Fourier transform infrared spectroscopy study of the secondary and tertiary structure of the reconstituted Na+/Ca2+ exchanger 70-kDa polypeptide

19F-NMR Probing of Ion-Induced Conformational Changes in Detergent-Solubilized and Nanodisc-Reconstituted NCX_Mj

Consecutive interactions of 3Na+ or 1Ca2+ with the Na+/Ca2+ exchanger (NCX) result in an alternative exposure (access) of the cytosolic and extracellular vestibules to opposite sides of the membrane, where ion-induced transitions between the outward-facing (OF) and inward-facing (IF) conformational states drive a transport cycle. Here, we investigate sub-state populations of apo and ion-bound species in the OF and IF states by analyzing detergent-solubilized and nanodisc-reconstituted preparations of NCX_Mj with 19F-NMR. The 19F probe was covalently attached to the cysteine residues at entry locations of the cytosolic and extracellular vestibules. Multiple sub-states of apo and ion-bound species were observed in nanodisc-reconstituted (but not in detergent-solubilized) NCX_Mj, meaning that the lipid-membrane environment preconditions multiple sub-state populations toward the OF/IF swapping. Most importantly, ion-induced sub-state redistributions occur within each major (OF or IF) state, where sub-state interconversions may precondition the OF/IF swapping. In contrast with large changes in population redistributions, the sum of sub-state populations within each inherent state (OF or IF) remains nearly unchanged upon ion addition. The present findings allow the further elucidation of structure-dynamic modules underlying ion-induced conformational changes that determine a functional asymmetry of ion access/translocation at opposite sides of the membrane and ion transport rates concurring physiological demands.

Linearly Polarized Infrared Spectroscopy for the Analysis of Biological Materials

The analysis of biological samples with polarized infrared spectroscopy (p-IR) has long been a widely practiced method for the determination of sample orientation and structural properties. In contrast to earlier works, which employed this method to investigate the fundamental chemistry of biological systems, recent interests are moving toward "real-world" applications for the evaluation and diagnosis of pathological states. This focal point review provides an up-to-date synopsis of the knowledge of biological materials garnered through linearly p-IR on biomolecules, cells, and tissues. An overview of the theory with special consideration to biological samples is provided. Different modalities which can be employed along with their capabilities and limitations are outlined. Furthermore, an in-depth discussion of factors regarding sample preparation, sample properties, and instrumentation, which can affect p-IR analysis is provided. Additionally, attention is drawn to the potential impacts of analysis of biological samples with inherently polarized light sources, such as synchrotron light and quantum cascade lasers. The vast applications of p-IR for the determination of the structure and orientation of biological samples are given. In conclusion, with considerations to emerging instrumentation, findings by other techniques, and the shift of focus toward clinical applications, we speculate on the future directions of this methodology.

Curcumin binds to the pre-fibrillar aggregates of Cu/Zn superoxide dismutase (SOD1) and alters its amyloidogenic pathway resulting in reduced cytotoxicity

Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease that affects motor neurons. Unfortunately, effective therapeutics against this disease is still not available. Almost 20% of familial ALS (fALS) is suggested to be associated with pathological deposition of superoxide dismutase (SOD1). Evidences suggest that SOD1-containing pathological inclusions in ALS exhibit amyloid like properties. An effective strategy to combat ALS may be to inhibit amyloid formation of SOD1 using small molecules. In the present study, we observed the fibrillation of one of the premature forms of SOD1 (SOD1 with reduced disulfide) in the presence of curcumin. Using ThT binding assay, AFM, TEM images and FTIR, we demonstrate that curcumin inhibits the DTT-induced fibrillation of SOD1 and favors the formation of smaller and disordered aggregates of SOD1. The enhancement in curcumin fluorescence on the addition of oligomers and pre-fibrillar aggregates of SOD1 suggests binding of these species to curcumin. Docking studies indicate that putative binding site of curcumin may be the amyloidogenic regions of SOD1. Further, there is a significant increase in SOD1 mediated toxicity in the regime of pre-fibrillar and fibrillar aggregates which is not evident in curcumin containing samples. All these data suggest that curcumin reduces toxicity by binding to the amyloidogenic regions of the species on the aggregation pathway and blocking the formation of the toxic species. Nanoparticles of curcumin with higher aqueous solubility show similar aggregation control as that of curcumin bulk. This suggests a potential role for curcumin in the treatment of ALS.

