Double-helical structures for polyxanthylic acid

Polyxanthylic acid has been found to exist in two different duplex forms, A_I and A_II. a_I, formed at pH5·7, occurs in a compact lattice with nearest neighbor molecules spaced at 2.11 nm. It has an axial translation per residue, h = 0·301 nm, and a rotation per residue, t = 36·0 °. The intensity distribution in its X-ray fiber diffraction pattern is analogous to that of A-RNA (h = 0·281 nm, t = 32·7 °). On the other hand A_II, formed at pH 8·0, has a less compact, statistically disordered crystal packing with nearest neighbors 2·35 nm apart. It has h = 0·252 nm and t = 32·7 ° and gives an X-ray intensity distribution essentially identical to A-DNA (h = 0·256 nm, t = 32·7 °). Similar right-handed helical duplex models, with flexible C-3′-endo sugar rings, have been developed for each molecular structure. Both have purine purine base-pairs, possibly triply hydrogen-bonded, and certainly with the same symmetry as Watson-Crick pairs but with a 0·2 nm greater C-1′ … C-1′ separation.     

Left-handed Helical Polynucleotides with D-Sugar Phosphodiester Backbones

Naturally occurring polynucleotides have right-handed helical confrontations in the solid state¹ and in solution². Poly(dI-dC)poly(dI-dC) was found to form a left-handed helix in spite of the D-sugar backbone. Also, L-adenylyl-(3′–5′)-L-adenosine synthesized by Tazawa et al⁴. takes up the left-handed stacked conformation. We had synthesized a dinucleoside monophosphate, 8,2′-anhydro-8-mercapto-9-β-D-arabinofuranosyladenine phosphoryl-(3′–5′)-8,2′-anhydro-8-mercapto-9-β-D-arabinofuranosyladenine (A^spA^s) (molecular structure Ia; see also ref. 5) and this compound has a left-handed stacked conformation. The two bases in Ia, having the D-sugar backbone, stacked along the left-handed helical axis; these bases are fixed at ?_CN = ?108° (syn-anti region) by the anhydro linkages.     

Studies on dithio-o-toluate copper(I) complexes with bis(diphenylphosphino)methane. Crystal structures of {di-μ3-dithio-o-toluato-S,S′,S′-bis[μ-bis(diphenylphosphino)methane-μ-dithio-o-toluato-S,S′]} tetracopper(I) and {di[μ-bis(diphenylphosphino)methane]bis(dithio-o-toluato-S,S′)} dicopper(I)

The structures of [(CuS₂CT)₂dppm]₂ (I) (T = o-tolyl; dppm = bis(diphenylphosphino)methane) and [CuS₂CTdppm]₂ (II) have been determined by X-ray methods. Crystals of I are monoclinic, space group P2₁/n, with a = 15.163(4), b = 18.691(5), c = 13.478(4) Å, β = 96.81(3)°, Z = 2; crystals of II are orthorhombic. space group Pccn, with a = 23.267(4), b = 13.016(3), c = 20.731(5) Å, Z = 4. The structures of I and II have been solved by Patterson and Fourier methods and refined by full-matrix least-squares to R = 0.082 for I and 0.092 for II. The structure of I consists of centrosymmetric tetranuclear complexes in which two pairs of Cu atoms are triply bridged by a dppm ligand and two dithiocarboxylate groups from the dithio-o-toluate ligands. These last behave differently: one of them through a sulphur atom is also bonded to a Cu atom of the other pair so forming a tetranuclear complex. The Cu atoms of each pair show different coordination: Cu(1) displays a distorted trigonal and Cu(2) a distorted trigonal pyramidal geometry. The structure of II consists of dimers, in which each copper atom, doubly bridged by two dppm ligands, completes a distorted trigonal pyramidal coordination through two sulphur atoms from dithio-o-toluate anions acting as chelating ligands. In both compounds the phenyl group of the dithio-o-toluate anions is orthogonal to the corresponding CS₂ group. Both complexes give methyldithio-o-toluate in high yields by reaction with methyl iodide.     

