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Kim YB, Lenz RW. Polyesters from microorganisms. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2001; 71:51-79. [PMID: 11217417 DOI: 10.1007/3-540-40021-4_2] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Bacterial polyesters have been found to have useful properties for applications as thermoplastics, elastomers, and adhesives and are biodegradable and biocompatible. Poly(3-hydroxyalkanoates) (PHAs) and poly(beta-malate) are the most representative polyesters synthesized by microorganisms. PHAs containing a wide variety of repeating units can be produced by bacteria, including those containing many types of pendant functional groups which can be synthesized by microorganisms that are grown on unnatural organic substrates. Poly(beta-malate) is of interest primarily for medical applications, especially for drug delivery systems. In this chapter, the bacterial production and properties of poly(3-hydroxyalkanoates) and poly(beta-malate) are described with emphasis on the former.
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227
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Goti A, Cacciarini M, Cardona F, Cordero FM, Brandi A. Total Synthesis of (−)-Rosmarinecine by Intramolecular Cycloaddition of (S)-Malic Acid Derived Pyrroline N-Oxide. Org Lett 2001; 3:1367-9. [PMID: 11348236 DOI: 10.1021/ol015747o] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction in text] Straightforward total syntheses of (-)-rosmarinecine have been achieved from L-malic acid derived pyrroline N-oxides by two novel useful cascade processes, which join the family of domino reactions. Both strategies, which furnished the target alkaloid in enantioenriched and enantiopure forms, respectively, allow complete control of configuration at all the three newly created contiguous stereogenic centers.
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228
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Hirose R, Suzuki T, Moriyama H, Sato T, Yamagishi A, Oshima T, Tanaka N. Crystal structures of mutants of Thermus thermophilus IPMDH adapted to low temperatures. PROTEIN ENGINEERING 2001; 14:81-4. [PMID: 11297665 DOI: 10.1093/protein/14.2.81] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Random mutagenesis on thermophilic 3-isopropylmalate dehydrogenases (IPMDH; EC 1.1.1.85) produced mutant enzymes which adapt to low temperatures. These mutants had higher activity at lower temperatures than the wild-type enzyme without losing high thermostability. Here we report three structures of the mutants of Thermus thermophilus IPMDH determined by X-ray diffraction which was adapted to a low-temperature environment. Two of them have unstable coenzyme binding states and the other one probably has a stable substrate binding state. The present research suggests that the adaptation is correlated with the binding of either coenzyme or the substrate.
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229
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Ahn JB, Yun CS, Kim KH, Ha DC. Access to 1-hydroxymethylpyrrolizidines utilizing malate enolate-imine condensation and ring-closing methathesis: synthesis of (-)-croalbinecine. J Org Chem 2000; 65:9249-51. [PMID: 11149882 DOI: 10.1021/jo0012187] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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230
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Doyle SA, Fung SY, Koshland DE. Redesigning the substrate specificity of an enzyme: isocitrate dehydrogenase. Biochemistry 2000; 39:14348-55. [PMID: 11087384 DOI: 10.1021/bi001458g] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite the structural similarities between isocitrate and isopropylmalate, isocitrate dehydrogenase (IDH) exhibits a strong preference for its natural substrate. Using a combination of rational and random mutagenesis, we have engineered IDH to use isopropylmalate as a substrate. Rationally designed mutations were based on comparison of IDH to a similar enzyme, isopropylmalate dehydrogenase (IPMDH). A chimeric enzyme that replaced an active site loop-helix motif with IPMDH sequences exhibited no activity toward isopropylmalate, and site-directed mutants that replaced IDH residues with their IPMDH equivalents only showed small improvements in k(cat). Random mutants targeted the IDH active site at positions 113 (substituted with glutamate), 115, and 116 (both randomized) and were screened for activity toward isopropylmalate. Six mutants were identified that exhibited up to an 8-fold improvement in k(cat) and increased the apparent binding affinity by as much as a factor of 80. In addition to the S113E mutation, five other mutants contained substitutions at positions 115 and/or 116. Most small hydrophobic substitutions at position 116 improved activity, possibly by generating space to accommodate the isopropyl group of isopropylmalate; however, substitution with serine yielded the most improvement in k(cat). Only two substitutions were identified at position 115, which suggests a more specific role for the wild-type asparagine residue in the utilization of isopropylmalate. Since interactions between neighboring residues in this region greatly influenced the effects of each other in unexpected ways, structural solutions were best identified in combinations, as allowed by random mutagenesis.
