The structure of horse methaemoglobin at 2-0 A resolution

The structure of horse methaemoglobin has been redetermined by phase extension and refinement. This has improved our knowledge of the haem geometry and the stereochemistry of the interfaces between the subunits, and confirmed the disorder of the C-terminal residues. Using new four-circle diffractometer data between the limiting spheres of radius 10 and 2.0 Å^?1, the co-ordinates determined by Perutz et al. (1968a,b) were subjected to successive cycles of real-space refinement into electron density maps calculated with observed ¦F¦ values and phases derived from the latest refined model, until the reliability index had dropped from an initial value of 0.45 to 0.23. The positions of the iron atoms relative to the planes of the porphyrin rings were refined separately, and checked by Fourier syntheses based on anomalous scattering and by difference Fourier syntheses calculated with coefficients from which the iron contributions had been removed. The general root-mean-squared error in atomic positions is 0.32 Å; the probable error in the displacement of the iron atoms from the porphyrin planes is 0.06 Å. The difference Fourier synthesis, obtained after refinement of the protein was complete, showed 41 bound water molecules per asymmetric unit and also revealed five errors in amino acid sequence, one of which was confirmed chemically.The secondary structures of the subunits are stabilized by hydrogen bonds formed by main-chain NH and CO groups either with each other or with nearby polar side-chains. There are few internal hydrogen bonds linking the various chain segments; many of the external polar side-chains help to stabilize the tertiary structure by forming hydrogen bonds with each other or through bound water molecules. Several of the helical segments are irregular and the terminal residues are disordered. The contacts between the subunits are more polar than the earlier 2.8 Å map had led us to believe, because it had failed to show up the 15 bound water molecules at the α₁β₁ and the four at the α₁β₂ contact. Their inclusion has raised the number of hydrogen bonds between neighbouring subunits at α₁β₁ from five to 17 or possibly 19, and at α₁β₂ from two to six or possibly seven. The remaining 22 water molecules are distributed over the internal cavity and the molecular surface; most of them make hydrogen bonds with at least two polar groups of the protein. Despite several amino acid differences, the structure of the α₁β₁ contact, including the bound water, is the same as in human deoxyhaemoglobin (Fermi, 1975).     

Structure of azide methemoglobin

We have compared the structures of horse azide methemoglobin and methemoglobin (MetHb) at 2.8 Å resolution by X-ray difference Fourier analysis. Of four low-spin liganded Hb derivatives (nitric oxide Hb, carbon monoxide Hb, cyanide MetHb, and azide MetHb), azide MetHb is closest in structure to MetHb. In azide MetHb the ligands are co-ordinated end-on at angles of about 125 ° to the heme axes, which is similar to the stereochemistry assumed by azide in binding to free heme. Because of its bent binding geometry, azide encounters less interference in binding and perturbs the protein structure less than carbon monoxide and cyanide, which are smaller, but prefer linear axial co-ordination to heme. Steric interactions between ligand and protein are greater on the β chain, where the E helix is pushed away from the heme relative to MetHb, than on the α chain. Iron position is the same and heme stereochemistry and position are very similar in azide MetHb and MetHb.     

Sensory adaptation mutants of E. coli.

The ability of E. coli to adapt to constant levels of attractant and repellent chemicals was studied by examining the patterns of flagellar movement in cells subjected to abrupt concentration changes. Wild-type bacteria exhibited transient responses to such stimuli, in support of previous findings. Nonchemotactic mutants of the cheX class responded to both attractants and repellents, but were unable to terminate these behavioral changes as long as the stimulating chemical was present. The sensory adaptation defect of cheX strains may be due to an inability to methylate several cytoplasmic membrane proteins that initiate changes in flagellar movement in response to chemoreceptor signals. Based on these results, possible mechanisms of stimulus transduction and sensory adaptation during chemotaxis are discussed.     

A secondary attachment site for bacteriophage lambda in trpC of E. coli.

We have determined the nucleotide sequence of a secondary lambda attachment site in trpC. Direct sequence analysis of lambdatrp transducing phage DNA fragments carrying the two prophage attachment sites reveals a 6 nucleotide homology in the crossover region which is a subset of the 15 nucleotide core sequence in the primary lambda attachment site: GCTTTTTTATACTAA. This 6 nucleotide sequence is also present in the intact trpC genome at the attachment site, as shown by analysis of trpC mRNA spanning this region.     

Structural aspects of thrombin specificity.

