Brownian dynamics simulations of aldolase binding glyceraldehyde 3-phosphate dehydrogenase and the possibility of substrate channeling.

Brownian dynamics (BD) simulations test for channeling of the substrate, glyceraldehyde 3-phosphate (GAP), as it passes between the enzymes fructose-1,6-bisphosphate aldolase (aldolase) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH). First, BD simulations determined the favorable complexes between aldolase and GAPDH; two adjacent subunits of GAPDH form salt bridges with two subunits of aldolase. These intermolecular contacts provide a strong electrostatic interaction between the enzymes. Second, BD simulates GAP moving out of the active site of the A or D aldolase subunit and entering any of the four active sites of GAPDH. The efficiency of transfer is determined as the relative number of BD trajectories that reached any active site of GAPDH. The distribution functions of the transfer time were calculated based on the duration of successful trajectories. BD simulations of the GAP binding from solution to aldolase/GAPDH complex were compared to the channeling simulations. The efficiency of transfer of GAP within an aldolase/GAPDH complex was 2 to 3% compared to 1.3% when GAP was binding to GAPDH from solution. There is a preference for GAP channeling between aldolase and GAPDH when compared to binding from solution. However, this preference is not large enough to be considered as a theoretical proof of channeling between these proteins.

Interactions of glyceraldehyde-3-phosphate dehydrogenase with G- and F-actin predicted by Brownian dynamics.

Brownian dynamics (BD) was used to simulate the binding of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) to G- and F-actin. High-resolution three-dimensional models (X-ray and homology built) of the proteins were used in the simulations. The electrostatic potential about each protein was predicted by solving the linearized Poisson-Boltzmann equation for use in BD simulations. The BD simulations resulted in complexes of GAPDH with G- or F-actin involving positively charged surface patches on GAPDH (Lyses 24, 69, 110 and 114) and negatively charged residues of the N- and C-termini (Asps 1, 25 and 363 and Glus 2, 4, 224 and 364) of actin. The actin residues all belong to subdomain 1. Although the positively charged surface patches of GAPDH are not close enough to each other to enhance their electrostatic potential, occasionally two subunits of the GAPDH tetramer may simultaneously interact with two neighboring monomers of F-actin. These results are different from those of fructose-1,6-bisphosphate aldolase, where quaternary structure directly influenced binding by two subunits combining their electrostatic potentials (see previous study, Ouporov et al., 1999, Biophys. J. 76: 17-27). Instead, GAPDH uses its quaternary structure to span the distance between two different actin subunits so that it can interact with two different actin subunits simultaneously.

Computer simulations of glycolytic enzyme interactions with F-actin.

Muscle actin and fructose-1,6-bisphosphate aldolase (aldolase) were chemically crosslinked to produce an 80 kDa product representing one subunit of aldolase linked to one subunit of actin. Hydroxylamine digestion of the crosslinked product resulted in two 40.5 kDa fragments, one that was aldolase linked to the 12 N-terminal residues of actin. Brownian dynamics simulations of muscle aldolase and GAPDH with F-actin (muscle, yeast, and various mutants) estimated the association free energy. Mutations of residues 1-4 of muscle actin to Ala individually or two in combination of the first four residues reduced the estimated binding free energy. Simulations showed that muscle aldolase binds with the same affinity to the yeast actin as to the double mutated muscle actin; these mutations make the N-terminal of muscle actin identical to yeast, supporting the conclusion that the actin N-terminus participates in binding. Because the depth of free energy wells for yeast and the double mutants is less than for native rabbit actin, the simulations support experimental findings that muscle aldolase and GAPDH have a higher affinity for muscle actin than for yeast actin. Furthermore, Brownian dynamics revealed that the lower affinity of yeast actin for aldolase and GAPDH compared to muscle actin, was directly related to the acidic residues at the N-terminus of actin.

Brownian dynamics simulations of interactions between aldolase and G- or F-actin.