Interactions of caveolin-1 scaffolding and intramembrane regions containing a CRAC motif with cholesterol in lipid bilayers

Caveolin-1 is a major structural protein of caveolae and specifically binds cholesterol (Chol). The caveolin scaffolding domain is thought to be involved in caveolin-Chol interaction through the sequence V94-T-K-Y-W-F-Y-R101, a motif that matches a cholesterol recognition amino-acid consensus (CRAC). In the present work, three CRAC-containing peptides, corresponding to caveolin-1 94-101, 82-101 and 93-126, were tested to study the role of the CRAC motif in the caveolin-Chol interaction in 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayers using differential scanning calorimetry (DSC), fluorescence and circular dichroism (CD). The Y97I substituents of the three peptides and one peptide segment corresponding to caveolin-1 101-126 that excludes the CRAC motif were also tested for comparison. Our results showed the potency of these CRAC-containing peptides in sequestering Chol into domains and the enhanced role of the intramembrane domain and scaffolding domain for the potency. Of the three CRAC-containing peptides, the peptide 93-126 was particularly effective in promoting Chol segregation, while the peptide 82-101 was less potent in promoting the formation of domains than the peptide 93-126, but was more potent than the peptide 94-101. The domain partition of DPPC/Chol bilayers was not observed in the presence of the peptide 101-126, in contrast to the case in the presence of the peptide 93-126 at the same concentrations of peptide and Chol. The potency of the CRAC motif in Chol segregation was lowered by the Y97I mutation. The difference in structure may be a factor that contributes to different effects of these peptides on the distribution of Chol in the lipid membrane.

Structural study of the catalytic domain of PKCzeta using infrared spectroscopy and two-dimensional infrared correlation spectroscopy

The secondary structure of the catalytic domain from protein kinase C zeta was studied using IR spectroscopy. In the presence of the substrate MgATP, there was a significant change in the secondary structure. After heating to 80 degrees C, a 14% decrease in the alpha-helix component was observed, accompanied by a 6% decrease in the beta-pleated sheet; no change was observed in the large loops or in 3(10)-helix plus associated loops. The maximum increase with heating was observed in the aggregated beta-sheet component, with an increase of 14%. In the presence of MgATP, and compared with the sample heated in its absence, there was a substantial decrease in the 3(10)-helix plus associated loops and an increase in alpha-helix. Synchronous 2D-IR correlation showed that the main changes occurred at 1617 cm(-1), which was assigned to changes in the intermolecular aggregated beta-sheet of the denaturated protein. This increase was mainly correlated with the change in alpha-helix. In the presence of MgATP, the main correlation was between aggregated beta-sheet and the large loops component. The asynchronous 2D-correlation spectrum indicated that a number of components are transformed in intermolecularly aggregated beta-sheet, especially the alpha-helix and beta-sheet components. It is interesting that changes in 3(10)-helix plus associated loops and in alpha-helix preceded changes in large loops, which suggests that the open loops structure exists as an intermediate state during denaturation. In summary, IR spectroscopy revealed an important effect of MgATP on the secondary structure and on the thermal unfolding process when this was induced, whereas 2D-IR correlation spectroscopy allowed us to show the establishment of the denaturation pathway of this protein.