CD correlation of C-2′substituted monocyclic carotenoids

The scope and limitation of circular dichroism (CD) correlations of several C-2′ substituted monocyclic monochiral, homodichiral and heterodichiral carotenoids have been investigated, aiming at the assignment of absolute configuration at C-2′ by using the diester and 2′-β-d-tetraacetylglucosyl derivative of (2′R)-plectaniaxanthin and a synthetic chiral C₄₅-carotene as key references. The correlations are based on the additivity hypothesis, the conformational rule and a comparison of CD spectra, preferably conservative ones. Quantitative aspects of the conformational rule are considered. Substituent effects at C-2′ and C-1′ have been studied. Absolute configurations are suggested for (2′)-phleixanthophyll (3S,2′S)-2′-hydroxyflexixanthin, (3R,2′S)-myxoxanthophyll, (3S,2′S-4-ketomyxoxanthophyll (3R,2′S)-myxol-2′-O-methyl methylpentoside and (2R,2′S)-Cp. 473 from relevant CD correlations. The chiralities of (2′S)-4-ketophleixanthophyll and (2R,6R,2′S)-A.g. 471 are suggested from biogenetic considerations. A chemosystematic consideration of chirality and source is included.     

Cytogenetic studies on natural intergeneric hybridization inAster alliances

Natural intergeneric hybrids betweenAster ageratoides subsp.ovatus (2n=36) andKalimeris incisa (2n=72) were found. All of the hybrids studied were found to have 2n=72, 18 more chromosomes than a regular F₁ hybrid. The hybrids were found to be of two types: one having 18 large chromosomes ofovatus, and the other having 9 large chromosomes of the same subspecies. In meiosis of the PMCs of the hybrid with 18 large chromosomes, a regular chromosome configuration, 36_II, was observed. In PMCs of the hybrid with 9 large chromosomes an irregularity of chromosome pairings was observed, showing varied chromosome configurations: 35_II+2_I, 34_II+4_I, 33_II+6_I, I_III+33_II+3_I, 1_IV+32_II+4_I, 32_II+8_I, 31_II+10_I, 29_II+14_I, 3_III+29_II+5_I. Most univalents were large, but a few were small. The hybrids with 18 large chromosomes were found to be partial amphidiploid and possessing double chromosome complements ofovatus. The hybrids with 9 large chromosomes were found to be the first backcrossed generation between the hybrid with 18 large chromosomes andK. incisa.     

‘Chargaff's Rules’ for Protein Folding: Stoichiometric Leitmotif Made Visible

Abstract

The complex between cobalt hexammine and decadeoxyoligomer d(CGTACGTACG) crystallizes into the space group P6₅ with unit cell constants a = b = 17.93Å, and c = 43.41Å. The molecules have the helix axis coincident with the crystal c-axis. The decamers stack on top of each other and form a quasi-continuous helix. The structure is disordered. The asymmetric unit is a dimer (pPyr-pPur)₂ with each base pair 60% of the time a C-G and 40% of the time a T-A. Restrainted least-squares refinement led to an R-factor of 25.5% for 506 observed reflections above the two-sigma level. The structure was found to have one strand in the Z_I-conformation and the other in the Z_II-conformation. The cobalt hexammine binds to two Z_II-chains of symmetrically related molecules. On one Z_II chain, two ammonia molecules of the cobalt hexammine bind to the N7 nitrogen and 06 oxygen atoms of the guanine bases and a third ammonia to the phosphate anionic oxygen atom of the preceding pyrimidine base, resulting in an “external” binding mode. On the other Z_II chain, one ammonia molecule of the cobalt hexammine binds only to the anionic oxygens of the phosphate group of the guanine bases, leading to an “internal” binding mode. Thus, the basis of the stabilization of Z-DNA by [Co(NH₃)₆]³⁺ is its binding to only guanine nucleotides. It is surmised that statistical disordering of deoxyoligonucleotide structures which take a Z conformation, depends on the length of the oligomer. That is to say, octamers and decamers (which cannot use an integral number of molecules for a 12 base pair repeat) form disordered structures whereas tetramers and hexamers form well ordered structures.     

