[19] Extraction of water-soluble enzymes and proteins from membranes

Proteolytic cleavage by the inner membrane peptidase (IMP) complex or Oct1 peptidase controls the localization of the yeast peroxiredoxin Prx1 to distinct mitochondrial compartments

Yeast Prx1 is a mitochondrial 1-Cys peroxiredoxin that catalyzes the reduction of endogenously generated H₂O₂ Prx1 is synthesized on cytosolic ribosomes as a preprotein with a cleavable N-terminal presequence that is the mitochondrial targeting signal, but the mechanisms underlying Prx1 distribution to distinct mitochondrial subcompartments are unknown. Here, we provide direct evidence of the following dual mitochondrial localization of Prx1: a soluble form in the intermembrane space and a form in the matrix weakly associated with the inner mitochondrial membrane. We show that Prx1 sorting into the intermembrane space likely involves the release of the protein precursor within the lipid bilayer of the inner membrane, followed by cleavage by the inner membrane peptidase. We also found that during its import into the matrix compartment, Prx1 is sequentially cleaved by mitochondrial processing peptidase and then by octapeptidyl aminopeptidase 1 (Oct1). Oct1 cleaved eight amino acid residues from the N-terminal region of Prx1 inside the matrix, without interfering with its peroxidase activity in vitro Remarkably, the processing of peroxiredoxin (Prx) proteins by Oct1 appears to be an evolutionarily conserved process because yeast Oct1 could cleave the human mitochondrial peroxiredoxin Prx3 when expressed in Saccharomyces cerevisiae Altogether, the processing of peroxiredoxins by Imp2 or Oct1 likely represents systems that control the localization of Prxs into distinct compartments and thereby contribute to various mitochondrial redox processes.

Characterization of the interactions between β-amyloid peptide and the membranes of human SK-N-SH cells

Interaction of β-amyloid peptide (Aβ) with cell membranes is thought to be an initial step in Alzheimer's disease (AD). However, some data are controversial and the underlying mechanisms remain unclear. In this report, two populations of Aβ were found in human SK-N-SH neuroblastoma cells. Notably, one of the Aβ populations was tightly inserted into the plasma membrane whilst the other was only peripherally associated with it. Here we show that reducing membrane cholesterol decreased the number of membrane-embedded Aβs and increased the number of membrane-attached Aβs. We also found that cholesterol depletion inhibited Aβ degradation and exacerbated Aβ-mediated cytotoxicity. Our detailed and direct observations provide specific insights into the mechanism of Aβ membrane-associated toxicity.

Importance of membrane structural integrity for RPE65 retinoid isomerization activity

Regeneration of visual chromophore in the vertebrate visual cycle involves the retinal pigment epithelium-specific protein RPE65, the key enzyme catalyzing the cleavage and isomerization of all-trans-retinyl fatty acid esters to 11-cis-retinol. Although RPE65 has no predicted membrane spanning domains, this protein predominantly associates with microsomal fractions isolated from bovine retinal pigment epithelium (RPE). We have re-examined the nature of RPE65 interactions with native microsomal membranes by using extraction and phase separation experiments. We observe that hydrophobic interactions are the dominant forces that promote RPE65 association with these membranes. These results are consistent with the crystallographic model of RPE65, which features a large lipophilic surface that surrounds the entrance to the catalytic site of this enzyme and likely interacts with the hydrophobic core of the endoplasmic reticulum membrane. Moreover, we report a critical role for phospholipid membranes in preserving the retinoid isomerization activity and physical properties of RPE65. Isomerase activity measured in bovine RPE was highly sensitive to phospholipase A(2) treatment, but the observed decline in 11-cis-retinol production did not directly reflect inhibition by products of lipid hydrolysis. Instead, a direct correlation between the kinetics of phospholipid hydrolysis and retinoid isomerization suggests that the lipid membrane structure is critical for RPE65 enzymatic activity. We also provide evidence that RPE65 operates in a multiprotein complex with retinol dehydrogenase 5 and retinal G protein-coupled receptor in RPE microsomes. Modifications in the phospholipid environment affecting interactions with these protein components may be responsible for the alterations in retinoid metabolism observed in phospholipid-depleted RPE microsomes. Thus, our results indicate that the enzymatic activity of native RPE65 strongly depends on its membrane binding and phospholipid environment.

