Isoprenoid Chain Research Articles

Significance of the 72-Membered Macrocyclic Structure Found in Archaeal Membrane Lipids: Model Studies of the Macrocyclic Tetraether Diphospholipids by Calorimetric, 31P NMR, and Electron Microscopic Analyses

Abstract Described in this paper are the characterizations of the synthetic 72-membered macrocyclic tetraether phospholipids (7, 8) and their acyclic congeners (9, 10), the hydrocarbon chains of which are unbranched straight chains instead of isoprenoid chains such as found in those of archaea. Thermal analyses by differential scanning calorimetry (DSC) clearly showed that the phase transition temperature (Tc) of the cyclic tetraether lipids 7 and 8 was rather lower than those of the corresponding acyclic counterparts 9 and 10. This trend was opposite to that of the diether lipids. The findings from 31P NMR and electron microscopic analyses suggested that the lipid polymorphism of 7 and 8 was quite different from that of 9 and 10. These results revealed that the cyclic structure in 7 and 8 contributed not only to the limitation of motional freedom at the hydrophobic region but also to the change of the lipid polymorphism in comparison with 9 and 10. Furthermore, it was found that these physicochemical as well as polymorphic properties were indistinguishable between the regioisomers 7 and 8 (or 9 and 10).

Synthesis of [ 11C] coenzyme Q-related compounds for in vivo estimation of mitochondrial electron transduction and redox state in brain

We have studied the synthesis of [ 11C]2,3-dimethoxy-5-methyl-6-(10-hydroxy)-decyl-1,4-benzoquinone (idebenone) and [ 11C]2,3-dimethoxy-5-methyl-1,4-benzoquinone (CoQ 0) by methylation of their respective desmethyl precursors using [ 11C]CH 3I for in vivo measurement of mitochondrial electron transfer and redox state. The [ 11C]idebenone was more lipophilic than [ 11C]CoQ 0; the latter became hydrophilic by reduction. Clearance of [ 11C]idebenone from mouse brain was more rapid than that of [ 11C]CoQ 0. The results indicated that modification of the isoprenoid side chain in [ 11C]CoQ is necessary to develop more suitable radiopharmaceuticals.

29] Determination of vitamin E forms in tissues and diets by high-performance liquid chromatography using normal-phase diol column

Publisher Summary This chapter discusses the determination of various forms of vitamin E in tissues and diets by high-performance liquid chromatography (HPLC) using normal-phase diol column. Vitamin E is a generic term that includes a mixture of tocopherols (T) and tocotrienols (T 3 ) that differs in the number and position of methyl groups on the fused chromanol ring and the absence or presence of three double bonds in the isoprenoid side chain. The present method for the determination of all the vitamin E forms in tissues eliminates the thawing step by pulverizing the tissue at dry ice temperature. Total vitamin E is extracted with hexane and analyzed directly by HPLC using diol column and fluorescence detection, without prior saponification of the sample. The method is modified for the analysis of diets to determine both free and esterified vitamin E. The chapter discusses the response factors of the different forms of vitamin E, the use of internal standards to quantitate vitamin E, and the structure and properties of the diol column. The diol column appears to combine the superior separation of normal-phase silica columns with the added stability and reproducibility that the epoxide structure of the packing material provides. The chapter concludes with a discussion of the influence of triacylglycerols on the quantitation of vitamin E using fluorescence detection.

Crystal structure of farnesyl protein transferase complexed with a CaaX peptide and farnesyl diphosphate analogue.

