Conformation-dependent participation of the protein in electron equivalent transfer to cytochrome c

When ferricytochrome c is reduced by H atoms (produced by pulse radiolysis) at neutral pH where it is in a closed protein configuration, a considerable percentage of the reduction proceeds through electron equivalent transfer via the protein.At pH 2.0, where cytochrome c is in an open configuration, H atoms reduce by adding directly to the heme porphyrin. The intermediate then observed is identified through similarity with that formed on ferriheme alone.     

Interaction of D-glucose with alkaline-earth metal ions. Synthesis, spectroscopic, and structural characterization of Mg(II)- and Ca(II)-D-glucose adducts and the effect of metal-ion binding on anomeric configuration of the sugar

The interaction of D-glucose with the hydrated alkaline-earth metal halides has been studied in solution, and adducts of the type Mg(D-glucose)X2.4 H2O, Ca(D-glucose)X2.4 H2O, and Ca(D-glucose)2X2.4 H2O, where X = Cl- and Br-, have been isolated, and characterized by means of F.t.-i.r. and 1H-n.m.r. spectroscopy, X-ray powder diffraction, and molar conductivity measurements. Spectroscopic and other evidence suggested that the Mg(II) ion in the Mg(D-glucose)X2.4 H2O adducts six-coordinate, binding to a D-glucose molecule (possibly via O-1 and O-2 atoms) and to four H2O molecules, whereas, in the corresponding 1:1 Ca-D-glucose adduct, the Ca(II) ion is possibly seven-coordinate, binding to a sugar moiety (through the O-1, O-2, and other sugar donor atoms) and to four H2O molecules. In 1:2 Ca(D-glucose)2X2.4 H2O, the calcium ion may be eight-coordinate, binding to two D-glucose molecules (possibly via the O-1 and O-2 atoms of each sugar moiety) and to four H2O molecules. The strong, sugar H-bonding network is rearranged upon D-glucose adduct-formation, and the alpha-anomeric configuration is favored by these metal cation coordinations.     

The oxidation of cytochrome c peroxidase by hydrogen peroxide. Characterization of products.

H2O2 reacts with cytochrome c peroxidase in a variety of ways. The initial reaction produces cytochrome c peroxidase Compound I. If more than a 10-fold excess of H2O2 is added to the enzyme, a portion of the H2O2 will react with Compound I to produce molecular oxygen. The remainder oxidizes the heme group and various amino acid residues in the protein. If less than a 10-fold excess of H2O2 is added to the enzyme, essentially all the H2O2 is utilized by oxidation of amino acid residues in the protein. The oxidation of the amino acid residues by H2O2 substantially modifies the reactivity of cytochrome c peroxidase. The modification of reactivity could be the direct result of amino acid oxidation or an indirect result caused by a perturbation of the protein structure at the active site. The products oxidized at pH 8 lose their ability to react with H2O2. The products oxidized at pH4 react with H2O2 but their reactivity toward Fe(CN)4-6 is substantially reduced.     

Sugar interaction with biologically active cis-PtCl2(NH3)2 (anticancer) and its inactive trans isomer

The interaction of D-glucuronic and D-gluconic acids with cis- and trans-PtCl2(NH3)2 (cisplatin and transplatin) has been investigated in aqueous solution and solid complexes of the type cis-[PtL(NH3)2]L.H2O and trans-[PtL2(NH3)2]L.H2O, where L = D-glucuronate or D-gluconate anions, are isolated and characterized by means of Fourier transform-infrared and 1H-NMR spectroscopy, and molar conductivity and X-ray powder diffraction measurements. Spectroscopic and other evidence indicated that the sugar anions bind monodentately in trans-[PtL2(NH3)2].H2O and bidentately in cis-[PtL(NH3)2]L.H2O complexes through the carboxylate oxygen atoms and other sugar donor groups. The strong sugar intermolecular hydrogen-bonding network is altered to that of the sugar-OH...NH3(H2O)...OH-sugar, upon platinum-ammine interaction. The D-glucuronate anion has the beta-anomer configuration both in the free salt and in these platinum-sugar complexes.     

