Fourier transform infrared study of proteins with parallel beta-chains

On 'Fourier transform infrared study of proteins with parallel β-chains' by Heino Susi, D. Michael Byler

In 1987, Susi & Byler published a groundbreaking paper for the determination of the secondary structure of proteins. Notably, they determined the characteristic signature of the β-strand in the infrared spectrum. As a result, Fourier-transform infrared spectroscopy became a general method to determine protein structure.

Evaluation of protein secondary structure from FTIR spectra improved after partial deuteration

FTIR spectroscopy has become a major tool to determine protein secondary structure. One of the identified obstacle for reaching better predictions is the strong overlap of bands assigned to different secondary structures. Yet, while for instance disordered structures and α-helical structures absorb almost at the same wavenumber, the absorbance bands are differentially shifted upon deuteration, in part because exchange is much faster for disordered structures. We recorded the FTIR spectra of 85 proteins at different stages of hydrogen/deuterium exchange process using protein microarrays and infrared imaging for high throughput measurements. Several methods were used to relate spectral shape to secondary structure content. While in absolute terms, β-sheet is always better predicted than α-helix content, results consistently indicate an improvement of secondary structure predictions essentially for the α-helix and the category called “Others” (grouping random, turns, bends, etc.) after 15 min of exchange. On the contrary, the β-sheet fraction is better predicted in non-deuterated conditions. Using partial least square regression, the error of prediction for the α-helix content is reduced after 15-min deuteration. Further deuteration degrades the prediction. Error on the prediction for the “Others” structures also decreases after 15-min deuteration. Cross-validation or a single 25-protein test set result in the same overall conclusions.

Conformation-dependent membrane permeabilization by neurotoxic PrP oligomers: The role of the H2H3 oligomerization domain

The relationship between prion propagation and the generation of neurotoxic species and clinical onset remains unclear. Several converging lines of evidence suggest that interactions with lipids promote various precursors to form aggregation-prone states that are involved in amyloid fibrils. Here, we compared the cytotoxicities of different soluble isolated oligomeric constructs from murine full-length PrP and from the restricted helical H2H3 domain with their effects on lipid vesicles. The helical H2H3 domain is suggested to be the minimal region of PrP involved in the oligomerization process. The discrete PrP oligomers of both the full-length sequence and the H2H3 domain have de novo β-sheeted structure when interacting with the membrane. They were shown to permeabilize synthetic negatively charged vesicles in a dose-dependent manner. Restricting the polymerization domain of the full-length PrP to the H2H3 helices strongly diminished the ability of the corresponding oligomers to associate with the lipid vesicles. Furthermore, the membrane impairment mechanism occurs differently for the full-length PrP oligomers and the H2H3 helices, as shown by dye-release and black lipid membrane experiments. The membrane damage caused by the full-length PrP oligomers is correlated to their neuronal toxicity at submicromolar concentrations, as shown by cell culture assays. Although oligomers of synthetic H2H3 could compromise in vitro cell homeostasis, they followed a membrane-disruptive pattern that was different from the full-length oligomers, as revealed by the role of PrP^C in cell viability assays.

Reversible Morphological Control of Cholecystokinin Tetrapeptide Amyloid Assemblies as a Function of pH

Most amyloid assemblies are seen as irreversible and exhibit polymorphism because their assembly is kinetically controlled and different structures are trapped during the aggregation process. However, in the specific case of peptide hormones, formation of amyloid assemblies for storage purposes has been reported. This suggests a strict control of assembly and the ability to disassemble upon hormone secretion. In the present work, we have sought to test these assertions with a short peptide, the cholecystokinin (or gastrin) tetrapeptide (CCK-4), that has been found in both gastrointestinal tract and central nervous system, and whose sequence is shared by a large number of hormones. We have thus studied in vitro this peptide's self-assembling properties in dense phases at different pH levels, thus mimicking in vivo storage conditions. The solubility and morphology of the supramolecular assemblies have been shown to vary with the pH. At low pH, the tetrapeptide exhibits a low solubility and forms microcrystals. At higher pH levels, peptide solubility increases and above a high enough concentration, peptide monomers self-assemble into typical amyloid fibrils of 10-20 nm diameter. The physical network formed by these fibrils results in a birefringent hydrogel phase. Despite the different morphological features exhibited at different pH, structural analysis shows strong similarities. Both supramolecular assemblies-microcrystals and fibrils-are structured by β-sheets. We also show that all these morphologies are reversible and can be either dissolved or changed into one another by switching the pH. In addition, we demonstrate that a modification in the charge sequence of the peptide by amino acid mutation modifies its self-assembly properties. In conclusion, just as the CCK-4 sequence is the minimal sequence required for a complete biological activity at CCK_B receptors in the brain, it is also sufficient to form amyloid fibers whose properties can be related to hormone storage and release purposes in vivo.

