Comparison of methods for sample preparation of individual rat cerebrospinal fluid samples prior to two-dimensional polyacrylamide gel electrophoresis

Different pre-treatment methods have been compared for two-dimensional mapping of individual rat cerebrospinal fluid samples based on acetone, trichloroacetic acid/acetone and methanol/acetone precipitation of proteins. Acetone precipitation following incubation with DTT gave the highest protein recovery (72%) and the largest number of protein spots (92 +/- 4) as well as minimizing the time taken.     

Cytochemical characterization of deoxyribonucleoprotein by UV-microspectrophotometry on heat denatured cell nuclei

Denaturation of double-stranded DNA into a single-stranded state can be studied by heating fixed cells attached to quartz slides and then determining the increase in nuclear UV-absorption at 265 nm by microspectrophotometry at room temperature. In order to prevent renaturation as the slides are cooled, formaldehyde is added to the solution in which heat denaturation is performed. The influence of formaldehyde concentration, duration of heating and ionic strength on the stability of DNA to heat denaturation has been examined. The standard method involves heating of ethanol/acetone fixed cells to temperatures between 22°C and 100°C in 0.15 M NaCl, 0.015 M sodium citrate containing 4% formaldehyde for 20 min followed by cooling to room temperature and mounting in glycerol.     

Heat Denaturation Profiles of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) and Rubisco Activase and the Inability of Rubisco Activase to Restore Activity of Heat-Denatured Rubisco

We compared the heat-denaturation profiles of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and Rubisco activase and further examined the ability of Rubisco activase to restore the activity of heat-denatured Rubisco originally reported (E. Sanchez de Jimenez, L. Medrano, and E. Martinez-Barajas [1995] Biochemistry 34: 2826-2831). Rubisco was heat-treated in both the carbamylated and uncarbamylated forms and in the presence and absence of 10 mM dithiothreitol (DTT). Both forms were highly resistant to heat denaturation and further protection was gained in the presence of DTT. A 50% loss in total activity occurred after 1 h at 57.5 and 55.2[deg]C for uncarbamylated Rubisco and at 60.2 and 59.6[deg]C for carbamylated Rubisco, in each case with and without DTT, respectively. In contrast, Rubisco activase lost 50% activity after only 5 min at 33[deg]C and the loss in activity was not affected by the presence of Rubisco. When Rubisco, heat-denatured to various extents, was incubated at room temperature with Rubisco activase or bovine serum albumin as a control, Rubisco activase did not have a significant specific ability to restore Rubisco activity. We conclude that Rubisco activase alone does not have the ability to restore the activity of heat-denatured Rubisco and is unlikely to protect or restore Rubisco activity from heat denaturation in vivo because it is more heat-labile than Rubisco.     

Isolation and partial characterization of the low-molecular-mass zinc/cadmium-binding protein from the testes of the patas monkey (Erythrocebus patas). Distinction from metallothionein.

The mammalian testes are generally quite susceptible to cadmium. A deficiency of metallothionein (MT), a metal-binding protein linked to Cd tolerance, has been observed in rat testes and may explain the sensitivity in rats. Little is known about the metal-binding proteins in primate testes. Thus this study examined the nature of these proteins in a non-human primate species, the patas monkey (Erythrocebus patas). In all cases proteins isolated from testes were compared with authentic MT isolated from the liver of a zinc-treated monkey. A low-molecular-mass Zn/Cd-binding protein was seen in testicular and hepatic cytosol after gel filtration. Neither protein had substantial amounts of associated copper. These proteins could be partially purified from both sources by heat treatment and acetone precipitation. When such extracts were further separated by reverse-phase h.p.l.c., four hepatic forms were isolated, all of which proved to be authentic MT by amino acid analysis. However, only two testicular forms were separated by h.p.l.c., both of which had amino acid compositions quite unlike that of MT, having a much lower cysteine content and amino acids which are absent from MT (leucine and phenylalanine). The testicular protein appeared to be uninducible by Zn treatment. These results suggest that the low-molecular-mass Cd/Zn-binding proteins in the patas testes are not MTs and further support the hypothesis that a MT deficiency may be an important determinate of the marked testicular sensitivity to Cd toxicity.     