Membrane-binding and enzymatic properties of RPE65

Regeneration of visual pigments is essential for sustained visual function. Although the requirement for non-photochemical regeneration of the visual chromophore, 11-cis-retinal, was recognized early on, it was only recently that the trans to cis retinoid isomerase activity required for this process was assigned to a specific protein, a microsomal membrane enzyme called RPE65. In this review, we outline progress that has been made in the functional characterization of RPE65. We then discuss general concepts related to protein-membrane interactions and the mechanism of the retinoid isomerization reaction and describe some of the important biochemical and structural features of RPE65 with respect to its membrane-binding and enzymatic properties.

Proteomic analysis of thioredoxin-targeted proteins in Escherichia coli

Thioredoxin, a ubiquitous and evolutionarily conserved protein, modulates the structure and activity of proteins involved in a spectrum of processes, such as gene expression, apoptosis, and the oxidative stress response. Here, we present a comprehensive analysis of the thioredoxin-linked Escherichia coli proteome by using tandem affinity purification and nanospray microcapillary tandem mass spectrometry. We have identified a total of 80 proteins associated with thioredoxin, implicating the involvement of thioredoxin in at least 26 distinct cellular processes that include transcription regulation, cell division, energy transduction, and several biosynthetic pathways. We also found a number of proteins associated with thioredoxin that either participate directly (SodA, HPI, and AhpC) or have key regulatory functions (Fur and AcnB) in the detoxification of the cell. Transcription factors NusG, OmpR, and RcsB, not considered to be under redox control, are also associated with thioredoxin.

Three phase partitioning: concentration and purification of proteins

Three phase partitioning (TPP) uses t-butanol and ammonium sulfate to precipitate enzymes and proteins from aqueous solutions. The method is useful both upstream with crude samples and downstream where a scaleable simple step is needed. About 25 enzymes and proteins have been isolated by various laboratories using TPP-t-butanol. The relation of t-butanol used in TPP, with n-butanol used as an extraction agent from Morton's work, is reviewed. Some t-butanol appears bound to TPP-precipitated proteins which are actually protein-t-butanol coprecipitates. They float above denser aqueous salts because bound t-butanol increases their buoyancy, similar to the behavior of many lipoproteins. On redissolving TPP-precipitated enzymes, total and specific activities usually are regained and sometimes increased. Sulfate ion-in large concentrations-likely exerts itself through its kosmotropic action as in conventional salting out. t-Butanol likewise appears to be a kosmotrope and crowding agent at room temperature or above, whereas C1 and C2 cosolvents (e.g., ethanol) do not so behave except at near or below zero temperatures. However, kosmotropy is not the entire origin of TPP, nor probably of conventional salting out. Electrostatic forces, capacity to force protein conformation tightening and protein hydration shifts, also contribute. Electrostatic forces, and the tendency for salt ions to bind and tighten protein molecule conformation, are indicated by the sharp pH dependency of both conventional salting out and TPP, around pH regions where proteins undergo conformation changes. Sulfate anion is densely-perhaps extraordinarily-hydrated, adding much to its effective size, and therefore it has a tendency to crowd or exclude proteins, when sulfate concentrations are in the 0.5 to 3 M range.

The yeast Rab escort protein binds intracellular membranes in vivo and in vitro

In both mammals and yeast, intracellular vesicular transport depends on the correct shuttling between membrane and cytosol of the Rab/Ypt small G proteins. Membrane association of these proteins requires prenylation by the Rab geranylgeranyl transferase that recognizes a complex formed by the Rab/Ypt protein and the Rab escort protein (REP). After prenylation the Rab/Ypt protein is delivered to the target membranes by REP. Little is known about the early steps of the Rab-REP complex formation and where this association occurs in the cell. Although prenylation is believed to take place in the cytosol, we show that the yeast Rab escort protein Mrs6 is present in both soluble and particulate fractions of cell extracts. Mrs6p is associated with the heavy microsomal fraction that contains endoplasmic reticulum-Golgi membranes but is absent in the plasma membrane, vacuoles, mitochondria, and microsomal subfraction associated with mitochondria. The solubilization pattern of the particulate pool of Mrs6p implies that this protein is peripherally but tightly associated with membranes via hydrophobic interactions and metal ions. We also report that the C terminus of Mrs6p is important for maintaining the solubility of the protein because its deletion or replacement with the C terminus of RabGDI results in a protein that localizes only to membranes.

