Electron transport components from methanogenic bacteria: The ferredoxin from Methanosarcinabarkeri (strain Fusaro)

A ferredoxin has been isolated from the methanogenic organism $\text{Methanosarcina}\text{barkeri}$ (strain Fusaro). The protein appears to be constituted by two identical subunits of molecular weight approx. 6000 daltons. The UV-visible spectrum of the protein is characterized by two broad absorption peaks centered at 410 and 300 nm and an absorbance ratio $\text{A}{}_{410}\text{A}{}_{300}\text{= 0.8}$. The molar extinction coefficients at 410 and 300 nm are 36,500 and 45,625 M^?1 cm^?1, respectively. The amino acid compsition of $\text{M.}\text{barkeri}$ ferredoxin shows a preponderance of acidic residues and lacks five amino acids. The protein contains 8 cysteine residues and approx. 7 iron atoms and 7–8 acid-labile sulfide groups per molecule which are indicative of the presence of two iron-sulfur clusters in the molecule. The N-terminal sequence shows a high degree of homology with the sequences of ferredoxins from $\text{Clostridium}\text{pasteurianum}\text{,}\text{Desulfovibrio}\text{gigas}$ and $\text{Desulfovibrio}\text{africanus}\text{.}\text{M.}\text{barkeri}$ ferredoxin functions as an electron carrier in the pyruvate dehydrogenase system. Its possible role in a variety of electron transfer reactions is discussed.     

Preliminary X-ray diffraction studies on a ferredoxin from the thermophilic archaebacterium,Thermoplasma acidophilum

A ferredoxin from the thermophilic archaebacterium, Thermoplasmaacidophilum, is supposed to contain two (4Fe-4S) active centers; one center could be linked by four cysteine residues to the protein and the other bonded with three cysteines and an unknown group. This ferredoxin has been crystallized by salting-out against 2.3 m-ammonium sulfate solution. The space group is P2₁2₁2 with cell dimensions of $\text{a = 59.20}\text{A}\text{?}\text{, b = 52.77}\text{A}\text{?}\text{and}\text{c = 41.28}\text{A}\text{?}$. Four molecules pack in the unit cell with $\text{V}{}_{\mathrm{<mtext>m</mtext>}}\text{= 2.03}\text{A}\text{?}{}^3\text{/dalton}$.     

Fluorescence X-ray absorption studies of rubredoxin and its model compounds

The X-ray absorption spectra of rubredoxin from Peptococcus aerogenes and of the model iron sulfur components prepared by Holm [Fe(S₂-O-xyl)₂] have been obtained in the oxidized and reduced forms using X-rays from synchrotron radiation at the Stanford Synchrotron Radiation Project. The spectra were measured both in transmission and by fluorescence, with the latter giving a several-fold higher signal-to-noise ratio for the protein. The edge spectra of the protein and the model compounds were extremely similar and both showed similar changes upon reduction. The best resolved change of the edge spectra upon reduction was a shift of the 1s-3d transition by ≈0.7 eV to lower energies. The EXAFS region of the spectra were converted to k-space and the data were fitted in order to determine first the average Fe-S distances, R_ave, and second their spread which, for rubredoxin, was described by a model wherein three Fe-S bonds had length R₃ and one R₁.Three different methods have been tried consisting essentially of fitting (1) both phase and amplitude simultaneously to the R₃, R₁ model, (2) phase alone to an R_ave model and using the phase to determine the spread of distance, and (3) using phase and amplitude to fit an R_ave model and then using the amplitudes alone to determine the spread of distances. The values of R_ave obtained for the oxidized state of rubredoxin were $\text{R}{}_{\mathrm{<mtext>ave</mtext>}}\text{= 2.265(13)}\text{A}\text{?}$ for the powder and 2.256(16) Å in solution. Upon reduction the value increased to 2.32(2) å. The spread of the distances was determined most accurately by the third method and was $\text{¦R}{}_3\text{— R}{}_1\text{¦= 0.04}{}^{\mathrm{+0.06}}{}_{\mathrm{?0.04}}\text{A}\text{?}$ for the oxidized powder and $\text{¦R}{}_3\text{— R}{}_1\text{¦= 0.08}$ for the reduced form. These values agree within combined experimental errors with the values found by extended X-ray absorption fine structure in the oxidized and reduced forms of Fe(S₂-O-xyl)₂, which also agreed with the previously published X-ray diffraction results.The agreement between the average distances in rubredoxin and the model compounds and the small spread allowable in the rubredoxin distances lead to the conclusion that any strain energy in the iron — sulfur bonds of Rub_ox is appreciably less than thermal energy. Hence the redox potential is not being regulated by strain in the iron — sulfur bond lengths.     

