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Biomedical subjects

D J Goss

Publications and source records attributed to D J Goss.

51 records · Page 3Linked to original sources
PubMed1984

Studies on the role of eukaryotic nucleotide exchange factor in polypeptide chain initiation.

Interactions of eukaryotic 5-dimethylaminonaphthalene-1-sulfonyl-initiation factor 2 (eIF-2) from rabbit reticulocytes and the guanine nucleotide exchange factor ( GEF ), Met-tRNAf, GTP, and GDP were monitored by changes in fluorescence anisotropy and radioactive filtration assays. At 1 mM Mg2+, radioactive filtration assays demonstrate that GEF is necessary for nucleotide exchange. We did not observe a GDP dependence in the association reaction of eIF-2 X GEF for GDP concentrations from 0.01 to 20 microM. This is in disagreement with the model: eIF-2 X GDP + GEF in equilibrium eIF-2 X GEF + GDP. The addition of GTP caused a decrease in fluorescence anisotropy which is interpreted as a dissociation of eIF-2 X GEF . We propose an asymmetrical model of ternary complex (eIF-2 X GTP X Met-tRNAf) formation where 1) GDP does not displace GEF and 2) GTP replaces GEF and presumably GDP. For reticulocyte eIF-2, phosphorylation of the alpha subunit greatly inhibits protein synthesis. This inhibition derives neither from failure of GEF to bind to eIF-2(alpha P) nor from greatly enhanced binding of GEF . The inhibition results from the requirement of very high levels of GTP (100 microM) to dissociate the eIF-2(alpha P) X GEF complex.

Eukaryotic Initiation Factor-2↗
PubMed1984

Oxygen equilibrium studies on carp-human hybrid hemoglobins.

Hybrid hemoglobins have been made in which one chain is derived from human hemoglobin and the other from carp hemoglobin. Both hybrid hemoglobins show low cooperativity in oxygen binding. Hybrid I (alpha carp: beta human) has a very small Bohr effect, whereas hybrid II (alpha human: beta carp) has a Bohr effect nearly as large as that for human hemoglobin. Both hemoglobins have P50's more closely resembling carp hemoglobin than human hemoglobin in the region of pH 7, and for both hybrids, as for carp, cooperativity virtually disappears at acid and alkaline pHs. Since both hybrids are formed from chains derived from cooperative parent hemoglobins, it is difficult to account for the low cooperativity in terms only of the T-state salt bridges and the alpha 1-beta 2 contacts involved in the R-T switch region. We suggest that the F9 Ser in the carp beta-chain as well as alpha 1-beta 1 interactions is important in controlling the allosteric transitions in these hybrids.

Animals↗
PubMed1984

Ligand binding kinetic studies on the hybrid hemoglobin alpha(carp):beta(human): a hemoglobin with a restricted allosteric range.

The preparation of native alpha- and beta-chains of carp hemoglobin and the preparation of the hybrid hemoglobin alpha(carp):beta(human), hybrid I, are described. CO association and dissociation kinetics were determined for the hybrid hemoglobin alpha(carp):beta(human) as a function of fractional saturation by stopped-flow and by flash and laser photolysis. Oxygen dissociation from the liganded distribution of conformers and overall oxygen association were studied by laser photolysis. An allosteric model was used to fit successfully all of the CO and oxygen kinetics and equilibria for this hybrid. In this model, it was assumed that the conformational changes were rapid with respect to ligand binding. A linear free-energy relationship relating rate constants and equilibrium constants was assumed in order to reduce the number of fitting parameters. In the allosteric model itself, it was assumed that L, but not c, varied with pH. For CO, the allosteric parameter c was 0.24; for oxygen, the value was 0.14. At pH 7, L was 80. In hybrid I, the calculated CO association rate constants for the R and T states differ by only a factor of 2. From the equilibrium data, with no assumptions as to the rate of conformational equilibrations , one can show that the allosteric model requires that the measured CO association constant from stopped-flow measurements be assigned to the T state. This state, however, is poised approximately midway between a carp-human T state and a carp hemoglobin R state. In this hybrid, neither chain shows normal R-state behavior; rather, the liganded state is also intermediate between R and T. In this hemoglobin, the low cooperativity appears to be associated with a very restricted range for the R-T conformational change.