The Impact of N-terminal Acetylation of α-Synuclein on Phospholipid Membrane Binding and Fibril Structure

Human α-synuclein (αS) has been shown to be N terminally acetylated in its physiological state. This modification is proposed to modulate the function and aggregation of αS into amyloid fibrils. Using bacterially expressed acetylated-αS (NTAc-αS) and endogenous αS (Endo-αS) from human erythrocytes, we show that N-terminal acetylation has little impact on αS binding to anionic membranes and thus likely not relevant for regulating membrane affinity. N-terminal acetylation does have an effect on αS aggregation, resulting in a narrower distribution of the aggregation lag times and rates. 2D-IR spectra show that acetylation changes the secondary structure of αS in fibrils. This difference may arise from the slightly higher helical propensity of acetylated-αS in solution leading to a more homogenous fibril population with different fibril structure than non-acetylated αS. We speculate that N-terminal acetylation imposes conformational restraints on N-terminal residues in αS, thus predisposing αS toward specific interactions with other binding partners or alternatively decrease nonspecific interactions.

Synergistic Inhibitory Effect of Peptide-Organic Coassemblies on Amyloid Aggregation

Inhibition of amyloid aggregation is important for developing potential therapeutic strategies of amyloid-related diseases. Herein, we report that the inhibition effect of a pristine peptide motif (KLVFF) can be significantly improved by introducing a terminal regulatory moiety (terpyridine). The molecular-level observations by using scanning tunneling microscopy reveal stoichiometry-dependent polymorphism of the coassembly structures, which originates from the terminal interactions of peptide with organic modulator moieties and can be attributed to the secondary structures of peptides and conformations of the organic molecules. Furthermore, the polymorphism of the peptide-organic coassemblies is shown to be correlated to distinctively different inhibition effects on amyloid-β 42 (Aβ42) aggregations and cytotoxicity.

Fourier transform infrared spectroscopy on external perturbations inducing secondary structure changes of hemoglobin

The secondary structure of proteins and their conformation are intimately related to their biological functions.

Insoluble protein assemblies characterized by fourier transform infrared spectroscopy

Fourier transform infrared (FTIR) spectroscopy is a useful tool for the structural characterization of insoluble protein assemblies, as it allows to obtain information on the protein secondary structures and on their intermolecular interactions. The protocols for FTIR spectroscopy and microspectroscopy measurements in transmission and attenuated total reflection modes will be presented and illustrated in the following examples: bacterial inclusion bodies, self-assembling peptides, thermal aggregates, and amyloid fibrils.

Characterization of recombinant antibodies for cancer therapy by infrared spectroscopy

Fourier transform infrared (FTIR) spectroscopy was used to study the structure of the recombinant antibodies 1E10, anti-CD20 and hR3, which are used as anti-cancer therapeutic drugs. We tested their sensitivity against different conditions and treatments such as pH, temperature, freeze-thaw cycles and drying, which are relevant for the practical usefulness of the drugs. All antibodies were stable against moderate temperature increases (up to 50 °C) and pH changes (range 5-9). 1E10 was sensitive to extreme pH values (pH 3 and 12), whereas hR3 was most sensitive to temperature (at and above 60 °C). We did not observe any significant changes upon freeze-thaw and drying treatments. The secondary structure content of all three antibodies was estimated to be similar to that of IgG with ∼64% β-sheet, 0% α-helix and ∼36% other structure.