Thermal Properties of Freeze-Concentrated Sugar-Phosphate Solutions

In order to understand the effect of phosphate salts on the freeze-concentrated glass-like transition temperature (T _g′) of aqueous sugar solutions, two types of sugar (glucose and maltose) and five types of phosphate salts (Na₃PO₄, Na₄P₂O₇, Na₅P₃O₁₀, K₃PO₄, and K₄P₂O₇) were employed, and the thermal properties of various sugar-phosphate aqueous systems were investigated using differential scanning calorimetry. The T _g′ of glucose increased with increasing sodium phosphates up to a certain phosphate ratio, decreasing thereafter. The maximum T _g′ value was slightly higher in the order of Na₃PO₄ > Na₄P₂O₇ ≥ Na₅P₃O₁₀. Maltose-sodium phosphate also showed a similar trend as glucose-sodium phosphate samples. However, the degree of T _g′-rise of maltose systems was much less than that of glucose. It is thought that the T _g′ elevated by the molecular interaction between sugar and phosphate ions will be reduced by hydrated sodium ions. In comparisons between potassium phosphate and sodium phosphate, it was found that sugar-potassium phosphates showed the lower maximum T _g′ at a lower phosphate ratio than sugar-sodium phosphates. In addition, the T _g′ of potassium phosphates dropped sharply in comparison with sodium phosphates at the high phosphate ratio. These results suggest that potassium phosphates are lower T _g′ than sodium phosphates, and that potassium ion plays a better plasticizer than sodium ion. A certain amount of sodium phosphates (Na₃PO₄ and Na₄P₂O₇) caused devitrification. Potassium phosphates, however, did not show devitrification which can be explained by the fact that potassium ion can be dynamically restricted by sugar.     

Unusual lipids and acylglucosylsterols from the roots of Livistona chinensis

A 70% ethanol extract from the roots of Livistona chinensis has been investigated, led to the isolation of 18 compounds, including two new 6′-O-acyl-β-d-glucosyl-β-sitosterols, 6′-O-(2″-hydroxyheptadecanoyl)-β-d-glucosyl-β-sitosterol (1) and 6′-O-(icosa-9″Z,12″Z-dienoyl)-β-d-glucosyl-β-sitosterol (2), two new keto esters, ethyl 16-(dodeca-4″′Z,7″′Z-dienyl)-29-oxo-15-(tetradeca-5″Z,8″Z,11″Z-trienyl) triacontanoate (7), and 16-hydroxy-8-oxohexadecyl tetradecanoate (9), a new unsaturated fatty acid, tetracosa-(11Z,14Z,18Z)-trienoic acid (8), as well as a new fatty alcohol, 10-decylnonadecane-1,19-diol (10). The structures of new compounds were elucidated, based on spectroscopic and chemical methods. The antiproliferative activity against four human tumor cell lines (K562, HL-60, HepG2, and CNE-1) was evaluated. Four compounds (1–3, 5) showed potent antiproliferative effects with the IC₅₀ of 10–100 μM. To our knowledge, this is the first report of the occurrence of 6′-O-acyl-β-d-glucosyl-β-sitosterol and 3-O-acyl-β-sitosterol in the genus Livistona. Keto fatty acids and their esters are also rare in higher plant.     

4-Azidophlorizin,a high affinity probe and photoaffinity label for the glucose transporter in brush border membranes

