Optimal Detergent Concentration Research Articles

Cryo-EM grid optimization for membrane proteins

SummaryCryo-EM grid preparation is an important bottleneck in protein structure determination, especially for membrane proteins, typically requiring screening of a large number of conditions. We systematically investigated the effects of buffer components, blotting conditions and grid types on the outcome of grid preparation of five different membrane protein samples. Aggregation was the most common type of problem which was addressed by changing detergents, salt concentration or reconstitution of proteins into nanodiscs or amphipols. We show that the optimal concentration of detergent is between 0.05 and 0.4% and that the presence of a low concentration of detergent with a high critical micellar concentration protects the proteins from denaturation at the air-water interface. Furthermore, we discuss the strategies for achieving an adequate ice thickness, particle coverage and orientation distribution on free ice and on support films. Our findings provide a clear roadmap for comprehensive screening of conditions for cryo-EM grid preparation of membrane proteins.

Expression, purification and reconstitution of the C-terminal transmembrane domain of scavenger receptor BI into detergent micelles for NMR analysis

Scavenger receptor class B type I (SR-BI), the high density lipoprotein (HDL) receptor, is important for the delivery of HDL–cholesteryl esters to the liver for excretion via bile formation. The focus on therapeutic strategies aimed at reducing cholesterol levels highlights the critical need to understand the structural features of SR-BI that drive cholesterol removal. Yet, in the absence of a high-resolution structure of SR-BI, our understanding of how SR-BI interacts with HDL is limited. In this study, we have optimized the NMR solution conditions for the structural analysis of the C-terminal transmembrane domain of SR-BI that harbors putative domains required for receptor oligomerization. An isotopically-labeled SR-BI peptide encompassing residues 405–475 was bacterially-expressed and purified. [U-15N]-SR-BI(405–475) was incorporated into different detergent micelles and assessed by 1H–15N-HSQC in order to determine which detergent micelle best maintained SR-BI(405–475) in a folded, native conformation for subsequent NMR analyses. We also determined the optimal detergent concentration used in micelles, as well as temperature, solution buffer and pH conditions. Based on 1H–15N-HSQC peak dispersion, intensity, and uniformity, we determined that [U-15N]-SR-BI(405–475) should be incorporated into 5% detergent micelles consisting of 1-palmitoyl-2-hydroxy-sn-glycero-3-phospho-[1′-rac-glycerol] (LPPG) and data collected at 40°C in a non-buffered solution at pH 6.8. Furthermore, we demonstrate the ability of SR-BI(405–475) to form dimers upon chemical crosslinking. These studies represent the first steps in obtaining high-resolution structural information by NMR for the HDL receptor that plays a critical role in regulating whole body cholesterol removal.

Characterization of Acid Sphingomyelinase Activity in Human Cerebrospinal Fluid

BackgroundAs a key enzyme in sphingolipid metabolism, acid sphingomyelinase (ASM) is involved in the regulation of cell fate and signaling via hydrolysis of sphingomyelin to form ceramide. While increased activity of the lysosomal form has been associated with various pathological conditions, there are few studies on secretory ASM limited only to cell models, plasma or serum.MethodsAn optimized assay based on a fluorescent substrate was applied to measure the ASM activity in cerebrospinal fluid (CSF) collected from mice and from 42 patients who were classified as controls based on normal routine CSF values.ResultsWe have detected ASM activity in human CSF, established a sensitive quantitative assay and characterized the enzyme’s properties. The enzyme resembles plasmatic ASM including protein stability and Zn2+-dependence but the assays differ considerably in the optimal detergent concentration. Significantly increased activities in the CSF of ASM transgenic mice and undetectable levels in ASM knock-out mice prove that the measured ASM activity originates from the ASM-encoding gene SMPD1. CSF localized ASM activities were comparable to corresponding serum ASM levels at their respective optimal reaction conditions, but no correlation was observed. The large variance in ASM activity was independent of sex, age or analyzed routine CSF parameters.ConclusionsHuman and mouse CSF contain detectable levels of secretory ASM, which are unrelated to serum ASM activities. Further investigations in humans and in animal models will help to elucidate the role of this enzyme in human disease and to assess its value as a potential biomarker for disease type, severity, progress or therapeutic success.