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231
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Viornery L, Saliba C, Daskiewicz JB, Bayet C, Comte G, Fenet B, Gutierrez G, Barron D. Phenylpropanoids from Umbilicus pendulinus. Chem Pharm Bull (Tokyo) 2000; 48:1768-70. [PMID: 11086910 DOI: 10.1248/cpb.48.1768] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Phytochemical investigation of the leaves of Umbilicus pendulinus afforded in addition to 2-O-caffeoyl malate, isoquercitrin and Z-venusol, the new isomer E-venusol. Special NMR experiments were carried out to elucidate the configuration of the two latter compounds.
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232
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Abstract
To develop a bioreactor for solid-to-solid conversions, the conversion of solid Ca-maleate to solid Ca-D-malate by permeabilized Pseudomonas pseudoalcaligenes was studied. In a bioreactor seeded with product (Ca-D-malate) crystals, growth of Ca-D-malate crystals is the last step in the solid-to-solid conversion and is described here. Crystal growth is described as a transport process followed by surface processes. In contrast to the linear rate law obeyed by the transport process, the surface processes of a crystal-growth process can also obey a parabolic or exponential rate law. Growth of Ca-D-malate crystals from a supersaturated aqueous solution was found to be surface-controlled and obeyed an exponential rate law. Based on this rate law, a kinetic model was developed which describes the decrease in supersaturation due to Ca-D-malate crystal growth as a function of the constituent ions, Ca(2+) and D-malate(2-). The kinetic parameters depended on temperature, but, as expected (surface-controlled), they were hardly affected by the stirring speed.
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233
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Gasslmaier B, Krell CM, Seebach D, Holler E. Synthetic substrates and inhibitors of beta-poly(L-malate)-hydrolase (polymalatase). EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:5101-5. [PMID: 10931193 DOI: 10.1046/j.1432-1327.2000.01573.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Polymalatase from Physarum polycephalum calalysed the hydrolysis of beta-poly[L-malate] and of the synthetic compounds beta-di(L-malate), beta-tetra(L-malate), beta-tetra(L-malate) beta-propylester, and L-malate beta-methylester. Cyclic beta-tri(L-malate), cyclic beta-tetra(L-malate), and D-malate beta-methylester were not cleaved, but were competitive inhibitors. The O-terminal acetate of beta-tetra(L-malate) was neither a substrate nor an inhibitor. L-Malate was liberated; the Km, Ki and Vmax values were measured. The appearance of comparable amounts of beta-tri(L-malate), and beta-di(L-malate) during the cleavage of beta-tetra(L-malate) indicated a distributive mechanism for small substrates. The accumulation of a series of oligomers, peaking with the 11-mer and 12-mer in the absence of higher intermediates, indicated that the depolymerization of beta-poly(L-malate) was processive. The results indicate that beta-poly(L-malate) is anchored at its OH-terminus by the highly specific binding of the penultimate malyl residue. The malyl moieties beyond 12 residues downstream from the OH-terminus extend into a diffuse second, electrostatic binding site. The catalytic site joins the first binding site, accounting for the cleavage of the polymer into malate residues. It is proposed that the enzyme does not dissociate from beta-poly(L-malate) during hydrolysis, when both sites are filled with the polymer. When only the first binding site is filled, the reaction partitions at each oligomer between hydrolysis and dissociation.
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234
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Faucci MT, Melani F, Mura P. 1H-NMR and molecular modelling techniques for the investigation of the inclusion complex of econazole with alpha-cyclodextrin in the presence of malic acid. J Pharm Biomed Anal 2000; 23:25-31. [PMID: 10898151 DOI: 10.1016/s0731-7085(00)00260-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Carrying on a study where the combination of alpha-cyclodextrin and malic acid was found to be the most effective in improving the solubility of econazole, an antifungal drug very poorly water soluble, in the present work 1H-NMR and nuclear overhauser effect (NOE) experiments and molecular modelling studies were performed to gain insight into the interactions in solution between such three components and the structure of the supposed multicomponent complex. Findings demonstrated that two different complexes can be simultaneously present in solution involving, respectively, the inclusion of econazole monochloro-phenyl group within the host cavity from the primary hydroxyl side of the cyclodextrin cavity, or that of the other phenyl group through the opposite side of the cavity. It was shown that also malic acid is strictly involved in the molecular assembly of the complex, particularly through interactions with primary hydroxyl groups of the cyclodextrin molecule. Molecular modelling studies allowed to elaborate possible geometric models of the multicomponent complex and to select the more energetically favourable conformations which complied better with experimental data. Results suggested the possible formation in solution of stable oligomeric aggregates constituted by the repeated concatenation of the three components.
