Secondary structure and temperature behavior of the acetylcholine receptor by Fourier transform infrared spectroscopy

Copper removal from aqueous solutions by white rot fungus Pleurotus ostreatus GEMB-PO1 and its potential in co-remediation of copper and organic pollutants

Addressing the environmental contamination from heavy metals and organic pollutants remains a critical challenge. This study explored the resilience and removal potential of Pleurotus ostreatus GEMB-PO1 for copper. P. ostreatus GEMB-PO1 showed significant tolerance, withstanding copper concentrations up to 2 mM. Its copper removal efficiency ranged from 64.56 % at 0.5 mM to 22.90 % at 8 mM. Transcriptomic insights into its response to copper revealed a marked upregulation in xenobiotic degradation-related enzymes, such as laccase and type II peroxidases. Building on these findings, a co-remediation system using P. ostreatus GEMB-PO1 was developed to remove both copper and organic pollutants. While this approach significantly enhanced the degradation efficiency of organic contaminants, it concurrently exhibited a diminished efficacy in copper removal within the composite system. This study underscores the potential of P. ostreatus GEMB-PO1 in environmental remediation. Nevertheless, further investigation is required to optimize the simultaneous removal of organic pollutants and copper.

Interactions between polyols and wheat biopolymers in a bread model system fortified with inulin: A Fourier transform infrared study

One of the ways to improve food safety and reduce community health risks is fortification of these products with inulin. Inulin, in spite of the effects and nutritional benefits, will also have undesirable effects on the quality and shelf life of bread. In this study, the interactions between polyols as improvers (i.e. glycerol, sorbitol and propylene glycol) and major biopolymers of wheat flour (i.e. starch and gluten) were examined in model systems fortified with Serish inulin by Fourier transform infrared (FTIR) spectroscopy. The changes in starch structure were estimated focusing on the ratios of the heights of the bands at 1047 and 1022 cm^-1 which expresses the quantity of ordered starch to amorphous starch. At first and 5th days of storage, this ratio of control sample was higher than polyol treated samples. It was proved from Gaussian-Lorenzian curve fitting that the relative contribution of characteristic peaks of β-turns and intramolecular β-sheets was consecutively increased when polyol proportion of models increased. Whereas, content of intermolecular β-sheets and α-helix was slightly decreased with increasing of polyols in the models. Briefly, polyols especially 5% propylene glycol, could be used to reduce the undesirable effects of inulin on the quality parameters of dough and bread.

Design and Evaluation of Lyophilized Fibroblast Growth Factor 21 and Its Protection against Ischemia Cerebral Injury

This study investigated the effect of the excipients, including glycine, mannitol, arginine, trehalose, sorbitol, and poloxamer188, on the stability of recombinant human fibroblast growth factor 21(FGF21) during the process of lyophilization and storage. The glass transition temperature (T_g), protein secondary structure, aggregation ratio, and the bioactivity of lyophilized FGF21 were measured. We furthermore investigated the effect of FGF21 against ischemia cerebral injury using the middle cerebral artery occlusion (MCAO) model in rats. The ischemia cerebral injury of MCAO rats was analyzed via 2,3,5-triphenyltetrazolium chloride and Nissl-staining. Endoplasmic reticulum (ER) stress related proteins were detected via Western blot. In this study, we found that aggregation was the primary mode of deterioration of lyophilized FGF21under accelerated storage conditions. Mannitol combined with trehalose and glycine formulations offers the most effective protein protection to reduce the aggregation. Administration of FGF21 protected cerebral ischemia and decreased ER stress related proteins in MCAO rats and PC12 cells.

Serish inulin and wheat biopolymers interactions in model systems as a basis for understanding the impact of inulin on bread properties: a FTIR investigation

In this study the interactions between Serish root inulin and the main biopolymer types of wheat flour namely gluten, starch and phospholipid, were investigated in different model systems using Fourier transform infrared (FTIR) spectroscopy to unravel the underlying physical mechanism by which inulin impacts dough and bread properties. Interactions of inulin with starch and phospholipid were not considerable compared to gluten, but it was also clear that the modes of these interactions varied with the type and the amount of additives used in model formulation. This study revealed that when inulin is added to gluten, water redistribution promotes partial dehydration of gluten and collapse of β-spirals into intermolecular β-sheet structures; this trans-conformations might be due to physical reasons are believed to further impact the poor quality of bread containing added inulin. Upon performing Gaussian-Lorenzian curve fitting, it was observed that by adding of inulin to model systems, the relative contribution of characteristic peaks of β-turn and intramolecular β-sheet was progressively decreased whereas intermolecular β-sheet and α-helix contents were increased.