hrpf of Xanthomonas campestris pv. vesicatoria encodes an 87-kDa protein with homology to NoIX of Rhizobium fredii

The gram-negative bacterium Xanthomonas campestris pv. vesicatoria is the causal agent of bacterial spot disease on pepper and tomato plants. The main hrp (hypersensitive reaction and pathogenicity) gene cluster in X. campestris pv. vesicatoria spans a 23-kb chromosomal region, comprising six complementation groups designated hrpA to hrpF. Analysis of the hrpF locus revealed a single open reading frame encoding HrpF (86.4 kDa). HrpF is predominantly hydrophilic, and contains two hydrophobic domains in the C terminus. An interesting feature is the presence of two imperfect direct repeats in the N-terminal region. Deletion studies showed that one repeat is sufficient for function. Epitope tagging of HrpF allowed detection of the protein in X. campestris pv. vesicatoria. Subcellular localization studies suggest that HrpF is both in the soluble fraction and in the inner membrane. Interestingly, HrpF is 48% identical (67% similar) to the Rhizobium fredii NoIX protein that is part of the host specificity locus. Since several Hrp proteins are believed to be components of the types of III hrp protein secretion apparatus, allowing export of proteins essential for the interaction with the plant, the possible role of hrpF and NoIX in secretion is discussed.

2,3-Oxidosqualene cyclase: from azasqualenes to new site-directed inhibitors

2,3-Oxidosqualene cyclases (OSC) are enzymes which convert 2,3-oxidosqualene (OS) into polycyclic triterpenoids such as lanosterol, cycloartenol, and alpha- and beta-amyrin. Our interest in the study of OSC is the development of new OSC inhibitors for potential use as hypocholesterolemic, antifungal, or phytotoxic drugs. In particular, we describe the biological activity and the mechanism of a series of acyclic azasqualene derivatives mimicking the C-2, C-8, and C-20 carbonium ions formed during OS cyclization. Some of these carbonium ion analogues are very promising as specific hypocholesterolemic agents. The toxicity, the biodistribution, and the pharmacokinetics of different azasqualene derivatives in mice are also presented. In order to obtain new, site-directed irreversible inhibitors of OSC, a series of squalene derivatives containing functional groups that can link covalently to an active-site thiol group was designed. Among these compounds, squalene maleimide was the most active toward mammalian OSC, whereas squalene Ellman behaved as an irreversible inhibitor of OSC from yeast.

Association of cytochrome b translational activator proteins with the mitochondrial membrane: implications for cytochrome b expression in yeast

The products of the nuclear genes CBS1 and CBS2 are both required for translational activation of mitochondrial apocytochrome b in yeast. We report the intramitochondrial localization of both proteins by use of specific antisera. Based on its solubilization properties the CBS1 protein is presumed to be a component of the mitochondrial membrane; the detergent concentrations needed to release CBS1 from mitochondria are almost the same as for cytochrome c1. In contrast, CBS2 behaves like a soluble protein, with some characteristics of a membrane-associated protein. A model is presented for translational activation of cytochrome b, which might also be applicable to translational regulation of other mitochondrial genes.

Purification and some properties of the squalene-tetrahymanol cyclase from Tetrahymena thermophila

The membrane-bound enzyme from Tetrahymena thermophila responsible for the conversion of squalene into the quasi-hopanoid tetrahymanol was purified 297-fold to near homogeneity. Purification involved solubilization by octylthioglucoside, chromatography on DEAE-trisacryl, hydroxyapatite and FPLC ion-exchange on Mono Q. The apparent KM was found to be 18 microM. 2,3-Iminosqualene and N,N-dimethyldodecylamine-N-oxide are effective inhibitors of the cyclase with I50 values of 50 and 30 nM, respectively. The cyclase has a molecular mass of 72 kDa as judged by electrophoresis in polyacrylamide gels under denaturating conditions. The optimal enzymatic activity was obtained at pH 7.0 and 30 degrees C. The solubilized enzyme needs the presence of detergent for maintaining activity. The influence of different detergents on cyclase activity was studied. Triton X-100 proved to be a strong inactivator of the enzyme. Solubilization of the cyclase in Tween 80 and digitonin inactivates the enzyme. However, its activity can be recovered by complementation of the assay buffer with octylthioglucoside above its critical micellar concentration. We suggest that this approach might be applicable to other membrane-bound proteins.