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235
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Abstract
Analysis of the content and distribution of organic acids in chickpea plants (Cicer arietinum L.) showed that malonate was the most abundant acid in roots and nodules, whereas malate was the main acid in leaves and stems. The highest concentration of malonate in roots was in the apices. Malonate metabolism did not appear to be directly related to abiotic stress. We suggest that malonate has a role as a defensive chemical in roots and nodules of chickpeas.
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236
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Osanai S, Nakamura K. Effects of complexation between liposome and poly(malic acid) on aggregation and leakage behaviour. Biomaterials 2000; 21:867-76. [PMID: 10735463 DOI: 10.1016/s0142-9612(99)00210-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The design and development of novel pH-sensitive liposomes were investigated to improve the release of liposome-encapsulated chemicals. Stable liposomes comprising of L-alpha-dipalmitoylphosphatidylcholine (DPPC) and poly(carboxylic acid) were prepared and characterized. Poly(malic acid) (PMLA) was chosen as a fusogen, because of its excellent biodegradability in physiological regions. Octyl groups introduced in the poly(malic acid) worked as anchors at the surface of the liposomes and made a remarkable contribution to complexing. The interaction between the liposomes and the polyacids was studied in terms of the change in size of the liposomes. The influences of molecular weight and amounts of polymer upon their characteristics, especially fusion, were discussed. The influences of pH change with respect to the association behavior of the liposomes such as aggregation and fusion were estimated by the particle size of the liposomes, turbidimetry of the solution and resonance energy transfer assay. From the results of these studies, it was shown that more tightly complexed liposomes aggregated and fused more positively with increasing acidity of the solution. The leakage of calcein entrapped in the inner aqueous phase of the liposomes increased with decreasing pH. The effect of pH on the liposome aggregation in a solution qualitatively paralleled that found in the leakage behavior.
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237
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Michielsen MJ, Frielink C, Wijffels RH, Tramper J, Beeftink HH. D-malate production by permeabilized Pseudomonas pseudoalcaligenes; optimization of conversion and biocatalyst productivity. J Biotechnol 2000; 79:13-26. [PMID: 10817338 DOI: 10.1016/s0168-1656(00)00220-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
For the development of a continuous process for the production of solid D-malate from a Ca-maleate suspension by permeabilized Pseudomonas pseudoalcaligenes, it is important to understand the effect of appropriate process parameters on the stability and activity of the biocatalyst. Previously, we quantified the effect of product (D-malate2 -) concentration on both the first-order biocatalyst inactivation rate and on the biocatalytic conversion rate. The effects of the remaining process parameters (ionic strength, and substrate and Ca2 + concentration) on biocatalyst activity are reported here. At (common) ionic strengths below 2 M, biocatalyst activity was unaffected. At high substrate concentrations, inhibition occurred. Ca2+ concentration did not affect biocatalyst activity. The kinetic parameters (both for conversion and inactivation) were determined as a function of temperature by fitting the complete kinetic model, featuring substrate inhibition, competitive product inhibition and first-order irreversible biocatalyst inactivation, at different temperatures simultaneously through three extended data sets of substrate concentration versus time. Temperature affected both the conversion and inactivation parameters. The final model was used to calculate the substrate and biocatalyst costs per mmol of product in a continuous system with biocatalyst replenishment and biocatalyst recycling. Despite the effect of temperature on each kinetic parameter separately, the overall effect of temperature on the costs was found to be negligible (between 293 and 308 K). Within pertinent ranges, the sum of the substrate and biocatalyst costs per mmol of product was calculated to decrease with the influent substrate concentration and the residence time. The sum of the costs showed a minimum as a function of the influent biocatalyst concentration.
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238
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Abstract
[reaction: see text] Pantocin B, an unusual antibiotic produced by Erwinia herbicola, effectively controls E. amylovora, the pathogen causing the plant disease fire blight. A total synthesis of pantocin B from L-alanine, glycine, and L-malic acid is reported.