In situ opening/closing of OmpG from E. coli and the splitting of β-sheet signals in ATR-FTIR spectroscopy

The pH dependent opening and closure of Escherichia coli OmpG is driven by the formation and breaking of hydrogen bridges in β-strands S11-S13. We have investigated the in situ secondary structural changes of OmpG with ATR-FTIR difference spectroscopy in order to detect the signals associated with the newly established interactions. Curve-fitting of OmpG in two pH conditions revealed the splitting and shifting of β-sheet signals upon opening of the channel. Besides secondary structure changes, there are also amino acid side chain signals that play active role in opening/closing of the channel. An interaction among positively charged arginines and negatively charged aspartic and glutamic acid residues is suggested upon closure of the channel while this interaction is abolished when the channel opens at higher pH.

Fourier transform infrared spectroscopy of intrinsically disordered proteins: measurement procedures and data analyses

A peculiar property of intrinsically disordered proteins (IDPs), or of intrinsically disordered domains, is the absence of a well-defined three dimensional structure under native conditions. Moreover, IDPs usually acquire a specific structure in the presence of different interactors. In this framework, Fourier transform infrared (FTIR) spectroscopy is a powerful tool to assess the disordered character of a protein and to study its induced folding. In this chapter, we will show the detailed experimental procedures to measure the FTIR spectra of protein samples and the spectral analyses required to obtain information on the protein secondary structures and aggregation.

Relationship between digestibility and secondary structure of raw and thermally treated legume proteins: a Fourier transform infrared (FT-IR) spectroscopic study

The secondary structure of proteins in legumes, cereals, milk products and chicken meat was studied by diffuse reflectance infrared spectroscopy in the region of the amide I band. Major secondary structure components ( β-sheets, random coil, α-helix, turns), together with the low- and high-frequency side contributions, were resolved and related to the in vitro digestibility behaviour of the different foods. A strong inverse correlation between the relative spectral weights of the β-sheet structures and in vitro protein digestibility values was measured. Structural modifications in legume proteins induced by autoclaving were monitored by the changes in the amide I spectra. The results indicate that the β-sheet structures of raw legume proteins and the intermolecular β-sheet aggregates, arising upon heating, are primary factors in adversely affecting the digestibility.

Qualification of FTIR spectroscopic method for protein secondary structural analysis

Fourier transform infrared (FTIR) spectroscopy is widely used to study protein secondary structure both in solution and in the solid state. The FTIR spectroscopic method has also been employed as a characterization method by the biopharmaceutical industry to determine the higher order structure of protein therapeutics, and to determine if any changes in protein conformation have occurred as a result of changes to process, formulation, manufacture, and storage conditions. The results of these studies are often included in regulatory filings; when comparability is assessed, the comparison is often qualitative. To demonstrate that the method can be quantitative, and is suitable for these intended purposes, the precision and sensitivity of the FTIR method were evaluated. The results show that FTIR spectroscopic analysis is reproducible with suitable method precision, that is, spectral similarity of replicate measurements is greater than 90%. The method can detect secondary structural changes caused by pH and denaturant. The sensitivity of the method in detecting structural changes depends on the extent of the changes and their impact on the resulting spectral similarity and characteristic FTIR bands. The results of these assessments are described in this paper.

The preservation and degradation of filamentous bacteria and biomolecules within iron oxide deposits at Rio Tinto, Spain

One of the keys to understanding and identifying life on other planets is to study the preservation of organic compounds and their precursor micro-organisms on Earth. Rio Tinto in southwestern Spain is a well documented site of microbial preservation within iron sulphates and iron oxides over a period of 2.1 Ma. This study has investigated the preservation of filamentous iron oxidising bacteria and organics through optical microscopy, scanning electron microscopy (SEM) and Fourier transform infra-red (FTIR) spectroscopy, from laboratory cultures of natural samples to contemporary natural materials to million-year old river terraces. Up to 40% elemental carbon and >7% nitrogen has been identified within microbial filaments and cell clusters in all samples through SEM EDS analyses. FTIR spectroscopy identified C-H(x) absorption bands between 2960 and 2800 cm(-1), Amide I and II absorption bands at 1656 and 1535 cm(-1), respectively and functional group vibrations from within nucleic acids at 917, 1016 and 1124 cm(-1). Absorption bands tracing the diagenetic transformation of jarosite to goethite to hematite through the samples are also identified. This combination of mineralogy, microbial morphology and biomolecular evidence allows us to further understand how organic fossils are created and preserved in iron-rich environments, and ultimately will aid in the search for the earliest life on Earth and potential organics on Mars.

