Comparison of helix-stabilizing effects of alpha,alpha-dialkyl glycines with linear and cycloalkyl side chains

The ability of alpha, alpha-di-n-alkyl glycines with linear and cyclic alkyl side chains to stabilize helical conformations has been compared using a model heptapeptide sequence. The conformations of five synthetic heptapeptides (Boc-Val-Ala-Leu-Xxx-Val-Ala-Leu-OMe, Xxx = Ac8c, Ac7c, Aib, Dpg, and Deg, where Ac8c = 1-aminocyclooctane-1-carboxylic acid, Ac7c = 1-aminocycloheptane-1-carboxylic acid, Aib = alpha-aminoisobutyric acid, Dpg = alpha,alpha-di-n-propyl glycine, Deg = alpha,alpha-di-n-ethyl glycine) have been investigated. In crystals, helical conformations have been demonstrated by x-ray crystallography for the peptides, R-Val-Ala-Leu-Dpg-Val-Ala-Leu-OMe, (R = Boc and acetyl). Solution conformations of the five peptides have been studied by 1H-nmr. In the apolar solvent CDCl3, all five peptides favor helical conformations in which the NH groups of residues 3-7 are shielded from the solvent. Successive NiH<-->Ni + 1H nuclear Overhauser effects over the length of the sequence support a major population of continuous helical conformations. Solvent titration experiments in mixtures of CDCl3/DMSO provide evidence for solvent-dependent conformational transitions that are more pronounced for the Deg and Dpg peptides. Solvent-dependent chemical shift variations and temperature coefficients in DMSO suggest that the conformational distributions in the Deg/Dpg peptides are distinctly different from the Aib/Acnc peptides in a strongly solvating medium. Nuclear Overhauser effects provide additional evidence for the population of extended backbone conformations in the Dpg peptide, while a significant residual population of helical conformations is still detectable in the isomeric Ac7c peptide in DMSO.     

Chloroplast inheritance and DNA variation in sweet, sour, and ground cherry

Sour cherry (Prunus cerasus L.) is an allotetraploid and both sweet cherry (P avium L.) and ground cherry (P. fruticosa Pall.) are the proposed progenitor species. The study investigated the maternal species origin(s) of sour cherry using chloroplast DNA (cpDNA) markers and a diverse set of 22 sweet, 25 sour, and 7 ground cherry selections. Two cpDNA restriction fragment length polymorphisms (RFLPs) and one polymerase chain reaction (PCR) fragment length polymorphism were identified among the 54 selections. The three polymorphisms considered together resolved four haplotypes. Analysis of sour cherry progeny indicated that the chloroplast genome is maternally inherited and therefore appropriate to use in determining maternal phylogenetic relationships. Ground cherry was found more likely than sweet cherry to be the maternal progenitor species of sour cherry since 23 of 25 of the sour cherry selections had the most prevalent ground cherry haplotype. However, the other two sour cherry selections tested had the most prevalent sweet cherry haplotype and a wild French sweet cherry selection had the most prevalent ground cherry haplotype. The results underscore the importance of using diverse Prunus germplasm to investigate phylogenetic relationships.     

Accumulation of methylmercury and inorganic mercury in the brain

Differences in metabolism between different mercury species are well recognized. Conclusions that only a minor demethylation of methylmercury takes place in the brain are based primarily on results from short term studies. Results from a number of studies on humans exposed for many years to methylmercury have shown high concentrations of inorganic mercury in the brain in relation to total mercury. Similar evidence is available from studies on monkeys exposed for several years to methylmercury. The results indicate that a significant accumulation of inorganic mercury takes place with time despite the fact that the demethylation rate is slow. Differences in biological halftimes between different mercury species will explain the results. Some data do still need confirmation using different analytical methods. There is reason to believe that the one-compartment model for methyl mercury cannot be used without reservations. Inorganic mercury has a complicated metabolism. After exposure to metallic mercury vapor, inorganic mercury, probably bound to selenium, accumulates in the brain. A fraction of the mercury is excreted, with a long biological halftime. Studies on rats and monkeys indicate that inorganic mercury penetrates the blood-brain barrier only to a very limited-extent.     