Aggregation gatekeeper and controlled assembly of Trpzip β-hairpins

Protein and peptide aggregation is an important issue both in vivo and in vitro. Herein, we examine the aggregation behaviors of two well-studied β-hairpins, Trpzip1 and Trpzip2. Previous studies suggested that Trpzip2 remains monomeric up to a concentration of ~15 mM whereas Trpzip1 readily aggregates at micromolar concentrations at acidic or neutral pH. This disparity is puzzling considering that these two peptides differ only in their turn sequences (i.e., GN vs NG). We hypothesize that these peptides can aggregate from their folded states via native edge-to-edge interactions and that the Lys8 residue in Trpzip2 is a more effective aggregation gatekeeper, because of a more favorable orientation. In support of this hypothesis, we find that increasing the pH to 13 or replacing Lys8 with a hydrophobic and photolabile Lys analogue, Lys(nvoc), leads to a significant increase in the aggregation propensity of Trpzip2, and that the aggregation of this Trpzip2 mutant can be reversed upon restoring the native Lys side chain via photocleavage of the nvoc moiety. In addition, we find that while both Trpzip1 and Trpzip2 form parallel β-sheet aggregates, the Lys(nvoc) Trpzip2 mutant forms antiparallel β-sheets and more stable fibrils. Taken together, these findings provide another example showing how sensitive peptide and protein aggregation is to minor sequence variation and that it is possible to use a photolabile non-natural amino acid, such as Lys(nvoc), to tune the rate of peptide aggregation and to control fibrillar 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.

Correlation between the OmpG secondary structure and its pH-dependent alterations monitored by FTIR

The channel activity of the outer-membrane protein G (OmpG) from Escherichia coli is pH-dependent. To investigate the role of the histidine pair His231/His261 in triggering channel opening and closing, we mutated both histidines to alanines and cysteines. Fourier transform infrared spectra revealed that the OmpG mutants stay-independent of pH-in an open conformation. Temperature ramp experiments indicate that the mutants are as stable as the open state of wild-type OmpG. The X-ray structure of the alanine-substituted OmpG mutant obtained at pH 6.5 confirms the constitutively open conformation. Compared to previous structures of the wild-type protein in the open and closed conformation, the mutant structure shows a difference in the extracellular loop L6 connecting beta-strands S12 and S13. A deletion of amino acids 220-228, which are thought to block the channel at low pH in wild-type OmpG, indicates conformational changes, which might be triggered by His231/His261.

Responses of Azospirillum brasilense to nitrogen deficiency and to wheat lectin: a diffuse reflectance infrared fourier transform (DRIFT) spectroscopic study

For the rhizobacterium Azospirillum brasilense, the optimal nutritional range of C:N ratios corresponds to the presence of malate (ca. 3 to 5 g l(-1) of its sodium salt) and ammonium (ca. 0.5 to 3 g l(-1) of NH4Cl) as preferred carbon and nitrogen sources, respectively. This microaerophilic aerotactic bacterium is known to have a narrow optimal oxygen concentration range of ca. 3 to 5 microM, which is 1.2% to 2% of oxygen solubility in air-saturated water under normal conditions. In this work, the effects of stress conditions (bound-nitrogen deficiency related to a high C:N ratio in the medium; excess of oxygen) on aerobically grown A. brasilense Sp245, a native wheat-associated endophyte, were investigated in the absence and presence of wheat germ agglutinin (WGA, plant stress protein and a molecular host-plant signal for the bacterium) using FTIR spectroscopy of whole cells in the diffuse reflectance mode (DRIFT). The nutritional stress resulted in the appearance of prominent spectroscopic signs of poly-3-hydroxybutyrate (PHB) accumulation in the bacterial cells; in addition, splitting of the amide I band related to bacterial cellular proteins indicated some stress-induced alterations in their secondary structure components. Similar structural changes were observed in the presence of nanomolar WGA both in stressed A. brasilense cells and under normal nutritional conditions. Comparative analysis of the data obtained and the relevant literature data indicated that the stress conditions applied (which resulted in the accumulation of PHB involved in stress tolerance) and/or the presence of nanomolar concentrations of WGA induced synthesis of bacterial cell-surface (glyco)proteins rich in beta-structures, that could be represented by hemagglutinin and/or porin.

