Crystal structure analysis of the tetragonal crystal form are preliminary molecular model of pig-heart citrate synthase

Structural and functional regulations by a disulfide bond designed in myoglobin like human neuroglobin

An artificial disulfide bond (Cys46-Cys61) was designed in the heme distal site of myoglobin, which regulates the conformation of the heme distal His64 and the protein reactivity, as confirmed by X-ray crystallography, EPR, and kinetic UV-vis studies. This study shows the successful design of a disulfide bond with suitable positions in globins, conferring a structure and function like those of the native human neuroglobin.

Redox regulation of Arabidopsis mitochondrial citrate synthase

Citrate synthase has a key role in the tricarboxylic (TCA) cycle of mitochondria of all organisms, as it catalyzes the first committed step which is the fusion of a carbon-carbon bond between oxaloacetate and acetyl CoA. The regulation of TCA cycle function is especially important in plants, since mitochondrial activities have to be coordinated with photosynthesis. The posttranslational regulation of TCA cycle activity in plants is thus far almost entirely unexplored. Although several TCA cycle enzymes have been identified as thioredoxin targets in vitro, the existence of any thioredoxin-dependent regulation as known for the Calvin cycle, yet remains to be demonstrated. Here we have investigated the redox regulation of the Arabidopsis citrate synthase enzyme by site-directed mutagenesis of its six cysteine residues. Our results indicate that oxidation inhibits the enzyme activity by the formation of mixed disulfides, as the partially oxidized citrate synthase enzyme forms large redox-dependent aggregates. Furthermore, we were able to demonstrate that thioredoxin can cleave diverse intra- as well as intermolecular disulfide bridges, which strongly enhances the activity of the enzyme. Activity measurements with the cysteine variants of the enzyme revealed important cysteine residues affecting total enzyme activity as well as the redox sensitivity of the enzyme.

Soft nanotube hydrogels functioning as artificial chaperones

Self-assembly of rationally designed asymmetric amphiphilic monomers in water produced nanotube hydrogels in the presence of chemically denatured proteins (green fluorescent protein, carbonic anhydrase, and citrate synthase) at room temperature, which were able to encapsulate the proteins in the one-dimensional channel of the nanotube consisting of a monolayer membrane. Decreasing the concentrations of the denaturants induced refolding of part of the encapsulated proteins in the nanotube channel. Changing the pH dramatically reduced electrostatic attraction between the inner surface mainly covered with amino groups of the nanotube channel and the encapsulated proteins. As a result, the refolded proteins were smoothly released into the bulk solution without specific additive agents. This recovery procedure also transformed the encapsulated proteins from an intermediately refolding state to a completely refolded state. Thus, the nanotube hydrogels assisted the refolding of the denatured proteins and acted as artificial chaperones. Introduction of hydrophobic sites such as a benzyloxycarbony group and a tert-butoxycarbonyl group onto the inner surface of the nanotube channels remarkably enhanced the encapsulation and refolding efficiencies based on the hydrophobic interactions between the groups and the surface-exposed hydrophobic amino acid residues of the intermediates in the refolding process. Refolding was strongly dependent on the inner diameters of the nanotube channels. Supramolecular nanotechnology allowed us to not only precisely control the diameters of the nanotube channels but also functionalize their surfaces, enabling us to fine-tune the biocompatibility. Hence, these nanotube hydrogel systems should be widely applicable to various target proteins of different molecular weights, charges, and conformations.

A stereocomplex platform efficiently detecting antigen-antibody interactions

Ultrathin poly(methyl methacrylate) (PMMA) stereocomplex films with macromolecularly double-stranded regular nanostructures were prepared by layer-by-layer assembly of isotactic and syndiotactic PMMAs on solid surfaces. Antibodies were immobilized through the Fc region-capturing protein A, which had been physically adsorbed on the complex film, and the binding of antigens to immobilized antibodies was quantitatively investigated by the quartz crystal microbalance technique. Greater amounts of protein A with native forms were adsorbed on the complex film than those on conventional single-component PMMA films. Antibodies with high target-binding activities were also immobilized on the complex film. A greater amount of antigens could be detected on the complex film. The activity of protein A was maintained on the complex for a long time even within a dried state. The mechanism for the preservation of protein native forms on the complex surface was speculated by analyzing the physical adsorption of proteins with various secondary structures. Stereocomplex films can be utilized as novel coating nanomaterials for efficiently detecting protein-protein interactions.