The crystallographic structure of acetyl-Cys-Val-Ile-selenoMet-COOH and alpha-hydroxyfarnesylphosphonic acid (alphaHFP) complexed with rat farnesyl protein transferase (FPT) (space group P61, a = b = 174. 13 A, c = 69.71 A, alpha = beta = 90 degrees, gamma = 120 degrees, Rfactor = 21.8%, Rfree = 29.2%, 2.5 A resolution) is reported. In the ternary complex, the bound substrates are within van der Waals contact of each other and the FPT enzyme. alphaHFP binds in an extended conformation in the active-site cavity where positively charged side chains and solvent molecules interact with the phosphate moiety and aromatic side chains pack adjacent to the isoprenoid chain. The backbone of the bound CaaX peptide adopts an extended conformation, and the side chains interact with both FPT and alphaHFP. The cysteine sulfur of the bound peptide coordinates the active-site zinc. Overall, peptide binding and recognition appear to be dominated by side-chain interactions. Comparison of the structures of the ternary complex and unliganded FPT [Park, H., Boduluri, S., Moomaw, J., Casey, P., and Beese, L. (1997) Science 275, 1800-1804] shows that major rearrangements of several active site side chains occur upon substrate binding.

The gerC locus of Bacillus subtilis, required for menaquinone biosynthesis, is concerned only indirectly with spore germination.

The gerC region of Bacillus subtilis comprises a tricistronic operon, encoding enzymes that catalyse the late stages of menaquinone biosynthesis. The gerC58 mutation is responsible for a severe growth defect; unsuppressed mutant cells grow as very short rods, which sometimes septate aberrantly. Cultures grow only to a low cell density, rapidly lose viability, and never sporulate. Unlinked suppressor mutations can restore near-normal growth. Several independent suppressed isolates were examined; all grew to normal cell length, but they showed, to varying extents, a residual defect in the placement of the cell division septum. The germination properties of the suppressed derivatives varied from normal to significantly slow in germination in all germinants; therefore, the combination of the gerC mutation and different suppressor alleles resulted in spores with very different germination properties. This suggests that any relationship between the gerC gene products and spore germination is indirect. The gerCC58 mutation maps in a gene encoding the catalytic subunit of the heptaprenyldiphosphate synthase, which is responsible for formation of the isoprenoid side chain of menaquinone-7, and it is proposed that the gerCA, gerCB and gerCC genes be renamed hepA, menG and hepB, respectively.

Biological significance of the side chain length of ubiquinone in Saccharomyces cerevisiae

Ubiquinone (UQ), an important component of the electron transfer system, is constituted of a quinone structure and a side chain isoprenoid. The side chain length of UQ differs between microorganisms, and this difference has been used for taxonomic study. In this study, we have addressed the importance of the length of the side chain of UQ for cells, and examined the effect of chain length by producing UQs with isoprenoid chain lengths between 5 and 10 in Saccharomyces cerevisiae. To make the different UQ species, different types of prenyl diphosphate synthases were expressed in a S. cerevisiae COQ1 mutant defective for hexaprenyl diphosphate synthesis. As a result, we found that the original species of UQ (in this case UQ-6) had maximum functionality. However, we found that other species of UQ could replace UQ-6. Thus a broad spectrum of different UQ species are biologically functional in yeast cells, although cells seem to display a preference for their own particular type of UQ.

98/02780 Petroleum land release—data availability: QGMJ QGMJ, 1998, 99, (1155), 39

