Resting state conformation of the MsbA homodimer as studied by site-directed spin labeling

MsbA is the ABC transporter for lipid A and is found in the inner membranes of Gram-negative bacteria such as Escherichia coli. Without MsbA present, bacterial cells accumulate a toxic amount of lipid A within their inner membranes. A crystal structure of MsbA was recently obtained that provides an excellent starting point for functional dynamics studies in membranes [Chang, and Roth (2001) Science 293, 1793-1800]. Although a structure of MsbA is now available, many questions remain concerning its mechanism of transport. Site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy is a powerful approach for characterizing local areas within a large protein structure in addition to detecting and following changes in local structure due to dynamic interactions within a protein. The quaternary structure of the resting state of the MsbA homodimer reconstituted into lipid membranes has been evaluated by SDSL EPR spectroscopy and chemical cross-linking techniques. SDSL and cross-linking results are consistent with the controversial resting state conformation of the MsbA homodimer found in the crystal structure, with the tips of the transmembrane helices forming a dimer interface. The position of MsbA in the membrane bilayer along with the relative orientation of the transmembrane helical bundles with respect to one another has been determined. Characterization of the resting state of the MsbA homodimer is essential for future studies on the functional dynamics of this membrane transporter.     

A comparative study on the structural differences of primate hemoglobins by spin labeling technique

The hemoglobins of human and five non-human primates were spin-labeled with N-(1-oxyl-2,2,6,6-tetramethyl-4-piperidinyl)iodoacetamide, and the ESR spectra of their deoxy, oxy, and carbonmonoxy forms were measured. The analyses of the spectra indicated that the local protein conformation in the vicinity of the spin-labeled cysteine residue at position 93(F9) in the beta-chain is slightly but significantly different among species, and that each hemoglobin shows a similar change in conformation upon conversion from the oxy form to the carbonmonoxy one except for human hemoglobin. Human hemoglobin was suggested to undergo a significantly different conformational change upon this conversion, indicating that it has unique characteristics among the primate hemoglobins.     

盐胁迫下盐地碱蓬体内无机离子含量分布特点的研究

用不同浓度NaCl溶液处理盐地碱蓬（Suaeda salsa)植株后,测定并比较老叶、幼叶及根部的无机离子含量和对K的选择性,叶片及根部的Na^ 、Cl^-含量随盐度的增加而升高,且累积趋势相似,盐胁迫下根部Na^ 、Cl^-及总离子含量（K^ 、Na^ 、Ca^2 ,NO3^-,Cl^-)明显低于叶片,说明盐地碱蓬地盐胁迫下,以叶片优先积累大量离子（如Na^ ,Cl^-) 为其适应特征。NaCl处理下,叶片的K^ ,Ca^2 含量低于对照,但随盐度的增加保持相对稳定,而根部K^ 含量,K/Na比、对K的选择性则高于叶片,这对盐胁迫下地上部的K^ 亏缺有一定补偿作用。低盐度处理（100mmol/LNaCl)促进NO3^-的吸收,另外随盐度的增加,叶片渗透势下降,渗透调节能力增强,幼叶渗透势低于老叶,但渗透调节能力相同。     

Effect of pH, ionic strength and univalent inorganic ions on the reconstitution of aspartate aminotransferase

1. The effect of pH change on the reconstitution of aspartate aminotransferase (EC 2.6.1.1), i.e. the reactivation of the apoenzyme with coenzyme (pyridoxal phosphate and pyridoxamine phosphate), was studied in the pH range 4.2-8.9 by using three buffer systems at concentrations ranging from 0.025 to 0.1m. 2. Although the profile of the reconstitution rate-pH curve in the range pH5.2-6.8 (covered by sodium cacodylate-HCl buffer) reflects the influence of the H(+) concentration on the reconstitution process, the profile of the curve in the pH ranges 4.2-5.6 and 7.2-8.25 (covered respectively by sodium acetate-acetic acid and Tris-HCl buffers) appears to be influenced by the ionic strength of the buffer. 3. The reconstitution is also influenced by univalent inorganic ions such as halide ions and, to a lesser extent, alkali metal ions, which are known to alter the water structure.     

