1 GPa [Kitchen, D.B., Reed, L.H. & Levy, R.M.(1992) Biochemistry 31, 10083-10093] and 500 MPa [Brunne, R.M. & van Gunsteren, W.F.(1993) FEBS Lett. 323, 215-217]. A possible explanation for the difference is the time scale of the experiments.

Effects of pH and KCl on the conformations of creatine kinase from rabbit muscle. Infrared, circular dichroic and fluorescence studies

The activity loss of creatine kinase (CK), observed at low pH (midpoint was 4.8) corresponded to the monomerization of the dimeric protein and was correlated with structural changes. The acid-induced unfolding was not complete at this pH, as probed by circular dichroic (CD) and fluorescence methods. Further decrease of pH, led to a second transition (midpoint was pH 3.5). The loss of activity was irreversible at pH 4.8 (< 20% native activity was recovered) while it was almost fully reversible (> 90% of native activity was recovered) for the enzyme incubated at pH 0.9-2.5. The amount of intermolecular beta-sheets (monitored with the 1620 cm-1 infrared component band) was maximal when the enzyme was incubated at pH 4.8, as a consequence of protein aggregation, while it was minimal at extremes of pH and at low ionic strength. Acid-induced and alkaline-induced denaturations promoted different structural changes, leading to distinct partially unfolded conformational states. The addition of KCl (from 0.05 M to 0.5 M) to an acidic solution of monomeric creatine kinase (pH 1.6) resulted in a highly cooperative transition from the partially unfolded conformation (UA) to the more compact conformation (A) with the properties of a molten globule, as probed by CD spectra and by fluorescence. The formation of intermolecular beta-sheets in the compact conformation was observed by infrared spectroscopy, indicating formation of unstable aggregates.

A Fourier-transform infrared spectroscopic investigation of the hydrogen-deuterium exchange and secondary structure of the 28-kDa channel-forming integral membrane protein (CHIP28)

Fourier-transform infrared spectroscopy (FTIR) has been employed to investigate the structural properties of the 28-kDa channel-forming integral membrane protein (CHIP28) present in phospholipid vesicles suspended in aqueous media. This study reports the FTIR spectra of this membrane protein present in H2O and 2H2O. The secondary structure of the protein was determined and found to consist of 36% alpha-helical and 42% beta-sheet structures. These results are in close agreement with the results of a previous CD study [Van Hoek, A. N., Wiener, M., Bicknese, S., Miercke, L., Biwersi, J. & Verkman, A. S. (1993) Biochemistry 32, 11,847-11,856]. However, the results differ from those given in an FTIR analysis by the same workers who recorded FTIR spectra of the CHIP28 protein in a dehydrated state. An unusually high extent of hydrogen-deuterium exchange of the peptide groups of this protein occurs. The magnitude of the spectral changes observed upon exposure of the protein to 2H2O is greater than has been observed with any other membrane protein previously studied. Thus, over 80% of the peptide groups exchange within 5 min and the amide I band maximum shifts to low frequency by approximately 20 cm-1. This high hydrogen-deuterium exchange observed with the CHIP28 protein is consistent with the presence of an aqueous pore within the protein structure.

Circular dichroism and Fourier transform infrared spectroscopic studies on the secondary structure of Saccharomyces cerevisiae and Escherichia coli phospho enolpyruvate carboxykinases

The secondary structure of Saccharomyces cerevisiae and Escherichia coli phospho enolpyruvate (PEP) carboxykinases was quantitatively examined using circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopies. From CD analyses, values of 24% alpha-helix and 38% beta-sheet were obtained for the E. coli enzyme, while the corresponding values for the S. cerevisiae PEP carboxykinase were 20% and 36%. Analysis of the amide I' infrared band indicated 20% alpha-helix and 36% beta-sheet for the S. cerevisiae enzyme, while for the E. coli protein values of 40% beta-sheet and between 9 and 36% alpha-helix could be inferred. It is concluded that the bacterial enzyme has more secondary structure elements than the yeast protein. No alteration of the CD or FTIR spectra was detected upon substrate or metal ion binding to any enzyme.