Animals↗
PubMed1984

Ligand binding kinetic studies on the hybrid hemoglobin alpha (human):beta (carp): a hemoglobin with mixed conformations and sequential conformational changes.

Oxygen and CO ligand binding kinetics have been studied for the hybrid hemoglobin (Hb) alpha (human):beta (carp), hybrid II. Valency and half-saturated hybrids were used to aid in the assignment of the conformations of both chains. In hybrid II, an intermediate S state occurs, in which one chain has R- and the other T-state properties. In HbCO at pH 6 (plus 1 mM inositol hexaphosphate), the human alpha-chain is R state and the carp beta-chain is T state. We have no evidence at this pH that the carp beta-chain ever assumes the R conformation. At pH 6, the human alpha-chain shows human Hb R-state kinetics at low fractional photolysis and T-state rates for CO ligation by stopped flow. At pH 7, the human-chain R-state rate slows toward a carp hemoglobin rate. The carp beta-chains, on the other hand, react 50% more rapidly in the liganded conformation than in carp hemoglobin, and while the human alpha-chains are in the R state, the two beta-chains appear to function as a cooperative dimer. In this hemoglobin, the chains appear to be somewhat decoupled near pH 7, allowing a sequential conformational change from the R state in which the beta-chains first assume T-state properties, followed by the alpha-chains. The rate of the R-T conformational change for the carp beta-chains is at least 300 times greater than that for the human alpha-chains. At pH 9, the R----T conformational transition rate is at least 200 times slower than that for human hemoglobin.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1983

The binding of ribosomal protein S1 to S1-depleted 30S and 70S ribosomes. A fluorescence anisotropy study of the effects of Mg2+.

We have determined the equilibrium constants for the binding of AEDANS-labelled S1 to S1-depleted 30S and 70S ribosomes. For "tight" ribosomes, the association of S1 increases with the sixth power of Mg2+ concentration, but for 30S subunits and "loose" ribosomes, there is virtually no dependence of the association on Mg2+ over the same concentration range, 2-10 mM in Mg2+. The binding of S1 to 70S ribosomes at 10 mM Mg2+ is stabilized by 2 kcal/mol compared to the binding to 30S subunits. When intact S1 binds to tight ribosomes, the fluorescence anisotrophy is that for virtually complete rotational immobilization. The anisotropies vary considerably with the preparation and treatment of both S1 and ribosomes and these variations are detailed here. The results suggest the linkage of Mg2+-dependent conformational changes in the intact ribosomes, perhaps including rRNA, and the binding of S1.

Escherichia coli↗
PubMed1982

Kinetic studies on the interaction of chain initiation factor 3 with 70 S Escherichia coli ribosomes and subunits.

The magnesium ion dependencies of several of the reaction rates for assembly of the Escherichia coli protein synthesis initiation complex have been determined as well as the effects of IF-3 (initiation factor 3) on the overall reaction of 30 S and 50 S ribosomal subunits. The reaction kinetics were studied by light-scattering changes as well as by changes in the fluorescence anisotropy of dansylated-IF-3. The full model for treating these processes consists of four reactions, three of which are thermodynamically independent. Conditions were chosen and techniques were employed that allowed three of the reactions to be studied individually. This allowed us to fit, with a single adjustable rate constant, all of the light-scattering changes that occurred upon flowing 30 S and 50 S ribosomal subunits against varying concentrations of both Mg2+ and IF-3. Preparations of IF-3 were found to react toward 30 S subunits with either of two markedly different binding rates. We find that the simplest model that explains both the light-scattering and anisotropy data for all IF-3 experiments is one that includes as a necessary step the association of 30 S-IF-3 with 50 S subunits to form a 70 S-IF-3 complex.

Escherichia coli↗
PubMed1982

The kinetics of ligand binding for diverse mammalian myoglobins and the effects of substitutions outside the heme cavity.