Monitoring and Optimizing Detergent Concentration For Membrane Protein Crystallization While Following Protein Homogeneity

Detergent concentration is critical to growing quality membrane protein crystals. Since the optimal detergent concentration lies just below the detergent phase boundary, the starting detergent concentration must be minimized for initial crystallization trials. However, the majority of Pure, Homogenous and Stable targets contain excessive levels of detergent micelles upon concentration using molecular weight cut-off filters. Size Exclusion Chromatography (SEC) and a Tetra Detector Array (refractometer, viscometer, light scattering, and UV detectors; TDA) are now being successfully utilized to monitor and optimize detergent concentration while assaying PDC homogeneity during purification and concentration for crystallization. In doing so, the oligomeric state, size, shape and the detergent:protein ratio of the Protein Detergent Complex (PDC) is measured.Five different membrane proteins using 3 different detergents (OG, DDM, and FC14) and 4 different methods will be presented where detergent was successfully minimized while maintaining PDC homogeneity. Methods utilized where ultra filtration (centrifugal and high-pressure molecular weight cut-off filters) plus SEC and dialysis, changing detergent isomer, Ni-NTA and ion exchange chromatography.Detergent micelle SEC retention volume, dn/dc, Rh, IV, mass and behavior on different molecular cut-off filters and formats are all being measured using TDA. As expected, there is a direct correlation of measured excess micelle concentration to crystal phase separation and diffraction quality. Unexpectedly, free micelles in the presence of PDCs tend to be highly retained on cut-off filters which would freely pass a pure detergent micelle system; therefore, when measuring whether a micelle is retained or passed through by specific molecular cut-off filters and formats, it must be measured using a PDC system and not just buffered detergent controls.

Annealing Prion Protein Amyloid Fibrils at High Temperature Results in Extension of a Proteinase K-resistant Core

Amyloids are highly ordered, rigid beta-sheet-rich structures that appear to have minimal dynamic flexibility in individual polypeptide chains. Here, we demonstrate that substantial conformational rearrangements occur within mature amyloid fibrils produced from full-length mammalian prion protein. The rearrangement results in a substantial extension of a proteinase K-resistant core and is accompanied by an increase in the beta-sheet-rich conformation. The conformational rearrangement was induced in the presence of low concentrations of Triton X-100 either by brief exposure to 80 degrees C or, with less efficacy, by prolonged incubation at 37 degrees C at pH 7.5 and is referred to here as "annealing." Upon annealing, amyloid fibrils acquired a proteinase K-resistant core identical to that found in bovine spongiform encephalopathy-specific scrapie-associated prion protein. Annealing was also observed when amyloid fibrils were exposed to high temperatures in the absence of detergent but in the presence of brain homogenate. These findings suggest that the amyloid fibrils exist in two conformationally distinct states that are separated by a high energy barrier and that yet unknown cellular cofactors may facilitate transition of the fibrils into thermodynamically more stable state. Our studies provide new insight into the complex behavior of prion polymerization and highlight the annealing process, a previously unknown step in the evolution of amyloid structures.

A continuous spectrophotometric assay for phospholipase A 2 activity

This paper describes a simple continuous spectrophotometric method for assaying phospholipase A 2 (PLA 2) activity. The procedure is based on a coupled enzymatic assay, using dilinoleoyl phosphatidylcholine as phospholipase substrate and lipoxygenase as coupling enzyme. The linoleic acid released by phospholipase was oxidized by lipoxygenase and then phospholipase activity was followed spectrophotometrically by measuring the increase in absorbance at 234 nm due to the formation of the corresponding hydroperoxide from the linoleic acid. The optimal assay concentrations of hog pancreatic phospholipase A 2 and lipoxygenase were established. PLA 2 activity varied with pH, reaching its optimal value at pH 8.5. Scans of the deoxycholate concentration pointed to an optimal detergent concentration of 3 mM. Phospholipid hydrolysis followed classical Michaelis–Menten kinetics ( V m =1.8 μ M/min, K m=4.5 μ M, V m/ K m =0.4 min −1). This assay also allows PLA 2 inhibitors, such as p-bromophenacyl bromide or dehydroabietylamine acetate, to be studied. This method was proved to be specific since there was no activity in the absence of phospholipase A 2. It also has the advantages of a short analysis time and the use of commercially nonradiolabeled and inexpensive substrates, which are, furthermore, natural substrates of phospholipase A 2.

Determination of the phospholipase activity of patatin by a continuous spectrophotometric assay.