New experimental approach to the estimation of rate of electron transfer from the primary to secondary acceptors in the photosynthetic electron transport chain of purple bacteria

A method for calculating the rate constant ($\text{K}{}_{\mathrm{<mtext>A</mtext><mtext>1</mtext><mtext>A</mtext><mtext>2</mtext>}}$) for the oxidation of the primary electron acceptor (A₁) by the secondary one (A₂) in the photosynthetic electron transport chain of purple bacteria is proposed.The method is based on the analysis of the dark recovery kinetics of reaction centre bacteriochlorophyll (P) following its oxidation by a short single laser pulse at a high oxidation-reduction potential of the medium. It is shown that in Ectothiorhodospira shaposhnikovii there is little difference in the value of $\text{K}{}_{\mathrm{<mtext>A</mtext><mtext>1</mtext><mtext>A</mtext><mtext>2</mtext>}}$ obtained by this method from that measured by the method of Parson ((1969) Biochim. Biophys. Acta 189, 384–396), namely: $\text{(4.5±1.4) · 10}{}^3\text{s}{}^{\mathrm{?1}}$ and $\text{(6.9±1.2) · 10}{}^3\text{s}{}^{\mathrm{?1}}$, respectively.The proposed method has also been used for the estimation of the $\text{K}{}_{\mathrm{<mtext>A</mtext><mtext>1</mtext><mtext>A</mtext><mtext>2</mtext>}}$ value in chromatophores of Rhodospirillum rubrum deprived of constitutive electron donors which are capable of reducing P⁺ at a rate exceeding this for the transfer of electron from A₁ to A₂. The method of Parson cannot be used in this case. The value of $\text{K}{}_{\mathrm{<mtext>A</mtext><mtext>1</mtext><mtext>A</mtext><mtext>2</mtext>}}$ has been found to be $\text{(2.7±0.8) · 10}{}^3\text{s}{}^{\mathrm{?1}}$.The activation energies for the A₁ to A₂ electron transfer have also been determined. They are 12.4 kcal/mol and 9.9 kcal/mol for E. shaposhnikovii and R. rubrum, respectively.     

Location of iron in the Fe2+-bleomycin complex as observed by 13C NMR spectroscopy.

The antineoplastic action of bleomycin is currently thought to arise from the degradation of cellular DNA by the iron-bleomycin complex. Bleomycin A₂ has one iron binding site as revealed by the iron-titrations of bleomycin monitored optically. To probe the structure of the Fe²⁺-bleomycin complex, we studied the paramagnetic effects of its high spin ferrous iron on the nuclear relaxation rates ($\text{1}\text{T}{}_1$) of the natural abundance carbon-13 atoms in the molecule. The presence of Fe²⁺ in bleomycin predominantly enhances the $\text{1}\text{T}{}_1$ of only four protonated carbon atoms in the molecule (C2, C3, C5, and C6). No other protonated carbon atoms are affected significantly. From the magnitudes of the paramagnetic effects of Fe²⁺ on the ¹³C relaxation rates, we obtain distances of 3.6, 4.1, 4.0, and 3.6 Å from the metal to the C2, C3, C5, and C6 carbon atoms, respectively. These results are consistent with the metal ion-chelation of the α-amino group of the terminal diaminopropionic acid residue and the pyrimidine ring but do not implicate any other parts of the bleomycin molecule in binding to iron.     

Damping of oscillations in the semiquinone absorption in reaction centers after successive flashes. Determination of the equilibrium between QA−QB and QAQB−

A quantitative model for the damping of oscillations of the semiquinone absorption after successive light flashes is presented. It is based on the equilibrium between the states Q_A^?Q_B and Q_AQ_B^?. A fit of the model to the experimental results obtained for reaction centers from Rhodopseudomonas sphaeroides gave a value of $\text{α =}\text{[}\text{Q}{}_{\mathrm{<mtext>A</mtext>}}{}^{\mathrm{?}}\text{Q}{}_{\mathrm{<mtext>B</mtext>}}\text{]}\text{([}\text{Q}{}_{\mathrm{<mtext>A</mtext>}}{}^{\mathrm{?}}\text{Q}{}_{\mathrm{<mtext>B</mtext>}}\text{] + [}\text{Q}{}_{\mathrm{<mtext>A</mtext>}}\text{Q}{}_{\mathrm{<mtext>B</mtext>}}{}^{\mathrm{?}}\text{])}\text{= 0.065 ± 0.005}$ (T = 21°C, pH 8).     