Solvated helical backbones: x-ray diffraction study of Boc-Ala-Leu-Aib-Ala-Leu-Aib-OMe.H2O

A second example of insertion of a water molecule into the helical backbone of an apolar peptide is presented here and compared to a similar occurrence in a longer peptide with the same type of sequence of residues, i.e., Boc-Aib-(Ala-Leu-Aib)3-OMe. The backbone of the title compound assumes an approximate 3(10)-helical form with three 4----1 hydrogen bonds. In the place of a fourth 4----1 hydrogen bond, a water molecule is inserted between O(1) and N(4), and acts as a bridge by forming hydrogen bonds N(4) ... W(1) (2.95 A) and W(1) ... O(1) (2.81 A). The water molecule participates in a third hydrogen bond with a neighboring peptide molecule, W(1) ... O(4) (2.91 A). The insertion of the water molecule causes the apolar peptide to mimic an amphiphilic helix. Crystals grown from ethyl acetate/petroleum ether (reported here) or from methanol/water solution are in space group P2(1)2(1)2(1) with a = 12.024(4) A, b = 15.714(6) A, c = 21.411(7) A, Z = 4 and dcalc = 1.124 g/cm3 for C32H58N6O9.H2O. The overall agreement factor R is 6.3% for 2707 reflections observed with intensities greater than 3 sigma(F) and the resolution is 0.90 A.     

Modular design of synthetic protein mimics. Characterization of the helical conformation of a 13-residue peptide in crystals

The incorporation of alpha-aminoisobutyryl (Aib) residues into peptide sequences facilitates helical folding. Aib-containing sequences have been chosen for the design of rigid helical segments in a modular approach to the construction of a synthetic protein mimic. The helical conformation of the synthetic peptide Boc-Aib-(Val-Ala-Leu-Aib)3-OMe in crystals is established by X-ray diffraction. The 13-residue apolar peptide adopts a helical form in the crystal with seven alpha-type hydrogen bonds in the middle and 3(10)-type hydrogen bonds at either end. The helices stack in columns, zigzag rather than linear, by means of direct NH...OC head to tail hydrogen bonds. Leucyl side chains are extended on one side of the helix and valyl side chains on the other side. Water molecules form hydrogen bonds with several backbone carbonyl oxygens that also participate in alpha-helix hydrogen bonds. There is no apparent distortion of the helix caused by hydration. The space group is P2(1)2(1)2(1), with a = 9.964 (3) A, b = 20.117 (3) A, c = 39.311 (6) A, Z = 4, and dx = 1.127 g/cm3 for C64H106N13O16.1.33H2O. The final agreement factor R was 0.089 for 3667 data observed greater than 3 sigma(F) with a resolution of 0.9 A.     

Conformation of the flexible bent helix of Leu1-zervamicin in crystal C and a possible gating action for ion passage

The membrane channel-forming polypeptide, Leu¹-zervamicin, Ac-Leu-Ile-Gln-Iva-Ile⁵-Thr-Aib-Leu-Aib-Hyp¹⁰-Gln-Aib-Hyp-Aib-Pro¹⁵-Phol (Aib: α-aminoisobutyric acid; Iva: isovaline; Hyp: 4-hydroxyproline; Phol: phenylalininol) has been analyzed by x-ray diffraction in a third crystal form. Although the bent helix is quite similar to the conformations found in crystals A and B, the amount of bending is more severe with a bending angle ≈ 47°. The water channel formed by the convex polar faces of neighboring helices is larger at the mouth than in crystals A and B, and the water sites have become disordered. The channel is interrupted in the middle by a hydrogen bond between the OH of Hyp (10) and the NH₂ of the Gln (11) of a neighboring molecule. The side chain of Gln (11) is wrapped around the helix backbone in an unusual fashion in order that it can augment the polar side of the helix. In the present crystal C there appears to be an additional conformation for the Gln (11) side chain (with ≈ 20% occupancy) that opens the channel for possible ion passage. Structure parameters for C₈₅H₁₄₀N₁₈O₂₂ · xH₂O · C₂H₅OH are space group P2₁2₁2₁, a = 10.337(2) Å, b = 28.387(7) Å, c = 39.864(11) Å, Z = 4, agreement factor R = 12.99% for 3250 data observed > 3σ(F), resolution = 1.2 Å. © 1994 John Wiley & Sons, Inc.     