A new phlorizin derivative ($\text{2′-O-(β-}\text{d}\text{-}\text{glucopyranosyl}\text{)-4-}\text{azidophloretin}$, 4-azidophlorizin) has been synthesized and its affinity for the d-glucose, Na⁺ co-transport system in brush border vesicles from intestinal and renal membranes has been compared with that of phlorizin. The extent of the reversible interaction of the ligand with the transporter in dim light has been evaluated from three separate measurements: (1) K′_i, the constant for fully-competitive inhibition of (Na⁺, Δψ)-dependent d-glucose uptake, (2) K′_d, the dissociation constant of 4-azido[³H]phlorizin binding in the presence of an NaSCN inward gradient, and (3) K″_i, the constant for fully-competitive inhibition of the specific ((Na⁺, Δψ)-dependent, d-glucose protectable) high-affinity [³H]phlorizin binding. In experiments with vesicles derived from rat kidney, all three constants (K′_i, K′_d and K″_i) were essentially equal and ranged between 3.2 and 5.2 μM, that is, the azide derivative has almost the same affinity for this transporter as phlorizin itself. On the other hand, compared to phlorizin, the 4-azidophlorizin has a lower affinity for the transporter in vesicles prepared from rabbit; its K′_i values are some 15–20-times larger than those determined with rat membranes. However, the affinity of the azide for the sugar transporter in membranes from either the intestine or kidney of the same animal species (rabbit or rat) was essentially the same. In spite of the lower affinity for the transporter in either membrane system from the rabbit, results described elsewhere (Hosang, M., Gibbs, E.M., Diedrich, D.F. and Semenza, G. (1981) FEBS Lett., 130, 244–248) indicate that 4-azidophlorizin is an effective photoaffinity label in this species also. Photolysis of the azide yields a reactive intermediate which reacts with a 72 kDa protein in rabbit intestine brush borders. Covalent labeling of this protein occurred under conditions which suggests that it is (a component of) the glucose transporter.     

Some observations on the minor products of the reaction of 2,2′-dilithiobiphenyl with mercuric chloride

Reaction of 2,2′-dilithiobiphenyl (formed from 2,2′-diiodobiphenyl and lithium in diethyl ether) with mercuric chloride gives the ortho-biphenylenemercury trimer (I) with 2,2′-bis(iodomercury)biphenyl (II) as an isolatable intermediate. The mass spectrum of impure 2,2′-bis(iodomercury)biphenyl at high sensitivity shows ion clusters which are interpreted as the ions of a polyphenyl iodomercury complex [Hg₃(C₆H₄)₄I₂] (III) which is identified as a further intermediate in the production of ortho-biphenylenemercury trimer and several iodomercury cations of general formula [Hg_xI_y]⁺, where x, y = 1, 2, 3. A fragmentation scheme is presented to account for these unusual iodomercury cations. Reaction mechanisms are presented to account for the production of II and III.     

Computational investigation of the geometric structures of [(CN)5PtTl(CN)n]n− (n=0, 1, 2 or 3)

[(CN)₅PtTl(CN)_n]ⁿ⁻ (n=0–3, complexes I–IV) have been studied computationally using quasi-relativistic gradient-corrected density functional theory. Good agreement is obtained with previous EXAFS and Raman data for complexes II–IV, but calculations significantly overestimate the PtTl bond length and underestimate ν(PtTl) for complex I. The addition of co-ordinating water molecules to the thallium atom in complexes I–III has little effect on complexes II and III, but significantly shortens the PtTl bond in complex I, bringing it into excellent agreement with experiment. The bond length shortening is traced to intramolecular hydrogen bonding. The total molecular bonding energies of hydrated I and I′ (in which the axial ligands on the thallium and platinum atoms are interchanged) are found to be very similar to one another, suggesting that complex I might exist as a mixture of isomers in solution.     

Individual Interactions of the b Subunits within the Stator of the Escherichia coli ATP Synthase

F_OF₁ ATP synthases are rotary nanomotors that couple proton translocation across biological membranes to the synthesis/hydrolysis of ATP. During catalysis, the peripheral stalk, composed of two b subunits and subunit δ in Escherichia coli, counteracts the torque generated by the rotation of the central stalk. Here we characterize individual interactions of the b subunits within the stator by use of monoclonal antibodies and nearest neighbor analyses via intersubunit disulfide bond formation. Antibody binding studies revealed that the C-terminal region of one of the two b subunits is principally involved in the binding of subunit δ, whereas the other one is accessible to antibody binding without impact on the function of F_OF₁. Individually substituted cysteine pairs suitable for disulfide cross-linking between the b subunits and the other stator subunits (b-α, b-β, b-δ, and b-a) were screened and combined with each other to discriminate between the two b subunits (i.e. b_I and b_II). The results show the b dimer to be located at a non-catalytic α/β cleft, with b_I close to subunit α, whereas b_II is proximal to subunit β. Furthermore, b_I can be linked to subunit δ as well as to subunit a. Among the subcomplexes formed were a-b_I-α, b_II-β, α-b_I-b_II-β, and a-b_I-δ. Taken together, the data obtained define the different positions of the two b subunits at a non-catalytic interface and imply that each b subunit has a different role in generating stability within the stator. We suggest that b_I is functionally related to the single b subunit present in mitochondrial ATP synthase.     