A wide range of novel diagenetic and catagenetic products of the diaromatic carotenoid isorenieratene, a pigment of the photosynthetic green sulphur bacteria Chlorobiaceae, has been identified in a number of sedimentary rocks ranging from Ordovician to Miocene. Compound identification is based on NMR, mass spectrometry, the presence of atropisomers, and stable carbon isotopes. Atropisomers contain an axially chiral centre which, in combination with other chiral centres, results in two or more diastereomers that can be separated on a normal GC column. Chlorobiaceae use the reverse TCA cycle to fix carbon, so that their biomass is enriched in 13C. High 13C contents of isorenieratene derivatives therefore support their inferred origins.Isorenieratene derivatives include C 40, C 33, and C 32, diaryl isoprenoids and short-chain aryl isoprenoids with additional aromatic and/or S-containing rings. C 33 and C 32 compounds are diagenetic products of C 33 and C 32 “carotenoids” formed from isorenieratene during early diagenesis through expulsion of toluene and m-xylene, respectively. Cyclisation of the polyene acyclic isoprenoid chain can proceed via an intramolecular Diels-Alder reaction, followed by aromatisation of the newly formed ring. Sulphurisation is also an important process during early diagenesis, competing with expulsion and cyclisation. Sulphur-bound isorenieratane is released during progressive diagenesis, due to cleavage of relatively weak SS and CS bonds. Cleavage of C-C bonds during aromatisation of newly formed rings and during catagenesis yields short-chain compounds. The inherent presence of a conjugated double bond system in carotenoids implies that similar diagenetic and catagenetic reactions can occur with all carotenoids.Chlorobiaceae live at or below the oxic/anoxic boundary layer and require both light and H 2S. The presence of isorenieratene or its diagenetic and catagenetic products in ancient sedimentary rocks and crude oils is therefore an excellent indication for photic zone anoxia in the depositional environment. Diagenetic and catagenetic products of isorenieratene are expected to find applications in reconstruction of palaeoenvironments and in oil-oil and oil-source rock correlation studies. Their presence in several petroleum source rocks suggests that anoxia is an important environmental parameter for the preservation of organic matter.

Enzymatic Aspects of Isoprenoid Chain Elongation.

Enzymatic Aspects of Isoprenoid Chain Elongation.

A high diffusion coefficient for coenzyme Q 10 might be related to a folded structure

We measured the lateral diffusion of different coenzyme Q homologues and analogues in model lipid vesicles using the fluorescence collisional quenching technique with pyrene derivatives and found diffusion coefficients in the range of 10 −6 cm 2/s. Theoretical diffusion coefficients for these highly hydrophobic components were calculated according to the free volume theory. An important parameter in the free volume theory is the relative dimension between diffusant and solvent: a molecular dynamics computer simulation of the coenzymes yielded their most probable geometries and volumes and revealed surprisingly similar sizes of the short and long homologues, due to a folded structure of the isoprenoid chain in the latter, with a length for coenzyme Q 10 of 21 Å. Using this information we were able to calculate diffusion coefficients in the range of 10 −6 cm 2/s, in good agreement with those found experimentally.

Electrochemical Measurement of Lateral Diffusion Coefficients of Ubiquinones and Plastoquinones of Various Isoprenoid Chain Lengths Incorporated in Model Bilayers

The long-range diffusion coefficients of isoprenoid quinones in a model of lipid bilayer were determined by a method avoiding fluorescent probe labeling of the molecules. The quinone electron carriers were incorporated in supported dimyristoylphosphatidylcholine layers at physiological molar fractions (<3 mol%). The elaborate bilayer template contained a built-in gold electrode at which the redox molecules solubilized in the bilayer were reduced or oxidized. The lateral diffusion coefficient of a natural quinone like UQ 10 or PQ 9 was 2.0 ± 0.4 × 10 −8 cm 2 s −1 at 30°C, two to three times smaller than the diffusion coefficient of a lipid analog in the same artificial bilayer. The lateral mobilities of the oxidized or reduced forms could be determined separately and were found to be identical in the 4–13 pH range. For a series of isoprenoid quinones, UQ 2 or PQ 2 to UQ 10, the diffusion coefficient exhibited a marked dependence on the length of the isoprenoid chain. The data fit very well the quantitative behavior predicted by a continuum fluid model in which the isoprenoid chains are taken as rigid particles moving in the less viscous part of the bilayer and rubbing against the more viscous layers of lipid heads. The present study supports the concept of a homogeneous pool of quinone located in the less viscous region of the bilayer.

