Biochemical characterization of canavalin, the major storage protein of jack bean

The structure of canavalin, a jack bean (Canavalis ensiformis) protein homologous to phaseolin, the major seed storage protein of Phaseolus vulgaris, has been investigated by x-ray crystallography and found to be a hexamer composed of three identical pairs of similar but nonidentical subunits related by a perfect 3-fold axis and pseudo dyad axes (strict C₃ and pseudo D₃). One member of each pair of subunits is derived from the amino terminal half of a precursor polypeptide of molecular weight 49,000 and the other from its carboxy terminal half. Thus, the crystallographic evidence indicates that the precursor polypeptide is a tandem duplicate and is structurally redundant (McPherson A. 1982 J Biol Chem 255: 10472). A number of physical and chemical properties of the protein in both the uncleaved and the cleaved form were investigated. These included the native molecular weights, amino acid analyses, number of exposed sulfhydryl groups, carbohydrate content, metal ion analysis, crystallization behavior, and the fate of the protein in developing seeds. It was also found that the purified precursor protein possesses a substantial level of α-d-mannosidase activity and seems to share a number of other physical and chemical properties with that enzyme.     

Adenosine triphosphatase from rat liver mitochondria. Crystallization and x-ray diffraction studies of the F1-component of the enzyme.

The homogeneous rat liver F1-ATPase preparation of Catterall and Pedersen (Catterall, W.A., and Pedersen, P.L. (1971) J. Biol. Chem. 246, 4987-4994) has been crystallized from a solution containing phosphate and ATP by precipitation with ammonium sulfate. Most of the resultant crystals are cubes of approximately 0.3 to 0.6 mm per side. X-ray precession photographs show that the crystals are rhombohedral, space group R32 (D37 NO155) with hexagonal cell dimensions a = 148 A, c = 368 A. The molecular weight of the asymmetric unit of the crystals is 190,000 or about half the molecular weight (384,000) of the rat liver enzyme indicating that the crystallographic 2-fold axes of symmetry coincide with a molecular symmetry axis. The crystals diffract to at least 3.5 A and therefore this is the first report of an ATPase preparation in which crystals suitable for x-ray analysis have been obtained.     

Nicotinamide adenine dinucleotide-specific glutamate dehydrogenase of Neurospora crassa. Isolation and sequences of several cyanogen bromide peptides from the NH2-terminal portion of the peptide chain

Previous studies of the amino acid sequence of the NAD-specific glutamate dehydrogenase of Neurospora crassa (EC 1.4.1.2) resulted in the assignments of peptides to four fragments, the longest being the COOH-terminal 669 residues of the protein. A further study of peptides derived by cyanogen bromide cleavage by different separation methods has yielded additional peptides that have provided new information concerning the sequence and has given overlaps of previously known sequences. This has permitted establishment of 313 residues in one sequence (fragment II). This is in addition to a sequence of 43 residues (fragment I) at the NH2-terminal end and a sequence of 669 residues (fragment III) previously established at the COOH-terminal end of the molecule. The present status of our knowledge of the overall sequence is given in the accompanying papers, together with some views regarding the conformation of the protein (Haberland, M.E., Chen, C.-W., and Smith, E.L. (1980) J. Biol. Chem. 255, 7993-8000, and Austen, B.M., Haberland, M.E., and Smith, E.L. (1980) J. Biol. Chem. 255, 8001-8004).     

Ca2+ control of actin filament length. Effects of macrophage gelsolin on actin polymerization