Patatin is a family of glycoproteins that accounts for 30-40% of the total soluble protein in potato (Solanum tuberosum L.) tubers. This protein has been reported to serve as a storage protein and also to exhibit lipid phospholipase activity. This paper describes a simple continuous spectrophotometric method for assaying patatin phospholipase activity. The procedure is based on a coupled enzymatic assay using [1,2-dilinoleoyl] PC as the phospholipase substrate and lipoxygenase as the coupling enzyme. In the procedure developed in this work, lipoxygenase oxidizes the linoleic acid released by the phospholipase activity of patatin. This activity can then be followed spectrophotometrically by recording the increase in absorbance at 234 nm that results from the formation of the corresponding hydroperoxide from linoleic acid by the action of lipoxygenase. The optimal assay concentrations of patatin and lipoxygenase were established. Phospholipase activity varied with pH, reaching its optimal value at pH 9.5. Scans of the deoxycholate concentration pointed to an optimal detergent concentration of 3 mM. Phospholipid hydrolysis followed classical Michaelis-Menten kinetics (Vm = 9.8 x 10(-3) micromol/min x microg protein, Km = 7.8 microM, Vm/Km = 1.3 min(-1) x microg protein). This method proved to be specific since there was no activity in the absence of patatin. It also had the advantages of a short analysis time and the use of commercially nonradiolabeled and inexpensive substrates, which are, furthermore, natural substrates of phospholipase.

Polyphosphoinositide Phospholipase C in Plasma Membranes of Wheat (Triticum aestivum L.)

Polyphosphoinositide-specific phospholipase C activity was present in plasma membranes isolated from different tissues of several higher plants. Phospholipase C activities against added phosphatidylinositol 4-phosphate (PIP) and phosphatidylinositol 4,5-bisphosphate (PIP(2)) were further characterized in plasma membrane fractions isolated from shoots and roots of dark-grown wheat (Triticum aestivum L. cv Drabant) seedlings. In right-side-out (70-80% apoplastic side out) plasma membrane vesicles, the activities were increased 3 to 5 times upon addition of 0.01 to 0.025% (w/v) sodium deoxycholate, whereas in fractions enriched in inside-out (70-80% cytoplasmic side out) vesicles, the activities were only slightly increased by detergent. Furthermore, the activities of inside-out vesicles in the absence of detergent were very close to those of right-side-out vesicles in the presence of optimal detergent concentration. This verifies the general assumption that polyphosphoinositide phospholipase C activity is located at the cytoplasmic surface of the plasma membrane. PIP and PIP(2) phospholipase C was dependent on Ca(2+) with maximum activity at 10 to 100 mum free Ca(2+) and half-maximal activation at 0.1 to 1 mum free Ca(2+). In the presence of 10 mum Ca(2+), 1 to 2 mm MgCl(2) or MgSO(4) further stimulated the enzyme activity. The other divalent chloride salts tested (1.5 mm Ba(2+), Co(2+), Cu(2+), Mn(2+), Ni(2+), and Zn(2+)) inhibited the enzyme activity. The stimulatory effect by Mg(2+) was observed also when 35 mm NaCl was included. Thus, the PIP and PIP(2) phospholipase C exhibited maximum in vitro activity at physiologically relevant ion concentrations. The plant plasma membrane also possessed a phospholipase C activity against phosphatidylinositol that was 40 times lower than that observed with PIP or PIP(2) as substrate. The phosphatidylinositol phospholipase C activity was dependent on Ca(2+), with maximum activity at 1 mm CaCl(2), and could not be further stimulated by Mg(2+).

Overproduction and high‐yield purification of phospholipase A from the outer membrane of Escherichia coli K‐12

The cloned gene for the outer-membrane-bound phospholipase A from Escherichia coli was placed under control of the strong PL promoter of phage lambda. Induction of PL resulted in a 250-fold overexpression up to about 2% total cellular protein. This overproduced enzyme was indistinguishable from the wild-type enzyme. A homogeneous phospholiphase A preparation was obtained in high yield from overproducing bacteria, using the zwitterionic detergent C12-Sulfobetaine and anion-exchange chromatography. Detergent gradients were found to exert great influence on the elution characteristics. Considerations for the choice of optimal detergent gradients are discussed. The purified enzyme migrated as a single 29-kDa band in SDS/polyacrylamide gels, and required Ca(II) for activity. Maximum activity was displayed by enzyme samples taken from solutions with detergent concentrations near the critical micelle concentration. However, upon switching from high to optimal detergent concentration, maximum activity was restored in several hours, probably reflecting a slow conformational transition of the protein. Because the final pure protein was found to hydrolyze phospholipids in the intact erythrocyte membrane, a densely packed bilayer, we assume that this protein is in its biological native state.