The significance of extracellular production and winter photosynthesis to estimates of primary production in a woodland stream community

Both winter photosynthesis and the release of extracellular DOC are commonly ignored in stream production studies. We examined these contributions in a second-order stream under a completely closed deciduous canopy. We estimate that in Sandy Run approximately 26% of the annual autochthonous particulate carbon is produced between December and March. Measured winter rates of photosynthesis were not significantly different than summertime rates. Contrary to implicit assumptions often made about stream primary productivity, winter production was as important as summer production. Highest rates of carbon assimilation, however, were measured in the spring and fall, and were significantly correlated with standing crops of stream algae as measured by chlorophyll concentration. The recovery of released DOC from stream algae indicated that this contribution was equivalent to 5% of the particulate contribution. Rates of DOC production were significantly correlated with rates of particulate production. We estimate that had winter photosynthesis and extracellular DOC production been ignored in Sandy Run, annual productivity would have been underestimated by about a third. This revised version was published online in July 2006 with corrections to the Cover Date.     

Phytosociological research on the montane coniferous forests of Greece: Mount Killini (NE peloponnisos—S Greece)

The montane coniferous forests and their degraded syntaxa included either in theQuercetalia ilicis or in theQuercetalia pubescenti-petraeae of the Meso- up to the Mountain-Mediterranean vegetation belts of Mount Killini, have been studied using the Braun-Blanquet method with 69 phytosociological relevés. The application of classification and ordination methods resulted in the recognition of seven forest and two scrub plant communities. These communities could be arranged along an altitudinal gradient. Their syntaxonomy and structure are described and the present horizontal and vertical arrangement of the coniferous syntaxa is mapped. From these syntaxa, 3 new associations and 1 new subassociation are described. The main factors influencing the differences in floristic composition, are altitude and human impact resulting in degradation of the coniferous forest associations. In addition, differences in soil parameters like pH, the presence of organic matter and nutrients appear to be important. Information on the site characteristics, structure and syndynamical position of the communities is given.     

Parallel and antiparallel aggregation of alpha-helices. Crystal structures of two apolar decapeptides X-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe (X = Boc, Ac)

An apolar helical decapeptide with different end groups, Boc- or Ac-, crystallizes in a completely parallel fashion for the Boc-analog and in an antiparallel fashion for the Ac-analog. In both crystals, the packing motif consists of rows of parallel molecules. In the Boc-crystals, adjacent rows assemble with the helix axes pointed in the same direction. In the Ac-crystals, adjacent rows assemble with the helix axes pointed in opposite directions. The conformations of the molecules in both crystals are quite similar, predominantly alpha-helical, except for the tryptophanyl side chain where chi 1 congruent to 60 degrees in the Boc- analog and congruent to 180 degrees in the Ac-analog. As a result, there is one lateral hydrogen bond between helices, N(1 epsilon)...O(7), in the Ac-analog. The structures do not provide a ready rationalization of packing preference in terms of side-chain interactions and do not support a major role for helix dipole interactions in determining helix orientation in crystals. The crystal parameters are as follow. Boc-analog: C60H97N11O13.C3H7OH, space group Pl with a = 10.250(3) A, b = 12.451(4) A, c = 15.077(6) A, alpha = 96.55(3) degrees, beta = 92.31(3) degrees, gamma = 106.37(3) degrees, Z = 1, R = 5.5% for 5581 data ([F] greater than 3.0 sigma(F)), resolution 0.89 A. Ac-analog: C57H91N11O12, space group P2(1) with a = 9.965(1) A, b = 19.707(3) A, c = 16.648(3) A, beta = 94.08(1), Z = 2, R = 7.2% for 2530 data ([F] greater than 3.0 sigma(F)), resolution 1.00 A.     

Quantification of the individual enantiomer plasma concentrations of the candidate antimalarial agent N-[2,6-dimethoxy-4-methyl-5-[(3-trifluoromethyl)phenoxyl]-8-quinolinyl]-1,4-pentanediamine (WR 238,605)

A high-performance liquid chromatographic method was developed to quantitate the plasma concentrations of the individual enantiomers of a candidate 8-aminoquinoline antimalarial agent WR 238,605 (I). The method employed one-step liquid extraction of a 0.5-ml plasma sample followed by direct injection of the extract through a chiral column and detection by fluorescence. Quantification was achieved using an internal standard. The limit of quantification was 10 ng/ml for each enantiomer. The method is sufficiently sensitive to quantitate the plasma concentrations of both enantiomers for 30 days following a single oral dose of 400 mg of the antimalarial agent administered as the racemic succinate salt to healthy human male volunteers. In nearly all samples taken 12 h to 30 days post-dose from three subjects, the difference in the plasma concentrations of the two enantiomers is less than 10%.