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239
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Damen EW, Wiegerinck PH, Braamer L, Sperling D, de Vos D, Scheeren HW. Paclitaxel esters of malic acid as prodrugs with improved water solubility. Bioorg Med Chem 2000; 8:427-32. [PMID: 10722165 DOI: 10.1016/s0968-0896(99)00301-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The synthesis of paclitaxel esters of malic acid is described. These compounds were found to have improved water solubility and are stable in solution at neutral pH. The C2' modified compounds behave as prodrugs, that is, paclitaxel is generated upon exposure to human plasma, whereas the C7 modified derivatives do not. 2'-Malyl paclitaxel sodium salt demonstrated enhanced antitumour activity and less toxicity in a P388 murine leukaemia in vivo model when compared to paclitaxel.
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240
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Bandell M, Lolkema JS. Stereoselectivity of the membrane potential-generating citrate and malate transporters of lactic acid bacteria. Biochemistry 1999; 38:10352-60. [PMID: 10441129 DOI: 10.1021/bi9907577] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The citrate transporter of Leuconostoc mesenteroides (CitP) and the malate transporter of Lactococcus lactis (MleP) are homologous proteins that catalyze citrate-lactate and malate-lactate exchange, respectively. Both transporters transport a range of substrates that contain the 2-hydroxycarboxylate motif, HO-CR(2)-COO(-) [Bandell, M., et al. (1997) J. Biol. Chem. 272, 18140-18146]. In this study, we have analyzed binding and translocation properties of CitP and MleP for a wide variety of substrates and substrate analogues. Modification of the OH or the COO(-) groups of the 2-hydroxycarboxylate motif drastically reduced the affinity of the transporters for the substrates, indicating their relevance in substrate recognition. Both CitP and MleP were strictly stereoselective when the R group contained a second carboxylate group; the S-enantiomers were efficiently bound and translocated, while the transporters had no affinity for the R-enantiomers. The affinity of the S-enantiomers, and of citrate, was at least 1 order of magnitude higher than for lactate and other substrates with uncharged R groups, indicating a specific interaction between the second carboxylate group and the protein that is responsible for high-affinity binding. MleP was not stereoselective in binding when the R groups are hydrophobic and as large as a benzyl group. However, only the S-enantiomers were translocated by MleP. CitP had a strong preference for binding and translocating the R-enantiomers of substrates with large hydrophobic R groups. These differences between CitP and MleP explain why citrate is a substrate of CitP and not of MleP. The results are discussed in the context of a model for the interaction between sites on the protein and functional groups on the substrates in the binding pockets of the two proteins.
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241
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Arthurs CE, Lloyd D. Kinetics, stereospecificity, and expression of the malolactic enzyme. Appl Environ Microbiol 1999; 65:3360-3. [PMID: 10427020 PMCID: PMC91505 DOI: 10.1128/aem.65.8.3360-3363.1999] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mass spectrometric measurement of carbon dioxide production was used to study malolactic fermentation (MLF) in Lactobacillus collinoides isolated from cider. The kinetics and stereospecificity of the malolactic enzyme (MLE) were studied, and the stoichiometry of the reaction sequence was investigated. The optimum pH for activity of the MLE was 4.9. MLF was more rapid (in both intact cells and cell extracts) when L-malic acid was used than when D-malic acid or the racemic mixture was added. The enzyme was found to be constitutively present in L. collinoides. Addition of L-malic acid (37 mM) to the growth medium resulted in increased MLE activity; addition of the D isomer alone or the racemic mixture resulted in lower activities. Addition of the main sugars in apple juice (fructose, sucrose, and glucose) to the growth medium in the presence of malic acid repressed production of MLE to similar extents in all three cases; in the absence of malic acid, instead of inhibiting MLF, addition of sugars to the growth medium somewhat increased the residual MLE activity.