Method for the estimation of the mean lorentzian bandwidth in spectra composed of an unknown number of highly overlapped bands

We introduce a method for the estimation of the mean Lorentzian bandwidth of the component bands in a spectrum. The method is computationally simple, using only the module of the Fourier transform of the spectrum, and its first derivative. Moreover, the presented method does not require knowledge of the number of bands in the spectrum, their band positions, or their band areas. Furthermore, it works on spectra containing Lorentzian bands, as well as Gaussian and Voigtian bands. Therefore, the introduced method seems especially well suited for obtaining a representative Lorentzian width for highly overlapped bands, independent of their number and Lorentzian/Gaussian character. We describe how different experimental limitations (spectral truncation, offset error, presence of noise, etc.) may affect the performance of the method, and when required we propose effective alternatives to minimize their effects. Finally, we show the application of the method to an experimental spectrum: the amide I band of a dry film of the solubilized ADP/ATP carrier. The estimation of the mean Lorentzian width can allow, for instance, for a more objective selection of the deconvolution width in Fourier self-deconvolution, allowing for a more objective and reliable analysis of the amide I band of proteins. The mean Lorentzian width can also be useful to obtain an estimation of the homogenous broadening and vibrational relaxation of the amide I vibration of proteins, without requiring complex pump-probe experiments.

Controlled immobilization of membrane proteins to surfaces for fourier transform infrared investigations

We show that it is possible to immobilize membrane proteins uniformly and reversibly as self-assembled (sub)monolayers on nitrilotriacetic acid-covered sensor surfaces via hexahistidine sequences present either in the protein or in lipid membranes. Fourier transform infrared spectra of such self-assembled (sub)monolayers deliver important structural information of the membrane proteins and are suited to screen the function of cellular receptors.

Time-resolved FTIR difference spectroscopy as tool for investigating refolding reactions of ribonuclease T1 synchronized with trans --> cis prolyl isomerization

The structurally well-characterized enzyme ribonuclease T1 was used as a model protein to further evaluate time-resolved Fourier transform IR difference spectroscopy in conjunction with temperature-jump techniques as a useful detection technique for protein folding studies. Compared to the wild-type protein, it was confirmed that the lack of one cis-proline bond at position 55 of the S54G/P55N variant is sufficient to significantly simplify and accelerate the refolding process. This result was sustained by the characterization of the early refolding events that occurred within the experimental dead time.

Dietary fats affect rat plasma lipoprotein secondary structure as assessed by Fourier transform infrared spectroscopy

This investigation was undertaken to determine by Fourier transform infrared spectroscopy the effects of diets enriched with fish, sunflower or olive oils on the secondary structure of plasma HDL and LDL from rats, as well as the effects on lipid unsaturation and acyl chain lengths. Controls were fed a commercial diet. In HDL, random coil conformation was relatively high in rats fed the fish diet, probably due to the irregular geometry of polyunsaturated fatty acids interacting with apoproteins. Parallel structural behaviors were observed for rats fed control and olive oil diets. The lowest lipid unsaturation level was found in HDL of rats fed olive oil, and acyl chain lengths were slightly increased by the three fats. Rats fed olive oil had the lowest percentage of LDL beta-sheets and these were more abundant in rats fed the fish oil diet. The least lipid unsaturation in LDL was in rats fed the olive oil diet. No significant differences in acyl chain lengths were observed. Certain protein conformational changes and/or apoprotein composition differences due to dietary fat may affect the binding between lipoproteins and their receptors in cells.