Catagenesis of light aromatic compounds in petroleum

Several aspects related to light aromatic compounds in petroleum are discussed: relative abundance in crude oils, possible associations between their contents and those of other major petroleum components, generation in radical and acid clay-catalyzed reactions from model compounds representing various petroleum components ( n-alkanes, isoprenoid alkanes, light naphthenic compounds, saturated polycyclic hydrocarbons, alkylaromatic compounds) and chemical mechanisms of aromatization during petroleum maturation. Model cracking reactions of various petroleum constituents indicate that light aromatic compounds are most likely formed during the petroleum catagenesis stage from a variety of sources, most importantly from compounds containing long n-alkyl and isoprenoid chains. The most probable sequence of events leading to aromatization includes cracking of saturated hydrocarbon chains to olefins, cracking of olefins to dienes, cyclization of dienes to cyclodienes and aromatization of cyclodienes. The molecular weight distribution of aromatic compounds in petroleum is most probably controlled by temperature and duration of the last stages of petroleum maturation. This distribution correlates with the distribution of n-alkanes as a function of their carbon number. Presented data on isomerization of individual aromatic compounds and aromatics distribution in crude oils suggest that aromatic compounds generated in cracking reactions undergo extensive isomerization and exchange of alkyl substituents. These reactions result in a nearly complete randomization of the types of alkyl substituents (mostly methyl and ethyl groups) and their positions in aromatic rings. These mixtures in most crude oils can be represented by thermodynamic equilibrium estimations for 200–300°C.

Total Synthesis of Archaeal 36-Membered Macrocyclic Diether Lipid.

Total synthesis of archaeal 36-membered macrocyclic diether lipid 2 is reported. The synthesis is based upon stereoselective preparation of functionalized isoprenoid chains, ether-linkage formation between the isoprenoid chains with a glycerol derivative, and the ultimate intramolecular dicarbonyl coupling using low-valent titanium known as McMurry coupling. This synthetic method has successfully provided the first practical route to chemically defined archaeal macrocyclic membrane lipids, which were not available because of the lack of synthetic access. Also described is a highly stereoselective and convenient synthesis of stereochemically homogeneous archaeal biphytanyl glycerol lipid 1.

Novel cyclised and aromatised diagenetic products of β-carotene in the Green River Shale

A suite of novel diagenetic products of β-carotene has been identified in an extract of a sample from the Green River Shale. Identification is mainly based on comparison of mass spectra with those of diagenetic products of another carotenoid, isorenieratene. These compounds were formed by (i) cyclisation and aromatisation of the polyene isoprenoid chain, (ii) explusion of toluene and m-xylene from the polyene isoprenoid chain, and (iii) aromatisation of the 1,1,5-trimethylcyclohex-5-enyl moieties resulting in 1,2-dimethylbenzene end groups. Reduction of the double bonds of β-carotene is the most important diagenetic process, however, as judged from the high relative amount of β-carotane (63% of quantified diagenetic products of β-carotene). These results indicate that the fossilisation potential of carotenoids is greater than previously thought.

Structures and properties of vitamin K and its radical anion predicted by a hybrid Hartree-Fock/density functional method

We present a hybrid Hartree-Fock/density functional study of 1,4-benzoquinone and a model of menaquinone-1, and predict the structures and vibrational frequencies of both the K 1 and K 2 forms of vitamin K and their radical anions. Our model compound includes only hydrogens as isoprenoid chain terminal groups, rather than the methyl groups present in actual menaquinone-1, for computational efficiency. Although the structures and frequencies found for vitamin K are significantly different from those found in the parent molecule 1,4-benzoquinone and its radical anion, calculated spin densities indicate that the odd electron is delocalized almost exclusively on the quinoid oxygens and ring of vitamin K. Isotropic hyperfine coupling constants are calculated for both radical anions using a Chipman basis set designed to give reliable spin properties. An electron affinity of 1.72 ± 0.05 eV is predicted for the model of menaquinone-1, but lowers to 1.68 ± 0.05 eV when the chain-terminal methyl groups are added.