Extraction of type-IV collagenase/gelatinase from plasma membranes of human cancer cells

Tumor proteinases are considered to be important in the process of cancer invasion and metastasis. We have proposed that the surface membrane localization of these proteinases places them in an optimal site to facilitate the invasion of surrounding extracellular matrix. In this study, we have used the organic solvent, n-butanol, and the detergent, n-octyl-glucoside, to sequentially extract metalloproteinases from crude plasma membranes of human RWP-I pancreatic cancer cells. Anion exchange chromatography and gel permeation chromatography were employed to further purify enzymes with the capacity to degrade gelatin, type-IV collagen, and carboxymethylated transferrin. Gelatin zymography was used to demonstrate proteinase bands of 92, 70 and 62-kDa. Immunoblotting of solubilized, partially purified pancreatic cancer plasma membrane proteins using polyclonal rabbit antibodies, which have specificity for type-IV collagenase/gelatinase, resulted in the recognition of a 70-kDa protein, but not the 92-kDa gelatinase. A type-IV collagenase/gelatinase of 68-kDa was similarly identified in A2058 human melanoma cancer cell plasma membranes.

Innate and acquired immune responses against Candida albicans in congenic B10.D2 mice with deficiency of the C5 complement component

Congenic mice, sufficient or deficient with respect to the C5 component of complement, were evaluated for their innate and acquired immune responses to Candida albicans. When unimmunized mice were challenged intravenously and sacrificed at intervals for cultural analyses of kidneys, it was clear that C5-sufficient mice were able to deal more effectively with C. albicans during the first week after challenge than C5-deficient mice. When immunized mice were challenged intravenously to assess the development of protective responses, an intact complement cascade appeared to contribute to the more rapid clearance of fungi during the first few weeks following challenge, but by the fourth week after challenge, the numbers of fungi had decreased significantly in both types of mice and were at levels which were not significantly different. No significant differences were detected in the development of delayed hypersensitivity or Candida-specific antibody between C5-sufficient and C5-deficient mice either. C5-deficient mice did have slightly elevated levels over the C5+ mice, but this may simply reflect the prolonged antigenic load during the first 3 weeks following intravenous challenge in both immune and nonimmune animals. The later-acting complement components, while appearing to contribute to the early inhibition of the growth of C. albicans in the nonimmune animal, had no adverse effect on the development of specific immune responses, in that delayed hypersensitive responses were equivalent between the two groups, antibody response was not significantly altered and the ultimate outcome of challenge in immunized animals was not affected.

Mechanism of release of integral proteins from rat liver microsomal membranes

The release of three integral enzymatic activities (NADH- and NADPH-cytochrome c reductase and 5'-nucleotidase) and total protein from washed rat liver microsomal membranes, upon simple incubation at 37 degrees C in aqueous media, was investigated. Release does not depend on contaminating proteases and is enhanced by alkaline pH. Total protein and enzyme release is consistent with a loss of phospholipids which are not recovered in the soluble phase. Following incubation at pH 9.0 large amounts of free fatty acids were recovered in the soluble phase, accounting for a ratio of 1/1 (w/w) with released protein. This evidence, together with the data available about densities (1.07-1.08 g/ml) and molecular weights (1 700 000-700 000) of the released enzymes, suggests that they are solubilized from microsomal membranes in the form of mixed micelles mostly formed by free fatty acids and integral proteins, probably owing to the activity of endogenous phospholipases on membrane lipids. Release of total protein and enzymatic activities is decreased by Ca2+, whose possible role in the phenomenon is discussed.

Two major non-collagenous glycoproteins in embryonic chick arteries

Glycoprotein-containing extracts were obtained from thoracic arteries of embryonic chicks by sequential treatment involving 6 M guanidinium chloride, purified bacterial collagenase, and 6 M guanidinium chloride plus 50 mM dithiothreitol. Two major glycopolypeptides, designated G1 and G2, having apparent mol. wts. of 140,000 and 130,000 respectively were detected by SDS/polyacrylamide gel electrophoresis. Equilibrium density gradient ultracentrifugation demonstrated G1 and G2 to be glycoproteins and not proteoglycans or glycosaminoglycans. Amino acid analysis of a glycoprotein-enriched fraction confirmed the non-collagenous nature of G1 and G2. The highly insoluble nature of these glycoproteins suggests that these species are intimately associated with the extracellular matrix. Glycoproteins of similar size were also extracted from wing tendons indicating that G1 and G2 may be common to the elastic tissues of the chick.