Structure of the pore-forming transmembrane domain of a ligand-gated ion channel

The structure of the pore-forming transmembrane domain of the nicotinic acetylcholine receptor from Torpedo has been investigated by infrared spectroscopy. Treatment of affinity-purified receptor with either Pronase or proteinase K digests the extramembranous domains (roughly 75% of the protein mass), leaving hydrophobic membrane-imbedded peptides 3-6 kDa in size that are resistant to peptide (1)H/(2)H exchange. Infrared spectra of the transmembrane domain preparations exhibit relatively sharp and symmetric amide I and amide II band contours centered near 1655 and 1545 cm(-)1, respectively, in both (1)H(2)O and (2)H(2)O. The amide I band is very similar to the amide I bands observed in the spectra of alpha-helical proteins, such as myoglobin and bacteriorhodopsin, that lack beta structure and exhibit much less beta-sheet character than is observed in proteins with as little as 20% beta sheet. Curve-fitting estimates 75-80% alpha-helical character, with the remaining peptides likely adopting extended and/or turn structures at the bilayer surface. Infrared dichroism spectra are consistent with transmembrane alpha-helices oriented perpendicular to the bilayer surface. The evidence strongly suggests that the transmembrane domain of the nicotinic receptor, the most intensively studied ligand-gated ion channel, is composed of five bundles of four transmembrane alpha-helices.

Differential interaction of equinatoxin II with model membranes in response to lipid composition

Equinatoxin II is a 179-amino-acid pore-forming protein isolated from the venom of the sea anemone Actinia equina. Large unilamellar vesicles and lipid monolayers of different lipid compositions have been used to study its interaction with membranes. The critical pressure for insertion is the same in monolayers made of phosphatidylcholine or sphingomyelin (approximately 26 mN m(-1)) and explains why the permeabilization of large unilamellar vesicles by equinatoxin II with these lipid compositions is null or moderate. In phosphatidylcholine-sphingomyelin (1:1) monolayers, the critical pressure is higher (approximately 33 mN m(-1)), thus permitting the insertion of equinatoxin II in large unilamellar vesicles, a process that is accompanied by major conformational changes. In the presence of vesicles made of phosphatidylcholine, a fraction of the protein molecules remains associated with the membranes. This interaction is fully reversible, does not involve major conformational changes, and is governed by the high affinity for membrane interfaces of the protein region comprising amino acids 101-120. We conclude that although the presence of sphingomyelin within the membrane creates conditions for irreversible insertion and pore formation, this lipid is not essential for the initial partitioning event, and its role as a specific receptor for the toxin is not so clear-cut.

Structural characterization of the C2 domain of novel protein kinase Cepsilon

Infrared spectroscopy (IR) and differential scanning calorimetry (DSC) were used to study the biophysical properties of the PKCepsilon-C2 domain, a C2 domain that possess special characteristics as it binds to acidic phospholipids in a Ca2+-independent manner and no structural information about it is available to date. When the secondary structure was determined by IR spectroscopy in H2O and D2O buffers, beta sheet was seen to be the major structural component. Spectroscopic studies of the thermal denaturation in D2O showed a broadening in the amide I' band starting at 45 degrees C. Curve fitting analysis of the spectra demonstrated that two components appear upon thermal denaturation, one at 1623 cm(-1) which was assigned to aggregation and a second one at 1645 cm(-1), which was assigned to unordered or open loop structures. A lipid binding assay has demonstrated that PKCepsilon-C2 domain has preferential affinity for PIP2 although it exhibits maximal binding activity for phosphatidic acid when 100 mol% of this negatively charged phospholipid was used. Thus, phosphatidic acid containing vesicles were used to characterize the effect of lipid binding on the secondary structure and thermal stability. These experiments showed that the secondary structure did not change upon lipid binding and the thermal stability was very high with no significant changes occurring in the secondary structure after heating. DSC experiments demonstrated that when the C2-protein was scanned alone, it showed a Tm of 49 degrees C and a calorimetric denaturation enthalpy of 144.318 kJ x mol(-1). However, when phoshatidic acid vesicles were included in the mixture, the transition disappeared and further IR experiments demonstrated that the protein structure was not modified under these conditions.