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242
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Geck MK, Kirsch JF. A novel, definitive test for substrate channeling illustrated with the aspartate aminotransferase/malate dehydrogenase system. Biochemistry 1999; 38:8032-7. [PMID: 10387047 DOI: 10.1021/bi983029c] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel method is presented that establishes definitively the existence or nonexistence of direct metabolite transfer between consecutive enzymes in a metabolic sequence. The procedure is developed with the specific example of channeling of oxaloacetate between Escherichia coli aspartate aminotransferase (AATase) and malate dehydrogenase (MDH). The assay is carried out in the presence of a large excess of inactive variants of AATase. These mutants would outcompete the much smaller quantities of wild-type AATase for any docking sites on MDH and thus decrease the rate of the coupled L-aspartate to oxaloacetate to malate sequence only if the direct metabolite transfer mechanism is operative. The results show that oxaloacetate is not transferred directly from AATase to MDH because no decrease in rate was observed in the presence of approximately 100 microM inactive mutants. This concentration is 10 times the physiological AATase concentration, which was determined in this work. The methodology can be applied generally.
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243
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Cammas S, Béar MM, Moine L, Escalup R, Ponchel G, Kataoka K, Guérin P. Polymers of malic acid and 3-alkylmalic acid as synthetic PHAs in the design of biocompatible hydrolyzable devices. Int J Biol Macromol 1999; 25:273-82. [PMID: 10416675 DOI: 10.1016/s0141-8130(99)00042-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Poly(beta-malic acid) and poly(beta-3-alkylmalic acid) derivatives, as synthetic polyhydroxyalkanoates (PHAs), present several advantages as macromolecular materials for temporary biomedical applications. Indeed, such polymers, which can be synthesized through different chemical and biological routes, have cleavable ester bonds in their backbone for hydrolytic degradation, stereogenic centres in the monomers units for controlling the macromolecular structure. bioassimilable or non-toxic repeating units and lateral chemical functions which can be adapted to specific requirements. The strategy for building such complex architectures, with one or several specific pendant groups, is based on the anionic ring-opening polymerization or copolymerization of the large family of malolactonic and 3-alkylmalolactonic acid esters. Because we are able to control the monomer synthesis and the polymerization step, we have been able to prepare different degradable materials for the biomedical field, such as: degradable associating networks made up by the association of random copolyesters containing a small percentage of hydrophobic moieties and beta-cyclodextrin copolymers; degradable macromolecular micelles constituted by degradable amphiphilic block copolymers of poly(beta-malic acid) as hydrophilic segments and poly(beta-alkylmalic acid alkyl esters) as hydrophobic blocks; and degradable nanoparticles made up by hydrophobic poly(beta-malic acid alkyl esters) derivatives. We have also prepared a terpolymer which exhibits growth factor-like properties in vivo. Finally, poly(beta-malic acid) has been used as an additive in the preparation of peritoneal dialysis bags.
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244
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Karsten WE, Hwang CC, Cook PF. Alpha-secondary tritium kinetic isotope effects indicate hydrogen tunneling and coupled motion occur in the oxidation of L-malate by NAD-malic enzyme. Biochemistry 1999; 38:4398-402. [PMID: 10194359 DOI: 10.1021/bi982439y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The NAD-malic enzyme from Ascaris suum catalyzes the divalent metal ion-dependent oxidative decarboxylation of L-malate to give pyruvate and CO2, with NAD+ as the oxidant. Alpha-secondary tritium kinetic isotope effects were measured with NAD+ or APAD+ and L-malate-2-H(D) and several different divalent metal ions. The alpha-secondary tritium kinetic isotope effects are slightly higher than 1 with NAD+ and L-malate as substrates, much larger than the expected inverse isotope effect for a hybridization change from sp2 to sp3. The alpha-secondary tritium kinetic isotope effects are reduced to values near 1 with L-malate-2-D as the substrate, regardless of the metal ion that is used. Data suggest the presence of quantum mechanical tunneling and coupled motion in the malic enzyme reaction when NAD+ and malate are used as substrates. Isotope effects were also measured using the D/T method with NAD+ and Mn2+ as the substrate pair. A Swain-Schaad exponent of 2.2 (less than the value of 3.26 expected for strictly semiclassical behavior) is estimated, suggesting the presence of other slow steps along the reaction pathway. With APAD+ and Mn2+ as the substrate pair, inverse alpha-secondary tritium kinetic isotope effects are observed, and a Swain-Schaad exponent of 3.3 is estimated, consistent with rate-limiting hydride transfer and no quantum mechanical tunneling or coupled motion. Data are discussed in terms of the malic enzyme mechanism and the theory developed by Huskey for D/T isotope effects as an indicator of tunneling [Huskey, W. P. (1991) J. Phys. Org. Chem. 4, 361-366].
