Long-range effects and conformational flexibility of aldolase

Targeting a moonlighting function of aldolase induces apoptosis in cancer cells

Muscle fructose-1,6-bisphosphate aldolase (ALDOA) is among the most abundant glycolytic enzymes in all cancer cells. Here, we show that the enzyme plays a previously unknown and critical role in a cancer cell survival. Simultaneous inhibition of ALDOA activity and interaction with F-actin cytoskeleton using ALDOA slow-binding inhibitor UM0112176 leads to a rapid cofilin-dependent loss of F-actin stress fibers which is associated with elevated ROS production, inhibition of ATP synthesis, increase in calcium levels, caspase activation and arrested cellular proliferation. These effects can be reproduced by silencing of ALDOA. The mechanism of pharmacological action is, however, independent of the catalytic function of the enzyme, specific to cancer cells, and is most deleterious to cells undergoing the epithelial–mesenchymal transition, a process facilitating cancer cell invasion. Our results demonstrate that the overabundance of ALDOA in cancer cells is associated with its moonlighting rather than catalytic functions. This may have significant implications for development of novel broad-based anti-cancer therapies.

Molecular dynamics study of naturally existing cavity couplings in proteins

Couplings between protein sub-structures are a common property of protein dynamics. Some of these couplings are especially interesting since they relate to function and its regulation. In this article we have studied the case of cavity couplings because cavities can host functional sites, allosteric sites, and are the locus of interactions with the cell milieu. We have divided this problem into two parts. In the first part, we have explored the presence of cavity couplings in the natural dynamics of 75 proteins, using 20 ns molecular dynamics simulations. For each of these proteins, we have obtained two trajectories around their native state. After applying a stringent filtering procedure, we found significant cavity correlations in 60% of the proteins. We analyze and discuss the structure origins of these correlations, including neighbourhood, cavity distance, etc. In the second part of our study, we have used longer simulations (≥100 ns) from the MoDEL project, to obtain a broader view of cavity couplings, particularly about their dependence on time. Using moving window computations we explored the fluctuations of cavity couplings along time, finding that these couplings could fluctuate substantially during the trajectory, reaching in several cases correlations above 0.25/0.5. In summary, we describe the structural origin and the variations with time of cavity couplings. We complete our work with a brief discussion of the biological implications of these results.

Redox proteomics of thiol proteins in mouse heart during ischemia/reperfusion using ICAT reagents and mass spectrometry

There is strong evidence for the involvement of reactive oxygen species in ischemia/reperfusion injury. Although oxidation of individual thiol proteins has been reported, more extensive redox proteomics of hearts subjected to ischemia/reperfusion has not been performed. We have carried out an exploratory study using mass spectrometry with isotope-coded affinity tags (ICAT) aimed at identifying reversible oxidative changes to protein thiols in Langendorff perfused isolated mouse hearts subjected to 20 min ischemia with or without aerobic reperfusion for 5 or 30 min. Reduced thiols were blocked by adding N-ethylmaleimide during protein extraction, then reversibly oxidized thiols in extracts of control perfused and treated hearts were reduced and labeled with the light and heavy ICAT reagents, respectively. Protein extracts were mixed in equal amounts and relative proportions of the isotope-labeled peaks were used to quantify oxidative changes between the control and the treated groups. Approximately 300 peptides with ICAT signatures were reliably identified in each sample, with 181 peptides from 118 proteins common to all treatments. A proportion showed elevated ICAT ratios, consistent with reversible thiol oxidation. This was most evident after early reperfusion, with apparent reversal after longer reperfusion. In comparison, there was gradual accumulation of protein carbonyls and loss of GSH with longer reperfusion. Many of the thiol changes were in mitochondrial proteins, including components of electron transport complexes and enzymes involved in lipid metabolism. The results are consistent with mitochondria being a major site of oxidant generation during early cardiac reperfusion and mitochondrial thiol proteins being targets for oxidation.