Compartmentation of proteins in cells is important to proper cell function. Interactions of F-actin and glycolytic enzymes is one mechanism by which glycolytic enzymes can compartment. Brownian dynamics (BD) simulations of the binding of the muscle form of the glycolytic enzyme fructose-1,6-bisphosphate aldolase (aldolase) to F- or G-actin provide first-encounter snapshots of these interactions. Using x-ray structures of aldolase, G-actin, and three-dimensional models of F-actin, the electrostatic potential about each protein was predicted by solving the linearized Poisson-Boltzmann equation for use in BD simulations. The BD simulations provided solution complexes of aldolase with F- or G-actin. All complexes demonstrate the close contacts between oppositely charged regions of the protein surfaces. Positively charged surface regions of aldolase (residues Lys 13, 27, 288, 293, and 341 and Arg 257) are attracted to the negatively charged amino terminus (Asp 1 and Glu 2 and 4) and other patches (Asp 24, 25, and 363 and Glu 361, 364, 99, and 100) of actin subunits. According to BD results, the most important factor for aldolase binding to actin is the quaternary structure of aldolase and actin. Two pairs of adjacent aldolase subunits greatly add to the positive electrostatic potential of each other creating a region of attraction for the negatively charged subdomain 1 of the actin subunit that is exposed to solvent in the quaternary F-actin structure.

A glycolytic enzyme binding domain on tubulin.

Cleavage of tubulin at tryptophan residues yielded several peptides, one of which strongly interacted with aldolase as determined by inhibition of aldolase activity. This peptide was identified as the C-terminal, residues 408-451, of the alpha-subunit of tubulin. Peptides with identical sequences to the C-terminal regions of the alpha- and beta-subunits of tubulin were synthesized to further characterize interactions with glycolytic enzymes. A 43-amino-acid C-terminal peptide from alpha-tubulin (residues 409-451) was found to have binding properties similar to those of native tubulin and was designated the tubulin glycolytic enzyme binding domain (T-GEBD-43mer).

Glycolytic enzymes and assembly of microtubule networks.

The ability of glycolytic enzymes, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), aldolase, pyruvate kinase (PK), and lactate dehydrogenase muscle-type (LDH(M)), to generate interactive microtubule networks was investigated. Bundles have previously been defined as the parallel alignment of several microtubules and are one form of microtubule networks. Utilizing transmission electron microscopy, interactive networks of microtubules as well as bundles were readily observed in the presence of GAPDH, aldolase, or PK. These networks appear morphologically as cross-linked microtubules, oriented in many different ways. Light scattering indicated that the muscle forms of GAPDH, aldolase, PK and LDH(m) caused formation of the microtubule networks. Triose phosphate isomerase (TPI) and lactate dehydrogenase heart-type (LDH(H)), glycolytic enzymes which do not interact with tubulin or microtubules, did not produce bundles, or interactive networks. Sedimentation experiments confirmed that the enzymes that cross-link also co-pellet with the microtubules. Such cross-linking of microtubules indicate that the enzymes are multivalent with the capability of simultaneous binding to more than one microtubule.

Effect of tubulin on the activity of the muscle isoenzyme of lactate dehydrogenase.

The interaction between muscle-type lactate dehydrogenase (LDHm) and tubulin was investigated by monitoring the combined effect of NADH and tubulin on steady-state kinetics and the combined effect of NADH and pH on complex formation between tubulin and the enzyme. Steady-state kinetics showed that LDHm is inhibited by tubulin. Experiments with heart-type lactate dehydrogenase (LDHh) showed that the inhibition is unique to the muscle-type enzyme. The magnitude of the inhibition is dependent upon the concentration of NADH as well as the pH of the buffer medium. The enzyme was less sensitive to inhibition at 50 microM NADH than at 10 microM NADH. Since this effect of NADH is not due to an ionic strength contribution, it is deemed to be specific. In contrast to the absence of tubulin, its presence induced a modification of the kinetic behavior of LDHm; i.e., the velocity dependence on NADH concentration displayed a marked sigmoid response. The inhibition of LDHm by tubulin is more pronounced at lower pH values than at higher pH values. The pH-dependent inhibitory profile is shifted to the left (i.e., pKa is decreased) with increasing concentrations of NADH. This pattern is remarkably similar to that observed for the binding of the enzyme on Sepharose immobilized tubulin and is consistent with the premise that inhibition is a result of interaction between these proteins. NAD+ was much less effective than NADH in dissociating LDHm from immobilized tubulin. Results from these in vitro studies are consistent with similar observations dealing with other glycolytic enzymes and cytoskeleton proteins, which show that enzyme catalytic properties are modified upon binding.

Binding constants and stoichiometries of glyceraldehyde 3-phosphate dehydrogenase-tubulin complexes.