Characterization of the Solubilized Plasma Membrane ATPase of Red Beet

The plasma membrane ATP-phosphohydrolase (ATPase) from red beet (Beta vulgaris L.) storage tissue was solubilized with the zwitterionic detergent Zwittergent 3-14 from a plasma membrane-enriched fraction which was extracted with the anionic detergent, sodium deoxycholate. For both the extraction of extraneous proteins by deoxycholate and the solubilization of active plasma membrane ATPase by Zwittergent 3-14, the optimal concentration of detergent was 0.1% (weight per volume) with a detergent to protein ratio of 1.0 (milligram per milligram). The properties of the solubilized ATPase were found to be similar to the membrane-bound enzyme with respect to pH optimum, substrate specificity, inhibitor sensitivity, and kinetics of K(+) stimulation. The solubilized ATPase preparation formed a rapidly turning over phosphoenzyme, the breakdown velocity of which was increased in the presence of 50 millimolar KCl. Solubilization with 0.1% Zwittergent 3-14 following extraction with 0.1% deoxycholate resulted in an increase in both ATPase activity and steady state phosphoenzyme level; however, a direct correspondence between the increase in ATPase activity and phosphorylation level did not exist. It is proposed that this discrepancy may be the result of a detergent-mediated modification of kinetic rate constants in the mechanism of the enzyme.

Endo-beta-D-galactosidases of Bacteroides fragilis and Escherichia freundii hydrolyze linear but not branched oligosaccharide domains of glycolipids of the neolacto series.

The specificities of the endo-beta-galactosidases of Bacteroides fragilis and Escherichia freundii towards linear and branched oligosaccharides of the lacto-N-glycosyl series were investigated using as substrates glycolipids containing (a) linear neolactotetra - or hexaosyl sequences, (b) branched biantennary neolactooctaosyl sequences, and (c) triantennary neolactononaor dodecaglycosyl sequences. Glycolipid and oligosaccharide hydrolysis products were identified by tlc and/or paper chromatography. The rate of hydrolysis was assessed in time course experiments in which the oligosaccharides released were quantified as 3H-labeled alditols. The salient observations were as follows. (i) With the substrates thus far tested in the present and a previous study ( Scudder , P., Uemura , K., Dolby , J., Fukuda, M.N., and Feizi , T. (1983) Biochem. J. 213, 485-494), the endo-beta-galactosidases from B. fragilis and E. freudii have indistinguishable specificities. (ii) The beta-galactosidic linkage of the branch point sequence (Formula: see text) is completely resistant to hydrolysis by these enzymes, although the unbranched sequence GlcNAc beta 1-3Gal beta 1-4GlcNAc/Glc is readily cleaved. (iii) At an optimal concentration of detergent, the endo-beta-galactosidase susceptibility of the GlcNAc beta 1-3Gal beta 1-4Glc sequence near the ceramide moiety of branched glycolipids is similar to that of the corresponding sequence in linear glycolipids.

Substrate specificity of two cationic lipases with high phospholipase A 1, activity purified from guinea pig pancreas II. Studies on glycerophospholipids

The substrate specificity of two cationic lipases with high phospholipase a 1 activity purified from guinea pig pancreas has been tested towards various natural and synthetic phospholipids. Natural glycerophospholipids carrying a 1-acyl-bond were degraded in the following order of decreasing activity: phosphatidylcholine = phosphatidylinositol > 1-acyl- sn-glycero-3-phosphocholine > phosphatidylethanolamine > phosphatidylglycerol. Sodium deoxycholate was an activator with all the phospholipids tested, each one requiring its own optimal concentration of detergent. Whereas 1-alkyl-2-acyl- sn-glycero-3-phosphocholine remained fully insensitive to enzyme degradation, 2-acyl- sn-glycero-3-phosphocholine was hydrolysed to some extent. However, additional experiments involving time-course hydrolysis revealed that this was entirely due to the migration of the 2-acyl-chain to the sn-1 position. From studies using racemic or enantiomeric phosphatidylcholines, it was concluded that the enzymes are not stereospecific. Activity against 1-acylpropanediolphosphocholine was much lower than with 1-acyl- sn-glycero-3-phosphocholine, indicating that the 2-hydroxyl group (or the 2-acyl-ester group) participates in the substrate reactivity through a strong inductive effect. Some activity could be detected against 1,3-diacylglycero-2-phosphocholine (β-phosphatidylcholine) and 1-acylglycol-2-phosphocholine. It is thus concluded that the failure of the lipases to hydrolyse the 2-acyl-bond in a natural phospholipid is due to the steric hindrance brought about by the acyl, alkyl or hydroxyl group present in the sn-1 position. The lipases might also be unable to hydrolyse acyl-ester bonds involving a secondary alcohol.