Adaptive evolution of the Streptococcus pyogenes regulatory aldolase LacD.1

In the human-pathogenic bacterium Streptococcus pyogenes, the tagatose bisphosphate aldolase LacD.1 likely originated through a gene duplication event and was adapted to a role as a metabolic sensor for regulation of virulence gene transcription. Although LacD.1 retains enzymatic activity, its ancestral metabolic function resides in the LacD.2 aldolase, which is required for the catabolism of galactose. In this study, we compared these paralogous proteins to identify characteristics correlated with divergence and novel function. Surprisingly, despite the fact that these proteins have identical active sites and 82% similarity in amino acid sequence, LacD.1 was less efficient at cleaving both fructose and tagatose bisphosphates. Analysis of kinetic properties revealed that LacD.1's adaptation was associated with a decrease in k(cat) and an increase in K(m). Construction and analysis of enzyme chimeras indicated that non-active-site residues previously associated with the variable activities of human aldolase isoenzymes modulated LacD.1's affinity for substrate. Mutant LacD.1 proteins engineered to have LacD.2-like levels of enzymatic efficiency lost the ability to function as regulators, suggesting that an alteration in efficiency was required for adaptation. In competition under growth conditions that mimic a deep-tissue environment, LacD.1 conferred a significant gain in fitness that was associated with its regulatory activity. Taken together, these data suggest that LacD.1's adaptation represents a form of neofunctionalization in which duplication facilitated the gain of regulatory function important for growth in tissue and pathogenesis.

Protein substrate discrimination in the quiescin sulfhydryl oxidase (QSOX) family

This work explores the substrate specificity of the quiescin sulfhydryl oxidase (QSOX) family of disulfide-generating flavoenzymes to provide enzymological context for investigation of the physiological roles of these facile catalysts of oxidative protein folding. QSOX enzymes are generally unable to form disulfide bonds within well-structured proteins. Use of a temperature-sensitive mutant of ubiquitin-conjugating enzyme 4 (Ubc4') as a model substrate shows that QSOX activity correlates with the unfolding of Ubc4' monitored by circular dichroism. Fusion of Ubc4' with the more stable glutathione-S-transferase domain demonstrates that QSOX can selectively introduce disulfides into the less stable domain of the fusion protein. In terms of intermolecular disulfide bond generation, QSOX is unable to cross-link well-folded globular proteins via their surface thiols. However, the construction of a septuple mutant of RNase A, retaining a single cysteine residue, demonstrates that flexible protein monomers can be directly coupled by the oxidase. Steady- and pre-steady-state kinetic experiments, combined with static fluorescence approaches, indicate that while QSOX is an efficient catalyst for disulfide bond formation between mobile elements of structure, it does not appear to have a significant binding site for unfolded proteins. These aspects of protein substrate discrimination by QSOX family members are rationalized in terms of the stringent steric requirements for disulfide exchange reactions.

Regulation of plant cytosolic aldolase functions by redox-modifications

From the five genes which code for cytosolic fructose 1,6-bisphosphate aldolases in Arabidopsis thaliana L., the cDNA clone of cAld2 (At2g36460), was heterologously expressed in E. coli and incubated under various oxidizing and reducing conditions. Covalent binding of a GSH moiety to the enzyme was shown by incorporation of biotinylated GSH (BioGEE) and by immunodetection with monoclonal anti-GSH serum. Nitrosylation after incubation with GSNO or SNP was demonstrated using the biotin-switch assay. Mass-spectrometry analysis showed glutathionylation and/or nitrosylation at two different cysteine residues: GSH was found to be attached to C68 and C173, while the nitroso-group was incorporated only into C173. Non-reducing SDS-PAGE conducted with purified wild-type and various Cys-mutant proteins revealed the presence of disulfide bridges in the oxidized enzyme, as described for rabbit muscle aldolase. Incubation of the purified enzyme with GSSG (up to 25 mM) led to partial and reversible inactivation of enzyme activity; NADPH, in the presence of the components of the cytosolic NADP-dependent thioredoxin system, could reactivate the aldolase as did DTT. Total and irreversible inactivation occurred with low concentrations (0.1 mM) of nitrosoglutathione (GSNO). Inactivation was prevented by co-incubation of cAld2 with fructose-1,6-bisphosphate (FBP). Nuclear localization of cAld2 and interaction with thioredoxins was shown by transient expression of fusion constructs with fluorescent proteins in isolated protoplasts.

