Protein organization in mouse liver peroxisomes.

Peroxisomes from mouse liver were fractionated with Triton X-114, a procedure which yields a detergent phase consisting of proteins containing hydrophobic binding sites, and a nondetergent, or aqueous, phase containing hydrophilic proteins. When this method was applied to peroxisomes from control mice, catalase and fatty acyl-CoA oxidase distributed to the aqueous phase, whereas the integral membrane protein, PMP68, and the bifunctional protein were recovered exclusively in the detergent phase. Urate oxidase distributed intermediate between these two phases. With peroxisomes from mice treated with the peroxisome proliferator clofibrate, the bifunctional protein was recovered in both the detergent and the aqueous phases, and urate oxidase was shifted toward the aqueous phase. Other analyses of the subperoxisomal distribution of the bifunctional protein were consistent with a proportion of this protein being tightly associated with the peroxisomal membrane, or with some other uncharacterized, poorly soluble, component. Sucrose gradient centrifugation of the aqueous phase resulting from Triton X-114 fractionation of peroxisomes revealed that a major proportion of catalase, fatty acyl-CoA oxidase, the bifunctional protein, and other unidentified proteins behaved as if associated under these conditions. In this respect, use of a higher concentration of Triton X-114 for peroxisome fractionation led to the partitioning of some catalase and fatty acyl-CoA oxidase to the detergent phase, indicating the presence of some detergent-accessible hydrophobic binding sites even on these proteins. These data have been interpreted as indicating matrix protein associations in vivo, associations which may be responsive to proliferator treatment.     

Method of purification of glucose oxidase by means of affinity chromatography on immunoabsorbent]

The possibility to purify glucose oxidase from Penicillium vitale on immunosorbent containing specific antibodies to the enzyme covalently bound with Sepharose 4B is studied. The method of affinity chromatography was applied, beside routine methods of fractionating blood serum proteins, to isolate specific antibodies from antiserum of rabbits immunized with glucose oxidase. Immobilized on Sepharose glucose oxidase was used as biospecific sorbent. Specific antibodies to the enzyme were isolated using chromatograpy of gamma-globulins mixture followed by protein desorption from the column with 1 M NaC1 and 3% glucose. Antibodies were immobilized by their covalent binding to activated Sepharose. The immunosorbent obtained was used to purify low active preparation of glucose oxidase by means of affinity chromatography under conditions worked out for the antibodies isolation. The enzyme was eluted from the column with 1 M NaC1 (pH 3.0) containing 3% glucose. 5-Fold purified enzyme preparation was isolated.     

Surfactant effects on protein structure examined by electrospray ionization mass spectrometry.

Electrospray ionization mass spectrometry (ESI-MS) has proven to be a useful tool for examining noncovalent complexes between proteins and a variety of ligands. It has also been used to distinguish between denatured and refolded forms of proteins. Surfactants are frequently employed to enhance solubilization or to modify the tertiary or quaternary structure of proteins, but are usually considered incompatible with mass spectrometry. A broad range of ionic, nonionic, and zwitterionic surfactants was examined to characterize their effects on ESI-MS and on protein structure under ESI-MS conditions. Solution conditions studied include 4% acetic acid/50% acetonitrile/46% H2O and 100% aqueous. Of the surfactants examined, the nonionic saccharides, such as n-dodecyl-beta-D-glucopyranoside, at 0.1% to 0.01% (w/v) concentrations, performed best, with limited interference from chemical background and adduct formation. Under the experimental conditions used, ESI-MS performance in the presence of surfactants was found to be unrelated to critical micelle concentration. It is demonstrated that surfactants can affect both the tertiary and quaternary structures of proteins under conditions used for ESI-MS. However, several of the surfactants caused significant shifts in the charge-state distributions, which appeared to be independent of conformational effects. These observations suggest that surfactants, used in conjunction with ESI-MS, can be useful for protein structure studies, if care is used in the interpretation of the results.     

Laser Raman spectroscopy of lipid-protein systems. Differences in the effect of intrinsic and extrinsic proteins on the phosphatidylcholine Raman spectrum.