Structure and dynamics of membrane proteins as studied by infrared spectroscopy

Infrared (IR) spectroscopy is a useful technique in the study of protein conformation and dynamics. The possibilities of the technique become apparent specially when applied to large proteins in turbid suspensions, as is often the case with membrane proteins. The present review describes the applications of IR spectroscopy to the study of membrane proteins, with an emphasis on recent work and on spectra recorded in the transmission mode, rather than using reflectance techniques. Data treatment procedures are discussed, including band analysis and difference spectroscopy methods. A technique for the analysis of protein secondary and tertiary structures that combines band analysis by curve-fitting of original spectra with protein thermal denaturation is described in detail. The assignment of IR protein bands in H2O and in D2O, one of the more difficult points in protein IR spectroscopy, is also reviewed, including some cases of unclear assignments such as loops, beta-hairpins, or 3(10)-helices. The review includes monographic studies of some membrane proteins whose structure and function have been analysed in detail by IR spectroscopy. Special emphasis has been made on the role of subunit III in cytochrome c oxidase structure, and the proton pathways across this molecule, on the topology and functional cycle of sarcoplasmic reticulum Ca(2+)-ATPase, and on the role of lipids in determining the structure of the nicotinic acetylcholine receptor. In addition, shorter descriptions of retinal proteins and references to other membrane proteins that have been studied less extensively are also included.

New structural insights into the refolding of ribonuclease T1 as seen by time-resolved Fourier-transform infrared spectroscopy

To get new structural insights into different phases of the renaturation of ribonuclease T1 (RNase T1), the refolding of the thermally unfolded protein was initiated by rapid temperature jumps and detected by time-resolved Fourier-transform infrared spectroscopy. The characteristic spectral changes monitoring the formation of secondary structure and tertiary contacts were followed on a time scale of 10(-3) to 10(3) seconds permitting the characterization of medium and slow folding reactions. Additionally, structural information on the folding events that occurred within the experimental dead time was indirectly accessed by comparative analysis of kinetic and steady-state refolding data. At slightly destabilizing refolding temperatures of 45 degrees C, which is close to the unfolding transition region, no specific secondary or tertiary structure is formed within 180 ms. After this delay all infrared markers bands diagnostic for individual structural elements indicate a strongly cooperative and relatively fast folding, which is not complicated by the accumulation of intermediates. At strongly native folding temperatures of 20 degrees C, a folding species of RNase T1 is detected within the dead time, which already possesses significant amounts of antiparallel beta-sheets, turn structures, and to some degree tertiary contacts. The early formed secondary structure is supposed to comprise the core region of the five-stranded beta-sheet. Despite these nativelike characteristics the subsequent refolding events are strongly heterogeneous and slow. The refolding under strongly native conditions is completed by an extremely slow formation or rearrangement of a locally restricted beta-sheet region accompanied by the further consolidation of turns and denser backbone packing. It is proposed that these late events comprise the final packing of strand 1 (residues 40-42) of the five-stranded beta-sheet against the rest of this beta-sheet system within an otherwise nativelike environment. This conclusion was supported by the comparison of refolding of RNase T1 and its variant W59Y RNase T1 that enabled the assignment of these very late events to the trans-->cis isomerization reaction of the prolyl peptide bond preceding Pro-39.

Physicochemical and immunological studies of the N-terminal domain of the Torpedo acetylcholine receptor alpha-subunit expressed in Escherichia coli

The nicotinic acetylcholine receptor (AChR) from the electric organ of Torpedo species is an oligomeric protein composed of alpha2 beta gamma delta subunits. Although much is known about its tertiary and quaternary structure, the conformation of the large extracellular domains of each of the subunits has not been analysed in detail. In order to obtain information about the spatial structure of the extracellular domain, we have expressed the N-terminal fragment 1-209 of the Torpedo californica AChR alpha-subunit in Escherichia coli. Two vectors coding for a (His)6 tag, either preceding or following the 1-209 sequence, were used and the recombinant proteins obtained (designated alpha1-209pET and alpha1-209pQE, respectively) were purified by affinity chromatography on a Ni2+-agarose column. The chemical structure of both proteins was verified by Edman degradation and mass spectrometry. The proteins were soluble in aqueous buffers but to make possible a comparison with the whole AChR or its isolated subunits, the recombinant proteins were analyzed both in aqueous solution and with the addition of detergents. The two proteins bound [125I]alpha-bungarotoxin with equal potency (KD approximately 130 nm, Bmax approximately 10 nmol.mg-1). Both were shown to interact with several monoclonal antibodies raised against purified Torpedo AChR. The circular dichroism (CD) spectra of the two proteins in aqueous solution revealed predominantly beta-structure (50-56%), the fraction of alpha-helices amounting to 32-35%. Nonionic (beta-octylglucoside) and zwitterionic (CHAPS) detergents did not appreciably change the CD spectra, while the addition of SDS or trifluoroethanol decreased the percentage of beta-structure or increased the alpha-helicity, respectively. The predominance of beta-structure is in accord with recent data on the N-terminal domain of the mouse muscle AChR alpha-subunit expressed in the mammalian cells [West et al. (1997) J. Biol. Chem. 272, 25 468]. Thus, expression in E. coli provides milligram amounts of the protein that retains several structural characteristics of the N-terminal domain of the Torpedo AChR alpha-subunit and appears to share with the latter a similar secondary structure. The expression of recombinant polypeptides representing functional domains of the AChR provides an essential first step towards a more detailed structural analysis.