Simulation of the amide I absorption of stacked β-sheets

Aggregated β-sheet structures are associated with amyloid and prion diseases. Techniques capable of revealing detailed structural and dynamical information on β-sheet structure are thus of great biomedical and biophysical interest. In this work, the infrared (IR) amide I spectral characteristics of stacked β-sheets were modeled using the transition dipole coupling model. For a test set of β-sheet stacks, the simulated amide I spectrum was analyzed with respect to the following parameters; intersheet distance, relative rotation of the sheets with respect to each other and the effect of number of sheets stacked. The amide I maximum shifts about 5 cm(-1) to higher wavenumbers when the intersheet distance between two identical β-sheets decreases from 20 to 5 Å. Rotation around the normal of one of the sheets relative to the other results in maximum intersheet coupling near 0° and 180°. Upon of rotation from 0° to 90° at an intersheet distance of 9 Å, the amide I maximum shifts about 3 cm(-1). Tilting of one of the sheets by 30° from the normal results in a shift of the amide I maximum by less than 1 cm(-1). When stacking several β-sheets along the normal, the amide I maximum shifts to higher wavenumbers with increasing stack size. The amide I maximum shifts about 6 cm(-1) when stacking four sheets with an intersheet distance of 9 Å. The study provides an aid in the interpretation of the IR amide I region for experiments involving β-sheets and creates awareness of the many effects that determine the spectrum of β-sheet structures.

Phosphoenolpyruvate and Mg2+ binding to pyruvate kinase monitored by infrared spectroscopy

Structural changes in rabbit muscle pyruvate kinase (PK) induced by phosphoenolpyruvate (PEP) and Mg(2+) binding were studied by attenuated total reflection Fourier transform infrared spectroscopy in combination with a dialysis accessory. The experiments indicated a largely preserved secondary structure upon PEP and Mg(2+) binding but also revealed small backbone conformational changes of PK involving all types of secondary structure. To assess the effect of the protein environment on the bound PEP, we assigned and evaluated the infrared absorption bands of bound PEP. These were identified using 2,3-(13)C(2)-labeled PEP. We obtained the following assignments: 1589 cm(-1) (antisymmetric carboxylate stretching vibration); 1415 cm(-1) (symmetric carboxylate stretching vibration); 1214 cm(-1) (C-O stretching vibration); 1124 and 1110 cm(-1) (asymmetric PO(3)(2-) stretching vibrations); and 967 cm(-1) (symmetric PO(3)(2-) stretching vibration). The corresponding band positions in solution are 1567, 1407, 1229, 1107, and 974 cm(-1). The differences for bound and free PEP indicate specific interactions between ligand and protein. Quantification of the interactions with the phosphate group indicated that the enzyme environment has little influence on the P-O bond strengths, and that the bridging P-O bond, which is broken in the catalytic reaction, is weakened by <3%. Thus, there is only little distortion toward a dissociative transition state of the phosphate transfer reaction when PEP binds to PK. Therefore, our results are in line with an associative transition state. Carboxylate absorption bands indicated a maximal shortening of the length of the shorter C-O bond by 1.3 pm. PEP bound to PK in the presence of the monovalent ion Na(+) exhibited the same band positions as in the presence of K(+), indicating very similar interaction strengths between ligand and protein in both cases.

