Alterations in the protein-synthesis, -degradation and/or -secretion rates in hepatic subcellular fractions of selenium-deficient mice.

Conformational studies of myelin basic protein (MBP) in solution generally have used protein purified in organic solvents and acid. The use of such conditions raises the possibility that the secondary structure reported for the basic protein represents a denatured state. Therefore we have purified this protein by using a procedure that avoids denaturants. Bovine myelin was extracted with 0.2 M-CaCl2 and the protein was purified from the supernatant by chromatography on Sephadex G-75. The conformation of the basic protein was characterized by using c.d. and 1H-n.m.r. spectroscopy. In solution, it appeared to be predominantly randomly coiled, with only small segments of persistent structure. However, in the presence of myristoyl lysophosphatidylcholine the secondary structure of MBP became more ordered, and sedimentation-velocity experiments showed that MBP aggregated. Comparison of our results with published data indicates that Ca2+-extracted basic protein behaves similarly to the protein purified by traditional methods with respect to its ordered conformation in solution in the absence and in the presence of lipid and with respect to its self-association. Thus its thermodynamically stable structure in aqueous solution appears to be a highly flexible coil.     

Preparation of template plasmids for cell-free protein synthesis using a regenerated anion-exchange column

In this report, we describe how reactions of cell-free protein synthesis can be successfully conducted using plasmids prepared with regenerated anion-exchange columns. When washed, stripped, and equilibrated with appropriated buffers, regenerated columns were able to be used repeatedly to prepare plasmids with consistent yield and purity. The regenerated columns exhibited comparable performance to a fresh column with respect to the efficiency of protein synthesis using the plasmids prepared from them. Overall, we expect that the presented results will contribute significantly to economizing the technology of cell-free protein synthesis as a practical method for protein production in preparative scales.     

Isoelectric focusing of high-molecular-weight protein complex under native conditions using agarose gel

The isolation and characterization of protein complexes are essential steps toward understanding cellular functions. A method for separating and characterizing high-molecular-weight protein complexes using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) with native agarose gel isoelectric focusing (IEF) is described. Using this method, fractions containing high-molecular-weight protein complexes were analyzed. The advantages of using native agarose gel IEF include the ability to concentrate the protein complexes and the ease of handling when performing 2D separations. Although limited with respect to the size of molecules and particles that may be separated, this method is useful for the isolation and characterization of high-molecular-weight protein complexes.     

Relative tolerance of mesostable and thermostable protein homologs to extensive mutation

Evolvability, designability, and plasticity of a protein are properties that are important to protein engineers, but difficult to quantify. Here, we directly compare homologous AroQ chorismate mutases from the thermophile Methanococcus jannaschii and the mesophile Escherichia coli with respect to their capacity to accommodate extensive mutation. The N-terminal helix comprising about 40% of these proteins was randomized at the genetic level using a binary pattern of hydrophobic and hydrophilic residues based on the respective wild-type sequences. Catalytically active library members were identified by a survival-selection assay in a chorismate mutase-deficient E. coli strain. Functional variants were found approximately approximately 10-times more frequently with the thermostable protein compared to its mesostable counterpart. Moreover, detailed sequence analysis revealed that functional M. jannaschii enzyme variants contained a smaller number of conserved residues and tolerated greater variability at individual sequence positions. Our results thus highlight the greater robustness of the thermostable protein with respect to amino acid substitution, while identifying specific sites important for constructing active enzymes. Overall, they support the notion that redesign projects will benefit from using a thermostable starting structure, even at very high mutational loads.     

Temporal variations in protein tyrosine phosphatase activity during cell proliferation and differentiation

Cellular oscillations in total extractable protein content and protein tyrosine phosphatase activity were analysed in proliferating and differentiating human acute promyelocytic leukaemic (HL-60) cell extracts. Differentiation was induced along the granulocytic pathway using all-trans retinoic acid (ATRA). High frequency rhythms with distinct, well defined waveforms of varying amplitude were observed for both the total protein content and for the enzyme activity of protein tyrosine phosphatase (PTP). Linear correlation analysis showed that there was no obvious relationship between the protein content and the corresponding PTP activity, suggesting that the periodic variations between these two components are relatively independent of each other. ATRA significantly altered the characteristics of the rhythms with respect to the period and amplitude and had a dampening effect on the oscillatory pattern of PTP activity. Modulation of such characteristics may be of significance with respect to the regulation of the differentiation processes and the possible reversal of transformation.     