The catalytic activity of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) decreased (almost linearly) as a function of increasing concentrations of tubulin; the total loss in activity was attained at a ratio of 1.2 to 1.8 tubulin dimer to GAPDH tetramer. Based on the inhibition data, a dissociation constant for the tubulin-GAPDH complex was calculated to be about 0.73 nM. The stoichiometry and the dissociation constants of the tubulin-GAPDH complex were found to be dependent upon the ionic strength of the assay media. Qualitatively similar results were obtained (i.e., inhibition and ionic strength effect) when the GAPDH-catalyzed reaction was measured in the presence of Sepharose-immobilized tubulin. The physical interaction between these two proteins, i.e., GAPDH and tubulin, was measured by the ability of one protein (immobilized on a Sepharose matrix) to copellet the other protein. By employing this copelleting technique, we measured the dissociation constant and stoichiometry of the immobilized tubulin-GAPDH complex to be about 6.4 nM and 0.91 tubulin dimer/GAPDH tetramer, respectively. The dissociation constant and stoichiometry thus obtained were found to be remarkably similar to those obtained by the tubulin-dependent GAPDH inhibition data. In contrast to these results, (soluble) tubulin had no effect on the catalytic activity of the immobilized GAPDH, albeit the soluble tubulin copelleted with the immobilized GAPDH. The dissociation constant and stoichiometry of immobilized GAPDH-tubulin complex were calculated to be 0.76 +/- 0.13 microM and 3.23 +/- 0.16 tubulin dimer/GAPDH tetramer, respectively. These data suggest that there are two classes of binding sites for tubulin on a tetrameric GAPDH; high-affinity and low-affinity sites. The enzyme is inhibited when tubulin binds at the high-affinity site while the catalytic function of the enzyme is unaffected when the tubulin binds at the low-affinity site. The latter site is suggested herein to be responsible for the cross-linking (bundling) of microtubules.

Glycolytic enzyme-tubulin interactions: role of tubulin carboxy terminals.

Tubulin and microtubules were modified with the protease, subtilisin. The modification reduced the length of alpha- or beta-tubulin by cleaving a peptide fragment from the C-terminals. Generation of alpha'beta'-tubulin, which is cleaved at both the alpha- and beta-subunit terminals, and alpha beta'-tubulin, which is cleaved at the beta-subunit C-terminal, have already been reported. In this work an isotype, alpha'beta-tubulin, was produced. The three modified tubulin isotypes were compared for their ability to interact with glycolytic enzymes. Cleavage of alpha led to a poorer interaction when tested via affinity chromatography. Tubulin also inhibits the activity of aldolase and glyceraldehyde 3-phosphate dehydrogenase. When the alpha-subunit C-terminal was intact, inhibition was greatest. These results imply that the C-terminal of the tubulin alpha-subunit is responsible for interactions with glycolytic enzymes.

Nonenzymatic incorporation of glucose and galactose into brain cytoskeletal proteins in vitro.

Initial studies demonstrated the loss of lysine and simultaneous appearance of glucitollysine in intracellular proteins following incubation with sugar. For example, when a crude nervous tissue cytoskeletal preparation was incubated in 100 mM glucose for 10 days, > 60% of the lysine residues were modified. Over 20% of the lysyl residues in a spinal cord neurofilament preparation are susceptible to Schiff base formation after one day and over 30% following five days of incubation with 100 mM glucose. When incubated with 100 mM galactose, F- and G-actin were found to be significantly modified in as few as 15 h, with > 70% of the lysyl residues lost. After 45 h of incubation, > 90% of the residues had been modified. These data also indicate that many of the lysyl residues in F- and G-actin are exposed and very susceptible to modification by sugar. This rapid and extensive modification of lysine in actin in vitro suggest that it may be modified in diabetic nervous tissue.

Effects of nonenzymatic glycation of subfragment-1 of myosin on interactions with actin.

Nonenzymatic bonding of reducing sugars to subfragment-1 of myosin (S-1) resulted in a reduction in actin-activated S-1 ATPase activity. Fructose caused a greater reduction than glucose. The Km for binding of actin to S-1 was significantly increased with sugar derivatization. In addition, sugar derivatization lowered the ability of S-1 to promote polymerization of G-actin. Western blot analysis demonstrated that glucose was nonenzymatically incorporated into the 50 and 20 kilodalton (kDa) fragments of S-1 with preponderance in the 20-kDa fragment. The reduced affinity of derivatized myosin for actin is indicated by the increased Km, the reduced ability to stimulate actin polymerization, and the positive Western blot reaction in the 20-kDa fragment.

Association of glycolytic enzymes with the cytoskeleton.