Organization of the oxygen-evolution enzyme complex studied by butanol/water phase partitioning of spinach photosystem II particles

The oxygen-evolving photosystem II particles prepared from spinach chloroplasts with brief sonication and Triton X-100 treatment were subjected to butanol/water phase partitioning. Three peripheral proteins of photosystem II having relative molecular masses of 33,000, 24,000, and 18,000 daltons and a part of the manganese atoms associated with photosystem II were partitioned into the aqueous phase, depending on the concentration of salt which was included in the suspension of the photosystem II particles. Quantitative analysis of the phase partitioning of the photosystem II particles under the various ionic conditions at pH 6.5 suggested the following: (a) two of the four atoms of manganese associated with photosystem II are located at a relatively hydrophilic environment and easily extracted from the membrane; (b) one of these "hydrophilic manganese atoms" is structurally in close proximity to the protein of the relative molecular mass of 33,000 daltons and stabilized by the protein specifically; (c) the protein of the relative molecular mass of 24,000 daltons as well as that of 33,000 daltons is involved in the stabilization of the other "hydrophilic manganese" in the membrane; (d) each of the three proteins has an independent binding site on the membrane and organizes a specific catalytic domain where oxidation of water is carried out efficiently in collaboration with the reaction center of photosystem II.     

Ortho-para spin isomers of the protons in the methylene group--possible implications for protein structure

The two hydrogen atoms attached to the carbon in the methylene group are of two different spin configurations, similar to those in the case of water: ortho, where the two proton spins are parallel to each other, and para, where they are antiparallel. The ortho configuration has three degenerate states, while the para configuration is singular, leading to a statistical ratio of these isomers 3:1 ortho/para. Such spin isomers are present in glycine and most chiral amino acids where they may induce broadening of structural zones, a possibility which remains to be assessed. The implications of this neglected possibility could be far-reaching, in particular with respect to protein structure and the origins of biochirality.     

Cyanide binding to cytochrome c peroxidase (H52L)

Cyanide binding to a cytochrome c peroxidase (CcP) variant in which the distal histidine has been replaced by a leucine residue, CcP(H52L), has been investigated as a function of pH using spectroscopic, equilibrium, and kinetic methods. Between pH 4 and 8, the apparent equilibrium dissociation constant for the CcP(H52L)/cyanide complex varies by a factor of 60, from 135 microM at pH 4.7 to 2.2 microM at pH 8.0. The binding kinetics are biphasic, involving bimolecular association of the two reactants, followed by an isomerization of the enzyme/cyanide complex. The association rate constant could be determined up to pH 8.9 using pH-jump techniques. The association rate constant increases by almost 4 orders of magnitude over the pH range investigated, from 1.8 x 10(2) M(-1) s(-1) at pH 4 to 9.2 x 10(5) M(-1) s(-1) at pH 8.6. In contrast to wild-type CcP, where the binding of HCN is the dominant binding pathway, CcP(H52L) preferentially binds the cyanide anion. Above pH 8, cyanide binding to CcP(H52L) is faster than cyanide binding to wild-type CcP. Cyanide dissociates 4 times slower from the mutant protein although the pH dependence of the dissociation rate constant is essentially identical for CcP(H52L) and CcP. Isomerization of the CcP(H52L)/cyanide complex is observed between pH 4 and 8 and stabilizes the complex. The isomerization rate constant has a similar magnitude and pH dependence as the cyanide dissociation rate constant, and the two reactions are coupled at low cyanide concentrations. This isomerization has no counterpart in the wild-type CcP/cyanide complex.     

A novel aco-type cytochrome-c oxidase from a facultative alkalophilic Bacillus: purification, and some molecular and enzymatic features.

A novel aco-type cytochrome-c oxidase was highly purified from the facultative alkalophilic bacterium, Bacillus YN-2000, grown at pH 10. The enzyme contained 9.0 nmol heme a/mg protein. It contained 1.23 mol of protoheme, 1.06 mol of heme c, 2.0 g atoms of copper, 2.5 g atoms of iron, and 1.8 g atoms of magnesium per mol of heme a. The enzyme molecule seemed to be composed of two subunits with Mrs of 52,000 and 41,600. On the basis of these results, the enzyme seemed to contain one molecule each of heme a, protoheme, and heme c per minimal structural unit (Mr, 93,600). Only protoheme among the three kinds of hemes in the enzyme reacted with CO and CN-. Heme a did not react with CO; cytochrome a3 did not seem to be present in the enzyme. The enzyme oxidized 314 mol of horse ferrocytochrome c per heme a per sec at pH 6.5 and the catalytic activity was 50% inhibited by 7.65 microM KCN. The enzymatic activity was found to be optimal at pH 6.0.     