A fluorescence study of the effects of pH and Mg2+ on the conformation of fructose 1,6-diphosphatase from spinach chloroplasts.

2-p-Toluidino-naphthalene-6-sulfonate is a sensitive fluorescent reporter group which can be used for the detection of the conformation of fructose 1,6-diphosphatase from spinach chloroplasts. When fructose 1,6-diphosphatase was added to a dilute solution of 2-p-toluidino-naphthalene-6-sulfonate at pH 9.0, the fluorescence intensity gradually increased. At this pH, the enzyme activity decreased at the same rate. However, at neutral pH (7.5), this time-dependent fluorescence change was not observed. In the presence of Mg2+, which is an activator of the enzyme, the fluorescence intensity was increased instantly and did not change for 30 min in the pH range 8.0--9.0. From the concentration dependence of the fluorescence intensity, the dissociation constant for Mg2+ was determined, Kdis = 3 mM. The effects of pH and Mg2+ on the conformation and activity of chloroplast fructose 1,6-diphosphatase are discussed.     

Nucleosome conformation: pH and organic solvent effects.

Monomer nucleosomes (nu 1) from chicken erythrocyte nuclei were examined in aqueous buffers (8 greater than pH greater than 3) and in solvent mixtures (i.e., water and ethanol, ethylene glycol, dioxane, dimethyl sulfoxide, 2-methyl-2,4-pentanediol, polyethylene glycol, sucrose, or urea). Circular dichroism, laser Raman spectroscopy of nu 1, and the fluorescence of nu 1 labeled with N-(3-pyrene) maleimide on thiol groups of H3 histone were employed to detect conformational transitions in nu 1. The results of pH studies were as follows: 5.5 greater than pH greater than 4.8, suppression of DNA ellipticity and no change of histone alpha-helix; 4.6 greater than pH greater than 4.2 an irreversible increase in the B character of DNA, a slight loss of histone alpha-helix, and a parallel loss of pyrene excimer fluorescence; 4 greater than pH, aggregation of nu 1 and protonation of the DNA bases C and A. Results obtained in the studies of nu 1 in solvent mixtures included the following: sharp conformational transitions that variously involved an increase in the B character of DNA, a slight loss of histone alpha-helix, and a loss of pyrene excimer. Different solvents required different concentrations to effect these conformational changes.     

A study into the effects of protein binding on nucleotide conformation.

In this study, we examine the effects of binding to protein upon nucleotide conformation, by the comparison of X-ray crystal structures of free and protein-bound nucleotides. A dataset of structurally non-homologous protein-nucleotide complexes was derived from the Brookhaven Protein Data Bank by a novel protocol of dual sequential and structural alignments, and a dataset of native nucleotide structures was obtained from the Cambridge Structural Database. The nucleotide torsion angles and sugar puckers, which describe nucleotide conformation, were analysed in both datasets and compared. Differences between them are described and discussed. Overall, the nucleotides were found to bind in low energy conformations, not significantly different from their 'free' conformations except that they adopted an extended conformation in preference to the 'closed' structure predominantly observed by free nucleotide. The archetypal conformation of a protein-bound nucleotide is derived from these observations.     

Comparative study on the active sites of ficin and papain by the spin labeling method

Ficin was alkylated with a series of haloacetamide spin labels with various distances between the spin probes and reactive groups. From the relation of these distances to the tau c values of the labels incorporated into protein, it was estimated that the depth of the active site hole of ficin is ca. 8 A. The results are somewhat different from those reported previously for papain (S. Nakayama et al. (1981) Biochem. Biophys. Res. Commun. 98, 471-475). Examination of the pH dependence of the ESR spectra for ficin and papain alkylated with an iodoacetamide or a maleimide spin label suggested that these enzymes have an amino acid residue of pKa 4 (probably a histidine residue) around the active site cysteine and that the active site conformations change at around pH 5.     