Laser Raman spectroscopy is used to examine the interactions of intrinsic and extrinsic proteins with the lipid layer structure. The interactions of cytochrome c and cytochrome c oxidase with lipids have been well established by others using a variety of techniques. Cytochrome c is thought to act as an extrinsic membrane protein while cytochrome c oxidase is thought to act as an intrinsic membrane protein. The lipid-cytochrome c and lipid cytochrome c oxidase systems are used to assist in interpreting the spectral changes due to extrinsic and intrinsic protein interactions. The two types of proteins examined produced differential changes in the lipid hydrocarbon C-H stretch Raman modes for both dimyristoyl and dipalmitoyl phosphatidylcholine. The plasma proteins albumin and fibrinogen were also found to differentially affect the lipid hydrocarbon C-H stretch Raman nodes. These proteins appear to interact with lipids in an extrinsic manner different from that of cytochrome c.     

The O2.- generating oxidase activation of bovine neutrophils. Evidence for synergism of multiple cytosolic factors in a cell-free system

Activation of the O2.- generating oxidase in neutrophils can be achieved with a cell-free oxidase-activating system, which consists of a high speed supernatant (cytosol), a particulate fraction enriched in plasma membrane, GTP-gamma-S, arachidonic acid and Mg ions. Cytosolic proteins from bovine neutrophils were fractionated by chromatography on Mono Q and Mono S columns into two fractions, neither of which was able to activate efficiently the membrane-bound oxidase. However, when combined and added to the cell-free system under optimized conditions, they acted synergistically, activating the oxidase to virtually the same extent as crude cytosol. This synergism demonstrates that more than one cytosolic factor is required for oxidase activation, and can be used to trace the cytosolic factors during the course of their purification.     

The fluorescent monomeric protein Kusabira Orange. Pressure effect on its structure and stability

The structure and stability of the fluorescent protein monomeric Kusabira Orange (mKO), a GFP-like protein, was studied under different pressure levels and in different chemical environments. At different pH values (between pH 7.4 and pH 4.0) and under a pressure up to 600 MPa (at 25 °C), mKO did not show significant fluorescence spectral changes, indicating a structural stability of the protein. In more extreme chemical conditions (at pH 4.0 in the presence of 0.8 M guanidine hydrochloride), a marked reduction of mKO fluorescence intensity emission was observed at pressures above 300 MPa. This fluorescence emission quenching may be due to the loss of the intermolecular bonds and, consequently, to the destructuration of the mKO chromophore structure. Since the electrostatic and hydrophobic interactions as well as the salt bridges present in proteins are usually perturbed under high pressure, the reduction of mKO fluorescence intensity emission is associated to the perturbation of the protein salt bridges network.     

Construction of a novel system for cell surface display of heterologous proteins on <Emphasis Type="Italic">Pichia pastoris</Emphasis>

A versatile vector was developed for heterologous proteins display on the cell surface of Pichia pastoris using the C-terminal half of alpha-agglutinin from Saccharomyces cerevisiae as a membrane anchor under the control of the alcohol oxidase 1 promoter (pAOX1). Multiple cloning sites and the sequence encoding the Xpress epitope (-Asp-Leu-Tyr-Asp-Asp-Asp-Asp-Lys-) were introduced into the vector for insertion of heterologous genes and selective cleavage of target proteins. Enhanced green fluorescence protein (EGFP) was used as a model protein to check the function of this vector. The expression of EGFP on the P. pastoris surface was confirmed by confocal laser scanning microscopy. Fluorescence microscopy and western blot analysis confirmed that EGFP can be successfully cleaved from the cell surface by treating with enterokinase.     