Water soluble receptors for human growth hormone from rabbit liver

Soluble receptors that bind human growth hormone have been prepared by incubation of liver membranes form pregnant female rabbits in 1 mM Tris buffer (ph 7.5 or 9.0) at 4 degrees C. Up to 29% of the growth hormone binding sites could be solubilized within 48 hours. The kinetics of binding of human growth hormone to the soluble receptor, the hormonal specificity and the binding parameters calculated by Scatchard analysis (Ka 2.2 x 10(9) M-1, capacity 409 fmole/mg) were essentially unchanged compared with those for the parent membrane-associated (particulate) receptor. Gel filtration on Ultrogel AcA22 indicated that the major binding peak eluted at a molecular weight of 300,000 daltons. Specificity studies showed that the soluble binding sites had a moderately high affinity for ovine prolactin (Ka integral of 1 x 10(8) M-1), but negligible affinity for insulin. Although aqueous extraction gives a lower yield of binding sites for human growth hormone than detergent extraction, it nevertheless avoids some of the problems associated with use of detergents and should facilitate the subsequent purification of the receptor in a relatively unaltered state. It may also have applicability for solubilization of other hormone receptor systems.

Isolation and partial characterization of proteoglycans from sheep lung parenchyma

Greater than 90% of the proteoglycans of sheep lung parenchyma, as measured by uronic acid, were solubilized employing a sequential procedure with guanidine hydrochloride, dithiothreitol and Triton X-100. The amounts solubilized were 68.7%, 16.2% and 5.9%, respectively. The guanidine hydrochloride extract was chromatographed using DEAE-cellulose in urea and eluted with increasing concentrations of NaCl. A major fraction (containing a 6.5-fold enrichment of uronic acid) was obtained with 0.5 M NaCl and further purified by Sepharose Cl-6B chromatography in guanidine hydrochloride. To demonstrate the presence of protein-linked glycosaminoglycans, the void volume peak containing protein and uronic acid was digested with papain and rechromatographed. Evidence for the presence of proteoglycans was obtained by observing an almost complete loss of uronic acid in the void volume and the appearance of a uronic acid peak in the included volume, migrating in the same area as single-chain glycosaminoglycans. Electrophoretic migration and disappearance of bands in electrophoresis after digestion with specific mucopolysaccharide lyases indicated that the small amount of uronic acid remaining in the void volume was hyaluronic acid whereas the included volume contained hyaluronic acid, heparan sulfate, chondroitin sulfates and/or dermatan sulfate.

The solubilisation of the membrane-bound D-alanyl-D-alanine carboxypeptidase of Bacillus coagulans NCIB 9365

Protoplast membranes and the particulate D,D-carboxypeptidase of Bacillus coagulans NCIB 9365 were extremely resistant to disruption by either detergents or urea. A combination of urea and the non-ionic detergent Genapol X-100 was required to achieve a significant solubilisation of membrane protein and D,D-carboxypeptidase in an active form; the pH optimum for this treatment was pH 7.5. Solubilisation of the enzyme was accompanied by a two-fold enhancement of activity. Kinetic results indicated that the enhancement may be due to an alteration in the conformation of the enzyme following disruption of membrane structure.

Calf-spleen nicotinamide--adenine dinucleotide glycohydrolase. Solubilization purification and properties of the enzyme

NAD glycohydrolase of calf spleen was solubilized with pancreatic lipase and purified approximatively 800-fold to a specific activity of 7 units/mg of protein by successive DEAE-cellulose and carboxymethyl-cellulose chromatography. The purified enzyme has a molecular weight of 24,000 and is characterized by a double band on disc gel electrophoresis. Some kinetic properties of the NAD-glycohydrolase-catalyzed hydrolsis of NAD have been examined using a titrimetric assay for enzyme activity. The reaction is subject to inhibition be excess of substrate, which disappears at high ionic strength and low pH. At a pH below 5 the kinetic displays an apparent activation by substrate. The effects of pH (4.5-9.0) on the kinetic parameters do not reveal an essential ionizable group in the catalytic process.