Gelsolin complexes with calcium (gelsolin-Ca2+) binds to the ends of actin filaments to which monomers add preferentially during elongation. It forms a stable complex with actin in a low ionic strength solution which does not normally favor the polymerization of actin. Gelsolin-Ca2+ increases the rate of nucleation of actin which precedes polymerization, but decreases the rate of elongation of the filaments. The final average length of filaments formed in the presence of gelsolin-Ca2+ is shorter and the equilibrium monomer concentration increases relative to actin polymerized in the absence of gelsolin-Ca2+. Gelsolin-Ca2+ also increases the number of actin filaments because the magnitude of the increase in monomer concentration is disproportionately small compared with the reduction in polymer length. In these respects, the population of actin filaments formed during polymerization in the presence of gelsolin-Ca2+ is similar to that resulting from the action of gelsolin on previously assembled actin filaments (Yin, H. L., Zaner, K. S., and Stossel, T. P. (1980) J. Biol. Chem. 255, 9494-9500). The calcium-dependent shortening of ects, the population of actin filaments formed during polymerization in the presence of gelsolin-Ca2+ is similar to that resulting from the action of gelsolin on previously assembled actin filaments (Yin, H. L., Zaner, K. S., and Stossel, T. P. (1980) J. Biol. Chem. 255, 9494-9500). The calcium-dependent shortening of ects, the population of actin filaments formed during polymerization in the presence of gelsolin-Ca2+ is similar to that resulting from the action of gelsolin on previously assembled actin filaments (Yin, H. L., Zaner, K. S., and Stossel, T. P. (1980) J. Biol. Chem. 255, 9494-9500). The calcium-dependent shortening of actin filaments is the primary mechanism for the dissolution of an actin gel by gelsolin. Therefore, the ability of gelsolin to produce short filaments irrespective of the initial state of assembly of the actin offers flexibility for controlling the network structure of the cytoplasm in which either the monomeric or polymeric form of actin molecules might predominate at different times.     

Identification of three phosphorylation sites on each heavy chain of Acanthamoeba myosin II

It has been previously demonstrated that the actin-activated Mg2+-ATPase activity of Acanthamoeba myosin II is inhibited by phosphorylation of its two heavy chains (Collins, J. H., and Korn, E. D. (1980) J. Biol. Chem. 255, 8011-8014). In this paper, it is shown that a partially purified kinase preparation from Acanthamoeba catalyzes the incorporation of 3 mol of phosphate into each mole of myosin II heavy chain. Tryptic digestion of the 32P-myosin, followed by two-dimensional peptide mapping, indicates that two of the three sites phosphorylated by the kinase in vitro correspond to the two major phosphorylation sites on the myosin heavy chain in vivo. Phosphorylation of myosin II in vitro by the kinase fraction completely inhibits the actin-activated Mg2+-ATPase activity of myosin II. Myosin II can be isolated in a highly phosphorylated, enzymatically inactive form, then dephosphorylated to an active form, and finally rephosphorylated to an inactive form. The Acanthamoeba kinase fraction catalyzes the phosphorylation of all three sites on the heavy chain of myosin II at virtually the same rate. From a comparison of the decrease in actin-activated Mg2+-ATPase activity with the amount of phosphate incorporated into myosin II, and from the results obtained previously by dephosphorylating myosin II (Collins, J. H., and Korn, E. D., (1980) J. Biol. Chem. 255, 8011-8014), it can be inferred that two of the sites phosphorylated in vitro act in a synergistic manner to inhibit the actin-activated myosin II Mg2+-ATPase.     

Mechanism of inactivation of monoamine oxidase by trans-2-phenylcyclopropylamine and the structure of the enzyme-inactivator adduct

Mitochondrial monoamine oxidase was inactivated with 2-[2-14C]phenylcyclopropylamine, dialyzed, and treated with acidic 2,4-dinitrophenylhydrazine. Contrary to the report of Paech et al. (Paech, C., Salach, J. I., and Singer, T. P. (1980) J. Biol. Chem. 255, 2700-2704), the 2,4-dinitrophenylhydrazone obtained was not that of 2-phenylcyclopropanone, but rather of cinnamaldehyde. Furthermore, denaturation of the labeled enzyme in the presence of sodium borohydride resulted in retention of 5.6 times more radioactivity than in its absence. Based on these results, a mechanism of inactivation of monoamine oxidase by 2-phenylcyclopropylamine and the structure of the enzyme-inactivator adduct are proposed.     

Copies of protein S6 in Escherichia coli ribosomes

A reinvestigation of the copy number of protein S6 in Escherichia coli ribosomes shows that there is only one copy of S6 in 30 S subunits and in 70 S ribosomes. The previously reported higher value (Subramanian, A. R. (1980) J. Biol. Chem. 255, 6941-6946) is shown to arise from the presence in the usual ribosome preparations of a protein which co-electrophoreses with S6 but does not react with S6 antiserum. This protein is removed when ribosomes are purified by passage through a sucrose gradient.     