In guinea pig sperm, aldolase A forms a complex with actin, WAS, and Arp2/3 that plays a role in actin polymerization

Glycolytic enzymes have, in addition to their role in energy production, other functions in the regulation of cellular processes. Aldolase A has been reported to be present in sperm, playing a key role in glycolysis; however, despite its reported interactions with actin and WAS, little is known about a non-glycolytic role of aldolase A in sperm. Here, we show that in guinea pig spermatozoa, aldolase A is tightly associated to cytoskeletal structures where it interacts with actin, WAS, and Arp2/3. We show that aldolase A spermatozoa treatment increases their polymerized actin levels. In addition, we show that there is a direct correlation between the levels of polymerized actin and the levels of aldolase A-actin interaction. Our results suggest that aldolase A functions as a bridge between filaments of actin and the actin-polymerizing machinery.

Thermodynamic analysis shows conformational coupling and dynamics confer substrate specificity in fructose-1,6-bisphosphate aldolase

Conformational flexibility is emerging as a central theme in enzyme catalysis. Thus, identifying and characterizing enzyme dynamics are critical for understanding catalytic mechanisms. Herein, coupling analysis, which uses thermodynamic analysis to assess cooperativity and coupling between distal regions on an enzyme, is used to interrogate substrate specificity among fructose-1,6-(bis)phosphate aldolase (aldolase) isozymes. Aldolase exists as three isozymes, A, B, and C, distinguished by their unique substrate preferences despite the fact that the structures of the active sites of the three isozymes are nearly identical. While conformational flexibility has been observed in aldolase A, its function in the catalytic reaction of aldolase has not been demonstrated. To explore the role of conformational dynamics in substrate specificity, those residues associated with isozyme specificity (ISRs) were swapped and the resulting chimeras were subjected to steady-state kinetics. Thermodynamic analyses suggest cooperativity between a terminal surface patch (TSP) and a distal surface patch (DSP) of ISRs that are separated by >8.9 A. Notably, the coupling energy (DeltaGI) is anticorrelated with respect to the two substrates, fructose 1,6-bisphosphate and fructose 1-phosphate. The difference in coupling energy with respect to these two substrates accounts for approximately 70% of the energy difference for the ratio of kcat/Km for the two substrates between aldolase A and aldolase B. These nonadditive mutational effects between the TSP and DSP provide functional evidence that coupling interactions arising from conformational flexibility during catalysis are a major determinant of substrate specificity.

Hemolytic anemia and severe rhabdomyolysis caused by compound heterozygous mutations of the gene for erythrocyte/muscle isozyme of aldolase, ALDOA(Arg303X/Cys338Tyr)

Aldolase (E.C. 4.1.2.13), a homotetrameric protein encoded by the ALDOA gene, converts fructose-1,6-bisphosphate to dihydroxyacetone phosphate and glyceraldehyde-3-phosphate. Three isozymes are encoded by distinct genes. The sole aldolase present in red blood cells and skeletal muscle is the A isozyme. We report here the case of a girl of Sicilian descent with aldolase A deficiency. Clinical manifestations included transfusion-dependent anemia until splenectomy at age 3 and increasing muscle weakness, with death at age 4 associated with rhabdomyolysis and hyperkalemia. Sequence analysis of the ALDOA coding regions revealed 2 novel heterozygous ALDOA mutations in conserved regions of the protein. The paternal allele encoded a nonsense mutation, Arg303X, in the enzyme-active site. The maternal allele encoded a missense mutation, Cys338Tyr, predicted to cause enzyme instability. This is the most severely affected patient reported to date and only the second with both rhabdomyolysis and hemolysis.