Investigation of immunoadsorbent efficiency and capacity for the isolation of tRNAs containing N6-(delta 2-isopentenyl)adenosine derivatives

Antibodies directed to modified nucleosides recognize the nucleoside (antigen) when it is present in an intact tRNA molecule. The general application of anti-nucleoside immunoadsorbent chromatography, however, has been greatly impeded by the apparent inefficiency and low capacity of conventional immunoadsorbents for transfer RNA. Antibodies specific for isopentenyladenosine (i6A) were employed to investigate the efficacy of various immunoadsorbents with respect to immobilization of antibody protein and with respect to their ability to bind i6A-containing tRNAs. Biologically active anti-i6A was recovered in high yield (80-88%) by affinity chromatography on i6A-adipate-Sepharose 4B or i6A-butane diglycidyl ether-Sepharose 4B using either 15% pyridine in phosphate-buffered saline or 0.2 M acetic acid as eluents. The binding capacity of various anti-i6A antibody immunoadsorbents was evaluated. While both anti-i6A antibody-protein A-agarose-iminothiolane (ITL) and anti-i6A antibody-protein A-agarose-dimethyl suberimidate showed a high capacity for i6A-tRNA, the latter column is much less efficient with respect to antibody immobilization. Under optimal conditions, the ITL immunoadsorbent binds 5-6 nmol of i6A/mg of antibody protein. With respect to bulk tRNA, 1 mg of antibody protein (ITL immunoadsorbent) binds all of the i6A-tRNA in a 1-mg sample.     

Potential errors in the measurement of total protein in male rat urine using test strips

Widely differing results were obtained for urinary protein determinations in male rats using 2 test strips and a quantitative Coomassie Blue sodium dodecyl sulphate method. A comparison of the sensitivity of the protein methods with respect to rat albumin and alpha 2U globulin was made; both test strips were found to be relatively insensitive to the presence of alpha 2U globulin. Resultant limitations of test strips in monitoring adult male rat urine protein concentrations are discussed.     

Kinetics of heat- and acidification-induced aggregation of firefly luciferase

The general approach to analysis of the kinetics of protein aggregation registered by the turbidimetric method has been elaborated. The terminal part of the kinetic curves is analyzed using a theoretical equation connecting the derivative of the apparent absorbance (A) with respect to time (dA/dt) and A (t is time). This analysis allows the limiting value of A at t--> infinity (A(lim)) and the order of aggregation with respect to protein (n) to be calculated. Approach proposed was applied to analysis of thermal and acidification-induced aggregation of firefly luciferase. In both cases the A(lim) value is a linear function of the protein concentration. The terminal part of the kinetic curves of thermal aggregation follows the first-order kinetics (n=1), whereas the kinetics of acidification-induced aggregation are characterized by the value of n higher than unity (n=1.29). The mechanism of nucleation-dependent aggregation has been discussed.     

Measurement of protein by dye-binding assay in the presence of metrizamide

Quantitative determination of protein using the binding of Coomassie Brilliant Blue G-250 was investigated with respect to interference with the density gradient material metrizamide, and compared with the corresponding interference using the Lowry method. The background absorption obtained with metrizamide in the absence of protein was less than 10% of that obtained with the Lowry method. In the presence of 0–4% metrizamide, parallel standard curves were obtained with 0–67 μg of protein in the samples. The curves overlapped in the range 0–40 μg of protein when metrizamide was included in the blanks. With up to 2% final concentration of metrizamide in the assay, the curves overlapped at all protein concentrations tested (0–67 μg). Correction for metrizamide interference is thus a simple procedure and a precise estimation of the metrizamide concentration is less critical than when the Lowry assay is used. The method is well suited for quantitation of protein in samples collected from metrizamide grandients.     

Affinity purification of specific DNA fragments using a lac repressor fusion protein

A new method for purification of specific DNA sequences using a solid phase technique has been developed based on a fusion between the Escherichia coli lac repressor gene (lacI) and the staphylococcal protein A gene (spa). The fusion protein, expressed in Escherichia coli, is active both in vivo and in vitro with respect to its three functional activities (DNA binding, IPTG induction, and IgG binding). The recombinant protein can be immobilized in a one-step procedure with high yield and purity using the specific interaction between protein A and the Fc-part of immunoglobulin G. The immobilized repressor can thereafter be used for affinity purification of specific DNA fragments containing the lac operator (lacO) sequence.     