The composition-dependence of the extent of reaction between a multivalent acceptor and a bivalent ligand: Implications of self-interaction of the ligand in precipitin effects

Theory is presented relating to the reversible interaction of an f-valent acceptor, A, with a bivalent ligand, B, which leads to the formation of a series of complexes comprising networks of alternating A and B molecules. An explicit expression is derived for the overall extent of reaction in terms of the total molar concentrations of reactants $\text{(}\text{m}{}_{\mathrm{A}}$ and $\text{m}{}_{\mathrm{B}}\text{)}$, the valency of the acceptor and the site-binding constant, k, governing the equilibria. It is shown by differentiation of this expression holding $\text{m}{}_{\mathrm{A}}$ (or $\text{m}{}_{\mathrm{B}}$) fixed that relations are available for the independent evaluation of f and k from a combination of precipitin and radioimmunoassay experiments. Moreover, it is established that dilution with solvent ($\text{m}{}_{\mathrm{A}}\text{/}\text{m}{}_{\mathrm{B}}$ fixed) cannot lead to the appearance of a precipitate with this type of crosslinking system. The latter observation forms the background for the development of theory pertaining to the joint operation of ligand dimerization, 2B?B₂, and crosslinking of the multivalent acceptor with bivalent B₂. The theoretical examination of this system is developed in terms of site-probability functions and involves the delineation of unique solutions for the extent of crosslinking reaction aided by the definition of the extent of binding in defined limits. It is shown with the use of numerical examples that the system involving self-associating ligand may result in the appearance of a precipitate on dilution with solvent and the conditions for the operation of this phenomenon are elucidated. It is noted that other types of ligand self-interaction may lead to similar effects in crosslinking systems, and the general principles emerging from this study are discussed in terms of systems in which antibody ligands are known to be involved in association reactions or are suspected to be so involved on the basis of precipitation effects observed on dilution with solvent.     

Low-temperature magnetic circular dichroism evidence for the conversion of four-iron-sulphur clusters in a ferredoxin from Clostridium pasteurianum into three-iron-sulphur clusters

Oxidation of the 8Fe ferredoxin from Clostridium pasteurianum with potassium ferricyanide, followed by purification on Sephadex G-25 and DE-23 cellulose columns, gives a protein with an intense EPR signal at g 2.01. The low-temperature magnetic circular dichroism (MCD) spectra of this species are different from those of the oxidized high-potential iron protein from Chromatium but identical with the spectra of ferredoxin II from Desulphovibrio gigas. On reduction of the ferricyanide-treated ferredoxin with sodium dithionite only a weak EPR signal with g factors of 2.05, 1.94 and 1.89 is obtained. The low-temperature MCD spectra are strongly temperature dependent with a form similar to those of dithionite-reduced D. gigas ferredoxin II. The MCD magnetization curves are dominated by a species with ground-state effective g factors of $\text{g}{}_{\mathrm{?}}$ 8.0 and g_⊥ 0.0, which are also similar to those determined recently by low-temperature MCD spectroscopy for D. gigas ferredoxin II. The MCD characteristics are quite different from those of dithionite-reduced ferredoxin from Cl. pasteurianum, untreated with ferricyanide. This establishes the close similarity of the iron-sulphur clusters in ferricyanide-treated Cl. pasteurianum ferredoxin and in D. gigas ferredoxin II. The latter is known to contain a single 3Fe centre, similar to that observed in ferredoxin I from Azotobacter vinelandii by X-ray crystallography. Therefore, it is concluded that the [4Fe-4S] clusters of Cl. pasteurianum ferredoxin are converted to 3Fe clusters on oxidation with ferricyanide.     

Heterozygote frequencies in small subpopulations.