Histochemical analysis of alcohol-lability and effects of inorganic ions on the metachromasia of galactogen

Summary Galactogen localised in the albumen gland of a land snail exhibited an intense and selective metachromatic reaction with azure A at pH 3.5 to 5.5. The metachromasia was labile towards alcoholic treatment. Methanol, ethanol, n-propanol and n-butanol in this order abolished the metachromasia with increasing efficiency. An interesting relationship between the capacity to abolish the galactogen metachromasia and the dielectric constants of these alcoholic solvents was also observed. The higher the dielectric constant of an alcohol the lower was its capacity to suppress the metachromasia of galactogen. Inorganic ions also suppressed the metachromasia of galactogen. Their capacity to suppress the metachromasia was a linear function of the charge carried by them. The pH dependence, effects of alcohol treatment and inorganic ions on the metachromasia of galactogen are considered in comparison with that of sulfomucins, sialomucins and hyaluronic acid. The importance of metachromasia techniques in the histochemical detection of galactogen is described.     

Non-erythroid beta spectrin interacting proteins and their effects on spectrin tetramerization

With yeast two-hybrid methods, we used a C-terminal fragment (residues 1697–2145) of non-erythroid beta spectrin (βII-C), including the region involved in the association with alpha spectrin to form tetramers, as the bait to screen a human brain cDNA library to identify proteins interacting with βII-C. We applied stringent selection steps to eliminate false positives and identified 17 proteins that interacted with βII-C (IP_βII-C s). The proteins include a fragment (residues 38–284) of “THAP domain containing, apoptosis associated protein 3, isoform CRA g”, “glioma tumor suppressor candidate region gene 2” (residues 1-478), a fragment (residues 74–442) of septin 8 isoform c, a fragment (residues 704–953) of “coatomer protein complex, subunit beta 1, a fragment (residues 146–614) of zinc-finger protein 251, and a fragment (residues 284–435) of syntaxin binding protein 1. We used yeast three-hybrid system to determine the effects of these βII-C interacting proteins as well as of 7 proteins previously identified to interact with the tetramerization region of non-erythroid alpha spectrin (IP_αII-N s) [1] on spectrin tetramer formation. The results showed that 3 IP_βII-C s were able to bind βII-C even in the presence of αII-N, and 4 IP_αII-N s were able to bind αII-N in the presence of βII-C. We also found that the syntaxin binding protein 1 fragment abolished αII-N and βII-C interaction, suggesting that this protein may inhibit or regulate non-erythroid spectrin tetramer formation.     

Estimation of lipid regions in a cytochrome oxidase-lipid complex using spin labeling electron spin resonance: Distribution effects on the spin label

The distribution of lipid in the cytochrome oxidase-lipid complex from beef heart mitochondria has been studied by the spin labeling electron spin resonance technique. The spectra of a phospholipid spin label incorporated in the complex reveals an immobilized (on the ESR time scale) component in addition to the fluid component which is found in aqueous dispersions of the extracted lipids. The first component corresponds to the domain of lipid influenced by the protein, and the second component to the remaining lipid. A theory taking into account not only the sizes of the lipid regions in which the spin label molecule distributes itself, but also the different affinities of the label for the two domains, has been developed. Taking advantage of the variation in spectra obtained with increasing amounts of spin label, computer calculations have been performed to estimate the distribution of lipid in the different regions of the cytochrome oxidase-lipid complex. An extrapolation of the amount of immobilized spin-labeled phospholipid to zero concentration of label allows a calculation of the number of fatty acid residues interacting with the protein to be made. It has been found that the number of aliphatic chains influenced by the protein is higher than that calculated for a single boundary layer around the protein. The approach used in this paper can be useful for studies of protein-lipid interactions in other systems.     

Probing the effect of transport inhibitors on the conformation of the mitochondrial citrate transport protein via a site-directed spin labeling approach