Chemical modification of D-amino acid oxidase. Amino acid sequence of the tryptic peptides containing tyrosine and lysine residues modified by fluorodinitrobenzene

D-Amino acid oxidase can be inactivated by covalent modification of predominantly tyrosine residue(s) at pH 7.4 by a low molar excess of fluorodinitrobenzene, which appears to act as an active site-directed reagent (Nishino, T., Massey, V., and Williams, C. H., Jr. (1980) J. Biol. Chem. 255, 3610-3616). Peptide mapping by high performance liquid chromatography of tryptic digests of protein modified with radiolabeled reagent revealed two major radioactive fractions with substantially different retention times which were not observed in protein modified in the presence of benzoate, a potent competitive inhibitor. Isolation and sequence analysis of the major radiolabeled peptides, as well as other direct chemical analyses, are presented which unambiguously demonstrate that these fractions represent modification of two different regions of the protein. The majority of the radiolabel was found within a 61-amino acid residue peptide containing an O-DNP-tyrosine residue exclusively at position 17. The substantial sequence surrounding this tyrosine residue indicates that it is different from that shown to react with N-chloro-D-leucine (Ronchi, S., Galliano, M., Minchiotti, L., Curti, B., Rudie, N. G., Porter, D. J. T., and Bright, H. J. (1980) J. Biol. Chem. 255, 6044-6046). The second fraction consisted of a 12-residue peptide containing an epsilon-DNP-lysine residue at position 5. Together, these two modified amino acids represented 0.89 mol of DNP incorporated/protein monomer. Both modifications must contribute to inactivation to account for the 90% decrease in enzymatic activity. Evidence is presented which suggests that both groups are within the active center of the enzyme and are modified in a mutually exclusive manner.     

Do DNA polymerases delta and alpha act coordinately as leading and lagging strand replicases?

The activity ratio of DNA polymerases delta and alpha in calf thymus was found to be invariably 1:1, irrespective of extraction procedure (8 types) and subcellular localization (cytoplasm, nucleus and microsomes). This was established by separation of the two forms by hydroxyapatite chromatography and by their response to specific inhibitors and monoclonal antibodies. This finding supports the dimeric DNA polymerase model [(1980) J. Biol. Chem. 255, 4290-4303], which proposes that DNA polymerases delta and alpha act coordinately as leading and lagging strand enzymes, respectively, at the replication fork.     

Potassium permeability and volume control in isolated rat hepatocytes

(1) The occurrence of volume-regulatory responses in isolated rat hepatocytes was investigated. After hypotonic shock, cells were able to shrink back to their normal volume within 15 min. By contrast, after hypertonic shock cells kept their shrunken volume for at least 15 min. (2) Na+-alanine cotransport increases K+ permeability in rat hepatocytes (Kristensen, L.O. (1980) J. Biol. Chem. 255, 5236-5243). It is shown here that this effect is due to cell swelling secondary to alanine accumulation rather than to the Na+-alanine cotransport itself.     

Differential activation of two protease-activated protein kinases from reticulocytes by a Ca2+-stimulated protease and identification of phosphorylated translational components

Two protein kinases have been partially purified from rabbit reticulocytes and shown to be activated by limited proteolysis with trypsin [S.M. Tahara and J.A. Traugh (1981) J. Biol. Chem. 256, 11558-11564; P.T. Tuazon, W.C. Merrick, and J.A. Traugh (1980) J. Biol. Chem. 255, 10954-10958]. Reticulocyte lysate was examined for protease activities which might be involved in activation of the protein kinases in vivo. Two neutral proteases, differentially activated by Fe2+ and Ca2+, were identified and partially purified. The Ca2+-stimulated protease specifically activated protease-activated kinase II; no effect was observed on protease-activated kinase I. The Fe2+-stimulated protease was not active on either protein kinase. The protease-activated kinases were examined using initiation factors (eIF) and 40-S ribosomal subunits as substrate. Protease-activated kinase I phosphorylated one subunit of eIF-3 (Mr 130000), eIF-4B and 40-S ribosomal protein S10. Protease-activated kinase II modified the beta subunit of eIF-2 (Mr 53000) and 40-S ribosomal protein S6. The substrate specificities are unique when compared with other cAMP-dependent and cAMP-independent protein kinases from reticulocytes.     