Hydroxylation of acetone by ethanol- and acetone-inducible cytochrome P-450 in liver microsomes and reconstituted membranes

Acetone oxidation in rat liver microsomes was induced 5- or 8-fold by the treatment of the animals with ethanol or acetone, respectively. The apparent Km of the reaction was 0.9 mM, a value lower than the concentration reported for plasma acetone under starvation conditions. The major acetone metabolite was identified as acetol by GC-MS. Acetone oxidation in microsomes was inhibited by typical P-450 inhibitors as well as by compounds (e.g. imidazole) known to interact with the ethanol-inducible P-450 form. Antibodies against this P-450 isozyme were inhibitory for the reaction in rabbit liver microsomes and this isozyme was the only one that showed acetone hydroxylation activity in reconstituted membranes. Imidazole inhibited the conversion of [14C]acetone into low-Mr compounds (e.g. glucose) in vivo. It is suggested that the ethanol- and acetone-inducible P-450 make use of acetone as an endogenous substrate in the utilization of the compound for, e.g. glucose production under conditions of starvation and diabetic ketoacidosis.     

Importance of storage conditions for the stability of zinc- and cadmium-induced metallothionein

We examined the storage stability of metallothionein (MT), a cysteine-rich protein that has diagnostic potential as a cancer marker and in the assessment of Zn status and heavy-metal toxicity. MT was rapidly degraded in samples of rat whole liver at -20 degrees C or -70 degrees C. MT in supernatants from heat-treated rat liver homogenates stored as 1:5 dilutions of liver from Zn- or Cd-induced rats were stable (recovery >98%) for 100 d at temperatures of -70 degrees C and -196 degrees C but not at -20 degrees C, regardless of the presence of dithiothreitol (DTT) or argon. The variability of MT measurement by the 109Cd-hemoglobin affinity assay was however greatest in samples from Zn-induced rats stored without DTT. The integrity of the MT protein in supernatants of heat-treated homogenates stored for 100 d was demonstrated by Sephadex G-75 chromatography. When heat-treated supernatants were stored as dilute solutions (1:125 of liver), MT was unstable regardless of treatment or storage temperature. Our findings show that liver MT is stable for at least 4 mo as a supernatant of a heat-treated homogenate (1:5 dilution of liver) when stored at or below -70 degrees C and in the presence of DTT.     

Refolding of partially and fully denatured lysozymes

Lysozyme refolding with high yields sometimes results from incomplete denaturation. Dithiothreitol (DTT) is a reductant commonly used to reduce and unfold disulfide-stabilized lysozymes. Through the use of fluorescence spectroscopy to access the extent of denaturation, we found that the rate and extent of denaturation highly depended on the concentration of DTT. Further, the denaturation exhibited a two-phase transition at a high DTT concentration with DTT at >100 mM and long denaturation time (>24 h) being needed for complete denaturation. A low DTT concentration and a short denaturation time resulted in fast refolding with high activity recovery, while a high DTT concentration and a long denaturation time resulted in slow refolding with low activity recovery. Hence, the renaturation of disulfide-containing lysozyme was highly affected by the extent of denaturation.     

Effects of alcohol on the solubility and structure of native and disulfide-modified bovine serum albumin

Differential precipitation of human plasma by ethanol is one of the most important processes for purifying therapeutic proteins, including human serum albumin. Better understanding of the effects of ethanol on the structure and stability of proteins is critical for effective and safe application of ethanol-induced protein precipitation. Here, we examined the effects of ethanol on the structure and solubility of bovine serum albumin (BSA) and SH-modified BSA. Ethanol caused BSA denaturation in a bimodal fashion, i.e., reduction of α-helix at low concentration and subsequent induction of the α-helical structure at higher concentration. In contrast, the solubility of BSA decreased monotonically. The secondary structure of SH-modified BSA was different from that of native BSA. Ethanol resulted in enhanced secondary structures of SH-modified BSA and decreased solubility monotonically. These results suggest the favorable interaction of ethanol with hydrophobic residues, leading to protein denaturation, but the unfavorable interaction with charged residues, leading to a reduction of protein solubility.     