The present investigation utilized the site-directed spin labeling method of electron paramagnetic resonance (EPR) spectroscopy to identify the effect of citrate, the natural ligand, and transport inhibitors on the conformation of the yeast mitochondrial citrate transport protein (CTP) reconstituted in liposomal vesicles. Spin label was placed at six different locations within the CTP in order to monitor conformational changes that occurred near each of the transporter’s two substrate binding sites, as well as at more distant domains within the CTP architecture. We observed that citrate caused little change in the EPR spectra. In contrast the transport inhibitors 1,2,3-benzenetricarboxylate (BTC), pyridoxal 5′-phosphate (PLP), and compound 792949 resulted in spectral changes that indicated a decrease in the flexibility of the attached spin label at each of the six locations tested. The rank order of the immobilizing effect was compound 792949 > PLP > BTC. The four spin-label locations that report on the CTP substrate binding sites displayed the greatest changes in the EPR spectra upon addition of inhibitor. Furthermore, we found that when compound 792949 was added vectorially (i.e., extra- and/or intra-liposomally), the immobilizing effect was mediated nearly exclusively by external reagent. In contrast, upon addition of PLP vectorially, the effect was mediated to a similar extent from both the external and the internal compartments. In combination our data indicate that: i) citrate binding to the CTP substrate binding sites does not alter side-chain and/or backbone mobility in a global manner and is consistent with our expectation that both in the absence and presence of substrate the CTP displays the flexibility required of a membrane transporter; and ii) binding of each of the transport inhibitors tested locked multiple CTP domains into more rigid conformations, thereby exhibiting long-range inter-domain conformational communication. The differential vectorial effects of compound 792949 and PLP are discussed in the context of the CTP homology-modeled structure and potential mechanistic molecular explanations are given.     

Muscular fatigue: effects of hydrogen ions and inorganic phosphate

During muscular fatigue two metabolites, hydrogen ions (H+) and inorganic phosphate (Pi), increase in concentration. The effect of increase in [H+] has been modeled mathematically for a system containing creatine kinase (EC 2.7.3.2), adenylate kinase (EC 2.7.4.3), and the appropriate concentrations of their substrates. Assuming that no other equilibrium reactions are involved, the result of acidification should be a useful increase in the ratio [ATP]/[ADP]. It is also shown by a reanalysis of earlier 31P NMR studies that the observed combination of increased [H+] and increased [Pi] leads to an increase in the monobasic phosphate concentration [Pi-] that is inversely proportional to the force of contraction. This suggests that Pi- may be a direct inhibitor of the actomyosin ATPase system.     

Effect of low pH on the conformation of Pseudomonas exotoxin A

Previously we examined factors involved in the entry mechanism of Pseudomonas exotoxin A (PTx) at the level of lipid-protein interactions (Farahbakhsh, Z. T., Baldwin, R. L., and Wisnieski, B. J. (1986) J. Biol. Chem. 261, 11404-11408). Exposure to a low pH environment appears to be an obligatory trigger of the entry pathway. In this report we describe the effect of pH upon the conformation of PTx. We have found that the intrinsic fluorescence of PTx is strongly dependent on pH, decreasing between pH 7.4 and 4.0 with a red shift in the emission lambda max. The changes are reversible and associated with the acquisition of a binding site for the fluorescent dye 1-anilino-8-naphthalenesulfonic acid (ANS). The fluorescence intensity of ANS in the presence of PTx increases with decreasing pH and is accompanied by a blue shift in emission spectra, indicative of exposure of hydrophobic surfaces. These changes are also reversible. Both the intrinsic fluorescence and ANS binding profiles show a dramatic dependence on pH, with the transitions centered on pH 5.0 and 4.5, respectively. Circular dichroism studies reveal a 9% decrease in alpha-helicity between pH 7.7 and 4. The susceptibility of toxin to trypsin cleavage is also a function of pH, increasing with decreasing pH. The pH 7.4 cleavage profile is regained when the acid-treated samples are brought back to pH 7.4. The conformational changes observed in these pH shift experiments are likely to be physiologically significant because the conditions closely resemble those that the toxin would encounter if entry into the cytoplasm of a cell involves escape from an endosomal compartment.     