VCD spectroscopic properties of the beta-hairpin forming miniprotein CLN025 in various solvents

Electronic and vibrational circular dichroism are often used to determine the secondary structure of proteins, because each secondary structure has a unique spectrum. Little is known about the vibrational circular dichroic spectroscopic features of the beta-hairpin. In this study, the VCD spectral features of a decapeptide, YYDPETGTWY (CLN025), which forms a stable beta-hairpin that is stabilized by intramolecular weakly polar interactions and hydrogen bonds were determined. Molecular dynamics simulations and ECD spectropolarimetry were used to confirm that CLN025 adopts a beta-hairpin in water, TFE, MeOH, and DMSO and to examine differences in the secondary structure, hydrogen bonds, and weakly polar interactions. CLN025 was synthesized by microwave-assisted solid phase peptide synthesis with N(alpha)-Fmoc protected amino acids. The VCD spectra displayed a (-,+,-) pattern with bands at 1640 to 1656 cm(-1), 1667 to 1687 cm(-1), and 1679 to 1686 cm(-1) formed by the overlap of a lower frequency negative couplet and a higher frequency positive couplet. A maximum IR absorbance was observed at 1647 to 1663 cm(-1) with component bands at 1630 cm(-1), 1646 cm(-1), 1658 cm(-1), and 1675 to 1680 cm(-1) that are indicative of the beta-sheet, random meander, either random meander or loop and turn, respectively. These results are similar to the results of others, who examined the VCD spectra of beta-hairpins formed by (D)Pro-Xxx turns and indicated that observed pattern is typical of beta-hairpins.

Native-like structure of proteins at a planar poly(acrylic acid) brush

Applying ATR-FTIR (attenuated total reflection Fourier transform infrared) and TIRF (total internal reflection fluorescence) spectroscopy, we have studied the secondary structure and aggregation properties of different proteins which are adsorbed at a poly(acrylic acid) (PAA) brush that covers a macroscopically large, planar surface. The PAA brush has been prepared on the surface of an ATR silicon crystal or a quartz plate. The preparation includes the deposition of a thin poly(styrene) film by spin-coating and the transfer of the diblock copolymer poly(styrene)-poly(acrylic acid) onto the hydrophobic film using the Langmuir-Schafer technique. It has been found that the proteins hen egg white lysozyme, bovine serum albumin, bovine alpha-lactalbumin, and bovine insulin adsorb spontaneously at a PAA brush at neutral pD values, albeit to different degrees. The secondary structure of the proteins was estimated from a decomposition of the amide I'-band in the observed ATR-FTIR spectra. Generally, the fractions of secondary structure elements recovered in this way were almost identical to those found when the proteins are native in solution. In addition, the tendency of insulin to form amyloid fibrils has also been tested when the protein is adsorbed at a planar PAA brush. Insulin is known to form amyloid fibrils in solution at low pH values and elevated temperatures. The experiments performed in this study suggest that a PAA brush does not promote fibril formation of insulin. Rather, insulin that is adsorbed at a PAA brush seems to be excluded from fibril formation pathways even at pD = 2 and 60 degrees C, where fibril formation of insulin is triggered in solution. Overall, the results of this study demonstrate that a planar PAA brush may serve as a mild environment for immobilized proteins.

Infrared spectroscopy of proteins

This review discusses the application of infrared spectroscopy to the study of proteins. The focus is on the mid-infrared spectral region and the study of protein reactions by reaction-induced infrared difference spectroscopy.

Functional, Hierarchically Structured Poly(diacetylene)s via Supramolecular Self-Assembly

The supramolecular self-assembly of macromonomers may serve as a first step to prepare well-defined, highly functionalized, hierarchically structured, conjugated polymers. Functional diacetylene macromonomers equipped with an oligopeptide segment designed to promote self-assembly into parallel beta-sheet type structures and a polydisperse, aliphatic coil segment to prevent global ordering give rise to supramolecular polymers with a tubular double-helical quarternary structure in organic solution. These supramolecular polymers may then be converted into the corresponding poly(diacetylene)s by UV irradiation under retention of their hierarchical structure.

