Structure analysis and molecular model of the selenoenzyme glutathione peroxidase at 2.8 Å resolution

The three-dimensional structure of bovine erythrocyte glutathione peroxidase, a tetrameric enzyme containing 4 gram atoms of selenium per mole (M_r = 84,000), has been determined at 2.8 Å resolution using the multiple isomorphous replacement method. By correlation calculations in Patterson space the tetramers were shown to exhibit molecular [222] symmetry, proving the monomers to be identical or at least very similar.The monomer consists of a single polypeptide chain of 178 amino acid residues. Its shape is nearly spherical with a radius of $\text{r ≈ 19}\text{A}\text{?}$. A tentative sequence corresponding to a partially refined model (R = 0.38) is given. Each subunit is built up from a central core of two parallel and two anti-parallel strands of pleated sheet surrounded by four α-helices. One of the helices runs antiparallel to the neighbouring β-strands giving rise to a βαβ substructure, an architecture that has been found in several other proteins e.g. flavodoxin, thioredoxin, rhodanese and dehydrogenases. A comparison of the glutathione peroxidase subunit structure with thioredoxin-S₂ revealed large regions of structural resemblance. The central four-stranded β structure together with two parallel α-helices resembles nearly 80% of the thioredoxin fold.The active sites of glutathione peroxidase are located in flat depressions on the molecular surface. Probably each active centre is built up by segments from two subunits. The catalytically active selenocysteines were found at the N-terminal ends of long α-helices and are surrounded by an accumulation of aromatic side-chains. A difference Fourier map between oxidized and substrate-reduced glutathione peroxidase as well as heavy-atom binding led to the conclusion that the two-electron redox-cycle involves a reversible transition of the active-site selenium from a selenenic acid (RSeOH) to a seleninic acid (RSeOOH).     

On the specificity of the uridine diphospho-N-acetylmuramyl-alanyl-D-glutamic acid: Diamino acid ligase of Bifidobacterium globosum

The peptidoglycan of Bifidobacterium globosum contains ornithine and lysine alternately in the same position of the peptide subunit. The uridine diphospho-N-acetylmuramyl-alanyl-D-glutamic acid: diamino acid ligase of this organism was purified 700-fold. Since the activities for the incorporation of ornithine and lysine into uridine diphospho-N-acetylmuramyl-tripeptide did not separate during purification and since the incorporation of ornithine is competitively inhibited by lysine and vice versa, both ornithine and lysine are assumed to be incorporated by one single enzyme. Studies on the specificity of the ligase toward analogs of ornithine have shown that the enzyme requires a diamino, monocarboxylic acid with 4–6 carbon atoms. Methylation of the -amino group or hydroxylation of the -carbon atom of lysine decreases the competitive properties of the analog, whereas the substitution of the -methylen group by sulfur (S-2-aminoethyl cysteine) results in a highly competitive compound.Abbreviations BSA bovine serum albumine - MurNAc N-acetyl-muramyl - DA diamino acid - Ala-DGlu--L-DA-DAla-D-Ala pentapeptide - Ala-DGlu--LDA tripeptide - Ala-DGlu dipeptide - DSM Deutsche Sammlung von Mikroorganismen - CEM clostridial enrichment medium     

Bicyclo[3,2,1]octanoid,neolignans from Aniba simulans

Six bicyclo[3,2,1]octanoid neolignans, isolated from the benzene extract of Aniba simulans Allen (Lauraceae) trunk wood, are shown to derive from two basic structures: 1-allyl-8-hydroxy-6-(3′-methoxy-4′,5′-methylenedioxyphenyl)-7-methyl-3-oxobicyclo[3,2,1]octane, substituted by 4-hydroxy, 4-hydroxy-5-methoxy, 4-methoxy or 4,5-dimethoxy groups; and 1-allyl-8-hydroxy-6-(3′-methoxy-4′,5′-methylenedioxyphenyl)-7-methyl-4-oxobicyclo[3,2,1]oct-2-ene, substituted by 3-hydroxy or 3-hydroxy-5-methoxy groups. The structural proposals are based on spectral data, interconversions synthesis of a derivative from the known (2R,3S,3aS)-3a-allyl-5-methoxy-2-(3′-methoxy,4′,5′-methylenedioxyphenyl)-3-methyl-2,3,3a,6-tetrahydro-6-oxobenzofuran.     

Dihydroisocoumarins and phthalide from wood samples infested by fungi

Wood samples, infested by fungi during storage, were shown to contain, besides the known 5-methyl-mellein, additional (3R)-8-hydroxy-3-methyl-3,4-dihydroisocoumarins substituted by 7-methyl, 5-formyl, 5-carboxy, 5-hydroxy, 5-methoxy, 6-methoxy-5-methyl and 6,7-dimethoxy-5-methyl groups, as well as 6-formyl-7-hydroxy-5-methoxy-4-methylphthalide. Several 2-methylchromanones were synthesized in order to show that this class of compounds can be distinguished from 3-methyl-3,4-dihydroisocoumarins by MS.     