Hysteretic behaviour of citrate synthase. Site-directed limited proteolysis

Limited proteolysis of citrate synthase by Astacus protease, chymotrypsin, clostripain, subtilisin and trypsin on primary fragmentation all yielded similarly sized large (Mr 35 000-36 000) and small fragments (Mr 13 500-14 000) but endoproteinase Lys-C gave fragments of Mr 40 500 and Mr 6500. The sites of the proteolytic attack were determined by Edman degradation of the fragmented synthase preparations, Chymotrypsin, subtilisin, trypsin and endoproteinase Lys-C hydrolyse the synthase at positions 323-324 (-Leu-Arg-), 321-322 (-Ala-Val-)/322-323 (-Val-Leu-), 313-314 (-Arg-Val-) and 366-367 (-Lys-Ala-), respectively. Chymotrypsin and subtilisin attack the small domain of the synthase at the loop between helices O and P very near to a catalytic residue, His-320, and abolish all synthase activities. Primary fragmentation by endoproteinase Lys-C and trypsin reduces the catalytic activity in the physiological overall reaction. Both fragmented enzyme species catalyse the hydrolysis and C-C bond cleavage reactions of citryl-CoA in a stimulated fashion compared to the steady-state rates of the native enzyme, and without hysteretic behaviour. The proteolytic cleavage occurs at acetyl-CoA binding sites within the small domain at the loops connecting helices O to P (trypsin) and Q to R (endoproteinase Lys-C) and reduces the affinity of acetyl-CoA. All of the altered kinetic properties of the fragmented enzyme species are related to this reduced affinity. The correlation between structure and function indicated above is strengthened by the unaltered affinity of oxaloacetate towards the fragmented synthase species. None of the proteolytic enzymes applied attacks oxaloacetate binding sites as defined by the structural work. Oxaloacetate inhibits the hydrolysis of citryl-CoA by the fragmented synthases (endoproteinase Lys-C, trypsin) competitively. An explanation is proposed. The isolated small and large fragments (endoproteinase Lys-C, trypsin) were enzymically inactive. Enzymic activity was restored on recombination of the fragments under denaturing conditions. Cleavage of the loops between helices O to P and Q to R by sequential fragmentation with endoproteinase Lys-C and trypsin inactivated the synthase completely. This result lends support to the idea that the open and closed crystal forms of the structural work are interconverted during the catalytic cycle.

Investigation of enzyme-substrate complexes by affinity chromatography. Application to pig heart citrate synthase

The relative affinities of Sepharose gels, to which coenzyme A (CoA-SH) and CoA-SH analogues were bound through a well defined site, for citrate synthase were determined. The relative eluting power of coenzyme derivatives for the CoA-SH-gel and the Matrex Gel Blue-bound enzyme was measured, and the influence of oxaloacetate on the binding of the enzyme investigated. From the results, the contributions of different parts of the coenzyme to its binding in the active site and kinetic concepts are derived and found to be in complete agreement with corresponding data for citrate synthase obtained from kinetic measurements reported in the literature. It is demonstrated for some other CoA-SH-specific enzymes that affinity chromatography is of value as an additional tool for the comparative investigation of binding sites of enzymes which depend on the same coenzyme.

Structural dynamics of human deoxyhemoglobin and hemochrome investigated by nuclear gamma resonance absorption (Mössbauer) spectroscopy

Mössbauer spectra of human deoxyhemoglobin and hemochrome frozen solutions, selectively enriched with 57Fe in either the alpha chains or the beta chains, were measured from 4.2 to 250 K. The Lamb-Mössbauer factor, ln f = 4II2 [x2]gamma/lambda 2, was calculated from these spectra and gives the structural dynamics of the iron atom (heme). Large differences in the mean-squared displacement, [x2]gamma, of the heme between hemochrome and deoxyhemoglobin at temperatures above 210 K were observed, demonstrating that when iron is bound to a rigid part of the protein (i.e., distal histidine in hemochrome), motions of the heme are suppressed (i.e., the dynamics are decreased). Comparison of the motions of these two hemoglobins proves that molecular diffusion can be neglected in an analysis of the dynamics below approximately 250 K.