Structure ofN-Acetylproline Amide in Liquid Water: Experimentally Measured and Numerically Simulated Infrared and Vibrational Circular Dichroism Spectra†

A few experimental and theoretical studies on the molecular structure of N-acetylproline amide (AP) in D2O solution have been reported recently. However, there is no consensus of the precise structure of AP in D2O because spectroscopically determined structures and a theoretically simulated one have been found to be different from one another. To determine its aqueous solution structure, IR and vibrational circular dichroism spectra of both L- and D-form AP solutions were measured. Molecular dynamics simulations with two different force fields and density functional theory calculations for the trans and cis rotamers of AP were performed to numerically simulate those spectra. Comparisons between experimentally measured and computationally simulated spectra directly suggest that the AP in water adopts a polyproline II-like conformation and that the force field parameter ff03 in the AMBER 8 suite of programs is more realistic and reliable in predicting molecular structure of AP in water than the ff99 in AMBER 7.

Synthesis and Characterization of Multiblock Copolymers Based on Spider Dragline Silk Proteins

Spider dragline silk with its superlative tensile properties provides an ideal system to study the relationship between morphology and mechanical properties of a structural protein. Accordingly, we synthesized two hybrid multiblock copolymers by condensing poly(alanine) [(Ala)(5)] blocks of the structural proteins (spidroin MaSp1 and MaSp2) of spider dragline silk with different oligomers of isoprene (2200 and 5000 Da) having reactive end groups. The synthetic multiblock polymer displayed similar secondary structure to that of natural spidroin, the peptide segment forming a beta-sheet structure. These multiblock polymers showed a significant solubility in the component solvents. Moreover, the copolymer which contains the short polyisoprene segment would aggregate into a micellar-like structure, as observed by TEM.

Characteristic two-dimensional IR spectroscopic features of antiparallel and parallel β-sheet polypeptides: Simulation studies

The antiparallel and parallel beta sheets are two of the most abundant secondary structures found in proteins. Although various spectroscopic methods have been used to distinguish these two different structures, the linear spectroscopic measurements could not provide incisive information for distinguishing an antiparallel beta sheet from a parallel beta sheet. After carrying out quantum-chemistry calculations and model simulations, we show that the polarization-controlled two-dimensional (2D) IR photon echo spectroscopy can be of critical use in distinguishing these two different beta sheets. Particularly, the ratio between the diagonal peak and the cross peak is found to be strongly dependent on the quasi-2D array of the amide I local-mode transition dipole vectors. The relative intensities of the cross peaks in the 2D difference spectrum of an antiparallel beta sheet are significantly larger than those of the diagonal peaks, whereas the cross-peak amplitudes in the 2D difference spectrum of a parallel beta sheet are much weaker than the main diagonal-peak amplitudes. A detailed discussion on the origin of the diagonal- and cross-peak intensity distributions of both the antiparallel and parallel beta sheets is presented by examining vibrational exciton delocalization, relative angles between two different normal-mode transition dipoles, and natures of the cross peaks in the 2D difference spectrum.

Temperature excursion infrared (TEIR) spectroscopy used to study hydrogen bonding between water and biomolecules

Water is a highly polar molecule that is capable of making four H-bonding linkages. Stability and specificity of folding of water-soluble protein macromolecules are determined by the interplay between water and functional groups of the protein. Yet, under some conditions, water can be replaced with sugar or other polar protic molecules with retention of protein structure. Infrared (IR) spectroscopy allows one to probe groups on the protein that interact with solvent, whether the solvent is water, sugar or glycerol. The basis of the measurement is that IR spectral lines of functional groups involved in H-bonding show characteristic spectral shifts with temperature excursion, reflecting the dipolar nature of the group and its ability to H-bond. For groups involved in H-bonding to water, the stretching mode absorption bands shift to lower frequency, whereas bending mode absorption bands shift to higher frequency as temperature decreases. The results indicate increasing H-bonding and decreasing entropy occurring as a function of temperature, even at cryogenic temperatures. The frequencies of the amide group modes are temperature dependent, showing that as temperature decreases, the amide group H-bonds to water strengthen. These results are relevant to protein stability as a function of temperature. The influence of solvent relaxation is demonstrated for tryptophan fluorescence over the same temperature range where the solvent was examined by infrared spectroscopy.