A possible role for protein phosphorylation in the activation of the respiratory burst in human neutrophils. Evidence from studies with cells from patients with chronic granulomatous disease

Two-dimensional gel electrophoresis was used to study protein phosphorylation in granules, membranes, and soluble fractions from human neutrophils that had been loaded with 32Pi. In resting cells, label was incorporated primarily into proteins of the membranes and the soluble supernatant; little appeared in the granules. Activation of 32P-loaded neutrophils resulted in an increase in the 32P content of a small number of membrane and soluble proteins without a change in the labeling of the granule fraction. The identity of the proteins affected by activation depended on the activating agent used; all of the activating agents, however, caused an increase in the labeling of a group of approximately 48-kDa proteins that appeared to be distributed between the membranes and the soluble supernatant. To investigate the role of phosphorylation in the activation of the respiratory burst oxidase, the incorporation of 32P into phosphoproteins was studied in neutrophils from patients with chronic granulomatous disease. When these cells were exposed to phorbol myristate acetate, one of the agents used for the activation of normal neutrophils, the 48-kDa proteins in the membranes and supernatants failed to take up additional 32P. Phosphorylation patterns in normal neutrophils activated under nitrogen were similar to the patterns seen with cells activated in air, suggesting that the differences in phosphorylation between normal and chronic granulomatous disease neutrophils did not represent secondary effects of the oxidants produced by the normal cells, but reflected primary biochemical differences between the normal and the defective phagocytes. We postulate from these results that the uptake of phosphate by the 48-kDa protein group may be involved in the activation of the respiratory burst oxidase.     

Evidence for essential histidine residues in bovine-liver mitochondrial monoamine oxidase.

Ethoxyformic acid anhydride, amino-1H-tetrazole, and photooxidation in the presence of rose bengal, which are reagents known to react with histidine residues of proteins, were shown to inactivate monoamine oxidase. Ethoxyformic acid anhydride reacted with about 6 histidine residues per 100 000 g of protein under the experimental conditions adopted and completely inactivated the enzyme. However, NH2OH reactivated the ethaxyformic acid derivative t only. Since NH2OH specifically deacylates N-ethoxyformylimidazole, it was shown that at least some of the histidine residues are essential for activity. In addition, photooxidation experiments in the presence of 0.01% rose bengal confirmed that only histidine residues of bovine hepatic monoamine oxidase are destroyed under the designated experimental conditions. About 9 histidine residues per 100 000 g of protein were destroyed during the photooxidation experiments. In the presence of substrate, kynuramine or benzylamine, only 7 histidine residues were destroyed, which indicates that 2 histidine residues per 100 000 g of protein are essential for activity.     

Utility of mass spectrometry for proteome ana lysis: part I. Conceptual and experimental approaches

This article is the first in a series of reviews intended as a tutorial providing the inexperienced, as well as the experienced, reader with an overview of principles of peptide and protein fragmentation in mass spectrometers for protein identification, surveying of the different types of instrument configurations and their combinations for protein identification. The first mass spectrometer was developed in 1899, but it took almost a century for the instrument to become a routine analytical method in proteomic research when fast atom bombardment ionization was developed, followed shortly by soft desorption/ionization methods, such as MALDI and electrospray ionization, to volatize biomolecules with masses of tens of kiloDaltons into the gas phase under vacuum pressure without destroying them. Thereafter, other soft ionization techniques that offered ambient conditions were also introduced, such as atmospheric pressure MALDI, direct analysis in real time, atmospheric-pressure solid analysis probe and hybrid ionization, sources of MALDI and electrospray ionization (e.g., two-step fused droplet electrospray ionization, laser desorption atmospheric-pressure chemical ionization, electrosonic spray ionization, desorption electrospray ionization, and electrospray-assisted laser desorption/ionization). The five basic types of mass analyzers currently used in proteomic research are the quadrupole, ion trap, orbitrap, Fourier transform ion cyclotron resonance and TOF instruments, which differ in how they determine the mass-to-charge ratios of the peptides. They have very different design and performance characteristics. These analyzers can be stand alone or, in some cases, put together in tandem or in conjunction with ion mobility mass spectrometry to take advantage of the strengths of each. Several singly or multiply charged fragment ion types, such as b, y, a, c, z, v, y and immonium ions are produced in the gas phase of the spectrometer. In the bottom-up sequencing approach for protein identification in a shotgun proteomic experiment, proteolytic digestion of proteins is accomplished by cleavage of the different bonds along the peptide backbone and/or side chain through a charge-directed transfer to the vicinity of the cleavage side. These various mass spectrometers and the types of ions produced have become important analytical tools for studying and analyzing proteins, peptides and amino acids.     