Effect of PbII on the Secondary Structure and Biological Activity of Trypsin

The effects of Pb(II) on the secondary structure and biological activity of trypsin have been examined by monitoring changes in its conductivity and IR and circular dichroism (CD) spectra. The results show that Pb(II) reacts with trypsin, and that the binding sites might be -OH and -NH groups in pepsin. The CD spectra indicate that interaction with Pb(II) significantly affects the secondary structure of trypsin, the beta-sheet-structure content being increased by about 42%, whilst those of alpha-helix and beta-turn structures are decreased by 13% and 21%, respectively. The results clearly demonstrate that Pb(II) affects the biological activity of trypsin by modifying its secondary structure. Most interesting is that Pb(II) up-regulates the activity of trypsin at low concentrations while down-regulating it at high concentrations.

Pharmacology of Brain Na+/Ca2+Exchanger: From Molecular Biology to Therapeutic Perspectives

In the last two decades, there has been a growing interest in unraveling the role that the Na+/Ca2+ exchanger (NCX) plays in the function and regulation of several cellular activities. Molecular biology, electrophysiology, genetically modified mice, and molecular pharmacology have helped to delve deeper and more successfully into the physiological and pathophysiological role of this exchanger. In fact, this nine-transmembrane protein, widely distributed in the brain and in the heart, works in a bidirectional way. Specifically, when it operates in the forward mode of operation, it couples the extrusion of one Ca2+ ion with the influx of three Na+ ions. In contrast, when it operates in the reverse mode of operation, while three Na+ ions are extruded, one Ca2+ enters into the cells. Different isoforms of NCX, named NCX1, NCX2, and NCX3, have been described in the brain, whereas only one, NCX1, has been found in the heart. The hypothesis that NCX can play a relevant role in several pathophysiological conditions, including hypoxia-anoxia, white matter degeneration after spinal cord injury, brain trauma and optical nerve injury, neuronal apoptosis, brain aging, and Alzheimer's disease, stems from the observation that NCX, in parallel with selective ion channels and ATP-dependent pumps, is efficient at maintaining intracellular Ca2+ and Na+ homeostasis. In conclusion, although studies concerning the involvement of NCX in the pathological mechanisms underlying brain injury during neurodegenerative diseases started later than those related to heart disease, the availability of pharmacological agents able to selectively modulate each NCX subtype activity and antiporter mode of operation will provide a better understanding of its pathophysiological role and, consequently, more promising approaches to treat these neurological disorders.

Hydrogen-deuterium exchange in membrane proteins monitored by IR spectroscopy: a new tool to resolve protein structure and dynamics

As more and more high-resolution structures of proteins become available, the new challenge is the understanding of these small conformational changes that are responsible for protein activity. Specialized difference Fourier transform infrared (FTIR) techniques allow the recording of side-chain modifications or minute secondary structure changes. Yet, large domain movements remain usually unnoticed. FTIR spectroscopy provides a unique opportunity to record (1)H/(2)H exchange kinetics at the level of the amide proton. This approach is extremely sensitive to tertiary structure changes and yields quantitative data on domain/domain interactions. An experimental setup designed for attenuated total reflection and a specific approach for the analysis of the results is described. The study of one membrane protein, the gastric H(+),K(+)-ATPase, demonstrates the usefulness of (1)H/(2)H exchange kinetics for the understanding of the molecular movement related to the catalytic activity.

Analysis of 1H/2H exchange kinetics using model infrared spectra

This paper investigates the different approaches that best retrieve band shape parameters and kinetic time constants from series of protein Fourier transform infrared (FT-IR) spectra recorded in the course of 1H/2H exchange. In this first approach, synthetic spectra were used. It is shown that 1H/2H exchange kinetic measurements can help resolve spectral features otherwise hidden because of the overlap of various spectral contributions. We evaluated the efficiency of Fourier self-deconvolution, synchronous/asynchronous correlation, difference spectroscopy, principal component analysis, inverse Laplace transform, and determination of the underlying spectra by global analysis assuming first-order kinetics with either known or unknown time constants. It is demonstrated that some strategies allow the extraction of both the time dependence and the spectral shape of the underlying contributions.