The mean fixation index within subpopulations (F_IS) has been defined as $\text{F}\text{̄}{}_{\mathrm{IS}}\text{= ∑w}{}_{\mathrm{i}}\text{F}{}_{\mathrm{ISi}}\text{or as}\text{F}\text{̂}{}_{\mathrm{IS}}\text{=}\text{∑w}{}_{\mathrm{i}}\text{p}{}_{\mathrm{i}}\text{q}{}_{\mathrm{i}}\text{F}{}_{\mathrm{ISi}}\text{∑w}{}_{\mathrm{i}}\text{p}{}_{\mathrm{i}}\text{q}{}_{\mathrm{i}}$. The latter definition is preferred because it can be obtained from the two other fixation indices, F_ST and F_IT and because it is unaffected by the mean gene frequency. The expected frequency of heterozygotes in small subpopulations of dioecious organisms will exceed Hardy-Weinberg expectations and this can be measured by $\text{F}\text{̂}{}_{\mathrm{IS}}$. In an isolated subpopulation of constant variance effective size $\text{N,}\text{F}\text{̂}{}_{\mathrm{IS}}$ rapidly tends to $\text{1 − 4N}{}^2\text{(N − 1 + [N}{}^2\text{+ 1]}{}^{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}\text{)}{}^2$. In the Island model of population structure, $\text{F}\text{̂}{}_{\mathrm{IS}}$ is approximately $\text{−(1 − m)}\text{N}\text{where}\text{m}$ is the immigration rate.When a sample is drawn from a natural population, the observed F_IS will depend upon the genetic structure of the population. The values of F_IS expected in three different types of population structure are discussed.     

Crystallographic studies of immunoglobulins: crystallization of the Fc fragment of rabbit IgG with and without cleavage of the inter-chain disulphide bridge

The Fc fragment was prepared from rabbit immunoglobulin G by digestion with papain, both with the inter-chain disulphide bond intact, and after reduction and alkylation. These two types of Fc crystallized in different, yet related forms, each with one dimer in the asymmetric unit. The covalently linked dimer crystallized in space group $\text{P2}{}_1\text{; a = 68.85 ± 0.05}\text{A}\text{?}\text{, b = 72.50 ± 0.05}\text{A}\text{?}\text{, c = 60.40 ± 0.05}\text{A}\text{?}$ and β = 105.1 ± 0.2 °. The reduced, non-covalently linked dimer also crystallized in space group $\text{P2}{}_1\text{; a = 81.55 ± 0.05}\text{A}\text{?}\text{, b = 55.65 ± 0.05}\text{A}\text{?}\text{, c = 68.85 ± 0.05}\text{A}\text{?}$ and β = 1051 ± 0.2 °. A non-crystallographic 2-fold axis relating the two identical polypeptide chains is clearly visible in the h0l projection of the second crystal form.     

The concept of high- and low-affinity reactions in bovine cytochrome c oxidase steady-state kinetics

(1) Analysis of the data from steady-state kinetic studies shows that two reactions between cytochrome c and cytochrome c oxidase sufficed to describe the concave Eadie-Hofstee plots ($\text{K}{}_{\mathrm{<mtext>m</mtext>}}\text{? 1 · 10}{}^{\mathrm{?8}}\text{M}$ and $\text{K}{}_{\mathrm{<mtext>m</mtext>}}\text{? 2 · 10}{}^{\mathrm{?5}}\text{M}$). It is not necessary to postulate a third reaction of $\text{K}{}_{\mathrm{<mtext>m</mtext>}}\text{? 10}{}^{\mathrm{?6}}\text{M}$. (2) Change of temperature, type of detergent and type of cytochrome c affected both reactions to the same extent. The presence of only a single catalytic cytochrome c interaction site on the oxidase could explain the kinetic data. (3) Our experiments support the notion that, at least under our conditions (pH 7.8, low-ionic strength), the dissociation of ferricytochrome c from cytochrome c oxidase is the rate-limiting step in the steady-state kinetics. (4) A series of models, proposed to describe the observed steady-state kinetics, is discussed.     

Preliminary x-ray crystallographic data for the semisynthetic non-covalent complex of residues 1 to 118 and 111 to 124 of bovine pancreatic ribonuclease

The enzymically active, semisynthetic complex formed by residues 1 through 118 and residues 111 through 124 of bovine pancreatic ribonuclease has been crystallized at pH 5.7 from $\text{(}\text{NH}{}_4\text{)}{}_2\text{SO}{}_4\text{CsCl}$ solutions. The crystals belong to space group P3₂21, have unit cell dimensions $\text{a}\text{and}\text{b = 64.4}\text{A}\text{?}\text{, c = 64.5}\text{A}\text{?}\text{,}\text{and}$ γ = 120° and are isomorphous with form M of ribonuclease A as well as forms W and R of ribonuclease S. They diffract well and may be expected to yield a structure defined to at least 3.0 Å resolution.     