Inheritance of leaf peroxidase isoenzymes in Nicotiana alata and linkage with the S-incompatibility locus

Summary Genetic analysis of peroxidase isoenzymes observed by electrophoresis shows that each of the two cathodic bands are controlled by one gene, respectively, P_I and P_II. Each gene has two allele forms; presence of activity (dominant) and absence of activity (recessive). The same situation is found for one anodic band; the three other anodic bands are controlled by a single gene with three active allele forms. No progenies seem to be produced from gametes P _I ^- P _II ^- (no activity of P_I or P_II). Investigation of the incompatibility system and the isoperoxidases demonstrates that the loci P_I, P_II and S are located in the same chromosome. P_I is closely linked to the S locus (3 cM); the distance between P_II and the S locus is 34 cM.     

Relative Stabilities and Transitions of DNA Conformations in 1:1 Electrolytes: A Theoretical Study

Abstract

We use a recently developed formalism (1) to calculate the salt dependent part of the free energy determining DNA conformational stability in 1:1 electrolytes. The conformations studied are the A,B,C and alternating-B right-handed forms and the Z₁Z_II left-handed forms of DNA. In the case of the B-Z₁ transition of d(G-C) · d(G-C) helices in NaCl solution, the free energy contribution considered suffices to describe the transition in a quantitative manner. The theory also predicts the occurrence of salt-induced B-A transitions which have been recently observed with poly[d(n²A-T)| and poly[d(G-C)|. In other cases, additional terms in the free energy balance, particularly due to hydration effects, must be at least as important as salt effects in determining conformational stability and structural transitions in solution. If diffuse ionic cloud electrostatic effects alone would dominate in all cases, the relative helical stabilities at 0.2 M monovalent salt would decrease in the order C > B > A > Z_II > Z₁ > alternating-B. At high salt concentrations (2.0 M - 5.0 M), the order would be alternating-B > Z, > A > Z_II > B > C.     

Low temperature spectral properties of subchloroplast fractions purified from spinach

Spinach (Spinacia oleracea L.) chloroplasts solubilized by digitonin were separated into five fractions by sucrose density gradient centrifugation. Three of the fractions, F_I, F_II, and F_III, corresponding to photosystem I, photosystem II, and the chlorophyll a/b complex, were purified further by two steps of diethylaminoethyl-cellulose chromatography followed by electrofocusing on an Ampholine column. The polypeptide patterns of the fractions were examined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and the spectral properties of the fractions at −196 C determined by absorption spectra, fourth derivative curves of the absorption spectra, fluorescence emission spectra, and fluorescence excitation spectra. The activity of purified F_II (photosystem II) was also assayed by the photoreduction of dichlorophenol-indophenol at room temperature using 1,5-diphenylcarbohydrazine as the electron donor and by the photoreduction of C-550 at −196 C. The different fractions showed unique polypeptide patterns and unique sets of low temperature-absorbing forms of chlorophyll. The fluorescence emission spectra of F_I, F_II, and F_III at −196 C were also unique with maxima at 734, 685 and 681 nm, respectively. F_I showed negligible emission at wavelengths shorter than 700 nm and the long wavelength tails of F_II and F_III in the 730 nm region were relatively small (approximately 10% of emission of their wavelength maxima). Addition of 0.1% Triton to F_I and F_II caused the longer wavelength absorbing forms of chlorophyll to shift to 670 nm and the fluorescence emission maxima (of both fractions) to shift to 679 nm at −196 C with an increase in the yield of fluorescence especially in the case of F_I.     