Expression, purification, and characterization of natural mutants of human aldolase B. Role of quaternary structure in catalysis

Fructaldolases (EC 4.1.2.13) are ancient enzymes of glycolysis that catalyze the reversible cleavage of phosphofructose esters into cognate triose (phosphates). Three vertebrate isozymes of Class I aldolase have arisen by gene duplication and display distinct activity profiles with fructose 1,6-bisphosphate and with fructose 1-phosphate. We describe the biochemical and biophysical characterization of seven natural human aldolase B variants, identified in patients suffering from hereditary fructose intolerance and expressed as recombinant proteins in E. coli, from which they were purified to homogeneity. The mutant aldolases were all missense variants and could be classified into two principal groups: catalytic mutants, with retained tetrameric structure but altered kinetic properties (W147R, R303W, and A337V), and structural mutants, in which the homotetramers readily dissociate into subunits with greatly impaired enzymatic activity (A149P, A174D, L256P, and N334K). Investigation of these two classes of mutant enzyme suggests that the integrity of the quaternary structure of aldolase B is critical for maintaining its full catalytic function.

Effect of acrylamide on aldolase structure. I. Induction of intermediate states

Acrylamide is a fluorescence quencher frequently applied for analysis of protein fluorophores exposure with the silent assumption that it does not affect the native structure of protein. In this report, it is shown that quenching of tryptophan residues in aldolase is a time-dependent process. The Stern-Volmer constant increases from 1.32 to 2.01 M-1 during the first 100 s of incubation of aldolase with acrylamide. Two tryptophan residues/subunit are accessible to quenching after 100 s of aldolase interaction with acrylamide. Up to about 1.2 M acrylamide concentration enzyme inactivation is reversible. Independent analyses of the changes of enzyme activity, 1ANS fluorescence during its displacement from aldolase active-site, UV-difference spectra and near-UV CD spectra were carried out to monitor the transition of aldolase structure. From these measurements a stepwise transformation of aldolase molecules from native state (N) through intermediates: I1, T, I2, to denatured (D) state is concluded. The maxima of I1, T, I2 and D states populations occur at 0.2, 1.0, 2.0 and above 3.0 M of acrylamide concentration, respectively. Above 3.5 M, acrylamide aldolase molecules become irreversibly inactivated.

Identification of conserved promoter elements for aldB and isozyme specific residues in aldolase B

The comparison of three complete aldolase B genes-including known and putative regulatory elements-is presented. The third aldolase B gene was provided by the complete aldB gene sequence (14803 bp) encoding the rabbit aldolase B isozyme. The promoter sequence alignment included the nonmammalian chicken aldolase B gene and confirms the promoter sequence conservation of those elements where trans-factor binding has been demonstrated in rat aldB. Moreover, the alignment reveals conserved sequences that may represent previously unidentified promoter elements that are present in all aldBs or specifically in the mammalian aldB promoters. One remarkable feature is a poly-purine segment found between the CAAT and TATA elements. In the mammalian promoters, this is exclusively a 9-10 bp poly-dA stretch. The avian promoter has an additional stretch of eight dG-bases immediately upstream of the poly-dA. Alignment of a portion of intron 1 of the chicken, human, and rabbit aldB genes reveals conserved sequences that are likely candidates for a reported positive activation sequence. In addition, the amino acid sequences of all eight known aldolase B isozymes is compared to the other vertebrate aldolases. A number of aldolase B-specific residues are identified that cluster in the carboxyl-portion of the sequence. With the exception of residue C268, these residues are not found near the active site, although, they are likely to be responsible for the substrate specificity of aldolase B.

Interaction of phosphonomethyl analog of dihydroxyacetone phosphate with rabbit muscle aldolase

Aldolase presents the same binding affinity for dihydroxyacetone phosphate and its phosphonomethyl analog, but the partition coefficient between the intermediates from the Michaelis complex to the eneamine is different. The effects of the structural modification of the triose phosphate substrate on the interaction with rabbit muscle aldolase are discussed in connection with the mechanistic pathway and the three-dimensional structure of the enzyme.

