3(10)-Helix adjoining alpha-helix and beta-strand: sequence and structural features and their conservation

Does the amino acid use at the terminal positions of an α‐helix become altered depending on the context—more specifically, when there is an adjoining 3₁₀‐helix, and can a single helical cylinder encompass the resultant composite helix? An analysis of 138 and 107 cases of 3₁₀–α and α–3₁₀ composite helices, respectively, found in known protein structures indicate that the secondary structural element occurring first imposes its characteristics on the sequence of the structural element coming next. Thus, when preceded by a 3₁₀‐helix, the preference of proline to occur at the N1 position of an α‐helix is shifted to the N2 position, a typical characteristic of the C‐terminal capping of the 3₁₀‐helix. When an α‐ or a 3₁₀‐helix leads into a helix of the other type, there is a bend at the junction, especially for the 3₁₀–α composite, with the two junction residues facing inward and buried within the structure. Thus a single helical cylinder may not properly represent a composite helix, the bend providing a means for the tertiary structure to assume a globular shape, very much akin to what a proline‐induced kink does to an α‐helix. The tertiary structural context in which β–3₁₀ and 3₁₀–β composites occurs can be different, causing the angle between the secondary structural elements in the two cases to be different. Composites of 3₁₀‐helices and β‐strands are much more conserved among members in families of homologous structures than those between two types of helices; in many of the former instances, the 3₁₀‐helix constitutes the loops in β‐hairpin or β–β‐corner motifs. The overall fold of the chain may be more conserved than the actual identify of the secondary structure elements in a composite. © 2005 Wiley Periodicals, Inc. Biopolymers 78: 147–162, 2005 This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Synthesis, solid-state characterization and antimicrobial activities of three different polymorphs of a copper(II) complex with 4-isopropyltropolone (hinokitiol)

There exist at least three different polymorphs in the copper(II) complex [Cu(hino)₂] with a hinokitiol ligand (Hhino; 4-isopropyltropolone¹). In addition to deep-green plate crystals 1a and deep-green rod crystals 1b, whose crystal structures have been recently reported, novel green needle crystals 1c of [Cu(hino)₂] were found, the crystal structure of which was here determined by single-crystal X-ray analysis. Since only one crystal structure has been reported for the copper(II) complex [Cu(trop)₂] with a tropolone ligand (Htrop), the polymorphism found in the crystals of [Cu(hino)₂] would be due to the presence of the isopropyl group on the tropolone ring. The synthetic conditions giving the three polymorphs in good yields were found and the crystals were characterized with elemental analysis, FT-IR, TG/DTA and X-ray powder diffraction (XPD) measurements, as well as solution molecular weight measurements for 1a. The solid-state magnetic behaviors or the temperature-dependent magnetic susceptibilities were measured with Superconductivity Quantum Interference Devices (SQUID): 1a showed a weak ferromagnetic interaction, 1b showed a paramagnetic nature with S=1/2, while 1c showed a weak antiferromagnetic interaction. The antimicrobial activities for selected bacteria, yeasts and molds were also measured in the water-suspension system: 1a and 1b showed no activity, while 1c showed modest activities, and these activities were compared with those of the neutral Hino and the anionic hino⁻ ligands.     

Oxidations of sulfur rich heterocycles - new S-oxides of the parent 1,2,4-trithiolane and its tetramethyl derivative: synthesis and structural investigations