A Molecular Dynamics Simulation of a Polyamine-Induced Conformational Change of DNA. A Possible Mechanism for the B to Z Transition

Abstract

A 75ps molecular dynamics simulation has been performed on a fully solvated complex of spermine with the B DNA decamer (dGdC)₅ · (dGdC)₅. The simulation indicates a possible mechanism by which polyamines might induce the formation of a left-handed helix, the B to Z transition. Spermine was initially located in the major groove, hydrogen bonded to the helix. During the simulation the ligand migrates deeper into the DNA, maintaining strong hydrogen bonding to the central guanine bases and destroying the Watson-Crick base pairing with their respective cytosines. Significant rotation of these and other cytosine bases was observed, in part due to interactions of the helix with the aminopropyl chains of spermine. An intermediate B_II conformation might be of importance in this process.     

FT-IR and 1H NMR spectroscopic evidence of sugar ring conformational change in NH4GpG on complexation to form cis-[Pt(NH3)2(GpG)]+

The conformational change of the ribose ring in NH₄GpG and cis-[Pt(NH₃)₂(GpG)]⁺ was confirmed by FT-IR spectroscopic evidence as being C2′-endo, C3′-endo, anti, gg sugar ring pucker in the solid state. These results were compared with ¹H NMR spectral data in aqueous solution. The FT-IR spectrum of NH₄GpG shows marker bands at 802 cm^?1 and 797 cm^?1 which are assigned to the C3′-endo, anti, gg sugar-phosphate vibrations of ribose (?pG) and ribose (Gp?), respectively. The FT-IR spectrum of cis-[Pt(NH₃)₂(GpG)]⁺ (with N7N7 chelation in the GpG sequence) shows a marker band at 800 cm^?1 which is assigned to the C3′-endo, and a new shoulder band at 820 cm^?1 related to a C2′-endo ring pucker. The ribose conformation of (?pG) moiety in NH₄-GpG, C3′-endo, anti, gg changes into C2′-endo, anti, gg when a platinum atom is chelated to N7N7 in the GpG sequence.     

The stereochemistry of hydroxylation of the carotenoid lutein in Calendula officinalis

Excised, opening inflorescences of Calendula officinalis incorporated (3RS, 5R)- and (3RS, 5S)-[2-¹⁴C,5-³H₁]mevalonates into the carotenoid fraction. The ¹⁴C:³H ratios of lutein isolated from these tissues showed the hydrogen atom at C-3 of the β-ring is derived from the 5-pro-S position of mevalonate, while that at C-3 of the ε-ring is derived from the 5-pro-R position of mevalonate. Oxidation of lutein to monoketolutein showed that both hydrogen atoms at the C-15,15′ central double bond are derived from the 5-pro-R position of mevalonate.     

Synthesis and conformational study of poly(0,0′-dicarbobenzoxy-L-β-3,4-dihydroxyphenyl-α-alanine)

High-molecular-weight poly(0,0′-dicarbobenzoxy-L -β-3,4-dihydroxyphenyl-α-alanine) was prepared by the N-carboxyanhydride method. From the results obtained by a study of the optical rotation, nuclear magnetic resonance, and solution infrared absorption, the conformation of poly(0,0′-dicarbobenzoxy-L -β-3,4-dihydroxyphenyl-α-alanine) depended greatly on the solvent taking a right-handed helix with [θ]₂₂₅ = ?13,600 ～ ?18,900 in alkyl halides, a left-handed helix with [θ]₂₂₈ = 22,100 ～ 24,800 in cyclic ethers or trimethylphosphate, and a random coil structure in dichloroacetic acid, trifluoroacetic acid, or hexafluoroacetone sesquihydrate. The polypeptide underwent a right-handed helix-coil transition in chloroform/dichloroacetic acid (or trifluoroacetic acid) mixed solvents and a left-handed helix-coil transition in dioxane/dichloroacetic acid (or trifluoroacetic acid) mixed solvents. The results were compared with those of poly(0-carbobenzoxy-L -tyrosine).