Pressure-induced structural rearrangements of bovine pancreatic trypsin inhibitor studied by FTIR spectroscopy

Fourier transform infrared (FTIR) spectroscopy combined with resolution enhancement techniques, second-derivative and difference spectroscopies, have been used to characterize pressure-induced changes in the structural rearrangements of bovine pancreatic trypsin inhibitor (BPTI) in D2O solution at 25.0 degrees C. According to the observed changes in the amide I' band up to 550 MPa, the secondary structure elements of BPTI, such as the alpha-helix, 3(10)-helix, beta-sheet, and beta-turn, are scarcely rearranged except for the loop structure of residues of 9-17 and 36-43. The polypeptide backbone is not extensively unfolded up to 550 MPa. The minor pressure-induced structural rearrangements are completely reversible. A further increase in pressure above 1000 MPa associated with the precipitation of BPTI in D2O buffer solution induces the partial structural rearrangements of the alpha-helix, beta-turn and/or 3(10)-helix, and beta-sheet. The polypeptide backbone of BPTI is not fully unfolded even above 1000 MPa. Most of the protected backbone amide protons involved in the beta-sheet remain intact in the pressure range where BPTI is not precipitated, while those involved in the alpha-helix and beta-turn and/or 3(10)-helix are exchanged with solvent deuterons. The protected backbone amide protons located near the surface regions are more easily exchanged with solvent deuterons by application of high pressure than those involved in the core.

Fourier transform infrared spectral evidences for protein conformational changes in immature cataractous human lens capsules accelerated by myopia and/or systemic hypertension

The possible changes in protein structures of the cataractous human lens capsules of the immature patients with myopia and/or systemic hypertension have been investigated using Fourier transform infrared (FT-IR) microspectroscopy. Second-derivative and deconvolution methods have been applied to obtain the position of the overlapping components of the amide I band and assign them to different secondary structures. Changes in the protein secondary structure and composition of amide I band were estimated quantitatively from Fourier self-deconvolution and curve fitting algorithms. The results indicate that myopia and/or systemic hypertension were found to significantly modify the protein secondary structure of the cataractous human lens capsules to increase the beta-type structure and random coil and decrease the alpha-helix structure. Myopia-induced conformational change in triple helix structure was more pronounced. In conclusion, myopia and/or systemic hypertension seem to modify the conformation of the protein structures in cataractous human lens capsule to change ionic permeation through lens capsule to accelerate the cataract formation of senile patients.

ATR-FTIR spectroscopic investigation of imipenem-susceptible and -resistant Pseudomonas aeruginosa isogenic strains

The primary mechanism of imipenem resistance in Pseudomonas aeruginosa has been ascribed to an outer membrane impermeability owing to a loss of expression of protein D2. Attenuated total reflection-Fourier transform infrared spectroscopy in conjunction with statistical methods has been used as a new approach to rapidly discriminate four isogenic strains of P. aeruginosa--susceptible, less susceptible, and highly resistant to imipenem-- and to follow the structural modifications related to this low permeability. Decomposition of the broad protein and carbohydrate contours into underlying Gaussians and comparison of the susceptible and highly resistant strain provided quantitative and ultrastructural information on these strains. This methodology allows for discrimination not of the mutation itself but of its consequences observed in the protein and carbohydrate absorption regions. Its association with other existing biochemical methods may be envisaged since it may allow for rapid orientation of investigations in the field of bacterial resistance diagnosis.