Mechanistic and stereochemical studies on the glycine reductase of Clostridium sticklandii.

Clostridial glycine reductase multienzyme complex which catalyses the reaction: Glycine + ADP + Pi + 2H leads to Acetate + ATP + NH3 was solubilised and fractionated essentially according to the method of Stadtman [T.C. Stadtman (1970) Methods Enzymol. 17A, 956--966] into two components: protein A and 'glycine reductase' fraction. A reconstituted system obtained by combining the two components in the presence of dithiothreitol catalysed the conversion of glycine into acetate concomitant with the phosphorylation of ADP to ATP. Using the reconstituted system, in which the unwanted enzyme activity catalyzing an exchange of the alpha hydrogen atoms of glycine with the protons of the medium had been greatly reduced, it was found that the conversion of (2RS)-[2-14C, 2-3H1]glycine (3H/14C = 7.16) into acetate (3H/14C = 7.03) was attended by the retention of both the C-2 hydrogen atoms of glycine. Conversion of (2S)-[2-2H1, 2-3H1]glycine and (2R)-[2-2H1, 2-3H1]glycine by the reconstituted system gave (2S)-acetate and (2R)-acetate respectively showing that the reductive deamination of glycine occurs through an inversion of configuration. The cumulative information available on the glycine reductase reaction is embodied in a hypothetical mechanism of action for the enzyme.     

The optimal fraction of hydrophobic residues required to ensure protein collapse

The hydrophobic interaction is the main driving force for protein folding. Here, we address the question of what is the optimal fraction, f of hydrophobic (H) residues required to ensure protein collapse. For very small f (say f<0.1), the protein chain is expected to behave as a random coil, where the H residues are "wrapped" locally by polar (P) residues. However, for large enough f this local coverage cannot be achieved and the thermodynamic alternative to avoid contact with water is burying the H residues in the interior of a compact chain structure. The interior also contains P residues that are known to be clustered to optimize their electrostatic interactions. This means that the H residues are clustered as well, i.e. they effectively attract each other like the H-monomers in Dill's HP lattice model. Previously, we asked the question: assuming that the H monomers in the HP model are distributed randomly along the chain, what fraction of them is required to ensure a compact ground state? We claimed there that f approximately p(c), where p(c) is the site percolation threshold of the lattice (in a percolation experiment, each site of an initially empty lattice is visited and a particle is placed there with a probability p. The interest is in the critical (minimal) value, p(c), for which percolation occurs, i.e. a cluster connecting the opposite sides of the lattice is created). Due to the above correspondence between the HP model and real proteins (and assuming that the H residues are distributed at random) we suggest that the experimental f should lead to percolating clusters of H residues over the highly dense protein core, i.e. clusters of the core size. To check this theory, we treat a simplified model consisting of H and P residues represented by their alpha-carbon atoms only. The structure is defined by the C(alpha)-C(alpha) virtual bond lengths, angles and dihedral angles, and the X-ray structure is best-fitted onto a face-centered cubic lattice. Percolation experiments are carried out for 103 single-chain proteins using six different hydrophobic sets of residues. Indeed, on average, percolating clusters are generated, which supports our theory; however, some sets lead to a better core coverage than others. We also calculate the largest actual hydrophobic cluster of each protein and show that, on average, these clusters span the core, again in accord with our theory. We discuss the effect of protein size, deviations from the average picture, and implications of this study for defining reliable simplified models of proteins.     

Studies on the linkage between spin equilibria and protein structure in carp ferric hemoglobin

The effects of protein conformation on the spin-state equilibria of several derivatives of carp hemoglobin have been examined. This has been done by measuring the pH dependence of the paramagnetic susceptibilities of these derivatives in the presence and absence of inositol hexakisphosphate, P6-inositol. In all cases the addition of P6-inositol at low pH and the lowering of the pH in the presence of P6-inositol shift the spin-state equilibrium in favor of the high-spin electronic configuration. The P6-inositol and pH dependence of these magnetic properties parallels the pH and P6-inositol dependence of the conformational state of the hemoglobin as determined in earlier studies and further supports a thermodynamic linkage between the electronic state of the iron atoms and the quaternary structure of the hemoglobin molecule.     