Biochemical characteristics of functionally active actin-like protein from liver mitochondria

The actin-like protein with a molecular weight of 42 kDa was obtained from the preparation of freshly isolated mitochondria of the rat liver using the method of immobilized DNAse affinity chromatography. The inhibitory ability of the isolated protein with respect to pancreatic DNAse I was the same as that of muscular actin. The native structure of the mitochondria protein is confirmed by the data of spectral analysis and its ability to globular-fibrillar transformation with an increased ionic strength of the solution. The polymerization ability as well as a stimulating effect of the actin-like protein of mitochondria on the ATPase activity of myosin is much less pronounced as compared to actin of skeletal muscles.     

Vaccinia virus-mediated high level expression and single step purification of recombinant Jak2 protein

Jak2 functions as a non-receptor tyrosine kinase and has been linked to pathologies such as cancer and cardiovascular disease. Because of this, many studies have tried to better understand its function. Unfortunately, very little information is known about its catalytic or biochemical properties as purification of significant amounts of functional Jak2 protein has been exceedingly difficult. Here, Jak2 was expressed in BSC-40 cells using a vaccinia virus-mediated expression system. Significant amounts ( approximately 10microg) of Jak2 protein were expressed from a single 100-mm cell culture dish. The protein was first harvested using three different methods of extraction to determine the relative efficiency of each lysis method with respect to Jak2 protein yield and catalytic activity. We found that lysis methods utilizing detergents increased the efficiency of protein extraction about 3-fold when compared to a method lacking detergent. However, with respect to catalytic activity, Jak2 isolated from cells using detergent-containing lysis buffers had significantly less catalytic activity than when compared to the method that was detergent free. Expression was then scaled up and Jak2 protein was purified via a one step immunoaffinity purification scheme using both the detergent-free and a modified detergent-containing method of extraction that maintained catalytic activity. In vitro kinase assays demonstrated that the purified product was highly catalytic as measured by its ability to tyrosine phosphorylate Stat1. Collectively, the results show that (1) Jak2 can be expressed at very high levels in mammalian cells, (2) it can be purified to homogeneity via a single step purification scheme, and (3) the purified product is biologically active.     

Isolation of plasma membrane from protoplasts of Lolium multiflorum (ryegrass) endosperm cells.

Plasma membranes have been isolated from protoplasts of suspension-cultured ryegrass (Lolium multiflorum) endosperm cells. The protoplast membrane is coated before cell disruption with murine myeloma protein J539, a galactose-binding immunoglobulin A. The plasma membrane is labelled with 125I by using chemically or enzymically catalysed iodination techniques, or, more conveniently, by using 125I-labelled myeloma protein J539, which enables the membrane to be simultaneously coated and labelled. Protoplast lysis is effected by gentle mechanical means after swelling in hypo-osmotic medium. The plasma-membrane fraction is recovered at low centrifugal forces by fractionation of cell lysates on a discontinuous sucrose/sorbitol gradient. The plasma-membrane fraction is enriched 96-fold on a protein basis with respect to the specific radioactivity of 125I-labeled myeloma protein J539 in the homogenate. Electron microscopy showed long membrane profiles often associated with one another.     

Microinjection of antibodies to a 62 kd mitotic apparatus protein arrests mitosis in dividing sea urchin embryos

Previously, we described a 62 kd protein that is a component of the isolated sea urchin mitotic apparatus. This protein is a substrate for an endogenous, calcium/calmodulin-dependent protein kinase also associated with the mitotic apparatus. Phosphorylation of the 62 kd protein directly correlates with the depolymerization of microtubules in isolated mitotic apparatuses. Here we report a test of the function of the 62 kd protein in vivo. Double labeling studies using a monoclonal antibody to tubulin and an affinity purified antibody specific for the 62 kd protein reveal that the 62 kd protein co-localizes with mitotic apparatus microtubules. When affinity purified antibodies to the 62 kd protein were microinjected into dividing sea urchin embryos, mitosis was blocked in a stage-specific manner. The results are discussed with respect to the role of the 62 kd protein in the metaphase-anaphase transition.     

Inhibition of protein kinase C activity by the Leishmania donovani lipophosphoglycan

Purified lipophosphoglycan from Leishmania donovani was found to inhibit the activity of protein kinase C isolated from rat brain. Protein kinase C inhibition by lipophosphoglycan was continuous for 30 minutes. The glycoconjugate was a competitive inhibitor with respect to diolein, a noncompetitive inhibitor with respect to phosphatidylserine, and had no significant effect on protein kinase M and protein kinase A. A possible physiological role of lipophosphoglycan as a negative effector of protein kinase C is suggested.     

Biochemical characterization of the Arabidopsis biotin synthase reaction. The importance of mitochondria in biotin synthesis.