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245
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Heun G, Lambov N, Zlatkov A, Peikov P, Doytchinova I, Gesheva K. Biodegradable cross-linked prodrug of the bronchial dilator Vephylline. 2. Kinetics and quantum chemical studies on the release mechanism. J Control Release 1999; 58:189-94. [PMID: 10053191 DOI: 10.1016/s0168-3659(98)00153-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Experimental thermodynamics studies and quantum chemical reaction path calculations on the hydrolytic degradation of Poly-vephyllinemalate microspheres in acidic and basic media were performed. It was possible to make a conclusion on the release mechanism of free Vephylline as follows: a hydrolytic cleavage of the ester bonds between molecular fragments of R,S-malic acid takes place and leads to a soluble oligoester fraction. Then, further hydrolysis of the ester bonds between the xanthine fragment and R, S-malic acid leads to the release of Vephylline as free base. The hydrolytic process takes place in acidic solution with rapid degradation of the ester bonds between the malic acid monomers and by far slower degradation of the ester bonds between the malic acid and Vephylline. In basic solution both steps of the hydrolysis are fast processes leading to a complete release of free Vephylline within 1 h. The process of Vephylline release is under entropic control. The experimental results are well correlated to the results obtained after kinetics investigation and after AM1 quantum chemically calculated energy barriers in the reaction path leading to the tetrahedral intermediates of the hydrolytic reactions. This conclusion is in good accordance with an indirect study on the release mechanism of Vephylline from its polymeric prodrug, paying attention to the biological response, reported previously.
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246
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Rose IA. How fumarase recycles after the malate --> fumarate reaction. Insights into the reaction mechanism. Biochemistry 1998; 37:17651-8. [PMID: 9922130 DOI: 10.1021/bi9821521] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recycling of yeast fumarase to permit repetition of its reaction chemistry requires two proton transfers and two conformational changes, in pathways that are different in detail but thematically similar in the two directions. In the malate --> fumarate direction, simple anions such as acetate accelerate the fumarate-off step producing E(H(f)), a fumarate-specific isoform that retains the C3R-proton of malate. Fumarate specificity is shown with S-2,3-dicarboxyaziridine, which is competitive vs fumarate and noncompetitive with malate as substrate. The steady-state level of E(H(f)), based on Kii (S-2,3-dicarboxyaziridine), is increased by D2O and decreased by imidazole acting as a general acid for conversion of E(H(f)) to E(H(f))H. E(H(f))H is fumarate-specific as shown by the inhibition pattern with ClO4-. The pKa of this step is approximately 7.25 based on the pH dependence of Kii (ClO4-). A conformational change occurs next as shown by high sensitivity of k(cat) but not k(cat)/Km, to the microviscosogen, glycerol, and change to a nonspecific isoform, E(H(mf))H, probably the same species formed in the fumarate --> malate direction from malate-specific intermediates by a different conformational change. Malate enters the cycle by reaction with E(H(mf))H and returns to E(m)H x malate after a second conformational change. When fumarate-off is slow, as in low anion medium, malate itself becomes an activator of malate --> fumarate. This effect occurs with changes in inhibition patterns suggestive of the bypass of the slow E(f) --> E(mf) conversion in favor of direct formation of E(mf) when free fumarate is formed. 3-Nitro-2-hydroxypropionate, a strong inhibitor of fumarase [Porter, D. J. T., and Bright, H. J. (1980) J. Biol. Chem. 255, 4772-4780] in its carbanion form, is competitive with both malate and fumarate. Therefore, 3-nitro-2-hydroxypropionic acid interacts with E(H(mf))H and not with E(m) or E(f) isoforms. Occurrence of two different conformational changes in the recycling process suggests that the reaction chemistry employs a two-step mechanism. The specificity of inhibition for E(H(mf))H is consistent with the expected intermediate of a carbanion mechanism, E(H)H x carbanion-. The proton transfers and conformational changes of recycling occur in the same sequence that is expected for this reaction chemistry. Several examples of ligand-activated conformational changes are reported.