1. We report rate constants for oxygen dissociation and for oxygen, carbon monoxide, azide, and cyanide binding to whale, horse, dog, beef and human myoglobins. 2. For azide binding, rate constants can vary by at least a factor of two for substitutions outside the heme cavity. Azide binding may be affected by a substitution at residue 66 in the E helix, a site suggested by Case & Karplus (1979) J. molec. Biol. 132, 343-368, to be on a reactive path to the heme. 3. The oxygen and CO data show that substitutions outside the heme cavity can affect rate constants by at least a factor of 1.5. 4. The oxygen equilibrium constant was correlated with the metabolite rate of the corresponding species, in accord with the Wyman (1966) J. biol. Chem. 241, 115-121, model for facilitated diffusion of oxygen.

Animals↗
PubMed1980

Rapid micro-isolation of mammalian oxymyoglobin for biophysical studies.

A rapid, single-step procedure is described for the isolation of mammalian oxymyoglobin for physical studies. The procedure employs a high-capacity, reusable, Hg-resin through which the myoglobin is filtered. The mammalian myoglobins for which sequences have been reported lack reactive cysteine. The column binds hemoglobin and other sulfhydryl-containing proteins, and retards other proteins. The procedure requires less than twenty minutes for the isolation of oxymyoglobin from homogenized muscle tissue. Virtually no metmyoglobin is formed. The yields are 2-3 times greater than by other methods. The procedure can easily be scaled down for isolation of myoglobin from a few milligrams of muscle. Identical rate constants for oxygen association, dissociation, and CO association were measured by laser photolysis for beef heart myoglobin prepared by this procedure and that of Yamazaki et al. (Yamazaki, I., Yokota, K. and Shikama, K. (1964) J. Biol. Chem. 239, 4151). Gel electrophoresis indicates that the preparation is at least 95% pure.

Animals↗
PubMed1980

Kinetic studies of the rates and mechanism of assembly of the protein synthesis initiation complex.

Rate constants for a number of the assembly reactions involved in forming Escherichia coli ribosome initiation complexes have been measured. These reactions were monitored in a stopped-flow device in which Rayleigh scattering and fluorescence anisotropy were followed as a function of time. Fluorescence was induced by laser excitation modulated at 50 kHz. Aminoacyl-tRNA, initiation factor 3 (IF3), and 70S ribosomes were labeled with fluorescent probes. The light-scattering and fluorescence data show that the antiassociation model for IF3 function cannot be correct. IF3 can be considered to act as an effector in an allosteric model for ribosome function. Fluorescence anisotropy stopped-flow experiments provided rate constants for the binding of IF3 to both 30S subunits and to the intact 70S ribosome. Aminoacyl-tRNA's and nucleotide triplets appear to bind rapidly to 70S ribosomes and then a slow first-order conformational change occurs.

Bacterial Proteins↗
PubMed1978

Rapid solid phase isolation of 20 specific tRNAs from Escherichia coli.

A solid phase procedure has been developed for the rapid isolation of all 20 species of tRNA from Escherichia coli. The overall yields for a single preparation cycle ranged from 62 to 96%, the average being 80%. The values for the amino acid acceptor activities of the tRNA species equaled those reported in the literature for highly purified tRNAs. Starting from crude tRNA, a given tRNA species can easily be isolated in less than 2 h. One milliliter of the resin, which is reusable, is sufficient for the isolation of 200 mg of a specific tRNA. The procedure requires a bifunctional reagent, one moiety of which (--SO2Cl) reacts with the amino acid on the aminoacylated tRNA, the other, with the --SH group on the resin. Thus, only the desired tRNA species is bound to the resin; any of the other tRNAs in the filtrate can be isolated in another cycle. Raising the pH results in deacylation and release from the resin of the desired tRNA species. For tRNA Cys, it is necessary to block the --SH of cysteine prior to reaction with the bifunctional reagent. Side reactions involving the bifunctional reagent. Side reactions involving the bifunctional reagent and tRNA are either easily reversible or negligible (less than 0.01%).

Amino Acids↗
PubMed1976

Kinetics of ribosome dissociation and subunit association studied in a light-scattering stopped-flow apparatus.