Secondary structure and stability of the bacterial carbohydrate-specific recognition proteins K88ab, AFA-1, NFA-1, and CFA-1

The conformation and thermodynamic stability of the four polymeric carbohydrate-specific bacterial recognition proteins K88ab, AFA-1, NFA-1, and CFA-1 and their monomeric subunits that can be obtained by variation of pH were studied by infrared spectroscopy and differential scanning microcalorimetry. For NFA-1, a pH-dependent dissociation of the polymeric form cannot be achieved due to the stronger interactions of the neighboring subunits. Generally, no alterations in secondary structure are observed between the monomeric and the polymeric proteins. All adhesins reveal a high degree of beta-sheet structure (40-55%), while the alpha-helix component is of minor importance (10-20%). The adhesins investigated in this study revealed unusually high denaturation temperatures (69-104 degrees C) and stabilizing Gibbs energies, delta G (40-125 kJ/mol), compared to common globular proteins. Statistical deconvolution of the DSC curves yields a two-state transition of K88ab, NFA-1, and the monomeric CFA-1 and the existence of intermediate states for AFA-1 and polymeric CFA-1 during the denaturation process. The irreversible denaturation of K88ab, AFA-1, and CFA-1 is explained by aggregation of the polypeptide chains forming a three-dimensional network of intermolecular beta-sheet-type structures. In contrast, denaturation of NFA-1 is completely reversible. At a physiologically relevant temperature of approximately 40 degrees C, we observe predenaturational events in the DSC curves of polymeric K88ab and NFA-1 with no concomittant changes in the secondary structure of these proteins.

Beta-sheet secondary structure of an LDL receptor domain from complement factor I by consensus structure predictions and spectroscopy

Low density lipoprotein receptor domains (LDLrs) represent a large cell surface receptor superfamily of consensus length 39 residues. Alignment of 194 sequences indicated highly conserved Cys and Asp/Glu residues, and a consensus secondary structure with three beta-strands was predicted. Sequence threading against known protein folds indicated consistency with small beta-sheet proteins. Complement factor I contains two LDLrs, and the second of these was successfully expressed using a bacterial pGEX system. FT-IR spectroscopy on this indicated a small amount of beta-sheet together with turns and loops. LDLr is proposed to have a beta-sheet structure in which the five biologically important Asp/Glu residues are located on an exposed loop.

Establishing isostructural metal substitution in metalloproteins using 1H NMR, circular dichroism, and Fourier transform infrared spectroscopy

Far-UV CD, 1H-NMR, and Fourier transform infrared (FTIR) spectroscopy are three of the most commonly used methods for the determination of protein secondary structure composition. These methods are compared and evaluated as a means of establishing isostructural metal substitution in metalloproteins, using the crystallographically defined rubredoxin from Desulfovibrio gigas and its well-characterized cadmium derivative as a model system. It is concluded that analysis of the FTIR spectrum of the protein amide I resonance represents the most facile and generally applicable method of determining whether the overall structure of a metalloprotein has been altered upon metal reconstitution. This technique requires relatively little biological material (ca. 300 micrograms total protein) and, unlike either CD or 1H-NMR spectroscopy, is unaffected by the presence of different metal ions, thus allowing the direct comparison of FTIR spectra before and after metal substitution.

Comparison of and limits of accuracy for statistical analyses of vibrational and electronic circular dichroism spectra in terms of correlations to and predictions of protein secondary structure

This work provides a systematic comparison of vibrational CD (VCD) and electronic CD (ECD) methods for spectral prediction of secondary structure. The VCD and ECD data are simplified to a small set of spectral parameters using the principal component method of factor analysis (PC/FA). Regression fits of these parameters are made to the X-ray-determined fractional components (FC) of secondary structure. Predictive capability is determined by computing structures for proteins sequentially left out of the regression. All possible combinations of PC/FA spectral parameters (coefficients) were used to form a full set of restricted multiple regressions with the FC values, both independently for each spectral data set as well as for the two VCD sets and all the data grouped together. The complete search over all possible combinations of spectral parameters for different types of spectral data is a new feature of this study, and the focus on prediction is the strength of this approach. The PC/FA method was found to be stable in detail to expansion of the training set. Coupling amide II to amide I' parameters reduced the standard deviations of the VCD regression relationships, and combining VCD and ECD data led to the best fits. Prediction results had a minimum error when dependent on relatively few spectral coefficients. Such a limited dependence on spectral variation is the key finding of this work, which has ramifications for previous studies as well as suggests future directions for spectral analysis of structure. The best ECD prediction for helix and sheet uses only one parameter, the coefficient of the first subspectrum. With VCD, the best predictions sample coefficients of both the amide I' and II bands, but error is optimized using only a few coefficients. In this respect, ECD is more accurate than VCD for alpha-helix, and the combined VCD (amide I' + II) predicts the beta-sheet component better than does ECD. Combining VCD and ECD data sets yields exceptionally good predictions by utilizing the strengths of each. However, the residual error, its distribution, and, most importantly, the lack of dependence of the method on many of the significant components derived from the spectra leads to the conclusion that the heterogeneity of protein structure is a fundamental limitation to the use of such spectral analysis methods. The underutilization of these data for prediction of secondary structure suggests spectral data could predict a more detailed descriptor.