The diverse physical associations of the glycolytic enzymes with structural components of the cell suggest that the glycolytic enzymes are not entirely soluble in the cell. The relatively low affinities of the associations are likely responsible for the apparently transient interactions. The binding phenomenon is suggested to regulate metabolism through changes in enzymatic activity and facilitates localized enrichment of the enzymes.

Hexokinase redistribution in vivo.

Heterogenous stock mice in addition to mice selectively bred to maximally differ in their severity of alcohol withdrawal seizures (withdrawal seizure-resistant (WSR) and withdrawal seizure-prone (WSP] were used to provide evidence in favor of the importance of the rapidly changing distribution of brain hexokinase (ATP: D-hexose 6-phosphotransferase, EC 2.7.1.1) (HK). An ischemic response at 15, 30, 60 and 120 s after killing showed a decreasing cerebellar cytosolic HK concentration of 31%, 15%, 14% and 10% while the cerebral concentrations were 23%, 13%, 13% and 14%, respectively. WSR and WSP mice given an acute i.p. dose of 4 g/kg of alcohol showed opposite HK responses. Cytosolic HK in WSR mice decreased 18.5%, while WSP mice showed an increase of 20.3% over paired saline-injected controls. When ischemia was allowed to proceed in WSP mice following an in vivo alcohol treatment, cytosolic HK decreased in parallel to mice not given alcohol. These data suggest that alcohol can cause an HK redistribution in vivo which could play a role in the differing sensitivities of WSR and WSP mice to alcohol related seizures.

Glycolytic enzyme interactions with tubulin and microtubules.

Interactions of the glycolytic enzymes glucose-6-phosphate isomerase, aldolase, glyceraldehyde-3-phosphate dehydrogenase, triose-phosphate isomerase, enolase, phosphoglycerate mutase, phosphoglycerate kinase, pyruvate kinase, lactate dehydrogenase type-M, and lactate dehydrogenase type-H with tubulin and microtubules were studied. Lactate dehydrogenase type-M, pyruvate kinase, glyceraldehyde-3-phosphate dehydrogenase, and aldolase demonstrated the greatest amount of co-pelleting with microtubules. The presence of 7% poly(ethylene glycol) increased co-pelleting of the latter four enzymes and two other enzymes, glucose-6-phosphate isomerase, and phosphoglycerate kinase with microtubules. Interactions also were characterized by fluorescence anisotropy. Since the KD values of glyceraldehyde-3-phosphate dehydrogenase, pyruvate kinase and lactate dehydrogenase for tubulin and microtubules were all found to be between 1 and 4 microM, which is in the range of enzyme concentration in cells, these enzymes are probably bound to microtubules in vivo. These observations indicate that interactions of cytosolic proteins, such as the glycolytic enzymes, with cytoskeletal components, such as microtubules, may play a structural role in the formation of the microtrabecular lattice.

Heteromerous interactions among glycolytic enzymes and of glycolytic enzymes with F-actin: effects of poly(ethylene glycol).

Interactions of glucose-6-phosphate isomerase (D-glucose-6-phosphate ketol-isomerase, EC 5.3.1.9), aldolase (D-fructose-1,6-bisphosphate D-glyceraldehyde-3-phosphate lyase, EC 4.1.2.13), glyceraldehyde-3-phosphate dehydrogenase (D-glyceraldehyde-3-phosphate:NAD+ oxidoreductase (phosphorylating), EC 1.2.1.12), triose-phosphate isomerase (D-glyceraldehyde-3-phosphate ketol-isomerase, EC 5.3.1.1), phosphoglycerate mutase (D-phosphoglycerate 2,3-phosphomutase, EC 5.4.2.1), phosphoglycerate kinase (ATP:3-phospho-D-glycerate 1-phosphotransferase, EC 2.7.3), enolase (2-phospho-D-glycerate hydro-lyase, EC 4.2.1.11), pyruvate kinase (ATP:Pyruvate O2-phosphotransferase, EC 2.7.1.40) and lactate dehydrogenase [S)-lactate:NAD+ oxidoreductase, EC 1.1.1.27) with F-actin, among the glycolytic enzymes listed above, and with phosphofructokinase (ATP:D-fructose-6-phosphate 1-phosphotransferase, EC 2.7.1.11) were studied in the presence of poly(ethylene glycol). Both purified rabbit muscle enzymes and rabbit muscle myogen, a high-speed supernatant fraction containing the glycolytic enzymes, were used to study enzyme-F-actin interactions. Following ultracentrifugation, F-actin and poly(ethylene glycol) tended to increase and KCl to decrease the pelleting of enzymes. In general, the greater part of the pelleting occurred in the presence of both F-actin and poly(ethylene glycol) and the absence of KCl. Enzymes that pelleted more in myogen preparations than as individual purified enzymes in the presence of poly(ethylene glycol) and the absence of F-actin were tested for specific enzyme-enzyme associations, several of which were observed. Such interactions support the view that the internal cell structure is composed of proteins that interact with one another to form the microtrabecular lattice.