Computer-assisted comparisons were made of the X-ray coordinates of all homologous atoms in the serine protease derivatives tosyl chymotrypsin Aα, tosyl elastase, and diisopropylphosphoryl trypsin. The results provided further quantitative support for the belief that sequence homology in proteins results in close similarity of conformation. On this basis, inferences were drawn about the three-dimensional structure of the serine protease thrombin, for which atomic coordinates have not yet been determined experimentally. Further, it was concluded that the unique specificity of thrombin, i.e., its selective cleavage of certain ArgGly bonds in fibrinogen, is unlikely to be due to the insertions in the amino acid sequence of thrombin or to differences in sequence in the region of the active site and binding pocket. It is possible, however, that the elongated A chain appended to thrombin may be a source of this specificity.     

Transfer of memory cells into antigen-pretreated hosts. I. Functional detection of migration sites for antigen-specific B cells.

The distribution of functionally active hapten-specific B memory cells was investigated. Using antigen-pretreated lethally irradiated recipients, a marked accumulation of adoptively transferred B memory cells was demonstrated in lymph nodes containing specific antigen, but not in lymph nodes containing non-cross-reacting hapten conjugates. This difference in responsiveness between lymph nodes containing specific versus those containing nonspecific antigen developed over a period 3–5 days after memory cell transfer. The localization of antigen specific cells was T-cell independent; both carrier-primed T helper cells and specific antigenic challenge, however, were required to trigger the localized B memory cells into antibody production. Specific B memory cell accumulation did not result from an expansion of the antigen-specific cell population due to local proliferation induced by antigen depots in the lymph nodes to challenge. Rather, the results indicated that recirculating B memory cells had progressively accumulated through retention by antigen in the lymph node. These findings suggest that, in the absence of T-cell help and specific antigenic challenge, B memory cells accumulate in lymphoid tissue (follicles) without responding and provide persistent local memory for the humoral immune response.     

Characterization of IL-2-dependent cytotoxic T-cell clones. III. Inhibition of killing activity by monosaccharides

The effects of monosaccharides on the cytotoxic activity of cytotoxic T lymphocytes (CTL) and three cloned long-term cytotoxic T-lymphocyte lines (CTLL) are compared. Uncultured CTL and clones CTLL-A2 and CTLL-A11 were derived from the peritoneal cavity of C57BL/6 mice immunized against the H-2Dd determinants on the BALB/c sarcoma Meth A. Clone CTLL-R5 was derived from spleen of (BALB/c X C57BL)F1 mice immunized against a unique determinant on the BALB/c radiation-induced leukemia RL male 1. The cell-surface phenotype of the clones is Lyt-1+,2+,3+. Cytotoxic activity of CTLL-A2 and CTLL-R5 as determined by a 4-hr 51Cr-release assay was inhibited over 50% by 1 mM 2-deoxy-D-glucose. CTLL-A11 and the uncultured cytotoxic T cells were more resistant to inhibition by 2DG (40% at 20 mM). Surprisingly, it was found that the addition of D-mannose, D-galactose, D-glucose, L-fucose, alpha-methyl-D-mannose, and N-acetyl-D-glucosamine also inhibited, in a dose-related manner, the cytotoxicity of CTLL-A2 and CTLL-A11. CTLL-R5 showed a more restricted inhibition pattern: only D-mannose and D-galactose were inhibitory. The mechanism of inhibition remains to be clarified.     

Conformational preferences of dopamine analogues for inhibition of norepinephrine N-methyltransferase. Conformationally defined adrenergic agents. 7

A series of analogues of dopamine (DA) with varying degrees of conformational flexibility have been examined as potential substrates or competitive inhibitors of the enzyme norepinephrine N-methyltransferase (NMT). A conformationally defined (rigid) analogue of the fully extended conformation of DA, 2-amino-6, 7-dihydroxybenzonorbornene hydrobromide ($\text{3}$; 6, 7-D2HX) proved to be a better substrate than the non-catechol parent 2-aminobenzonorbornene ($\text{4}$; 2HX). However, analogues $\text{3}$ and $\text{4}$ displayed equivalent competitive inhibitory activity toward phenylethanolamine (PEA). Neither 6, 7-ADTN (5), a DA analogue in the 2-aminotetralin (2AT) system, nor 6, 7-DTHIQ ($\text{7}$), a DA analogue in the tetrahydroisoquinoline (THIQ) system, showed substrate activity; 6, 7-ADTN was a poorer competitive inhibitor than the parent 2AT but 6, 7-DTHIQ was a better competitive inhibitor than its parent, THIQ ($\text{8}$). A tricyclic conformationally defined analogue $\text{9}$ of 6, 7-ADTN was devoid of either substrate or inhibitory activity. From these results it may be concluded that a fully extended side chain conformation is required for NMT substrate activity, and the better substrate activity for 6, 7-D2HX compared to $\text{4}$ is consistent with a proper catechol orientation for interaction with the norepinephrine (NE) binding site of NMT.     