FT-IR spectroscopy of the major coat protein of M13 and Pf1 in the phage and reconstituted into phospholipid systems

FT-IR spectroscopy has been applied to study the secondary structure of the major coat protein of Pf1 and M13 as present in the phage and reconstituted in DOPG and mixed DOPC/DOPG (4/1) bilayers. Infrared absorbance spectra of the samples were examined in dehydrated films and in suspensions of D2O and H2O. The secondary structure of the coat protein is investigated by second-derivative analysis, Fourier self-deconvolution, and curve fitting of the infrared bands in the amide I region (1600-1700 cm-1). It is found that, in dehydrated films of Pf1 and M13 phage, the amide I region contains three bands located at about 1633, 1657, and 1683 cm-1, that are assigned to hydrogen-bonded turn, alpha-helix/random coil, and non-hydrogen-bonded turn, respectively. From a comparison of the infrared spectra in dehydrated film with those in aqueous suspension, the percentages of secondary structure were found with an accuracy of about +/- 5%. For the coat protein of Pf1 phage, the FT-IR quantification gives 69% alpha-helix conformation, 19% turn structure, and 12% random coil structure. For Pf1 coat protein in the membrane-embedded state, the amount of alpha-helix is 57%, whereas 42% is in a turn structure and 1% in a random coil structure. The same assignment strategy was used for the analysis of the data obtained for M13 coat protein reconstitution into phospholipid systems. For M13 coat protein in the phage, this gives 75% alpha-helix conformation, 21% turn structure, and 4% random coil structure.(ABSTRACT TRUNCATED AT 250 WORDS)

A comparison of infrared spectra of proteins in solution and crystalline forms

Fourier transform infrared spectroscopy has been used to compare the structure of a range of proteins in solution and in the form of single crystals. An infrared microscope was used to record the spectra of single crystals of the proteins. The proteins studied in this way were hen egg white lysozyme, bovine pancreatic ribonuclease A, bovine gamma-II crystallin, human serum amyloid P component, Endothia parasitica pepsin and Mucor pusillus pepsin. The amide I and amide II bands in the FTIR spectra of these proteins were analysed using derivative procedures thereby providing information on the secondary structure. The crystals were held under a vapour of mother liquor to reduce the effects of dehydration. A comparison of the spectra revealed that spectra recorded from crystals of lysozyme, ribonuclease A and gamma-II crystallin are nearly identical to those recorded from the proteins in solution. However, differences are observed between the spectra of serum amyloid P component, Endothia parasitica pepsin and Mucor pusillus pepsin in solution compared with that of the crystalline form These differences are suggested to be due to rearrangements of turn structures within the protein structure.

Thermal and pH stabilities of alkaline phosphatase from bovine intestinal mucosa: a FTIR study

The inactivation of alkaline phosphatase (AP) from bovine intestinal mucosa caused by lowering the p2H from 10.4 to 5.4 or by increasing the temperature from 25 degrees C to 70 degrees C were not followed by significant FTIR changes, indicating that the native conformation of AP was preserved under these conditions. Further decrease of p2H from 5.4 to 3.4 leaded to small infrared spectral changes of AP in the amide I' and amide II regions that were similar to the infrared spectral changes of AP induced by raising the temperature from 70 degrees C to 80 degrees C. The increase of temperature from 70 degrees C to 80 degrees C promoted the formation of intermolecular beta-sheets at the expense of some alpha-helix structures as evidenced by the appearance of the 1684 cm-1 and 1620 cm-1 component bands and the disappearance of the 1651-1657 cm-1 component band. This conformational change was followed by a sharp increase of the 2H/H exchange rate. CD spectra confirmed the FTIR results and were very sensitive to the variation of alpha-helix content while FTIR spectra were more receptive to the changes of beta-sheet structures.

The use and misuse of FTIR spectroscopy in the determination of protein structure

Fourier transform infrared (FTIR) spectroscopy is an established tool for the structural characterization of proteins. However, many potential pitfalls exist for the unwary investigator. In this review we critically assess the application of FTIR spectroscopy to the determination of protein structure by (1) outlining the principles underlying protein secondary structure determination by FTIR spectroscopy, (2) highlighting the situations in which FTIR spectroscopy should be considered the technique of choice, (3) discussing the manner in which experiments should be conducted to derive as much physiologically relevant information as possible, and (4) outlining current methods for the determination of secondary structure from infrared spectra of proteins.