Whereas oxidation of 1,2,4-trithiolane (1) with 1 molar equiv. of m-chloroperbenzoic acid (mCPBA) yielded 1,2,4-trithiolane 4-oxide (3) and a small amount of 1,2,4-trithiolane 1-oxide (2), the reaction with 2.5 molar equiv. of mCPBA afforded exclusively 1,2,4-trithiolane 1,4-dioxide (trans-7). The oxidation of 3,3,5,5-tetramethyl-1,2,4-trithiolane (4) with peroxyacetic acid (1 molar equiv. H₂O₂/AcOH) gave a mixture of regioisomeric 3,3,5,5-tetramethyl-1,2,4-trithiolane 4-oxide (6) as a major product and only traces of 1-oxide 5. Using 2.5 molar equiv. of peroxyacetic acid in reaction with 4 a mixture of both stereoisomers of 3,3,5,5-tetramethyl-1,2,4-trithiolane 1,4-dioxides cis-8 and trans-8 was isolated. Furthermore, 4 was oxidized to 3,3,5,5-tetramethyl-1,2,4-trithiolane 1,1,4,4-tetraoxide (9) using 6 molar equiv. of peroxyacetic acid. The molecular structures of 3, trans-7, trans-8 and 9 were unambiguously established by X-ray structure analysis. Compounds 1-4, trans-7, trans-8 and 9 were investigated by Raman spectroscopy. Ab initio calculations were used to obtain the optimized geometries and the vibrational wavenumbers of the title compounds. The vibrational assignment was accomplished by using the calculated harmonic wavenumbers and their Raman intensities. The calculated values of both structural parameters and the vibrational modes fitted in with experimental data. The spectroscopic changes observed in the spectra were correlated with the structural parameters in order to gain information about the influence of the oxidation on the molecule structure. The experimental data indicated, that in comparison with starting 1,2,4-trithiolanes 1 and 4 their oxidized derivatives showed remarkable shortening of the S-S bonds.     

Random biochemical networks: the probability of self-sustaining autocatalysis

We determine conditions under which a random biochemical system is likely to contain a subsystem that is both autocatalytic and able to survive on some ambient 'food' source. Such systems have previously been investigated for their relevance to origin-of-life models. In this paper we extend earlier work, by finding precisely the order of catalysation required for the emergence of such self-sustaining autocatalytic networks. This answers questions raised in earlier papers, yet also allows for a more general class of models. We also show that a recently described polynomial-time algorithm for determining whether a catalytic reaction system contains an autocatalytic, self-sustaining subsystem is unlikely to adapt to allow inhibitory catalysation--in this case we show that the associated decision problem is NP-complete.     

Phenology of flowering and starch accumulation in grape (Vitis vinifera L.) cuttings and vines

BACKGROUND AND AIMS: A reliable protocol for flowering and fruiting in cuttings was developed with the aim of (a) studying inflorescence and flower development in grapevine cuttings and field plants, and (b) assisting haploid plant production. METHODS: Inflorescence and flower development was studied in 'Gewurztraminer' (GW) and 'Pinot Noir' (PN) grape vines and cuttings grown in a glasshouse, along with variations in starch in the flowers. As there is a strong relationship between flower development and starch, the starch content of reproductive structures was estimated. KEY RESULTS: Inflorescence and flower development were similar in the vines and cuttings with consistent differences between the two cultivars. Indeed, the ontogenesis of male and female organs is not synchronous in GW and PN, with both female and male meiosis occurring earlier in PN than in GW. Moreover, changes of starch reserves were similar in the two plant types. CONCLUSIONS: Cuttings have a similar reproductive physiology to vines, and can be used to study grape physiology and to develop haploid plants.     

Two members of the Glomeromycota form distinct ectendomycorrhizas with <Emphasis Type="Italic">Alzatea verticillata</Emphasis>, a prominent tree in the mountain rain forest of southern Ecuador

Mycorrhizas formed by members of the Glomeromycota with roots of Alzatea verticillata (Alzateaceae, Malpighiales), a characteristic tree of the neotropical mountain rain forest in southern Ecuador, were investigated using light microscopy. Two morphotypes are described. One morphotype forms very fine, fan-shaped branches in the intercellular space of the inner cortical layer. The fungus most probably belongs to the so-called fine endophytes. A second morphotype was distinguished by its larger hyphae and intercellular, ctenoid branches. In both morphotypes, arbuscules were formed, but vesicles and intraradical spores were lacking. The results show, for the first time, arbuscular mycorrhizas with abundant intercellular, finger-like branches resembling appressoria and reminiscent of the Hartig net structure in ectomycorrhizas. The Hartig net is known as a place for nutrient exchange and a similar function is presumed here. Consequently, the described morphotypes should be classified as ectendomycorrhizas. The presented results are also a contribution for distinguishing members of Glomeromycota by their vegetative structures.     