4-Thioflavins as active site probes of flavoproteins. Reactions with sulfite

4-Thioflavins react with sulfite under aerobic conditions to yield highly fluorescent products with absorption maxima around 410 nm. These products have been identified as 4-hydroxy-4-sulfonylflavins, and have been shown to arise from a series of reactions following the O2-dependent reoxidation of an intermediate with absorption maxima at 363 and 465 nm. Under anaerobic conditions, the same intermediate is formed, but decays to a 350 nm absorbing species, which is probably the N(5)-sulfite adduct of 4-thioflavin. A plausible mechanism is described for the formation of the derivatives, and several of their chemical and physical properties are described. Distinctly different results between different proteins are obtained when sulfite reacts with enzyme-bound 4-thioflavins. 4-Thio-FAD-D-amino acid oxidase and 4-thio-FMN-lactate oxidase react rapidly to yield the N(5)-sulfite adducts, as occurs with the native enzymes. 4-Thio-FAD-p-hydroxybenzoate hydroxylase reacts slowly in a manner paralleling the reaction with the free 4-thioflavins.     

The protein-tethered lipid bilayer: a novel mimic of the biological membrane

A new concept of solid-supported tethered bilayer lipid membrane (tBLM) for the functional incorporation of membrane proteins is introduced. The incorporated protein itself acts as the tethering molecule resulting in a versatile system in which the protein determines the characteristics of the submembraneous space. This architecture is achieved through a metal chelating surface, to which histidine-tagged (His-tagged) membrane proteins are able to bind in a reversible manner. The tethered bilayer lipid membrane is generated by substitution of protein-bound detergent molecules with lipids using in-situ dialysis or adsorption. The system is characterized by surface plasmon resonance, quartz crystal microbalance, and electrochemical impedance spectroscopy. His-tagged cytochrome c oxidase (CcO) is used as a model protein in this study. However, the new system should be applicable to all recombinant membrane proteins bearing a terminal His-tag. In particular, combination of surface immobilization and membrane reconstitution opens new prospects for the investigation of functional membrane proteins by various surface-sensitive techniques under a defined electric field.     

Control of l-amino acid oxidase in Neurospora crassa by different regulatory circuits

l-Amino acid oxidase is synthesized in Neurospora crassa in response to three different physiological stimuli: (i) starvation in phosphate buffer, (ii) mating, and (iii) nitrogen derepression in the presence of amino acids. During starvation in phosphate buffer, or after mating, l-amino acid oxidase synthesis occurred in parallel with that of tyrosinase. Exogenous sulfate repressed the formation of the two enzymes in starved cultures, but not in mated cultures. Sulfate repression was relieved by protein synthesis inhibitors, suggesting that the effect of sulfate required the synthesis of a metabolically unstable protein repressor. With amino acids as the sole nitrogen source only l-amino acid oxidase was produced. Under these conditions enzyme synthesis was repressed by ammonium and was insensitive to sulfate. Biochemical evidence suggested that the l-amino acid oxidase formed under the three different conditions was the same protein. Therefore, the expression of l-amino acid oxidase appeared to be under the control of least two regulatory circuits. One, also controlling tyrosinase, seems to respond to developmental signals related to sexual morphogenesis. The other, controlling other enzymes of the nitrogen catabolic system, is used by the organism to obtain nitrogen from alternative sources such as proteins and amino acids.     

Pressure-dependent changes in the solution structure of hen egg-white lysozyme

The "rules" governing protein structure and stability are still poorly understood. Important clues have come from proteins that operate under extreme conditions, because these clarify the physical constraints on proteins. One obvious extreme is pressure, but so far little is known of the behavior of proteins under pressure, largely for technical reasons. We have therefore developed new methodology for calculating structure change in solution with pressure, using NMR chemical shift changes, and we report the change in structure of lysozyme on going from 30 bar to 2000 bar, this being the first solution structure of a globular protein under pressure. The alpha-helical domain is compressed by approximately 1%, due to tighter packing between helices. The interdomain region is also compressed. By contrast, the beta-sheet domain displays very little overall compression, but undergoes more structural distortion than the alpha-domain. The largest volume changes tend to occur close to hydrated cavities. Because isothermal compressibility is related to volume fluctuation, this suggests that buried water molecules play an important role in conformational fluctuation at normal pressures, and are implicated as the nucleation sites for structural changes leading to pressure denaturation or channel opening.     