Studies of triose phosphate isomerase by hydrogen exchange

The (3)H-H exchange of chicken muscle and rabbit muscle triose phosphate isomerases was studied. Their behaviour was mostly very similar. ;Exchange-in' (acquisition of radioactivity when protein was incubated in (3)H(2)O) was measured at 37 degrees C and at pH7.5, and the rates of exchange of the native and liganded enzymes were compared. Inhibitors and substrates retarded exchange, substrates showing the most marked effect; structural rearrangements in the enzyme may thus play some part in catalysis. The inhibitor phosphoglycollate affected the rabbit enzyme, but had little or no effect on the chicken enzyme. ;Exchange-out' (loss of radioactivity from protein previously labelled by incubation in (3)H(2)O) was measured by hollow-fibre dialysis. When ligand was removed during the course of dialysis (by replacing buffer that contained ligand with buffer that lacked ligand) there was a prompt decrease in the number of labelled H atoms of the protein. Analysis of the curves provides some information about the number and half-lives of the responsive H atoms. Ligands decrease the motility of the protein and affect about one-fifth of the chain. Low concentrations of glycerol 3-phosphate have an effect that is greater than expected.     

The occurrence of a reductase of delta2-carboxylic acids in Clostridium kluyveri with a stereospecificity different from that of butyryl-CoA dehydrogenase (author's transl)]

A Clostridia strain (R-strain) which hydrogenates tiglinate (1b) and alpha-methylcinnamate (1c) in the presence of hydrogenase gas in 2H2O to (2R, 3S)2-methyl-[2,3-2H]butyrate (5b, H = 2H) and (alphaR, betaR)alpha-methyl[alpha,beta-2H]dihydrocinnamate (5c, H = 2H), respectively, was isolated. The configuration at C-3 was determined by 1H-NMR spectroscopy in the presence of Eu(fod)3. The stereochemistry of this hydrogenation is the mirror image of that which has been determined with intact cells of another strain of Clostridium kluyveri (S-strain). In the presence of hydrogen gas, the R-strain hydrogenates crotonate in 2H2O to butyrate with the following deuterium distribution: C-2, 1.85; C-3, 1.35; and C-4, 0.63 deuterium atoms. Crotonate seems to be the substrate of two reductases with sterically different actions. Tiglinate (1b) and alpha-methylcinnamate, however, are hydrogenated only by that reductase which is different from the butyryl-CoA dehydrogenase.     

Carbon-13 nuclear magnetic resonance spectroscopy of [2-13C]carboxymethylcytochrome c.

Horse heart cytochrome c has been carboxymethylated under various reaction conditions using [2-13C]bromoacetate. Direct analysis of reaction products using 13C nuclear magnetic resonance spectroscopy shows that the protein can be much more extensively modified than has previously been assumed. The proximity of one carboxymethylmethionine residue to the paramagnetic center of the ferric protein allows it to be distinguished from a more constant carboxymethylmethionine residue on the basis of the chemical shift of its labeled methylene group. Refolding of cytochrome c after alkylation at low pH apparently gives a different configuration of modified methionine residues within the protein compared to that produced by alkylation at neutral pH in the presence of cyanide.     

Replacement of the axial histidine ligand with imidazole in cytochrome c peroxidase. 1. Effects on structure

Replacement of the axial histidine ligand with exogenous imidazole has been accomplished in a number of heme protein mutants, where it often serves to complement the functional properties of the protein. In this paper, we describe the effects of pH and buffer ion on the crystal structure of the H175G mutant of cytochrome c peroxidase, in which the histidine tether between the heme and the protein backbone is replaced by bound imidazole. The structures show that imidazole can occupy the proximal H175G cavity under a number of experimental conditions, but that the details of the interaction with the protein and the coordination to the heme are markedly dependent on conditions. Replacement of the tethered histidine ligand with imidazole permits the heme to shift slightly in its pocket, allowing it to adopt either a planar or distally domed conformation. H175G crystallized from both high phosphate and imidazole concentrations exists as a novel, 5-coordinate phosphate bound state, in which the proximal imidazole is dissociated and the distal phosphate is coordinated to the iron. To accommodate this bound phosphate, the side chains of His-52 and Asn-82 alter their positions and a significant conformational change in the surrounding protein backbone occurs. In the absence of phosphate, imidazole binds to the proximal H175G cavity in a pH-dependent fashion. At pH 7, imidazole is directly coordinated to the heme (d(Fe--Im) = 2.0 A) with a nearby distal water (d(Fe--HOH) = 2.4 A). This is similar to the structure of WT CCP except that the iron lies closer in the heme plane, and the hydrogen bond between imidazole and Asp-235 (d(Im--Asp) = 3.1 A) is longer than for WT CCP (d(His--Asp) = 2.9 A). As the pH is dropped to 5, imidazole dissociates from the heme (d(Fe--Im) = 2.9 A), but remains in the proximal cavity where it is strongly hydrogen bonded to Asp-235 (d(Im--Asp) = 2.8 A). In addition, the heme is significantly domed toward the distal pocket where it may coordinate a water molecule. Finally, the structure of H175G/Im, pH 6, at low temperature (100 K) is very similar to that at room temperature, except that the water above the distal heme face is not present. This study concludes that steric restrictions imposed by the covalently tethered histidine restrain the heme and its ligand coordination from distortions that would arise in the absence of the restricted tether. Coupled with the functional and spectroscopic properties described in the following paper in this issue, these structures help to illustrate how the delicate and critical interactions between protein, ligand, and metal modulate the function of heme enzymes.     