Quantitation of yeast total proteins in sodium dodecyl sulfate–polyacrylamide gel electrophoresis sample buffer for uniform loading

Proteins in sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS–PAGE) sample buffer are difficult to quantitate due to SDS and reducing agents being in the buffer. Although acetone precipitation has long been used to clean up proteins from detergents and salts, previous studies showed that protein recovery from acetone precipitation varies from 50 to 100% depending on the samples tested. Here, this article shows that acetone precipitates proteins highly efficiently from SDS–PAGE sample buffer and that quantitative recovery is achieved in 5 min at room temperature. Moreover, precipitated proteins are resolubilized with urea/guanidine, rather than with SDS. Thus, the resolubilized samples are readily quantifiable with Bradford reagent without using SDS-compatible assays.     

Functional activation of beta-adrenergic receptors by thiols in the presence or absence of agonists

Treatment of beta-adrenergic receptor with dithiothreitol (DTT) or other thiol compounds caused its functional activation in the presence or absence of agonist ligands. Such activation was observed in reconstituted unilamellar phospholipid vesicles that contained beta-adrenergic receptors, purified to greater than or equal to 95% homogeneity from turkey erythrocyte plasma membranes, and the stimulatory GTP-binding protein of the adenylate cyclase system (Gs) purified from rabbit liver. Incubation of the vesicles with 2-10 mM DTT at 0 degrees C for 1 h increased the rate (4-5-fold) and the extent (3-4-fold) of activation of Gs by guanosine 5'-O-(3-thiotriphosphate) (GTP gamma S) binding, an effect about equivalent to the addition of beta-adrenergic agonists. Treatment with DTT also markedly potentiated the ability of agonists to stimulate GTP gamma S binding, increasing the initial rate about 10-fold. DTT treatment was as effective as agonist in stimulating GTPase activity, and maximal stimulation was obtained when DTT-treated vesicles were assayed in the presence of agonist. Other thiol compounds produced effects similar to those of DTT but were at least 10-fold less potent. Stimulation of GTP gamma S binding or GTPase activity required active receptor, and treatment of the receptor with DTT prior to reconstitution also increased its efficacy. There was no effect of DTT on Gs alone. Thus, the site of action of DTT appears to be on the beta-adrenergic receptor itself, and the reduction of disulfides and the binding of agonist act synergistically to activate the receptor. DTT treatment made the receptor more labile to thermal denaturation. Inclusion of cholesterol or cholesteryl-hemisuccinate (5-25%) in the vesicles protected the reduced receptor against such denaturation and enhanced its recovery during reconstitution. No effect of cholesterol or cholesteryl-hemisuccinate was observed on the stability of the nonreduced receptor, which was comparable to that observed in native membranes.     

Heat Denaturation and Emulsifying Properties of Plasma Protein

The effects of pH and NaCl on the denaturation of plasma protein during heat treatment were investigated, as well as the relationship between protein structure and emulsifying properties. When the plasma protein solution (1% w/v) was heated at 80°C, precipitation was accelerated by the presence of NaCl. The measurement of SH groups, surface hydrophobicity and CD spectrum revealed that denaturation occurs easily by heat treatment in the neutral pH region and in the presence of NaCl. The emulsifying activity index (EAI) did not change much after heat treatment at pH 3 irrespective of the presence of NaCl, but it decreased about 60% after heat treatment at pH 7 in the absence of NaCl. Gel filtration patterns indicated that a high molecular weight peak arose upon heat treatment at neutral pH. We concluded that the decrease in EAI was owing to the polymerization of serum albumin and γ-globulin, which are the main components of plasma protein, and disulfide bonds participated in this process.     