Hysteretic behaviour of citrate synthase. Alternating sites during the catalytic cycle

Chemically and stereochemically pure (3S)-citryl-CoA was prepared enzymically and used as a substrate for citrate synthase to investigate the previously determined unexpectedly low rate of hydrolysis of the (3RS)-substrate. The unnatural R-diastereomer of this mixture is not inhibitory. At low enzyme concentrations the rate of citryl-CoA hydrolysis was linear until the reaction went near to completion; the hydrolysis approached Michaelis-Menten kinetics at high enzyme concentrations. In between these concentration extremes a biphasic rate dependence was detectable, where a fast initial phase lasting a few seconds was followed by a slow steady-state phase. Citrate synthase was characterized as a hysteretic enzyme existing in two interconvertible forms, which were designated according to their functions as hydrolase E and ligase E'. The hysteretic behaviour originates in the cleavage of citryl-CoA to acetyl-CoA and oxaloacetate. This reaction occurs on the ligase form E', which represents a trap for enzyme form E, the hydrolase. The conclusions given above are strengthened by the ordinary hydrolysis kinetics of (2S)-malyl-CoA, a substrate that is not subject to cleavage of the C-C bond on the synthase. The results satisfy the kinetic criterion for citryl-CoA being an intermediate of the physiological synthase reaction and, therefore, establish the oscillation of the synthase between hydrolase and ligase states during the catalytic cycle. A disorganization of these oscillations can be achieved by limited tryptic proteolysis of the synthase.

Citrate synthase from a Gram-positive bacterium. Purification and characterization of the Bacillus megaterium enzyme

Citrate synthase was purified to homogeneity from a Gram-positive bacterium (Bacillus megaterium) for the first time. The Mr of the native enzyme was determined to be 84 000 (S.E.M. +/- 5000). Sodium dodecyl sulphate/polyacrylamide-gel electrophoresis and gel filtration in guanidinium chloride revealed a single protein species of Mr 40 300 (S.E.M. +/- 4400), indicating a dimeric enzyme. This dimeric structure was confirmed by cross-linking the native enzyme with dimethyl suberimidate and with glutaraldehyde, followed by electrophoretic analysis. The enzyme follows Michaelis-Menten kinetics with respect to both substrates, acetyl-CoA and oxaloacetate, and is sensitive to non-specific inhibition by a range of adenine nucleotides. In both molecular and catalytic properties the citrate synthase closely resembles the enzyme from eukaryotic sources and contrasts markedly with the larger, hexameric, enzyme from Gram-negative bacteria.

Citrate synthase of Tetrahymena pyriformis: evolutionary and regulatory aspects

Citrate synthase (EC 4.1.3.7) from Tetrahymena pyriformis has been purified 185-fold. The molecular weight of the native enzyme was determined to be 120,000. The enzyme is labile at low ionic strength, but can be stabilized by KCl and glycerol. It is activated by KCl at low (below 60 mM) or high concentrations, and inhibited by divalent cations (Mn2+, Mg2+, Ca2+). The Michaelis constants are 0.1 mM for oxalacetate and 0.01 mM for acetyl-CoA. The kinetics with oxalacetate exhibit negative cooperativity, with a nH = 0.66. Among the metabolites tested, only ATP and GTP can inhibit the enzyme but Mg2+ relieves the ATP inhibition. Incubation with sulfhydryl reagents (DTNB) in the absence of its substrates results in a rapid inactivation of the enzyme. It is concluded that Tetrahymena citrate synthase is closer to the enzyme from Gram-positive bacteria than to those of eucaryotes.