Biotin synthase, encoded by the bio2 gene in Arabidopsis, catalyzes the final step in the biotin biosynthetic pathway. The development of radiochemical and biological detection methods allowed the first detection and accurate quantification of a plant biotin synthase activity, using protein extracts from bacteria overexpressing the Arabidopsis Bio2 protein. Under optimized conditions, the turnover number of the reaction was >2 h(-1) with this in vitro system. Purified Bio2 protein was not efficient by itself in supporting biotin synthesis. However, heterologous interactions between the plant Bio2 protein and bacterial accessory proteins yielded a functional biotin synthase complex. Biotin synthase in this heterologous system obeyed Michaelis-Menten kinetics with respect to dethiobiotin (K(m) = 30 microM) and exhibited a kinetic cooperativity with respect to S-adenosyl-methionine (Hill coefficient = 1.9; K(0.5) = 39 microM), an obligatory cofactor of the reaction. In vitro inhibition of biotin synthase activity by acidomycin, a structural analog of biotin, showed that biotin synthase reaction was the specific target of this inhibitor of biotin synthesis. It is important that combination experiments using purified Bio2 protein and extracts from pea (Pisum sativum) leaf or potato (Solanum tuberosum) organelles showed that only mitochondrial fractions could elicit biotin formation in the plant-reconstituted system. Our data demonstrated that one or more unidentified factors from mitochondrial matrix (pea and potato) and from mitochondrial membranes (pea), in addition to the Bio2 protein, are obligatory for the conversion of dethiobiotin to biotin, highlighting the importance of mitochondria in plant biotin synthesis.     

Rapid assay of binding of tumor-promoting phorbol esters to protein kinase C1

Protein kinase C is generally accepted to be a receptor protein of tumor-promoting phorbol esters. The binding of [3H]phorbol-12,13-dibutyrate to protein kinase C can be assayed by a rapid filtration procedure using a glass-fiber filter that has been treated with a cationic polymer, polyethylenimine. The phorbol ester specifically binds to the protein kinase only in the presence of phosphatidylserine and calcium. Non-specific binding is less than 10%, at most, of the total binding. The binding is linear with respect to the concentration of protein kinase C, is dependent on the concentrations of phorbol ester and phosphatidylserine in a saturative manner, and is inhibited by diacylglycerol (an endogenous activator of the protein kinase).     

The major basic proteins of bull seminal vesicle secretion

We have employed HPLC on reversed phase columns to analyse the major basic proteins from bull seminal vesicle secretion. The identification of proteins was achieved by comparison with authentic protein samples from bull seminal plasma as well as immunological characterisation using antisera directed against the latter proteins. The major basic proteins from bull seminal plasma: bull seminal proteinase inhibitor II (BUSI II), the seminal ribonuclease BS1, the protein P6 as well as the antimicrobial protein were also identified as the main constituents of the fraction of basic proteins derived from seminal vesicle secretion. FPLC using Mono S HR columns was also found to resolve the mixture of basic proteins and proved to be especially useful with respect to the isolation of the antimicrobial protein from basic proteins of seminal vesicle secretion. The identity of the antimicrobial protein from bull seminal plasma with the respective protein from seminal vesicle secretion was confirmed by amino-acid analysis and comparison of tryptic peptide patterns by HPLC. The antimicrobial protein was isolated from seminal vesicle secretion with a yield of 3 mg/ml of secretion.     

MD simulation of subtilisin BPN' in a crystal environment.

In this paper we present a molecular dynamics (MD) simulation of subtilisin BPN' in a crystalline environment containing four protein molecules and solvent. Conformational and dynamic properties of the molecules are compared with each other and with respect to the X-ray structure to test the validity of the force field. The agreement between simulated and experimental structure using the GROMOS force field is better than that obtained in the literature using other force fields for protein crystals. The overall shape of the molecule is well preserved, as is the conformation of alpha-helices and beta-strands. Structural differences are mainly found in loop regions. Solvent networks found in the X-ray structure were reproduced by the simulation, which was unbiased with respect to the crystalline hydration structure. These networks seem to play an important role in the stability of the protein; evidence of this is found in the structure of the active site. The weak ion binding site in the X-ray structure of subtilisin BPN' is occupied by a monovalent ion. When a calcium ion is placed in the initial structure, three peptide ligands are replaced by 5 water ligands, whereas a potassium ion retains (in part) its original ligands. Existing force fields yield a reliable method to probe local structure and short-time dynamics of proteins, providing an accuracy of about 0.1 nm.