Ethanol production by thermophilic bacteria: metabolic control of end product formation in Thermoanaerobium brockii.

Specific changes in the chemical and microbial composition of Thermoanaerobium brockii fermentations were compared and related to alterations of process rates, end product yields, and growth parameters. Fermentation of starch as compared with glucose was associated with significant decreases in growth rate and intracellular fructose-1,6-bisphosphate concentration and with a dramatic increase in the ethanol/lactate product ratio. Glucose or pyruvate fermentation in the presence of acetone was correlated with increased substrate consumption, growth (both rate and yield), acetate yield, and quantitative reduction of acetone to isopropanol in lieu of normal reduced fermentation products (i.e., H2, ethanol, lactate). Acetone altered pyruvate phosphoroclastic activity of cell extracts in that H2, lactate, and ethanol levels decreased, whereas the acetate concentration increased. Glucose fermentation in the presence of exogenous hydrogen was associated with inhibition of endogenous H2 production and either increased ethanol/acetate product ratios and decreased growth at less than 0.5 atm (51 kPa) of H2 or total growth inhibition at 1.0 atm (102 kPA). The effects of exogenous hydrogen on glucose fermentation were totally reversed by the addition of acetone. Glucose fermentation in coculture with Methanobacterium thermoautotrophicum correlated with increased growth (both rate and yield), acetate yield, and the formation of methane in lieu of monoculture reduced products. In coculture, but not monoculture, T. brockii grew on ethanol as the energy source, and acetate and methane were the end products as a direct consequence of hydrogen consumption by the methanogen.     

Protein precipitation of diluted samples in SDS‐containing buffer with acetone leads to higher protein recovery and reproducibility in comparison with TCA/acetone approach

Proteomic approaches are extremely valuable in many fields of research, where mass spectrometry methods have gained an increasing interest, especially because of the ability to perform quantitative analysis. Nonetheless, sample preparation prior to mass spectrometry analysis is of the utmost importance. In this work, two protein precipitation approaches, widely used for cleaning and concentrating protein samples, were tested and compared in very diluted samples solubilized in a strong buffer (containing SDS). The amount of protein recovered after acetone and TCA/acetone precipitation was assessed, as well as the protein identification and relative quantification by SWATH‐MS yields were compared with the results from the same sample without precipitation. From this study, it was possible to conclude that in the case of diluted samples in denaturing buffers, the use of cold acetone as precipitation protocol is more favourable than the use of TCA/acetone in terms of reproducibility in protein recovery and number of identified and quantified proteins. Furthermore, the reproducibility in relative quantification of the proteins is even higher in samples precipitated with acetone compared with the original sample.     

Development of a method for the efficient release of N-glycans from glycoproteins generating native deglycosylated proteins

In many cases, it is desirable to maintain the native status of the target glycoproteins when they are deglycosylated. However, most conventional deglycosylation process often causes the irreversible denaturation of the target glycoproteins. In the present study, we developed a deglycosylation method that could obtain the native deglycosylated proteins employing Png1p-ΔH1, which was confirmed to tolerate high concentration of dithiothreitol (DTT). To prove this process, ribonuclease B (RNase B) and Yeast carboxypeptidase (CPY) were employed as the targeting glycoproteins. Our results confirmed that both of them could be completely deglycosylated in the presence of high concentration DTT and could be refolded when DTT was removed. The circular dichroism spectroscopy (CD) measurement of refolded CPY and RNase B indicated that the structure of deglycosylated proteins had recovered their native status. This method offers the possibility of efficiently releasing N-linked glycans from glycoproteins and obtaining the native target proteins.     

Energy efficiency of acetone,butanol, and ethanol (ABE) recovery by heat-integrated distillation

Bioprocess and Biosystems Engineering - Acetone, butanol, and ethanol (ABE) is an alternative biofuel. However, the energy requirement of ABE recovery by distillation is considered elevated...     