The association-dissociation kinetics of ribosomes from Escherichia coli have been studied under various conditions in a light-scattering stopped-flow apparatus. The dissociation reaction at 2 mg/ml at 25 degrees C, induced by lowering the MgCl2 concentration from 18 to 3 mM, can best be described by three independent first-order processes with rate constants of 15 s-1, 0.9 s-u, and 3 X 10(-2) s-1, the slowest process comprising about 60% of the overall reaction. The fraction of ribosomes dissociating with the fastest rate (15 s-1) is concentration dependent and becomes negligible at 0.1 mg/ml9 Ribosomes treated with puromycin also show three dissociation rates with essentially the same rate constants as the nontreated samples. The dissociation induced by a high KCl concentration (0.85 MKCl, 18 mM MgCl) also shows three first-order phases with the same rate constants as for the dissociation induced by lowering the MgCl2 concentration. The formation of 70S ribosomes from 30S and 50S subunits, induced by increasing the MgCl2 concentration from 2 to 21 mM, follows second-order biphasic kinetics. A detailed analysis of the kinetic results shows that the two principal ribosomal forms must have one type of subunit in common. When the association data are analyzed assuming that the kinetic heterogeneity arises from two forms of only one subunit, the rate constants are found to be 6.4 X 10(6) and 1.05 X 10(6) M-1 s-1. Sequential flow experiments show that the rapid and slow association species are to be identified, respectively, with phases II (0.9 s-1) and III 0.03 s-1) of dissociation. Relaxation measurements show that these correspond to type B ("loose") and A ("tight") ribosomes, respectively. Tight and loose ribosomes were isolated by sucrose density centrifugation, and dissociation and association kinetic studies confirmed the above assignments. Furthermore, the rate constants for these ribosoems agreed within experimental error with rate constants derived from analysis of the multiphasic kinetic data. The association rate constants are for ribosomes dissociated by dilution with the appropriate buffer immediately before recording the kinetics of association. Ribosomes dissociated by dialysis overnight against 2 mM MgCl2 show an association rate constant for the slower association reaction (type-A ribosome) that is about four times smaller, whereas the rate constant for the faster process is roughly the same. The activation energies of the dissociation reactions, whether induced by lowering the MgCl2 concentration or increasing the KCl concentration, and the association raaction induced by increasing the MgCl2 concentration are less than 3.5 kcal/mol. The rate constants of the dissociation at 3 mM MgCl2 and of the association reaction at 21 mM MgCl2 do not vary between pH 7.2 and 8.4. When 30S and 50S subunits are flowed against buffer containing 20 mM spermidine, the association process is monophasic, with an association constant k - 6 X 10(6) M-1 s-1...

Binding Sites↗
PubMed1975

Kinetic light scattering studies on the dissociation of hemoglobin from Lumbricus terrestris.

The kinetics of the pH-induced dissociation of the 3 X 10(6) mol wt hemoglobin from Lumbricus terrestris (the earthworm) have been studied in a light-scattering stopped-flow apparatus. The ligand dependent dissociation data were fit well by a simple sequential model. The data for CO and oxyhemoglobin are consistent with Hb12 leads to 2Hb6 leads to 12Hb. Methemoglobin at pH 7 appears to be hexameric and the dissociation is consistent with the model: Hb6 leads to 6Hb. In a sequential decay scheme for which light-scattering changes are monitored, the relative amounts of rapid and slow phase are determined by the rate constants as well as the molecular weights of intermediate species. Assignment of the hexameric intermediate is supported by an investigation of the sensitivity of the theoretical kinetic curves to the molecular weights of the intermediates. This assignment is further supported by the following: (1) the same model will fit the data for oxy- and CO-hemoglobin at all three temperatures (a 24-29-fold variation in rate constants), (2) evidence from electron microscopy shows hexameric forms, and (3) methemoglobin is apparently stable as a hexamer at pH 7. When CO replaces O2 as the ligand, the dissociation rate increases by a factor of four. The met is about 20 times faster than the initial oxyhemoglobin dissociation rate, but perhaps more relevant for comparing dissociation of the hexamer, the met rate was respectively 100 times and 500 times faster than that for the assumed hexameric forms of CO- and oxy-hemoglobin. The activation energies for the dodecamer to hexamer dissociation and for the dissociation of the hexamer to smaller forms were about 30 kcal/mol for oxy-, CO-, and methemoglobin.

Carbon Monoxide↗