Trimethyl-p-benzoquinone Provides Excellent Structural, Spectroscopic, and Thermochemical Models for Plastoquinone-1 and Its Radical Anion

Trimethyl-p-benzoquinone (TMQ) has been proposed to furnish an accurate thermochemical model for plastoquinones, key electron acceptors in oxygenic photosynthetic electron transfer. Free energy perturbation/molecular dynamics simulations combined with hybrid Hartree−Fock/density functional (HF/DF) calculations confirm that TMQ and plastoquinone-1 have approximately equal aqueous one-electron reduction potentials, within the accuracy of the calculations. HF/DF calculations using the B3LYP/6-31G(d) method also show that TMQ and its radical anion have (1) structures almost identical to those of PQa model for plastoquinone-1 without the isoprenoid chain's methyl groupsand its radical anion, respectively, have (2) spin densities for TMQ•- and PQ•- which differ by 0.01 electrons at most, and have (3) key CO and CC stretching frequencies for the TMQ/PQ and TMQ•-/PQ•- pairs differing by only 1−8 cm-1. Thus, TMQ and TMQ•- are excellent models for the structures, spin densities, and vibrational frequencies of plast...

Diagenetic and catagenetic products of isorenieratene: Molecular indicators for photic zone anoxia

A wide range of novel diagenetic and catagenetic products of the diaromatic carotenoid isorenieratene, a pigment of the photosynthetic green sulphur bacteria Chlorobiaceae, has been identified in a number of sedimentary rocks ranging from Ordovician to Miocene. Compound identification is based on NMR, mass spectrometry, the presence of atropisomers, and stable carbon isotopes. Atropisomers contain an axially chiral centre which, in combination with other chiral centres, results in two or more diastereomers that can be separated on a normal GC column. Chlorobiaceae use the reverse TCA cycle to fix carbon, so that their biomass is enriched in 13C. High 13C contents of isorenieratene derivatives therefore support their inferred origins.Isorenieratene derivatives include C 40, C 33, and C 32, diaryl isoprenoids and short-chain aryl isoprenoids with additional aromatic and/or S-containing rings. C 33 and C 32 compounds are diagenetic products of C 33 and C 32 “carotenoids” formed from isorenieratene during early diagenesis through expulsion of toluene and m-xylene, respectively. Cyclisation of the polyene acyclic isoprenoid chain can proceed via an intramolecular Diels-Alder reaction, followed by aromatisation of the newly formed ring. Sulphurisation is also an important process during early diagenesis, competing with expulsion and cyclisation. Sulphur-bound isorenieratane is released during progressive diagenesis, due to cleavage of relatively weak SS and CS bonds. Cleavage of C-C bonds during aromatisation of newly formed rings and during catagenesis yields short-chain compounds. The inherent presence of a conjugated double bond system in carotenoids implies that similar diagenetic and catagenetic reactions can occur with all carotenoids.Chlorobiaceae live at or below the oxic/anoxic boundary layer and require both light and H 2S. The presence of isorenieratene or its diagenetic and catagenetic products in ancient sedimentary rocks and crude oils is therefore an excellent indication for photic zone anoxia in the depositional environment. Diagenetic and catagenetic products of isorenieratene are expected to find applications in reconstruction of palaeoenvironments and in oil-oil and oil-source rock correlation studies. Their presence in several petroleum source rocks suggests that anoxia is an important environmental parameter for the preservation of organic matter.

6 イソプレノイド生合成における鎖延長機構 : 中鎖プレニル二リン酸合成酵素遺伝子のクローニングとその解析(口頭発表の部)

6 イソプレノイド生合成における鎖延長機構 : 中鎖プレニル二リン酸合成酵素遺伝子のクローニングとその解析(口頭発表の部)

Polyprenyl diphosphate synthase essentially defines the length of the side chain of ubiquinone.