Fourier transform infrared spectroscopy investigations of protein structure

Infrared spectroscopy can provide insight into protein structure. This technique is sensitive to the backbone amide arrangement of peptide and protein molecules. In many cases, complementary as well as more expansive information is obtained as opposed to information obtained by other methods that examine the molecule's environmental surroundings, require molecular probes, or perhaps cannot investigate the molecule in its native environment. The foundation for spectroscopic differences between the various secondary structures arises not only from geometrical differences and hydrogen bond variations but also transition dipole coupling between neighboring oscillators. Theoretical predictions of protein spectra have been made using normal mode analysis and combined with experimental data. At present the amide I band has provided the most insight into secondary structure. Even more convincing results are obtained when both H2O and D2O are used as solvents. Recent advances in computerized technology and mathematical techniques have expanded the potential contributions of infrared spectroscopy in the area of protein structural determination. However, the limitations of resolution enhancement and curve-fitting techniques must be taken into consideration. The parameters must be carefully and optimally chosen and evaluated on a case-by-case basis. The subjectivity of these techniques makes a thorough understanding of the algorithms necessary, especially those commercially available. Infrared spectroscopy continues to provide insight into protein and peptide structures under biologically relevant conditions that enable the structure-function relationships for such molecules to be better understood.

The conformational analysis of peptides using Fourier transform IR spectroscopy

Fourier transform infrared spectroscopy (FTIR) can be used for conformational analysis of peptides in a wide range of environments. Measurements can be performed in aqueous solution, organic solvents, detergent micelles as well as in phospholipid membranes. Information on the secondary structure of peptides can be derived from the analysis of the strong amide I band. Orientation of secondary structural elements within a lipid bilayer matrix can be determined by means of polarized attenuated total reflectance-FTIR spectroscopy. Hydrogen-deuterium exchange can be monitored by the analysis of the amide II band. This review gives some example of peptide systems studied by FTIR spectroscopy. Studies on alamethicin and alpha-aminoisobutyric acid containing peptides have shown that FTIR spectroscopy is a sensitive tool for identifying 3(10)-helical structures. Changes in the structure of the magainins upon interaction with charged lipids were detected using FTIR spectroscopy. Tachyplesin is an example of a beta-sheet containing membrane active peptide. Polarized ir spectroscopy reveals that the antiparallel beta-sheet structures of tachyplesin are oriented parallel to the membrane surface. Synthesis of peptides corresponding to functionally/structurally important regions of large proteins is becoming increasingly popular. FTIR spectroscopy has been used to analyze the structure of synthetic peptides corresponding to the ion-selective pore of the voltage-gated potassium channel. In biomembrane systems these peptides adopt a highly helical structure. Under conditions, where these peptides are aggregated the presence of some intermolecular beta-sheet structure can also be detected.

Purification and secondary structural analysis of tissue inhibitor of metalloproteinases-1

In connective tissue diseases such as rheumatoid arthritis, the matrix metalloproteinases are the primary enzymes involved in tissue degradation. Tissue inhibitor metalloproteinases-1 (TIMP-1) is a specific inhibitor of these enzymes, which is thought to regulate their action in vivo. The structure and function of TIMP-1 may therefore be important as the basis for the rational design of therapeutic agents. This paper describes a simple and effective method for the purification of sufficient quantities of TIMP-1 for spectroscopic studies. Circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopy have, together, showed TIMP-1 to be mostly in a beta-sheet conformation, with significant amounts of alpha-helix and beta-turn. Two-dimensional nuclear magnetic resonance spectroscopy indicated a correspondingly high proportion of beta-sheet. CD and FTIR have also shown TIMP-1 to have high thermostability.

Structure and thermal stability of the extracellular fragment of human transferrin receptor at extracellular and endosomal pH

Fourier transform infrared spectroscopy has been used to study the solution structure and thermal stability of the extracellular fragment of human transferrin receptor (tfRt) at extracellular and endosomal pH. At extracellular pH tfRt is composed of 56% alpha-helix, 19% beta-sheet and 14% turns. Upon acidification to endosomal pH the alpha-helical content of the protein is reduced and the beta-sheet content increased by nearly 10%. At extracellular pH, the midpoint temperature of thermal denaturation (Tm) for the loss of secondary and tertiary structure, and the formation of aggregated structures, is 71 degrees C. At endosomal pH this temperature is reduced by approximately 15 degrees C. The apparent entropies of thermal denaturation indicate that the native structure of tfRt at endosomal pH is far more flexible than at extracellular pH.