The conformation of eukaryotic cytochrome c around residues 39, 57, 59 and 74.

1H-n.m.r. studies of horse, tuna, Candida krusei and Saccharomyces cerevisiae cytochromes c showed that each of the proteins contains a similar cluster of residues at the bottom of the protein that assists in shielding the haem from the solvent. The relative positions of the residues forming these clusters vary continuously with temperature, and they change with the change in protein redox state. This conformational heterogeneity is discussed with reference to the conformational flexibility of cytochrome c around residues 57, 59 and 74. Spectroscopic measurements of pKa values for Lys-55 (horse and tuna cytochromes c) and His-33 and His-39 (C. krusei and S. cerevisiae cytochromes c) are in excellent agreement with expectations based on chemical-modification studies of horse cytochrome c. [Bosshard & Zürrer (1980) J. Biol. Chem. 255, 6694-6699] and on the X-ray-crystallographic structure of tuna cytochrome c [Takano & Dickerson (1981) J. Mol. Biol. 153, 79-94, 95-115].     

On the active sites of the [NiFe] hydrogenase from Desulfovibrio gigas. M?ssbauer and redox-titration studies

The [NiFe] hydrogenase isolated from Desulfovibrio gigas was poised at different redox potentials and studied by M?ssbauer spectroscopy. The data firmly establish that this hydrogenase contains four prosthetic groups: one nickel center, one [3Fe-xS], and two [4Fe-4S] clusters. In the native enzyme, both the nickel and the [3Fe-xS] cluster are EPR-active. At low temperature (4.2 K), the [3Fe-xS] cluster exhibits a paramagnetic M?ssbauer spectrum typical for oxidized [3Fe-xS] clusters. At higher temperatures (greater than 20 K), the paramagnetic spectrum collapses into a quadrupole doublet with parameters magnitude of delta EQ magnitude of = 0.7 +/- 0.06 mm/s and delta = 0.36 +/- 0.06 mm/s, typical of high-spin Fe(III). The observed isomer shift is slightly larger than those observed for the three-iron clusters in D. gigas ferredoxin II (Huynh, B. H., Moura, J. J. G., Moura, I., Kent, T. A., LeGall, J., Xavier, A. V., and Münck, E. (1980) J. Biol. Chem. 255, 3242-3244) and in Azotobacter vinelandii ferredoxin I (Emptage, M. H., Kent, T. A., Huynh, B. H., Rawlings, J., Orme-Johnson, W. H., and Münck, E. (1980) J. Biol. Chem. 255, 1793-1796) and may indicate a different iron coordination environment. When D. gigas hydrogenase is poised at potentials lower than -80 mV (versus normal hydrogen electrode), the [3Fe-xS] cluster is reduced and becomes EPR-silent. The M?ssbauer data indicate that the reduced [3Fe-xS] cluster remains intact, i.e. it does not interconvert into a [4Fe-4S] cluster. Also, the electronic properties of the reduced [3Fe-xS] cluster suggest that it is magnetically isolated from the other paramagnetic centers.     

An active site-tyrosine-containing heptapeptide from D-amino acid oxidase

The flavoenzyme D-amino acid oxidase (Eo) is rapidly chlorinated by N-chloro-D-leucine (Rudie, N.G., Porter, D.J.T., and Bright, H.J. (1980) J. Biol. Chem. 255, 498-508). We have carried out chymotryptic digestion of E0-36Cl2 and find that all of the radiolabel is located in a heptapeptide having [3.5-36Cl2]chlorotyrosine as the COOH-terminal residue. This heptapeptide, having the sequence -Asp-Leu-Glu-Arg-Gly-Ile-Tyr-, is located within a larger fragment obtained previously from cyanogen bromide cleavage of E0. These results demonstrate that the target for chlorination in E0 must be a single tyrosine residue and provide, when taken together with previous findings, the first clear evidence for the identity and location of an active site residue in the polypeptide chain of D-amino oxidase.     