Molecular cloning and expression in E. coli of a yeast gene coding for beta-galactosidase.

The yeast Kluyveromyces lactis synthesizes a beta-galactosidase (EC 3.2.1.32) which is inducible by lactose. We have isolated the gene that codes for this enzyme using recombinant DNA techniques. K. lactis DNA was partially digested with the restriction endonuclease Eco R1 and joined to Eco R1-digested pBR322 plasmid DNA using DNA ligase. ligase. A lac-mutant of Escherichia coli lacking the structural gene for beta-galactosidase was transformed with ligated DNA. Three lac+ transformants containing recombinant plasmids were selected. Two of the plasmids (pK15 and pK17) contain four Eco R1-K. lactis DNA fragments having molecular weights of 2.2, 1.4, 0.55 and 0.5 x 10(6) daltons. The other plasmid (pK16) lacks the smallest fragment. E. coli carrying any of these plasmids produce beta-galactosidase activity that has a sedimentation coefficient and immunological determinants that are nearly identical to K. lactis beta-galactosidase and distinctly different from E. coli beta-galactosidase. DNA-DNA hybridization studies show that the four Eco R1 fragments in pK15 hybridize to K. lactis but not to E. coli DNA.     

DNA-dependent RNA-polymerases from Artemia embryos. characterization of polymerases I and II from nauplius larvae.

Partial purification and characterization of DNA-dependent RNA-polymerases from nauplius larvae of the brine shrimp, Artemia salina, are described. Fractionation of solubilized RNA-polymerases on columns of DEAE-cellulose yielded partially purified preparations of RNA polymerases I and II. The properties of these enzymes were found to be similar to properties of corresponding enzymes from other animal sources. A significant change in the relative amounts of polymerases I and II occurs between 36 and 72 hr of development. Polymerase activity obtained from 36-hr nauplii consisted of approximately equal amounts of polymerases I and II, whereas polymerase II accounted for more than 80% of the activity recovered from 72-hr nauplii. Total polymerase activity was lower at 72 than at 36 hr. The significance of these changes in relation to the decrease in RNA synthesis in vivo that occurs after 36 hr is discussed.     

Mitochondrial development during myogenesis.

The enzymatic and ultrastructural pattern of mitochondrial differentiation was investigated during myogenesis. Succinate cytochrome C reductase (SCR), a mitochondrial enzyme complex, increased in activity in developing chick thigh muscle in vivo and in vitro. SCR increase in vitro occurred subsequent to myoblast fusion and correlated with the period of increasing creatine phosphokinase (CPK) activity. Fusion-arrest and Ca²⁺-reversal experiments indicated an apparent coordination between CPK and SCR enzymatic increases and fusion. Analysis of SCR activity in fibroblast cultures suggested that the enzymatic increases observed in differentiating muscle cultures reflected myocyte differentiation, rather than fibroblast contamination or a unique property of the tissue culture environment. Morphological transitions in the myogenic mitochondria were temporally correlated with increased SCR activity. During myogenesis, the mitochondria enlarged in length and volume, exhibited an increase in matrix density, oriented in parallel to the long axis of the myofibrils, and contained increased numbers of parallel cristae. Many mitochondria in fusion-inhibited muscle cultures resembled those found in prefusion myoblasts, although mature mitochondria were observed in some fusion-blocked cells. Quantitative stereological analyses of these mitochondrial changes parallel the biochemical data and suggest that ultrastructural and enzymatic changes in the mitochondria are an integral part of myodifferentiation.     

Phosphoprotein phosphatase activity of rat liver nuclear membrane.

Nuclear membranes from rat liver contain a phosphoprotein phosphatase activity capable of dephosphorylating endogenous nuclear membrane phosphoproteins. This activity was also expressed towards the ³²P-labeled exogenous phosphoprotein substrates phosvitin and lysine-rich histone. Differential effects of altered ionic strength, EDTA, pyrophosphate, and 2-mercaptoethanol on the phosphatase activity towards the two exogenous substrates suggest the presence of multiple phosphatases in the nuclear membrane. ATP, ADP, and sodium fluoride inhibited activity towards both exogenous substrates, while cyclic AMP or cyclic GMP at 10^?6M had no apparent effect.     