Evidence from inhibitor studies for conformational changes of citrate synthase

1. Substrate analogue CoA derivatives were applied as inhibitors of citrate synthase. Substitution of the acyl-CoA oxygen next to sulfur by hydrogen was without marked influence on the affinity. 2. Carboxymethyl-CoA, a structural analogue of enolic acetyl-CoA, was characterized as a transition state analogue by an affinity 100-fold higher than that of acetyl-CoA. Ks of the binary inhibitor-enzyme complex was high (230 microM) but that of the ternary inhibitor-oxaloacetate-enzyme complex was 0.07 microM. Both enzyme subunits bound the inhibitor independently, also in the presence of oxaloacetate. 3. (3R,S)-3,4-Dicarboxy-3-hydroxybutyl-CoA, an analogue of citryl-CoA, inhibited the overall reaction noncompetitively against acetyl-CoA and against oxaloacetate; it was a competitive inhibitor against the hydrolysis and cleavage reactions of (3S)-citryl-CoA. Kinetic data suggest that this inhibitor represents an intermediate analogue. 4. The results given above indicate conformational changes of the synthase during the catalytic cycle. In the proposed mechanism the free enzyme represents a hydrolase which in the presence of oxaloacetate, by a well-known conformational change, is converted into a ligase. If both substrates are present, the ligase is reconverted into the hydrolase upon formation of the intermediate, (3S)-citryl-CoA.

Primary structure of porcine heart citrate synthase

The sequence of 437 amino acid residues of porcine heart citrate synthase [citrate oxaloacetate-lyase (pro-3S-CH2COO leads to acetyl-CoA), EC 4. 1. 3. 7] has been determined by the alignment of fragments generated by cleavage with cyanogen bromide and with trypsin. Isolation of the peptides was facilitated by recent developments in the high-performance liquid chromatography of peptide mixtures. The alignment of these peptides was consistent with that previously deduced from fragments derived by restricted cleavage of citrate synthase by limited proteolysis and cleavage of aspartyl-prolyl bonds and asparaginyl-glycyl bonds. The enzyme contains a modified amino acid, trimethyllysine, at residue 368, showing that the enzyme is subjected to post-translational modification.

Limited proteolysis of pig heart citrate synthase by subtilisin, chymotrypsin, and trypsin

Pig heart citrate synthase was subjected to limited proteolytic attack by subtilisin, chymotrypsin, and trypsin in the presence of palmitoyl-CoA. Initial proteolysis by all three proteolytic enzymes resulted in cleavage of the monomeric subunit (Mr 45 000 +/- 3000) into a large (Mr 35 000-38 500) and a small (Mr 9000 +/- 3000) into a large (Mr 35 000-38 500) and a small (Mr 9000-12 000) fragment. Further proteolysis of the large subunit produced a secondary fragment (Mr 31 000-36 000). The small (Mr 9000-12 000) fragment was stable in the presence of subtilisin but was substantially degraded by both chymotrypsin and trypsin. The actual molecular weight of fragments varied with the choice of the proteolytic enzyme. Limited proteolysis was absolutely dependent on the presence of palmitoyl-CoA and resulted in complete inhibition of the catalytic activity of the enzyme. Citrate, ammonium sulfate, and especially oxaloacetate provided complete protection against proteolysis whereas acetyl-CoA, CoASH, NADH, and ATP were ineffective. Reaction of rabbit anti-citrate synthase with citrate synthase and its proteolytic fragments indicated that the main antigenic region lay primarily in the small fragment. The products of subtilisin cleavage were isolated by gel filtration under denaturing conditions. The large (Mr 35 000-38 500) fragment contained the amino-terminal (approximately)336 amino acids and the small fragment contained the remaining carboxyl-terminal amino acids. The results are discussed in relation to the structure of citrate synthase.

Studies on a mutant form of Escherichia coli citrate synthase desensitised to allosteric effectors

Naturally occurring citrate synthases fall into distinct molecular and catalytic types. Gram-negative bacteria produce a 'large' enzyme, allosterically inhibited by NADH and, in the facultative anaerobes such as Escherichia coli, also by 2-oxoglutarate. On the other hand, Gram-positive bacteria and all eukaryotes produce a 'small' citrate synthase which is insensitive to these metabolites. As a complement to structure-function studies we have explored the possibility of genetically altering one type of citrate synthase to the other. By mutagenesis and suitable selection we have succeeded in isolating a mutant of E. coli whose citrate synthase is both 'small' and insensitive to NADH and 2-oxoglutarate. Some characteristics of the enzyme are described. Such mutant enzymes offer a novel approach to the study of citrate synthase, its regulation and its natural diversity.