Demonstration of tubulin-glycolytic enzyme interactions using a novel electrophoretic approach.

A gel electrophoretic technique was used to demonstrate an interaction with the soluble enzymes aldolase, glyceraldehydephosphate dehydrogenase, pyruvate kinase and muscle type lactate dehydrogenase to the cytoskeletal protein tubulin. It is suggested that tubulin, like actin, is a key cytoskeletal structure with which soluble proteins may associate.

Sample preparation for inositol measurement: Sep-Pak C18 use in detergent removal.

The enzymatic-fluorometric method of myo-inositol quantitation by L.C. MacGregor and F.M. Matschinsky (1984, Anal. Biochem. 141, 382-389) has proved to be very useful in accurately measuring small amounts of myo-inositol. Although this procedure is quite satisfactory, relatively high concentrations of detergents, salts, NADH, and malate interfere. To extend the usefulness of the MacGregor and Matschinsky method we report here an extraction procedure which removed the interfering substances, yet allowed the recovery of close to 100% of the inositol. The procedure involved first passing the sample through a Sep-Pak C18 cartridge to remove detergent and then through a mixed-bed resin to remove the ionic constituents. The procedure with the Sep-Pak C18 cartridge is applicable to a wide variety of biological samples requiring detergent removal.

Extraction of glycolytic enzymes: myo-inositol as a marker of membrane porosity.

Detergent extraction of brain slices and mouse fibroblast 3T3 cells was performed to determine rates and relative amounts of extraction of inositol versus the glycolytic enzymes. The two detergents, Triton X-100 and Brij 58, led to similar results for extraction of myo-inositol. The extraction of enzymes from brain slices or cells varied with the detergent. In brain slices, a buffered solution containing 0.2% of the detergent Brij 58 led to the extraction of 85% of the inositol before 3% of the aldolase or before 37% of either lactate dehydrogenase or triose phosphate isomerase was extracted. In contrast, with 0.1% Triton X-100 in isotonic phosphate-buffered saline, when 70% of the inositol was extracted, 33% of the aldolase and 48% of the triose phosphate isomerase were extracted. Lesser amounts of aldolase and glyceraldehyde phosphate dehydrogenase were extracted than most of the other glycolytic enzymes under all conditions, implying that these enzymes may be interacting with non-extractable subcellular components. In 3T3 cells, both detergents were of similar effectiveness for inositol extraction. Triton X-100 caused 89% of the inositol to be released and Brij 58 caused 84% to be released. With the enzymes, Brij 58 caused between 15 and 38% extraction and Triton X-100 caused between 61 and 85% extraction of the different glycolytic enzymes. Thus Brij 58 was as effective as Triton X-100 in inositol extraction but not nearly as effective in glycolytic enzyme extraction. The results demonstrate that inositol leakage from tissues or cells is a better indicator of detergent-mediated alterations in membrane porosity than glycolytic enzyme leakage.(ABSTRACT TRUNCATED AT 250 WORDS)

Glycolytic enzyme levels in synaptosomes.

The specific activities of glucosephosphate isomerase, aldolase, triosephosphate isomerase, glyceraldehydephosphate dehydrogenase, phosphoglycerate kinase, phosphoglycerate mutase, pyruvate kinase and lactate dehydrogenase were all higher in the synaptoplasmic fraction from rat brain than in 100,000 g supernatant fraction of rat brain homogenates when the supernatants were prepared in high ionic strength solutions. Four enzymes in synaptosomes and two enzymes in homogenates were associated with particulate fractions as indicated by the large increase in specific activity of the enzymes when samples were treated with 0.3 M KCl before centrifugation. Glucosephosphate isomerase, aldolase, pyruvate kinase and lactate dehydrogenase were the enzymes that showed a large increase in specific activity following salt treatment of isolated, synaptosomal membrane while aldolase and pyruvate kinase were the two enzymes which showed a large increase in specific activity in the high speed supernatant fractions. Because the specific activities of many enzymes are found to be elevated not only in synaptosomes but in synaptosomal membrane fractions it is suggested that these enzymes may provide the potential for significantly enhanced glycolysis at these locations.