Cooperativity between pepsin and crystallization of calcium carbonate in distilled water

Cooperativity between pepsin and crystallization of calcium carbonate in distilled water was studied. The results show that vaterite was formed under the influence of pepsin and the crystalline product was a composite of vaterite and pepsin. The component of this material was similar to that of nacre. At the same time, the crystallization of calcium carbonate had also an important effect on the secondary structure of the pepsin. The secondary structure of the pepsin was characterized through FT-IR technology. The result indicated that the pure pepsin is composed of 24.38% alpha-helices, 29.91% beta-sheets, 39.32% beta-turns and 6.49% random structures and the pepsin in the CaCO(3)-pepsin solution is composed of 2.09% alpha-helices, 93.304% beta-sheets, 4.592% beta-turns and 0.006% random structure. During the crystallization of the calcium carbonate from the pepsin solution, the secondary structure of the pepsin transformed. These results showed that there was cooperativity between the crystallization of vaterite and the pepsin. The cooperative mechanism is discussed.

Measurement of absolute values of hemoglobin oxygenation in the brain of small rodents by near infrared reflection spectrophotometry

Reflection near infrared spectroscopy (reNIRS) has been proposed as a novel technique for the measurement of absolute values of total hemoglobin (tHb), oxygenated hemoglobin (oxHb), hemoglobin saturation (SO2), and cytochrome aa3 oxidation status (oxCyt aa3) in living tissue. In this study, we evaluated reNIRS during physiological cerebral blood flow conditions in rats (n=6) and during the induction of global cerebral ischemia in gerbils (n=6). ReNIRS parameters were assessed over the exposed cerebral cortex and compared to regional cerebral blood flow (rCBF) data obtained by laser Doppler flowmetry. Under physiological conditions, reNIRS measurements reflected the large intra- and interindividual variability of oxHb and tHb in the brain. The absolute values obtained by reNIRS for tHb (6.3 +/- 1.7 mg/ml), oxHb (3.7 +/- 1.1 mg/ml), and SO2 (61 +/- 5%) matched expected values. In contrast, measurements of oxCyt aa3 were unstable and results unreliable. reNIRS reliably detected cerebral ischemia, verified by a reduction of rCBF to 11% of baseline. tHb dropped to 74 +/- 7% of baseline (P<0.001), reflecting ischemic microvascular vasoconstriction. oxHb and SO2 dropped to expected near-zero values (2 +/- 4 and 3 +/- 5% of baseline, respectively; P<0.001). We conclude that reNIRS provides reliable and reproducible absolute values for brain tissue tHb, oxHb, and SO2 in small rodents. Determination of physiological values requires measurements at multiple locations, while cerebral ischemia is reliably detected by continuous recordings at a single location.

Study of amide-proton exchange of Escherichia coli melibiose permease by attenuated total reflection-Fourier transform infrared spectroscopy: evidence of structure modulation by substrate binding

The accessibility of Escherichia coli melibiose permease to aqueous solvent was studied following hydrogen-deuterium exchange kinetics monitored by attenuated total reflection-Fourier transform infrared spectroscopy under four distinct conditions where MelB forms different complexes with its substrates (H(+), Na(+), melibiose). Analysis of the amide II band upon (2)H(2)O exposure discloses a significant sugar protection of the protein against aqueous solvent, resulting in an 8% less exchange of the corresponding H(+)*melibiose*MelB complex compared with the protein in the absence of sugar. Investigation of the amide I exchange reveals clear substrate effects on beta-sheet accessibility, with the complex H(+)*melibiose*MelB being the most protected state against exchange, followed by Na(+)*melibiose*MelB. Although of smaller magnitude, similar changes in alpha-helices plus non-ordered structures are detected. Finally, no differences are observed when analyzing reverse turn structures. The results suggest that sugar binding induces a remarkable compactness of the carrier's structure, affecting mainly beta-sheet domains of the transporter, which, according to secondary structure predictions, may include cytoplasmic loops 4-5 and 10-11. A possible catalytic role of these two loops in the functioning of MelB is hypothesized.