The synthesis and characterization of a cationic technetium(V) phenylimido complex. The X-ray crystal structure of [TcCl2(NPh)(PMe2Ph)3](BPh4)

The reaction of the neutral Tc(V) phenylimido complex [TcCl₃(NPh)(PPh₃)₂] with excess PMe₂Ph in refluxing MeOH gives the cationic, tris-dimethylphenylphosphine complex [TcCl₂(NPh)(PMe₂Ph)₃]⁺, which is isolated as the tetraphenylborate salt. The IR spectrum of the crystalline product shows a medium intensity band at 1102 cm⁻¹ which is assigned to ν(TcN) from the phenylimido core. The ¹H NMR spectrum of the diamagnetic complex shows a series of multiplets in the aryl region and three distinct signals near 2 ppm from the phosphine methyl groups. The X-ray crystal structure, which is the first for a cationic technetium organoimido complex, shows a meridional arrangement of phosphine ligands with a chloride ligand coordinated trans to the phenylimido unit. The TcN bond length of 1.711(2) Å is consistent with the dianionic nature of the organonitrogen core. The Tc---N---C bond angle of 178.8(2)° reflects the sp hybridization of the phenylimido nitrogen atom. The coordination geometry is best described as a distorted octahedron. Crystal data for C₅₄H₅₈BCl₂NP₃Tc: triclinic space group

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. Structure solution based on 9986 observed reflections converged at R = 3.65%, R_w = 5.43%, GOF = 1.82.     

The 19-electron Fe(I) state in tentacled iron sandwiches: synthesis, stability, Mössbauer spectroscopy, electronic structure and chain effect

The extremely air-sensitive 19-electron [Fe^ICp hexaalkylbenzene)] complexes (alkyl = n-propyl, n-butyl, n-pentl) have been synthesized; variable-temperature Mössbauer data indicate a drastic decrease of the quadrupole splitting upon increasing temperature which does not correspond to a Boltzmann population of the upper Kramer's doublet due to the ‘chain effect’. It is proposed that an increasing proportion of the 17-electron Fe(I) state is involved as the chain length increases.     

Trilobite taphonomy and ecology in Upper Ordovician carbonate buildups in Dalarna, Sweden

A major ecological grouping of the trilobites in the Upper Ordovician Boda Limestone buildups in Dalarna is outlined, based primarily on the modes of occurrences in the Jutjärn quarry. The so-called pockets are analysed with regard to their trilobite contents and distribution within a carbonate buildup. The pockets are of two general types. One consists of narrow opened fissures along bedding planes. The matrix of these may contain either of the peculiar blind Isocolus sjoegreni or Ityophorus undulatus , both of which appear to have been cavernous species, possibly belonging to the Bathyuracea (or Leiostegiacea). In addition, small proetids used the fissures for moulting. The other kind of pocket is a cavity largely filled with sediment from the surface of the buildup. The size is considerable, in rare cases up to many tens of cubic metres. Although the buildups housed about 90 trilobite species, each of these pockets is dominated by one or two out of seven large species. Of these, six are illaenids, the seventh the illaenid-like cheirurid Holotrachelus punctillosus. Usually only pygidia and cranidia are found. These species may have lived gregariously around the rims of the cavities. The remaining species, about 85% of the trilobite fauna, appear to have lived on the surface of the buildups. The largest group is the proetids with some 20 species (in addition to those known from pockets). Cheirurinids and lichids contribute with some 15 species each, and there are six odontopleurids. The distinctness of the 'community' is indicated by the circumstance that only three species are shared with contemporaneous level-bottom faunas in Sweden.