The involvement of a multicopper oxidase in iron uptake by the green algae Chlamydomonas reinhardtii

In the unicellular green algae Chlamydomonas reinhardtii, high-affinity uptake of iron (Fe) requires an Fe(3+)-chelate reductase and an Fe transporter. Neither of these proteins nor their corresponding genes have been isolated. We previously identified, by analysis of differentially expressed plasma membrane proteins, an approximately 150-kD protein whose synthesis was induced under conditions of Fe-deficient growth. Based on homology of internal peptide sequences to the multicopper oxidase hephaestin, this protein was proposed to be a ferroxidase. A nucleotide sequence to the full-length cDNA clone for this ferroxidase-like protein has been obtained. Analysis of the primary amino acid sequence revealed a putative transmembrane domain near the amino terminus of the protein and signature sequences for two multicopper oxidase I motifs and one multicopper oxidase II motif. The ferroxidase-like gene was transcribed under conditions of Fe deficiency. Consistent with the role of a copper (Cu)-containing protein in Fe homeostasis, growth of cells in Cu-depleted media eliminated high-affinity Fe uptake, and Cu-deficient cells that were grown in optimal Fe showed greatly reduced Fe accumulation compared with control, Cu-sufficient cells. Reapplication of Cu resulted in the recovery of Fe transport activity. Together, these results were consistent with the participation of a ferroxidase in high-affinity Fe uptake in C. reinhardtii.     

External labeling of galactose in surface membrane glycoproteins of the intact myelin sheath.

The molecular organization of surface galactose residues in glycoproteins of the intact myelin sheath was investigated using the enzymatic membrane probe, galactose oxidase. Rat spinal cords treated under physiological conditions with this nonpermanent probe were labeled specifically in galactose residues by reduction with tritiated sodium borohydride. The enzymatically modified proteins from isolated myelin were analyzed electrophoretically and their specific radioactivities determined. Results indicated tritium label associated with a surprising variety of high molecular weight proteins. The most extensively labeled peak corresponded to the major myelin glycoprotein as indicated by the coincidence of tritium label with that of [14C]fucose used as an internal marker for the glycoproteins. The radioactivity associated with this protein was 1.1 to 2.7 times higher after treatment with galactose oxidase when compared to reduction in the absence of the enzyme and 1.4 to 4.8 times higher when oxidized and reduced after prior treatment with neuraminidase. The results suggest a complex heterogeneity of minor glycoproteins associated with isolated myelin. It is concluded that from this complexity of glycoproteins, a major glycoprotein is at least partially localized on the external surface of either the intact myelin sheath or the closely associated oligodendroglial plasma membrane. Such a localization of this glycoprotein and the probable localization of the other glycoproteins enhances their potential role in specific interactions in the process of mpyelination or myelin maintenance.     

Adaptation of the mitochondrial systems of Rhodotorula gracilis to low oxygen pressure.

The obligate aerobic yeast, Rhodotorula gracilis, was grown in a liquid minimal medium at 1 mm Hg partial pressure of oxygen, conditions under which growth (measured as the increase in total protein) is reduced to 30% of the maximum rate. A significant increase in the ratio between mitochondrial oxidative enzymes and total protein occurs rapidly under these conditions. A concurrent increase in the ratio area of mitochondria/area of cytoplasm was also observed. The relative increase in mitochondrial enzymes, oxidase activities and mitochondrial membranes is due to the inhibition affecting the increase in cytoplasmic structures more significantly than the increase in mitochondrial structures at low pO2. The difference between mitochondrial and cytoplasmic syntheses cannot be ascribed to changes in the availability of ATP but it might rest with some other oxygen-utilising process (pyrimidine redox coenzymes, synthesis of sterols). The experimental conditions studied appear to offer a valuable tool for the investigation of the relationships between mitochondrial and cytoplasmic structures.     