Some properties of uridine-5′-diphospho-N-acetylgalactosamine:Hematoside N-acetylgalactosaminyltransferase at early and late stages of embryonic development of chicken retina

Some properties of the uridine-5′-diphospho-N-acetylgalactosamine:hematoside N-acetylgalactosaminyltransferase were studied in retina tissue from chick embryos at 7 and 14 days of development. The Vmax was about 6-fold higher in retinas from 14 day embryos than in retinas from 7 day embryos. No differences were found either in the apparent Michaelis constant for both donor nucleotide and acceptor glycolipid, or in the optimal detergent concentration, or in the stability upon storage at −14°C or heating at 50°C. Mixtures of homogenates of retinas from 7 day and from 14 day embryos gave the activity values expected for samples free of effectors diffusible and in excess. From experiments of partial delipidation of retina homogenates and reconstitution with lipid from retina homogenates from one or the other age, no indications were found that the activity was modulated by developmental changes in the lipid environment of the enzyme. Taken together, the results suggest that the increase of activity during development was not due to qualitative changes in the catalytic characteristics of the enzyme.

Elongation of DNA complementary to the 5' end of the avian sarcoma virus genome by the virion-associated RNA-dependent DNA polymerase.

RNA-dependent DNA synthesis in a virion-associated reaction has been described as being dependent upon the detergent concentration used for disruption of the virion. In this study, the Triton X-100 concentration was found to affect the elongation of the initially synthesized DNA complementary to the last approximately 100 nucleotides at the 5' end of the RNA (cDNA100). Whereas elongation of cDNA100 increased with time of incubation at the optimal detergent concentration, this process was retarded at higher detergent concentrations. At the optimal detergent concentration, elongated DNA was of low chemical complexity, indicating that extension of cDNA100 occurred at a unique site on the RNA. Higher than optimal detergent concentrations resulted in nonspecific elongation and in DNA of high chemical complexity. This was shown by oligopyrimidine tract analysis. Furthermore, actinomycin D was observed to inhibit the elongation of cDNA100 at the optimal detergent concentration. The nature of the elongation process was elucidated by analysis of DNA synthesized in a virion-associated reaction in the presence of bacteriophage Qbeta RNA. At the optimal detergent concentration DNA complementary only to avian sarcoma virus RNA was synthesized, whereas at higher concentrations DNA was copied from both avian sarcoma virus and Qbeta RNA. We conclude that the elongation mechanism of cDNA100 is affected by the detergent concentration and elongation is unspecific at higher than optimal detergent concentrations. The mechanism by which the nonionic detergent stimulates DNA synthesis has not yet been resolve. We assume that other factors in addition to DNA polymerase are involved in elongation of cDNA100.

Trihexosylceramide α-galactosidase of human leucocytes

Trihexosylceramide, isolated from human kidney and labelled in the terminal galactose position by oxidation with galactose oxidase and reduction with sodium boro[ 3H]hydride, was used to study some of the properties of human leucocyte α-galactosidase. The enzyme was inactive in the absence of detergent. Of all the detergents tested a crude sodium taurocholate preparation displayed the greatest activity. The optimal detergent concentration varied from 2 to 4 mg/ml depending on the protein concentration and indicating that the enzyme activity was dependent on the protein/detergent ratio. Because of its influence in regulating enzyme activity, it is essential that care must be taken to ensure that the protein/detergent ratio of all incubation mixtures is kept relatively constant whenever the diagnosis of Fabry's disease is attempted.

In vitro synthesis of full-length DNA transcripts of Rous sarcoma virus RNA by viral DNA polymerase.

Varying the concentration of Triton X-100, a nonionic detergent used to promote the DNA polymerase activity of Rous sarcoma virus in an endogenous reaction, showed a very sharp peak at about 0.02% (vol/vol) for optimal DNA synthesis. The yield of DNA at this concentration of Triton exceeded yields obtained at concentrations above the optimum by a factor of 2-5 for the 90-min reaction. At optimal Triton concentration, about 1-7% of the DNA made in the absence of actinomycin and about 4-10% of the DNA made in the presence of actinomycin was 2.5 X 10(6) daltons or greater, as estimated by formamide polyacrylamide gel electrophoresis and by alkaline sucrose gradient sedimentation. No large DNA was obtained at higher than optimal Triton concentrations. The large DNA molecules were rendered totally resistant to single-strand specific nuclease S1 after hybridization to an excess of viral RNA. It was concluded that at optimal detergent concentration, the viral DNA polymerase can synthesize full-size DNA transcripts of viral RNA.