Insights into the mechanism of Rad51 recombinase from the structure and properties of a filament interface mutant

Rad51 protein promotes homologous recombination in eukaryotes. Recombination activities are activated by Rad51 filament assembly on ssDNA. Previous studies of yeast Rad51 showed that His352 occupies an important position at the filament interface, where it could relay signals between subunits and active sites. To investigate, we characterized yeast Rad51 H352A and H352Y mutants, and solved the structure of H352Y. H352A forms catalytically competent but salt-labile complexes on ssDNA. In contrast, H352Y forms salt-resistant complexes on ssDNA, but is defective in nucleotide exchange, RPA displacement and strand exchange with full-length DNA substrates. The 2.5 Å crystal structure of H352Y reveals a right-handed helical filament in a high-pitch (130 Å) conformation with P6₁ symmetry. The catalytic core and dimer interface regions of H352Y closely resemble those of DNA-bound Escherichia coli RecA protein. The H352Y mutation stabilizes Phe187 from the adjacent subunit in a position that interferes with the γ-phosphate-binding site of the Walker A motif/P-loop, potentially explaining the limited catalysis observed. Comparison of Rad51 H352Y, RecA–DNA and related structures reveals that the presence of bound DNA correlates with the isomerization of a conserved cis peptide near Walker B to the trans configuration, which appears to prime the catalytic glutamate residue for ATP hydrolysis.     

Indirect regulation of the intestinal H+-coupled amino acid transporter hPAT1 (SLC36A1)

A H(+)-coupled amino acid transporter has been characterised functionally at the brush border membrane of the human intestinal cell line Caco-2. This carrier, hPAT1 (human Proton-coupled Amino acid Transporter 1) or SLC36A1, has been identified recently at the molecular level and hPAT1 protein is localised to the brush border membrane of human small intestine. hPAT1 transports both amino acids (e.g., beta-alanine) and therapeutic agents (e.g., D-cycloserine). In human Caco-2 cells, hPAT1 function (H(+)/amino acid symport) is associated with a decrease in intracellular pH (pH(i)), which selectively activates the Na(+)/H(+) exchanger NHE3, and thus maintains pH(i) and the driving force for hPAT1 function (the H(+) electrochemical gradient). This study provides the first evidence for regulation of hPAT1 function. Activation of the cAMP/protein kinase A pathway in Caco-2 cell monolayers either using pharmacological tools (forskolin, 8-br-cAMP, [(11,22,28)Ala]VIP) or physiological activators (the neuropeptides VIP and PACAP) inhibited hPAT1 function (beta-alanine uptake) at the apical membrane. Under conditions where NHE3 is inactive (the absence of Na(+), apical pH 5.5, the presence of the NHE3 inhibitor S1611) no regulation of beta-alanine uptake is observed. Forskolin and VIP inhibit pH(i) recovery (NHE3 function) from beta-alanine-induced intracellular acidification. Immunocytochemistry localises NHERF1 (NHE3 regulatory factor 1) to the apical portion of Caco-2 cells where it will interact with NHE3 and allow PKA-mediated phosphorylation of NHE3. In conclusion, we have shown that amino acid uptake via hPAT1 is inhibited by activators of the cAMP pathway indirectly through inhibition of NHE3 activity.