Cytoskeletal proteins used as marker of differentiation in mouse terato;carcinoma cells

The cyclic AMP receptor protein (CRP) of Escherichia coli has been crystallized. The crystals are orthorhombic, space group $\text{P2}{}_1\text{2}{}_1\text{2}{}_1\text{, a = 46.5}\text{A}\text{?}$, b = 97.1 Å, $\text{c = 105.4}\text{A}\text{?}$, with one dimeric CRP molecule per asymmetric unit.     

Some observations on a new type of point average molecular weight

A new type of (reduced) point average molecular weight A¹, is described. Several interesting properties are developed: (i) $\text{A}{}^1\text{=}\text{reduced}$ weight average molecular weight over the whole cell, $\text{A}{}_{\mathrm{<mtext>w</mtext>}}{}^{\mathrm{o}}\text{A}{}^1\text{(}\text{meniscus}\text{) = A}{}_{\mathrm{<mtext>w</mtext>}}\text{(}\text{meniscus}\text{); (iii) A}{}^1\text{(}\text{zero concentration}\text{) =}\text{reduced}$ number average molecular weight, A_n (meniscus). In addition, its usefulness in extracting the meniscus concentration, J(a), and in examining heterogeneous systems such as mucus glycoproteins, are discussed. The evaluation and application of $\text{A}{}^1$ requires only simple computational facilities, without the use for large-scale multiple data acquisition and recycling techniques.     

Asymmetric or symmetric? Cytosolic modulation of human erythrocyte hexose transfer

(1) The Michaelis-Menten parameters for hexose transfer in erythroctes, erythrocyte ghosts and inside-out vesicles at 20°C were determined using the light scattering method of Sen and Widdas ((1962) J. Physiol. 160, 392–403). (2) The external $\text{K}{}_{\mathrm{<mtext>m</mtext>}}$ for infinite-cis exit of d-glucose in cells and ghosts is $\text{3.6 ± 0.5}\text{mM}$. (3) Dilution of cellular solute (up to × 90 dilution) by lysing and resealing cells in varying volumes of lysate is without effect on the $\text{V}{}_{\mathrm{<mtext>m</mtext>}}$ for net d-glucose exit. The $\text{K}{}_{\mathrm{<mtext>m</mtext>}}$ for net exit, however, falls from $\text{32.4 ± 3.7}\text{mM}$ in intact cells to $\text{12.9 ± 2.3}\text{mM}$ in ghosts. This effect is reversible. (4) Infinite-cis net d-glucose uptake measurements in cells and ghosts reveal the presence of a low $\text{K}{}_{\mathrm{<mtext>m</mtext>}}$, high affinity internal site of $\text{5.9 ± 0.8}\text{mM}$. The $\text{V}{}_{\mathrm{<mtext>m</mtext>}}$ for net glucose entry increases from $\text{23.2 ± 3.7}\text{mmol/l per min}$ in intact cells to $\text{55.4 ± 6.3}\text{mmol/l per min}$ in ghosts. (5) The external $\text{K}{}_{\mathrm{<mtext>m</mtext>}}$ for infinite-cisd-glucose exit in inside-out vesicles is $\text{6.8 ± 2.7}\text{mM}$. The kinetics of zero-transd-glucose exit from inside-out vesicles are changed markedly when cellular solute (obtained by lysis of intact cells) is applied to either surface of inside-out vesicles. When solute is present externally, the $\text{K}{}_{\mathrm{<mtext>m</mtext>}}$ and $\text{V}{}_{\mathrm{<mtext>max</mtext>}}$ for zero-trans exit are decreased by up to 10-fold. When solute is present at the interior of inside-out vesicles, $\text{V}{}_{\mathrm{<mtext>max</mtext>}}$ for zero-trans exit is reduced; $\text{K}{}_{\mathrm{<mtext>m</mtext>}}$ for exit is unaffected. In the nominal absence of cell solute, transfer is symmetric in inside-out vesicles. The orientation of transporter in the bilayer is unaffected by the vesiculation procedure. (6) External application of cellular solute to ghosts reduces $\text{V}{}_{\mathrm{<mtext>max</mtext>}}$ for d-glucose exit but is without effect on the external $\text{K}{}_{\mathrm{<mtext>m</mtext>}}$ for infinite-cis exit. (7) The inhibitory potency of cell lysate on hexose transfer is lost following dialysis indicating that the factors responsible for transfer modulation are low molecular weight species. (8) We consider the hexose transfer in human erythrocytes is intrinsically symmetric and that asymmetry of transfer is conferred by interaction of the system with low molecular weight cytosolic factors.