Analogs of natural lipids. II. Polymorphic behavior of the tris-Homo acyl derivatives of cyclopentane-1,2,3-triols

The polymorphic behavior of the three series of tris-homoacyl (C_14:0, C_16:0 and C_18:0) cyclopentane-1,2,3-triol analogs of the natural saturated triglycerides has been studied using differential thermal analysis, Fourier transform infrared spectroscopy, and X-ray diffraction. It was found that the triglyceride analogs derived from the 1,2,3/0 and 1,2/3 cyclopentanetriols exhibit different polymorphic behavior than that of the natural triglycerides. The analogs derived from 1,3/2 cyclopentanetriol, however, were found to parallel the polymorphic behavior of the natural triglycerides quite closely. This polymorphic behavior is discussed in terms of the different configurations which the chains assume in each of the triglyceride analogs.     

Sodium-dependent amino acid transport in preimplantation mouse embryos. III. Na+-k+-atpase-linked mechanism in blastocysts.

Mouse blastocysts collapse in cytochalasin B (CB), reexpand (accumulate fluid) in control medium, but cannot reexpand in ouabain, an inhibitor of Na⁺K⁺-ATPases. These ATPases, then, seem to be necessary for fluid accumulation in blastocysts. Since intact blastocysts are relatively insensitive to ouabain, CB seems to make it possible for ouabain to reach the Na⁺K⁺-ATPases localized on the blastocoelic surface. CB-Collapsed blastocysts were found to transport alanine and lysine at the same rate as intact blastocysts, indicating that, in 1 hr, amino acids are transported into the cells of the intact blastocyst, and not into the fluid-filled blastocoel. Transport rates in CB-collapsed blastocysts do not exceed those in intact blastocysts, suggesting that hypothetical amino acid carriers are located only on the external blastocyst surface. Most important, ouabain strongly inhibits sodium-dependent alanine transport in CB-collapsed blastocysts, but not in intact blastocysts, providing strong evidence that Na⁺K⁺-ATPases, localized on the blastocoelic surface, are necessary for this transport. Ouabain does not inhibit sodium-independent lysine transport in CB-collapsed blastocysts. Thus, the dependency of both sodium-dependent amino acid transport and fluid accumulation upon Na⁺K⁺-ATPases, and the separate localization of amino acid carriers and these ATPases, provides functional evidence for an epithelial tissue type of mechanism for sodium-dependent amino acid transport in mouse blastocysts.     

Na+-dependent amino acid transport in preimplantation mouse embryos. II. Metabolic inhibitors and nature of the cation requirement.

Experiments were conducted in order to determine the energy source and nature of the cation dependency of [³H]methionine transport in preimplantation mouse embryos. The energy source of methionine transport was studied at the late four-cell and early blastocyst stages. The embryos, raised in vitro, were incubated for 1 hr in inhibitor(s) of energy metabolism and then transferred for 1 hr to medium that contained inhibitor(s) and ³H-methionine. These inhibitor studies suggest that respiration and glycolysis are needed to maintain uptake of methionine in early blastocysts. Late four-cell embryos seem to utilize respiration alone for transport.The cation dependency of methionine transport was studied at the late morula and early blastocyst stages. The kinetics of methionine uptake by early blastocysts in Na⁺-depleted media indicate a competitive type of inhibition. The uptake of methionine by early blastocysts is relatively resistant to ouabain and unaffected by K⁺-free medium. In contrast, methionine uptake by late morula-stage embryos is markedly inhibited by ouabain and K⁺-free medium in 1 hr. These results suggest that 1) Na⁺ serves to increase the affinity of methionine for the carrier in early blastocysts, 2) the cation gradients do not supply a major fraction of the energy required for methionine transport, and/or the gradients are difficult to perturb once the blastocyst has formed, and 3) putative Na⁺ pumps may be localized on the blastocoelic surface of the blastocysts.     

Enzyme assays using permeabilized cells of Neurospora.

A procedure is described for the preparation of homogeneous, steady-state cultures of germinated conidia of Neurospora crassa. Permeabilization of such cells has been accomplished by a combination of toluene-ethanol and freeze-thaw treatments. These permeabilized cells have been used for the determination of enzyme activities. The method has been shown to be rapid and rellable and is applicable to nuclear, mitochondrial, and cytosolic enzymes.