Ubiquinone, known as a component of the electron transfer system in many organisms, has a different length of the isoprenoid side chain depending on the species, e.g., Escherichia coli, Saccharomyces cerevisiae and humans have 8, 6, and 10 isoprene units in the side chain, respectively. No direct evidence has yet shown what factors define the length of the side chain of ubiquinone. Here we proved that the polyprenyl diphosphate that was available in cells determined the length of the side chain of ubiquinone. E. coli octaprenyl diphosphate synthase (IspB) was expressed with the mitochondrial import signal in S. cerevisiae. Such cells produced ubiquinone-8 in addition to the originally existing ubiquinone-6. When IspB was expressed in a S. cerevisiae COQ1 defective strain. IspB complemented the defect of the growth on the non-fermentable carbon source. Those cells had the activity of octaprenyl diphosphate synthase and produced only ubiquinone-8. These results opened the possibility of producing the type of ubiquinone that we need in S. cerevisiae simply by expressing the corresponding polyprenyl diphosphate synthase.

Chemistry, Nutritional Sources, Tissue Distribution and Metabolism of Vitamin K with Special Reference to Bone Health

Vitamin K occurs in anture as a series of compounds with a common 2-methyl-1,4 naphthoquinone nucleus and differing isoprenoid side chains at the 3 position. They comprise a single major plant form, phylloquinone with a phytyl side chain and a family of bacterially synthesized menaquinones (MKs) with multiprenyl side chains.The major dietary source to humans is phylloquinone for which the chief food contributors are green, leafy vegetables followed by certain vegetable oils (soybean, rapeseed and olive oils). Recent analyses by high pressure liquid chromatography are now providing a wide-ranging database of phylloquinone in foods. Menaquinones are found in moderate concentrations in only a few foods such as cheeses (MK-8 and MK-9). A wider spectrum of MKs is synthesized by the gut microflora, and their intestinal absorption probably accounts for most of the hepatic stores, particularly those with very long side chains (MKs-10–13) synthesized by members of the genus Bacteroides. The site of absorption of floral MKs is not known, but reasonable concentrations are found in the terminal ileum where bile salt-mediated absorption is possible.Both phylloquinone and menaquinones are bioactive in hepatic gamma-carboxylation but long-chain MKs are less well absorbed. Liver stores of vitamin K are relatively small and predominantly MKs-7–13. The hepatic reserves of phylloquinone (∼10% of the total) are labile and turn over at a faster rate than menaquinones. Trabecular and cortical bone appear to contain substantial concentrations of both phylloquinone and menaquinones. A majority (∼60–70%) of the daily dietary intake of phylloquinone is lost to the body by excretion, which emphasizes the need for a continuous dietary supply to maintain tissue reserves.

Pigment-protein interactions in Rhodobacter sphaeroides Y photochemical reaction center; comparison with other reaction center structures

Structural characteristics of pigments and cofactors are analyzed in the X-ray structure of the Rhodobacter sphaeroides (Y strain) photochemical reaction center, recently refined at 3 A resolution (Arnoux B, Gaucher JF, Ducruix A and Reiss-Husson F (1995) Acta Cryst D51: 368–379). As several structures are now available for these pigment-protein complexes from various Rhodobacter sphaeroides strains and for Rhodopseudomonas viridis, a detailed comparison was done for highlighting converging structural results as well as for pointing to incidental differences. Comparison of mean plane orientations and distances, and also direct superposition of the pigment arrays, indicated that the best agreement between all the structures concerned the dimer and the bacteriopheophytin of the A branch. In the Y reaction center structure the pentacoordination of the Mg++ atoms of the bacteriochlorophylls, and the H bonding pattern of the porphyrin conjugated carbonyls are consistent with the better resolved Rhodobacter sphaeroides recently published structure (Ermler U, Fritzsch G, Buchanan SK and Michel H (1995) Structure 2:925–936). Discrepancies between the various Rhodobacter sphaeroides structures are larger for the quinones, particularly the secondary one. In the Y reaction center structure the phytyl and isoprenoid chains of the cofactors are defined and their local mobility was evaluated by analyzing the temperature factor and the density of neighbouring atoms. Significant differences were observed between the A and B branches, and, within each branch, from the dimer to the quinone molecules.