Monoamine oxidase, an intracellular probe of oxygen pressure in isolated cardiac myocytes

The activity of monamine oxidase, an enzyme located almost exclusively at the outer mitochondrial membrane, toward the substrate phenylethylamine is used to report the oxygen pressure at the outer mitochondrial membrane of intact cardiac myocytes isolated from hearts of adult rats. The rate of substrate oxidation, under the conditions used, follows the Michaelis-Menten relation, and accordingly can be used as a measure of the local chemical activity of dissolved oxygen. The oxygen pressure at the outer mitochondrial membrane of myocytes, at rest and after 2- to 3-fold stimulation of respiratory oxygen consumption, differs from the extracellular oxygen pressure by at most 2 torr. This implies that most of the large, about 20 torr, difference in oxygen pressure between capillary lumen and mitochondria of the working heart must be extracellular. At physiologically relevant concentrations of the substrates phenylethylamine and norepinephrine, monoamine oxidase activity is relatively insensitive to extracellular oxygen pressure in the range 155 to 8 torr, suggesting a limited role for regulation of biogenic amine oxidation by oxygen availability.     

A carboxy-terminal peptide from p47-phox is a substrate for phosphorylation by protein kinase C and by a neutrophil protein kinase.

Agonist-activated phosphorylation of neutrophil proteins including p47-phox, a cytosolic component of the respiratory burst oxidase, has been implicated in the signal transduction cascade which leads to activation of the superoxide generating respiratory burst. We have previously reported (J. Biol. Chem. 265, 17550-59) that in a cell-free activation system consisting of cytosol plus plasma membrane from human neutrophils, diacylglycerol acts synergistically with an anionic amphiphile such as sodium dodecyl sulfate (SDS) to augment superoxide generation and assembly of the oxidase, and that p47 phosphorylation can occur under these conditions. Herein, we show that a peptide corresponding to a carboxy terminal sequence of p47-phox is a substrate for phosphorylation both by purified protein kinase C (a mixture of alpha, beta, and gamma forms) and by a distinct kinase or kinases present in neutrophil cytosol. Based on its activator requirements, the neutrophil kinase differs from classical protein kinase C, but may be a protein kinase C variant, based on inhibition by a protein kinase C peptide. Although in the cell-free system phosphorylation occurs under conditions which are similar to those for activation of superoxide generation, phosphorylation is not required for activation (1). Rather, protein assembly or aggregation which occurs under activation conditions may also promote phosphorylation.     

Engineering of Aerococcus viridans L-lactate oxidase for site-specific PEGylation: characterization and selective bioorthogonal modification of a S218C mutant

A defined bioconjugate of Aerococcus viridans L-lactate oxidase and poly(ethylene glycol) 5000 was prepared and characterized in its structural and functional properties in comparison to the unmodified enzyme. Because the L-lactate oxidase in the native form does not contain cysteines, we introduced a new site for chemical modification via thiol chemistry by substituting the presumably surface-exposed serine-218, a nonconserved residue in the amino acid sequence, with cysteine. The resulting S218C mutant was isolated from Escherichia coli and shown in kinetic assays to be similarly (i.e., about half as) active as the native enzyme, thus validating the structure-guided design of the mutation. Using maleimide-activated methoxypoly(ethylene glycol) 5000 in about 10-fold molar excess over protein, the S218C mutant was converted in high yield (94%) into PEGylated derivative, while the native enzyme was totally unreactive under equivalent conditions. PEGylation caused only a relatively small decrease (30%) in the specific activity of the S218C mutant, and it did not change the protein stability. PEGylation went along with enhancement of the apparent size of the homotetrameric L-lactate oxidase in gel permeation chromatography, from 170 kDa to 250 kDa. The protein hydrodynamic diameter determined by dynamic light scattering increased from 11.9 nm in unmodified S218C mutant to 16.4 nm in the PEGylated form. Site-selective PEGylation of the mutated L-lactate oxidase, using orthogonal maleimide-thiol coupling, could therefore facilitate incorporation of the enzyme into biosensors currently employed for determination of blood L-lactate levels, and it could also support different applications of the enzyme in applied biocatalysis.