FTIR reveals structural differences between native beta-sheet proteins and amyloid fibrils

The presence of beta-sheets in the core of amyloid fibrils raised questions as to whether or not beta-sheet-containing proteins, such as transthyretin, are predisposed to form such fibrils. However, we show here that the molecular structure of amyloid fibrils differs more generally from the beta-sheets in native proteins. This difference is evident from the amide I region of the infrared spectrum and relates to the distribution of the phi/psi dihedral angles within the Ramachandran plot, the average number of strands per sheet, and possibly, the beta-sheet twist. These data imply that amyloid fibril formation from native beta-sheet proteins can involve a substantial structural reorganization.

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.

Determining ?-sheet stability by Fourier transform infrared difference spectra

We describe here a new method for determining the conformational stability of antiparallel beta-sheets. Due to coupling between the transition dipoles, beta-sheet conformations typically exhibit a characteristic high-frequency amide I component centered at approximately 1680 cm(-1). Using one beta-sheet protein and two small beta-hairpins, we demonstrate that this high-frequency component, which is fairly narrow (approximately 8-10 cm(-1)), can be quantitatively resolved and used in thermal stability determination. Compared with the commonly used CD and fluorescence techniques, this ir method offers advantages. Since the area of this high-frequency component is only proportional to the folded population, it eliminates the need for a priori information of the folded and unfolded baselines encountered in other methods. Thus, it is applicable to a variety of beta-sheet systems.

Spectroscopic investigation on gel-forming ?-sheet assemblage of peptide derivatives

The conformational studies of peptide derivatives A and B in a gel state were studied by using circular dichroism (CD), Fourier transformed infrared (FTIR), and fluorescence spectroscopic techniques. Birefringence and electron microscopic studies were carried out to characterize the morphological aspects of the fibrils in the gel. The FTIR spectra of the peptides show the absence of free NH in the gel state, implying that the intermolecular hydrogen-bond formation is the driving force for the aggregation. The CD spectrum of the peptide gels shows the presence of antiparallel and parallel beta-sheet conformation for peptide derivatives A and B, respectively. Electron microscopic studies (EM) of the peptide derivatives A and B reveal that peptide A formed rigid, rod-like structures without cross-linking and peptide B formed loose fibrils organized into highly noncovalently cross-linked mesh-like structural aggregates. Peptide A was much more soluble in alcoholic solvents than peptide B, and no birefringence was observed with Congo red (CR) staining in the temperature range of 0-80 degrees C. The spectroscopic studies indicate that peptide B consists of domains having a significant amount of beta-sheet structure and exhibiting golden yellow birefringence between 53 and 56 degrees C when stained with Congo red. On the other hand, peptide A gives no evidence of birefringence under polarized light. Fluorescence probe binding studies with pyrene in gel state with peptides A and B indicates the polarity in the interior of the aggregates. The data presented in the present work indicate that peptide B forms fibrils, which is similar to amyloid aggregates that are present in biological systems.

Effects of ELF magnetic field on membrane protein structure of living HeLa cells studied by Fourier transform infrared spectroscopy

The effects of exposure to a 50 Hz magnetic field (maximum of 41.7 to 43.6 mT) on the membrane protein structures of living HeLa cells were studied using attenuated total reflection infrared spectroscopy. One min of such exposure shifted peak absorbance of the amide I band to a smaller wave number, reduced peak absorbance of the amide II band, and increased absorbance at around 1600 cm(-1). These results suggest that exposure to the ELF magnetic field has reversible effects on the N-H inplane bending and C-N stretching vibrations of peptide linkages, and changes the secondary structures of alpha-helix and beta-sheet in cell membrane proteins.