The emerging three-dimensional structure of a receptor. The nicotinic acetylcholine receptor

The nicotinic acetylcholine receptor is the neurotransmitter receptor with the most-characterized protein structure. The amino acid sequences of its five subunits have been elucidated by cDNA cloning and sequencing. Its shape and dimensions (approximately 12.5 nm x 8 nm) were deduced from electron-microscopy studies. Its subunits are arranged around a five-fold axis of pseudosymmetry in the order (clockwise) alpha H gamma alpha L delta beta. Its two agonist/competitive-antagonist-binding sites have been localized by photolabelling studies to a deep gorge between the subunits near the membrane surface. Its ion channel is formed by five membrane-spanning (M2) helices that are contributed by the five subunits. This finding has been generalized as the Helix M2 model for the superfamily of ligand-gated ion channels. The binding site for regulatory non-competitive antagonists has been localized by photolabelling and site-directed-mutagenesis studies within this ion channel. Therefore a three-dimensional image of the nicotinic acetylcholine receptor is emerging, the most prominent feature of which is an active site that combines the agonist/ competitive-antagonist-binding sites, the regulatory site and the ion channel within a relatively narrow space close to and within the bilayer membrane.

Aggregation of rhDNase occurred during the compression of KBr pellets used for FTIR spectroscopy

PURPOSE

To determine if a protein changes when it is compressed into a KBr pellet for FTIR spectroscopy measurement in the solid state, using recombinant human deoxyribonuclease I (rhDNase) as an example.

METHODS

Lyophilized rhDNase with KBr compressed at different pressures were analyzed by FTIR spectroscopy, size exclusion HPLC and enzymatic activity assay. Different protein/KBr weight ratios and residual water contents were studied for their possible effects on aggregation.

RESULTS

Depending on the pressure, a loss of enzymatic activity accompanied by an increase in soluble high molecular weight aggregates of the protein (up to approximately 15%) was demonstrated. Aggregation was reduced to less than 5% by a suitable dilution of the protein in KBr (1 in 1000). In contrast, water content variability (1-11 wt. %) did not affect aggregation.

CONCLUSIONS

The findings emphasize the importance to examine for protein integrity when using the KBr method for FTIR sample preparation. Protein aggregation may be minimized by optimizing the sample preparation condition such as changing the protein/KBr weight ratio.

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.

Surface-core relationships in human low density lipoprotein as studied by infrared spectroscopy

The secondary structure of human apolipoprotein B at 37 degrees C is estimated to be 24% alpha-helix, 23% beta-sheet, 6% beta-turns, 24% unordered structure, and 24% "beta-strands," characterized by a band around 1618 cm-1, and consistent with extended string-like chains in contact with the lipid moiety not forming beta-sheets. When cooled to a temperature below the cholesteryl ester transition at 30 degrees C, the ordering of the low density lipoprotein core results in reversible changes in the protein conformation, decreasing the apparent amount of alpha-helix, beta-strand, and unordered structure below 30 degrees C and increasing beta-sheet and beta-turns. Lowering the ionic strength affects the core-associated transitions, shifting their temperature from 30 to 20 degrees C, and modifying protein conformation below the transition. An additional thermal event is observed at 75 degrees C, leading to irreversible protein denaturation. In the broad temperature range between the 30 and 75 degrees C transitions, apolipoprotein B is stable toward both temperature and ionic strength changes. After thermal denaturation, the protein retains a certain degree of ordered structure.

Infrared spectroscopic studies of lyophilization- and temperature-induced protein aggregation

Recent studies have clearly demonstrated that Fourier transform IR spectroscopy can be a powerful tool for the study of protein stabilization during freeze-drying and for optimizing approaches to prevent lyophilization-induced protein aggregation. The purpose of the current review is to provide an overview of these topics, as well as an introduction to the study of protein secondary structure with IR spectroscopy. We will start with a general summary of the theories and practices for processing and interpreting protein IR spectra. We will then review the current literature on the use of IR spectroscopy to study protein structure and the effects of stabilizers during lyophilization. Next we will concentrate specifically on protein aggregation. The bulk of the research and the key assignments of spectral features in protein aggregates come from studies of the effects of high and low temperature on proteins. Therefore, we will first consider this topic. Finally, we will summarize the recent theoretical and applied work on lyophilization-induced aggregation.