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247
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Urbauer JL, Bradshaw DE, Cleland WW. Determination of the kinetic and chemical mechanism of malic enzyme using (2R,3R)-erythro-fluoromalate as a slow alternate substrate. Biochemistry 1998; 37:18026-31. [PMID: 9922171 DOI: 10.1021/bi981820f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
(2R,3R)-erythro-Fluoromalate, but not the threo isomer, is a slow substrate for chicken liver malic enzyme with either NADP or 3-acetylpyridine-NADP (APADP) as the other substrate. The Km for erythro-fluoromalate is similar to that of malate, but the turnover number with NADP is 3300-fold slower, although 5.5-fold faster with APADP than with NADP. Deuteration of fluoromalate at C-2 gave an isotope effect on V/K of 1.39 with NADP and 3.32 with APADP. With NADP, the 13C isotope effects at C-4 were 1.0490 with unlabeled and 1.0364 with deuterated fluoromalate. With APADP, the corresponding values were 1.0138 and 1.0087. These data show that the mechanism is stepwise with both nucleotide substrates, in contrast to the reaction of malate and APADP, which was postulated to be concerted by Karsten et al. [Karsten, W. E., and Cook, P. F. (1994) Biochemistry 33, 2096-2103], a conclusion recently shown to be correct by Edens et al. [Edens, W. A., Urbauer, J. L., and Cleland, W. W. (1997) Biochemistry 36, 1141-1147]. To explain the effect of deuteration on the 13C isotope effect with APADP, it is necessary to assume a secondary 13C isotope effect at C-4 on the hydride transfer step of approximately 1.0064 (assuming 5.7 as the intrinsic primary deuterium isotope effect and 1.054 as the product of the 13C equilibrium isotope effect on hydride transfer and the intrinsic 13C isotope effect on decarboxylation). The secondary 13C isotope effect on hydride transfer is thought to result from hyperconjugation between the carbonyl group and C-4 of the enzyme-bound fluorooxaloacetate intermediate.
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Imada K, Inagaki K, Matsunami H, Kawaguchi H, Tanaka H, Tanaka N, Namba K. Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 A resolution: the role of Glu88 in the unique substrate-recognition mechanism. Structure 1998; 6:971-82. [PMID: 9739088 DOI: 10.1016/s0969-2126(98)00099-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND 3-Isopropylmalate dehydrogenase (IPMDH) and isocitrate dehydrogenase (ICDH) belong to a unique family of bifunctional decarboxylating dehydrogenases. Although the ICDH dimer catalyzes its reaction under a closed conformation, known structures of the IPMDH dimer (without substrate) adopt a fully open or a partially closed form. Considering the similarity in the catalytic mechanism, the IPMDH dimer must be in a fully closed conformation during the reaction. A large conformational change should therefore occur upon substrate binding. RESULTS We have determined the crystal structure of IPMDH from Thiobacillus ferrooxidans (Tf) complexed with 3-isopropylmalate (IPM) at 2.0 A resolution by the molecular replacement method. The structure shows a fully closed conformation and the substrate-binding site is quite similar to that of ICDH except for a region around the gamma-isopropyl group. The gamma group is recognized by a unique hydrophobic pocket, which includes Glu88, Leu91 and Leu92 from subunit 1 and Val193' from subunit 2. CONCLUSIONS A large movement of domain 1 is induced by substrate binding, which results in the formation of the hydrophobic pocket for the gamma-isopropyl moiety of IPM. A glutamic acid in domain 1, Glu88, participates in the formation of the hydrophobic pocket. The C beta and C gamma atoms of Glu88 interact with the gamma-isopropyl moiety of IPM and are central to the recognition of substrate. The acidic tip of Glu88 is likely to interact with the nicotinamide mononucleotide (NMN) ribose of NAD+ in the ternary complex. This structure clearly explains the substrate specificity of IPMDH.
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Wang X, Gong CS, Tsao GT. Bioconversion of fumaric acid to succinic acid by recombinant E. coli. Appl Biochem Biotechnol 1998; 70-72:919-28. [PMID: 9627403 DOI: 10.1007/bf02920202] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Succinic acid was produced efficiently from fumaric acid by a recombinant E. coli strain DH5 alpha/pGC1002 containing multicopy fumarate reductase genes. The effects of initial fumaric acid and glucose concentration on the production of succinic acid were investigated. Succinic acid reached 41 to over 60 g/L in 48.5 h starting with 50 to 64 g/L fumaric acid. Significant substrate inhibition was observed at initial fumaric acid concentration of 90 g/L. L-Malic acid became the major fermentation product under these conditions. Provision of glucose (5-30 g/L) to the fermentation medium stimulated the initial succinic acid production rate over two folds.
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