Role of supernatant protein factor and anionic phospholipid in squalene uptake and conversion by microsomes

Supernatant protein factor (SPF), a cytosolic protein (Mr = 47,000) stimulates microsomal squalene epoxidase activity 4- to 10-fold in the presence of anionic phospholipid such as phosphatidylglycerol (PG) (Saat, Y., and Bloch, K. (1976) J. Biol. Chem. 251, 5155-5160). This effect has been ascribed to substrate translocation from inactive to active pools within the membrane of the endoplasmic reticulum (Friedlander, E. J., Caras, I. W., Lin, L. F. H., and Bloch, K. (1980) J. Biol. Chem. 255, 8042-8045). Here we show that SPF and PG also stimulate squalene uptake per se by microsomes as well as stimulate squalene epoxidase. Microsomes preloaded with substrate in the presence of SPF and PG show full epoxidase activity. They do not require further addition of these factors during enzyme assay. Addition of SPF and PG to assay mixtures containing microsomes preloaded with substrate in the presence of SPF and PG did not further increase epoxidase activity. We also show that PG tightly binds to microsomes. This binding of PG is essential for the response of microsomal epoxidase to SPF. Solubilized microsomal enzymes have been reconstituted and show high epoxidase activity. In this system, SPF and PG do not stimulate the conversion of squalene into products.     

Zn(II)-induced dimerization of human carbonmonoxy hemoglobin

Binding of Zn(II) to the carbon monoxide complex of human hemoglobin was shown by equilibrium sedimentation and sedimentation velocity experiments at pH 7.0 to induce the dissociation of liganded tetramers to dimers but not to monomers. These results provide direct confirmation of previous kinetic and gel filtration experiments (R. D. Gray, (1980) J. Biol. Chem.255, 1812–1818) that Zn(II) binding to liganded hemoglobin produces a change in aggregation state of liganded hemoglobin.     

Identification of the malK gene product. A peripheral membrane component of the Escherichia coli maltose transport system

The malK gene product of Escherichia coli has been identified through the use of a previously described technique that employs gene fusions (Shuman, H. A., Silhavy, T. J., and Beckwith, J. R. (1980) J. Biol. Chem. 255, 168-174). This protein, along with the four other products of the malB locus, comprise the complete maltose transport system. The malK protein has a molecular weight of approximately 40,000 and is located in the cell envelope. In mutant strains which lack another component of the transport system, the malG protein, the malK protein is located in the cytoplasm. This alteration in location suggests that the malK protein is associated with the inner surface of the cytoplasmic membrane via an interaction with the malG protein.     

Diphtheria toxin. Site and configuration of ADP-ribosylation of diphthamide in elongation factor 2

Diphtheria toxin inactivates protein synthesis elongation factor 2 by catalyzing the ADP-ribosylation of a novel derivative of histidine, diphthamide, in the protein (Van Ness, B. G., Howard, J. B., and Bodley, J. W. (1980) J. Biol. Chem. 255, 10710-10716). In this report, we describe experiments involving nuclear Overhauser enhancement NMR spectroscopy which were undertaken to elucidate the site of ADP-ribosylation of diphthamide and the configuration of the glycosidic bond formed by the toxin. The essential result of these experiments is that, in ribosyl-diphthamide obtained by enzymatic digestion of ADP-ribosyl-elongation factor-2, the H-5 imidazole proton is near the R-4 proton of ribose. This result and others are consistent with the interpretation that diphtheria toxin covalently attaches ADP-ribose to the imidazole N-1 of diphthamide via an alpha-glycosidic linkage.     

Association of phosphofructokinase and aldolase with the membrane of the intact erythrocyte

The binding of phosphofructokinase and aldolase to the membrane of the intact human erythrocyte was assessed by the rapid hemolysis/filtration method of Kliman and Steck (Kliman, H. J., and Steck, T. L. (1980) J. Biol. Chem. 255, 6314-6321). We found that about 50% of the phosphofructokinase was membrane-bound in fresh red cells prior to hemolysis. Binding was not significantly altered by deoxygenation. Approximately 40% of aldolase was membrane-associated in fresh red cells. In outdated, blood-banked red cells, aldolase was 73% membrane-bound while, following metabolic repletion, 40% of the enzyme was membrane-associated. These results support the hypothesis that certain glycolytic enzymes in the red cell are membrane-bound in a rapidly reversible and metabolically sensitive fashion.