Subunit dissociation,unfolding, and inactivation of bothrojaracin,a C-type lectin-like protein from snake venom

Snake venoms contain a large number of hemostatically active proteins that are structurally related to Ca(2+)-dependent animal lectins. These proteins, called C-type lectin-like proteins (CLPs), are generally found as heterodimers composed of two homologous subunits linked by a disulfide bond. Here, bothrojaracin (BJC), a CLP from Bothrops jararaca venom that is also a thrombin inhibitor, has been used as a model to study the subunit dissociation and unfolding of CLPs from snake venom. Dithiothreitol (DTT) up to 10 mM produces minor effects on the tertiary structure and activity of BJC. On the other hand, chromatographic studies and fluorescence polarization measurements indicate that the interchain disulfide bond is disrupted by DTT, although the dimeric association is maintained. Treatment of BJC with urea produces a progressive red shift in the emission spectra of the tryptophan residues, and circular dichroism measurements show that BJC retains significant secondary structure in the presence of 8 M urea, suggesting only partial unfolding. The effects of urea are fully reversible, as there is complete recovery of BJC activity after removal of the denaturing agent. Addition of DTT to a protein sample previously treated with 8 M urea produces a slightly larger spectral shift than that observed with urea alone. Furthermore, in this condition BJC loses its secondary structure, and its subunits are dissociated. After removal of urea and DTT, BJC is inactive toward thrombin, suggesting the irreversibility of their combined action. Altogether, our data show that (i) BJC is highly resistant to urea or DTT effects, requiring the simultaneous action of both agents to fully denature the protein, and (ii) BJC monomers are tightly associated, and the presence of DTT combined with high urea concentrations is necessary to disrupt them. On the basis of these results we propose the first denaturation model for a CLP from snake venom.     

AOT/异辛烷反胶束萃取纯化胰蛋白酶及酶变性失活问题的解决

用反胶束技术分离纯化蛋白质,具有高选择性、易于大规模操作等优点,具有良好的工业应用前景。但是离子型表面活性剂形成的反胶束体系萃取蛋白质容易引起蛋白质的变性,这是由于离子型表面活性剂的强电荷作用所导致的。对用AOT/异辛烷反胶束体系从胰酶粗提物中萃取胰蛋白酶进行了研究,通过在反胶束相加入乙醇,解决了反胶束萃取蛋白质时蛋白质变性失活的问题。并且由于乙醇的加入大大减少了分相的时间,简化了实验步骤,优化了实验方法,使此技术在工业上的大规模应用成为可能。通过优化各种实验条件,胰蛋白酶的前萃取率达到90%,反萃取率接近100%。最终得率为88%。纯化后的比活提高了5倍多,从300U/mg左右提高到了1800U/mg。     

Heavy meromyosin from skipjack tuna, Euthynus pelamis. Preparation and enzymic properties.

A method was developed to obtain heavy meromyosin (HMM) from the tryptic digest of skipjack tuna dorsal myosin. The tuna HMM thus obtained was shown to be homogeneous on gel filtration-gel electrophoresis, and on ultracentrifugation. The sedimentation constant (S20,w) was estimated to be 6.1S for tuna HMM. The ATPase activity of tuna dorsal HMM was found to be very similar to that of rabbit skeletal HMM in many respects: KCl concentration dependence, pH dependence, effect of pCMB, kinetic parameters (Vmax and Ka) in actin activation, and Arrhenius activation energy. The only difference found between tuna HMM and rabbit HMM was in heat denaturation behavior: the ATPase activities of tuna HMM were approximately four times as sensitive to heat inactivation as those of rabbit HMM. Thus, tuna HMM should represent a good experimental material for investigations of the molecular basis of susceptibility to denaturation, and of the characteristics of fish myosins in general. A new type of heat denaturation of myosin was observed. It occurred in a very early stage of heat treatment of either tuna dorsal myosin or rabbit skeletal myosin; however, it did not occur upon heat treatment of HMM of either tuna or rabbit, and it was detectable in terms of the Mg-ATPase activity only when the activity was measured in the presence of untreated actin.