Conformational changes upon dissociation of a globular protein from pea: a Fourier transform infrared spectroscopy study

Fourier transform infrared spectroscopy shows that the secondary structure of legumin, a globular protein from pea seeds, is composed of 41% beta-sheets and 16% alpha-helices and furthermore reveals the presence of beta-turns. The conformation prediction from the analysis of the amino-acid sequence of legumin using hydrophobic cluster analysis reveals that the C-terminal part of the alpha-polypeptide is devoid of defined secondary structures, whereas the beta-polypeptide is highly ordered. Comparison with analogous 11S globulins from other plant families indicates that ordered domains are highly preserved, phenomenon that may be associated with the similarity of the quaternary structure of these proteins. The results also reveal the presence of a large hypervariable region, located at the surface of the protein, that could be at the origin of the different functional properties of the 11S type globulins. The step-by-step destruction of the quaternary oligomeric structure of the native protein is accompanied by conformational changes that depend on the dissociation conditions. Whereas acylation leads to a decrease of the alpha-helix content by 10% at the expense of the beta-sheet content, addition of sodium perchlorate results in the conversion of 10% of the protein secondary structure from beta-sheet to unordered. These observations provide further evidence of the existence of different monomeric states that differ from their secondary structure and, therefore, exhibit different surface-active properties.

Spectroscopic characterization of conformational differences between PrPC and PrPSc: an alpha-helix to beta-sheet transition

Although no chemical modifications have been found to distinguish the cellular prion protein PrPC from its infectious analogue PrPSc, spectroscopic methods such as Fourier transform infrared (FTIR) spectroscopy reveal a major conformational difference. PrPC is rich in alpha-helix but is devoid of beta-sheet, whereas PrPSc is high in beta-sheet. N-terminal truncation of PrPSc by limited proteolysis does not destroy infectivity but it increases the beta-sheet content and shifts the FTIR absorption to lower frequencies, typical of the cross beta-pleated sheets of amyloids. Thus the formation of PrPSc from PrPC involves a conformational transition in which one or more alpha-helical regions of the protein is converted to beta-sheet. This transition is mimicked by synthetic peptides, allowing predictions of domains of PrP involved in prion diseases.

Fourier transform infrared spectroscopy and differential scanning calorimetry of transferrins: human serum transferrin, rabbit serum transferrin and human lactoferrin

Fourier transform infrared spectroscopy (FTIR) and differential scanning calorimetry (DSC) have been used to investigate the solution structure and thermal stability of human serum transferrin (HST), human lactoferrin (HLF) and rabbit serum transferrin (RST) in their diferric and apo forms. Our study shows that: (A) The secondary structure of all the proteins studied (estimated in H2O) was in the range 43-53% alpha-helix and 23-28% beta-sheet. These values differ markedly from previously reported circular dichroism (CD) data. This is attributed to the fact that FTIR and CD measure different aspects of secondary structure (hydrogen bonding and dihedral angles, respectively). (B) The secondary structural content of the proteins is not altered by iron binding or release. However, the iron-free proteins undergo a greater extent of 1H-2H exchange than the diferric proteins indicating that significant structural changes do occur upon iron binding/release. (C) The removal of iron leads to thermal destabilization of HST, HLF and RST. Structural variation in the apo transferrins is indicated by the observation of a single irreversible DSC transition for apo human lactoferrin, a double DSC transition for apo human serum transferrin (one reversible) and a broad irreversible asymmetric DSC transition for apo rabbit serum transferrin. FTIR spectroscopy shows that a distinct loss of protein secondary structure occurs at the transition temperatures shown by DSC.

Conformation changes of beta-lactoglobulin: an ATR infrared spectroscopic study of the effect of pH and ethanol

Fourier transform infrared spectroscopy has been applied to investigate the secondary structural changes of beta-lactoglobulin in water/ethanol mixtures. The studies were carried out at two different pHs and at high protein concentrations. The spectra were recorded using an attenuated total reflection cell. The amide I band of beta-lactoglobulin in water reveals large amounts of intra extended beta-sheet structure. About 20% ethanol, beta-lactoglobulin unfolds and beta-strand formation is observed. alpha-Helices are built up by increasing the ethanol concentration up to 30%. In 50% ethanol, beta-lactoglobulin gels providing the apparent pH are neutral. The secondary structural changes of beta-lactoglobulin were observed on the similarity maps obtained by Principal Component Analysis.