The core of the tetrameric mycobacterial porin MspA is an extremely stable beta-sheet domain

MspA is the major porin of Mycobacterium smegmatis mediating the exchange of hydrophilic solutes across the cell wall and is the prototype of a new family of tetrameric porins with a single central pore of 10 nm in length. Infrared and circular dichroism spectroscopy revealed that MspA consists mainly of antiparallel beta-strands organized in a coherent domain. Heating to 92 and 112 degrees C was required to dissociate the MspA tetramer and to unfold the beta-sheet domain in the monomer, respectively. The stability of the MspA tetramer exceeded the remarkable stability of the porins of Gram-negative bacteria for every condition tested and was not reduced in the presence of 2% SDS and at any pH from 2 to 14. These results indicated that the interactions between the MspA subunits are different from those in the porins of Gram-negative bacteria and are discussed in the light of a channel-forming beta-barrel as a core structure of MspA. Surprisingly, the channel activity of MspA in 2% SDS and 7.6 m urea at 50 degrees C was reduced 13- and 30-fold, respectively, although the MspA tetramer and the beta-sheet domain were stable under those conditions. Channel closure by conformational changes of extracellular loops under those conditions is discussed to explain these observations. This study presents the first experimental evidence that outer membrane proteins not only from Gram-negative bacteria but also from mycobacteria are beta-sheet proteins and demonstrates that MspA constitutes the most stable transmembrane channel protein known so far. Thus, MspA may be of special interest for biotechnological applications.

Ile-Lys-Val-Ala-Val (IKVAV)-containing laminin alpha1 chain peptides form amyloid-like fibrils

The Ile-Lys-Val-Ala-Val (IKVAV) sequence derived from laminin-1 promotes cell adhesion, neurite outgrowth, and tumor growth and metastasis. Here, we examined amyloid formation of an IKVAV-containing peptide (LAM-L: AASIKVAVSADR, mouse laminin alpha1 chain 2097-2108). The LAM-L peptide was stained with Congo red and exhibited fibrils in electron microscopy with a characteristic cross-beta X-ray diffraction pattern. Further, infrared spectra of LAM-L suggested a beta-sheet structure. These results indicate that LAM-L forms amyloid-like fibrils. We also examined amyloid-like fibril formation of LAM-L analogs. The neurite outgrowth activity of the LAM-L analogs was closely related to their amyloid-like fibril formation.

Changes in protein conformation and dynamics upon complex formation of brain-derived neurotrophic factor and its receptor: investigation by isotope-edited Fourier transform IR spectroscopy

The interactions of brain-derived neurotrophic factor (BDNF) with the extracellular domain of its receptor (trkB) are investigated by employing isotope-edited Fourier transform IR (FTIR) spectroscopy. The protein secondary structures of individual BDNF and trkB in solutions are compared with those in their complex. The temperature dependence of the secondary structures of BDNF, trkB, and their complex is also investigated. Consistent with the crystal structure, we observe by FTIR spectroscopy that BDNF in solution contains predominantly beta strands (approximately 53%) and relatively low contents of other secondary structures including beta turns (approximately 16%), disordered structures (approximately 12%), and loops (approximately 18%) and is deficient in alpha helix. We also observe that trkB in solution contains mostly beta strands (52%) and little alpha helix. Conformational changes in both BDNF and trkB are observed upon complex formation. Specifically, upon binding of BDNF, the conformational changes in trkB appear to involve mostly beta turns and disordered structures while the majority of the beta-strand conformation remains unchanged. The IR data indicate that some of the disordered structures in the loop regions are likely converted to beta strands upon complex formation. The FTIR spectral data of BDNF, trkB, and their complex indicate that more amide NH groups of trkB undergo H-D exchange within the complex than those of the ligand-free receptor and that the thermal stability of trkB is decreased slightly upon binding of BDNF. The FT-Raman spectra of BDNF, trkB, and their complex show that the six intramolecular disulfide bonds of trkB undergo significant conformational changes upon binding of BDNF as a result of changes in the tertiary structure of trkB. Taken together, the FTIR and Raman data are consistent with the loosening of the tertiary structure of trkB upon binding of BDNF, which leads to more solvent exposure of the amide NH group and decreased thermal stability of trkB. This finding reveals an intriguing structural property of the neurotrophin ligand-receptor complex that is in contrast to other ligand-receptor complexes such as a cytokine-receptor complex that usually shows protection of the amide NH group and increased thermal stability upon complex formation.