Neoflavonoids and the cinnamylphenol kuhlmannistyrene from Machaerium kuhlmannii and M. Nictitans

The trunkwood of Machaerium kuhlmannii contains methyl palmitate, 3-O-acetyloleanolic acid and sitosterol; the benzene derivatives 2,3-dimethoxyphenol, 2,6-dimethoxyphenol, 2-hydroxy-3-methoxyphenol, 2,3-dimethoxybenzaldehyde and methyl 3-(2-hydroxy-4-methoxyphenyl)-propionate; the isoflavonoids formononetin and (6aS,11aS)-medicarpin; the neoflavonoids (R)-3,4-dimethoxydalbergione, (R)-3,4-dimethoxydalbergiquinol, kuhlmanniquinol [(R)-3-(4-hydroxyphenyl)-3-(5-hydroxy-2,3,4-trimethoxyphenyl)-propene], dalbergin, kuhlmannin (6-hydroxy-7,8-dimethoxy-4-phenylcoumarin) and kuhlmannene (6-hydroxy-7,8-dimethoxy-4-phenylchrom-3-ene), as well as the cinnamylphenol kuhlmannistyrene [Z-1-(5-hydroxy-2,3,4-trimethoxybenzyl)-2-(2-hydroxyphenyl)-ethylene]. Five of these compounds, in addition to (R)-4′-hydroxy-3,4-dimethoxydalbergione, were also isolated from a trunkwood extract of M. nictitans. Structural assignments were confirmed by chemical interconversion and by the synthesis of (±)-kuhlmanniquinol.     

Mucronulatol,mucroquinone and mucronucarpan,isoflavonoids from Machaerium mucronulatum and M. villosum

Additionally to the cinnamylphenols described in a previous paper, wood samples of Machaerium mucronulatum and M. villosum contain isoflavones, besides (?)-duartin, (?)- and (±)-mucronulatol [(3S)- and rac-7,3′-dihydroxy-2′,4′-dimethoxyisoflavan], (?)-mucroquinone [(3S)-2-methoxy-5-(7-hydroxy-8-methoxychroman-3-yl)-1,4-benzoquinone] and (+)-mucronucarpan [(6aS,11aS)-2,10-dihydroxy-3,9-dimethoxypterocarpan]. The constitutions of mucronulatol, mucroquinone and mucronucarpan were deduced by spectra and degradations, and confirmed by syntheses.     

Variabilin,a 6a-hydroxypterocarpan from Dalbergia variabilis

Bark and wood of the creeper Dalbergia variabilis contain the previously described friedelin, O-acetyl-oleanolic acid, formononetin, 8-O-methylretusin, (+)-vestitol, (±)-mucronulatol, (+)- and (±)-medicarpin, besides (+)-variabilin [(6aR,11aR)-6a-hydroxy-3,9-dimethoxypterocarpan]. This structure was confirmed by the conversion of (+)-variabilin into di-O-methylcoumestrol.     

Absolute configurations of isoflavans

The absolute configurations of isoflavans and isoflavanquinones isolated from Cyclolobium, Dalbergia and Machaerium species were established by comparison of their ORD curves with that of (3S)-5,7,3′,4′-tetra-methoxyisoflavan and (3S)-7,4′-dimethoxyisoflavan-2′,5′-quinone, respectively. The assignments were checked by the ozonolysis of the isoflavan (?)-duartin to (R)-paraconic acid and the oxidation of isoflavans to isoflavanquinones. The PMR spectra of the dihydropyran ring of the isoflavans are discussed in terms of the preferred conformation of this ring.     

Deductive biology—Some cautious steps

For certain environments, the Darwinian model allows unique prediction of a function that any surviving system adapted to such an environment has to perform. This is the case for those environments that determine a “survival functional” of position in space-time of known shape. Purely temporal survival functionals can be distinguished from spatial and mixed ones. In each case, there exists an optimum path in combined physical and (reduced) metabolic space. Dependent on the admissible error, approximate solutions of different complexity are sufficient. All solutions possess an afferent, a central, and an efferent part. Within this general frame, specific, “probably simplest”, solutions are proposed for adaptive chemotaxis, insect locomotion, lower vertebrates locomotion, higher vertebrates locomotion, chronobiological systems, and immune systems, respectively—or rather, for the underlying functionals. Presented at the Society for Mathematical Biology Meeting, University of Pennsylvania, Philadelphia, August 19–21, 1976.