Identification of neuronal isozyme specific residues by comparison of goldfish aldolase C to other aldolases

A 2061 bp cDNA encoding a goldfish (Carassius auratus) aldolase was isolated from a goldfish brain library. The deduced 362 amino acid sequence is more similar to vertebrate brain (aldolase C) and muscle aldolases (aldolase A) than to the liver isozymes (aldolase B). Northern blot analysis indicates strong expression of the mRNA in brain but not in liver or muscle, which indicates that this is aldolase C rather than aldolase A. Analysis of all known vertebrate aldolase amino acid sequences reveals five residues; Leu-57, Arg-314, Thr-324, Glu-332, and Gly-350 that are present exclusively in aldolase Cs. The goldfish clone possesses all five residues. The residues are primarily located in the carboxyl-terminal region of the enzyme and may play a role in determining the neuronal isozyme-specific properties of the enzyme. Furthermore, the existence of an aldolase C in a teleost fish has implications with respect to the timing of genome duplication events that are thought to have been critical in vertebrate evolution.

Amide hydrogen exchange determined by mass spectrometry: application to rabbit muscle aldolase

The protein fragmentation/mass spectrometry method described by Zhang and Smith [(1993) Protein Sci. 2, 522-531] has been extended to measure amide hydrogen exchange rates in rabbit muscle aldolase, a homotetramer with M(r) = 157,000. Following a period of deuterium exchange, the partially deuterated protein was proteolytically fragmented into peptides whose deuterium contents were determined by directly coupled HPLC fast atom bombardment mass spectrometry. Hydrogen exchange rates were determined for amide hydrogens located in short segments derived from 85% of the aldolase backbone. Isotopic exchange rate constants spanning the range from 100 to 0.001 h-1 were determined for the exchange-in times used in this study (2.5 min to 44 h). The exchange rates for amide hydrogens located within short segments differed by as much as 10(4), demonstrating that local structural features dramatically affect the isotopic exchange rates in large proteins. A high level of correlation between the slowing of hydrogen exchange and intramolecular hydrogen bonding in aldolase was found. An exception to this correlation occurs at the subunit interface, where the amide hydrogens in one peptide segment with few amide hydrogen bonds have slower exchange rates than expected, suggesting that the amide hydrogens in this region are effectively shielded from the deuterated solvent. Isotope patterns observed for most peptides were binomial, indicating that hydrogen exchange proceeds through the EX2 mechanism (uncorrelated exchange). However, bimodal isotope patterns were found for peptides derived from three short segments of aldolase (including residues 58-64, 279-283, and 326-337), suggesting structural differences in these regions. A high level of correlation was found between crystallographic B-factors and amide hydrogen exchange rates, suggesting an isotopic exchange mechanism involving localized low-amplitude, high-frequency motions that do not require collective motion of many residues. From a methodology viewpoint, these results demonstrate that the combination of protein fragmentation with mass spectrometry is a useful method for determining the rates at which amide hydrogens located over major portions of large proteins undergo isotopic exchange.

Effects of chirality and substituents at carbon 3 in dihydroxyacetone-phosphate analogues on their binding to rabbit muscle aldolase

A series of dihydroxyacetone-phosphate (DHAP) analogues has been synthesized, differing in their stereochemistry and functionality at C-3. The kinetic effects of these compounds on the enzyme aldolase (EC 4.1.2.13) have been studied and differing modes of action observed. Competitive and time dependent reversible inhibition have been shown to take place both with and without borohydride detected formation of an immonium ion.

A data-based reaction mechanism for type I fructose bisphosphate aldolase

The structures of three type I fructose-1,6-bisphosphate aldolases have been determined and the common residues surrounding the Schiff base-forming Lys residue located. Armed with this information, it is now possible to propose a mechanism for this ubiquitous enzyme which is consistent with the recorded biochemical data. An interesting, but by no means mandatory, feature of the reaction mechanism is that catalysis can proceed without exchange with the solvent.