Temperature and pH dependence of the self-association of human spectrin

The self-association of human spectrin between 21 and 35 degrees C and between pH 6.5 and 9.5 has been studied at sedimentation equilibrium. For a given set of solution conditions between pH 6.5 and 8.5, coincidence of omega function plots as a function of total spectrin concentration (0-2 g/L) indicated that equilibrium was attained and that no significant concentration of solute was incapable of participating in the self-association reaction. Above pH 8.5, however, irreversible aggregation occurred, inferred from a failure of overlap in the omega function and molecular weight distributions. The behavior of spectrin can best be described by a cooperative isodesmic model, in which the promoter for association is the heterodimer and for which K12 is between 10(6) and 10(7) M-1 (depending on pH and temperature) and all other K are approximately 10(6) M-1. The returned values of the second viral coefficient for this model fall within the range calculated from the charge and Stokes radius of spectrin. Association appears to be favored slightly by decreased temperature and by decreased pH. The pH dependence resides only in K12 and is consistent with the presence of a single group, possibly histidine, displaying a slightly higher pKa value in the tetramer than in the dimer. The association reaction appears to be driven by the loss of enthalpy associated with release of strain in the heterodimer. The association sites appear to be conserved in the association reactions, consistent with the images from electron microscopy.(ABSTRACT TRUNCATED AT 250 WORDS)     

Experimental study of the combined effects of pH and salinity on the bioaccumulation of inorganic mercury in the crayfish Astacus leptodactylus

ABSTRACT

The combined effects of pH and salinity were investigated on the bioaccumulation of inorganic mercury in the Turkish crayfish Astacus leptodactylus, at the whole organism and organ levels. Effects on the ionic balance were also analysed during the acclimatization phase and after 3 and 15 days of exposure, via the direct route. The experimental protocol, based on a complete factorial design, took into account nine experimental conditions, resulting from the combination of three levels for pH (6, 7.5 and 9) and for salinity (1, 10 and 100 mM Cl-). The results showed an important Hg accumulation in the organs or tissues in direct contact with the surrounding medium, e.g. gills and carapace. The effects of the nine pH and salinity conditions were complex and variable from one organ to another. Correlations were studied between chemical species concentrations in the water (HgCl₂, HgOHCl, HgCl₃-,HgCl₄², Hg(OH)₂) and amounts of metal accumulated in the different organs. A positive correlation was found between the neutral species HgCl₂ and metal accumulated in the gills and in the carapace. Perturbations of the haemolymph ionic concentrations were no significant, except for Na⁺ after 3 days of exposure.     

An electro-optic study of human erythrocyte spectrin dimers. The presence of calcium ions does not alter spectrin flexibility

In order to determine whether the presence of Ca2+ increases the stiffness of the highly elongated and flexible spectrin molecules, we have carried out a birefringence relaxation study of isolated human erythrocyte spectrin dimers. Our measurements indicate no significant change in the flexibility of spectrin in solutions containing 0-10(-3) M Ca2+. This finding indicates that decreased spectrin flexibility is not the major functional mechanism underlying the decreased erythrocyte deformability reported as result of elevated intracellular levels of Ca2+. We find that the persistence length of spectrin dimers is less than 20 nm and is not dependent on the Ca2+ concentration.     

In vivo effects of metal ions on conformation and mechanical performance of silkworm silks

BackgroundThe mechanism of silk fiber formation is of particular interest. Although in vitro evidence has shown that metal ions affect conformational transitions of silks, the in vivo effects of metal ions on silk conformations and mechanical performance are still unclear.MethodsThis study explored the effects of metal ions on silk conformations and mechanical properties of silk fibers by adding K⁺ and Cu^2 + into the silk fibroin solutions or injecting them into the silkworms. Aimed by CD analysis, FTIR analysis, and mechanical testing, the conformational and mechanical changes of the silks were estimated. By using BION Web Server, the interactions of K⁺ and N-terminal of silk fibroin were also simulated.ResultsWe presented that K⁺ and Cu^2 + induced the conformational transitions of silk fibroin by forming β-sheet structures. Moreover, the mechanical parameters of silk fibers, such as strength, toughness and Young's modulus, were also improved after K⁺ or Cu^2 + injection. Using BION Web Server, we found that potassium ions may have strong electrostatic interactions with the negatively charged residues.ConclusionWe suggest that K⁺ and Cu^2 + play crucial roles in the conformation and mechanical performances of silks and they are involved in the silk fiber formation in vivo.General significanceOur results are helpful for clarifying the mechanism of silk fiber formation, and provide insights for modifying the mechanical properties of silk fibers.