Conformational analysis of hemopexin by Fourier-transform infrared and circular dichroism spectroscopy

Hemopexin is a serum glycoprotein that binds heme with the highest known affinity of any characterized heme-binding protein and plays an important role in receptor-mediated cellular heme uptake. Complete understanding of the function of hemopexin will require the elucidation of its molecular structure. Previous analysis of the secondary structure of hemopexin by far-UV circular dichroism (CD) failed due to the unusual positive ellipticity of this protein at 233 nm. In this paper, we present an examination of the structure of hemopexin by both Fourier-transform infrared (FTIR) and circular dichroism spectroscopy. Our studies show that hemopexin contains about 55% beta-structure, 15% alpha-helix, and 20% turns. The two isolated structural domains of hemopexin each have secondary structures similar to hemopexin. Although there are significant tertiary conformational changes indicated by the CD spectra, the overall secondary structure of hemopexin is not affected by binding heme. However, moderate changes in secondary structure do occur when the heme-binding domain of hemopexin associates with heme. In spite of the exceptionally tight binding at neutral pH, heme is released from the bis-histidyl heme-hemopexin complex at pH 5.0. Under this acidic condition, hemopexin maintains the same overall secondary structure as the native protein and is able to resume the heme-binding function and the native structure of the heme-protein (as indicated by the CD spectra) when returned to neutral pH. We propose that the state of hemopexin identified in vitro at pH 5.0 resembles that of this protein in the acidic environment of the endosomes in vivo when hemopexin releases heme during receptor-mediated endocytosis.

Secondary structure of the nicotinic acetylcholine receptor: implications for structural models of a ligand-gated ion channel

The secondary structure and effects of two ligands, carbamylcholine and tetracaine, on the secondary structure of affinity-purified nicotinic acetylcholine receptor (nAChR) from Torpedo has been studied using Fourier transform infrared spectroscopy (FTIR). FTIR spectra of the nAChR were acquired in both 1H2O and 2H2O buffer and exhibit spectral features indicative of a substantial alpha-helical content with lesser amounts of beta-sheet and random coil structures. The resolution enhancement techniques of Fourier self-deconvolution and Fourier derivation reveal seven component bands contributing to both the amide I band and amide I' band contours in 1H2O and 2H2O, respectively. Curve-fitting estimates of the nAChR secondary structure are consistent with the qualitative analysis of the FTIR spectra as follows: 39% alpha-helix, 35% beta-sheet, 6% turn, and 20% random coil. Of particular interest is the estimated alpha-helical content as this value places restrictions on models of the nAChR transmembrane topology and on the types of secondary structures that may contribute to functional domains, such as the ligand-binding site. The estimated alpha-helical content is sufficient to account for four transmembrane alpha-helices in each nAChR subunit as well as a substantial portion of the extracellular and/or the cytoplasmic domains. FTIR spectra were also acquired in the presence and absence of 1 mM carbamylcholine and 5 mM tetracaine to examine the effects of ligand binding on the secondary structure of the nAChR. The similarity of the spectra, even after spectral deconvolution, indicates that the secondary structure of the nAChR is essentially unaffected by desensitization.(ABSTRACT TRUNCATED AT 250 WORDS)

Residues 377-389 from the delta subunit of Torpedo californica acetylcholine receptor are located in the cytoplasmic surface

Torpedo californica acetylcholine receptor (AcChR) enriched, sealed vesicles have been specifically labeled on the cytoplasmic surface with pyridoxal 5'-phosphate (Perez-Ramirez, B., and Martinez-Carrion, M., 1989, Biochemistry 28, 5034-5040). After chromatography of the peptide fragments produced by trypin digestion of labeled AcChR, several fractions containing the phosphopyridoxyl label were obtained. Edman degradation identified one of the fractions, with sequence SRSELMFEKQSER, as corresponding to residues 377-389 in the delta subunit (primary structure). The latter must be a cytoplasmic region of this transmembranous protein, and residue delta K385 must reside in a water-soluble exposed domain of the cytosolic side of the membrane. Introduction of phosphopyridoxyl residues allows for their potential use as probes of conformational changes in the cytosolic surface of the receptor molecule.