Recognition of nucleic acid bases and base-pairs by hydrogen bonding to amino acid side-chains

Sequence-specific protein-nucleic acid recognition is determined, in part, by hydrogen bonding interactions between amino acid side-chains and nucleotide bases. To examine the repertoire of possible interactions, we have calculated geometrically plausible arrangements in which amino acids hydrogen bond to unpaired bases, such as those found in RNA bulges and loops, or to the 53 possible RNA base-pairs. We find 32 possible interactions that involve two or more hydrogen bonds to the six unpaired bases (including protonated A and C), 17 of which have been observed. We find 186 "spanning" interactions to base-pairs in which the amino acid hydrogen bonds to both bases, in principle allowing particular base-pairs to be selectively targeted, and nine of these have been observed. Four calculated interactions span the Watson-Crick pairs and 15 span the G:U wobble pair, including two interesting arrangements with three hydrogen bonds to the Arg guanidinum group that have not yet been observed. The inherent donor-acceptor arrangements of the bases support many possible interactions to Asn (or Gln) and Ser (or Thr or Tyr), few interactions to Asp (or Glu) even though several already have been observed, and interactions to U (or T) only if the base is in an unpaired context, as also observed in several cases. This study highlights how complementary arrangements of donors and acceptors can contribute to base-specific recognition of RNA, predicts interactions not yet observed, and provides tools to analyze proposed contacts or design novel interactions.     

The interaction of cationic antimicrobial peptides with vesicles containing synthetic glycolipids as models of the outer membrane of gram-negative bacteria.

Two simple lipid A analogues methyl 2,3-di-O-tetradecanoyl-alpha-D-glucopyranoside (GL1) and methyl 2,3-di-O-tetradecanoyl-alpha-D-glucopyranoside 4-O-phosphate (GL2) were synthesized and used for preparing mixed phosphocholine vesicles as models of the outer membrane of gram-negative bacteria. The interaction of these model membranes with magainin 2, a representative of the alpha-helical membrane active peptides, and apidaecin Ib and drosocin, two insect Pro-rich peptides which do not act at the level of the cellular membrane, were studied by CD and dye-releasing experiments. The CD spectra of apidaecin Ib and drosocin in the presence of GL1- or GL2-containing vesicles were consistent with largely unordered structures, whereas, according to the CD spectra, magainin 2 adopted an amphipathic alpha-helical conformation, particularly in the presence of negatively charged bilayers. The ability of the peptides to fold into amphipathic conformations was strictly correlated to their ability to bind and to permeabilize phospholipid as well as glycolipid membranes. Apidaecin Ib and drosocin, which are unable to adopt an amphipathic structure, showed negligible dye-leakage activity even in the presence of GL2-containing vesicles. It is reasonable to suppose that, as for the killing mechanism, the two classes of antimicrobial peptides follow different patterns to cross the bacterial outer membrane.     

Influence of ultraviolet-B radiation on growth,prevalence of deformities,and susceptibility to predation in Cascades frog (<Emphasis Type="Italic">Rana cascadae</Emphasis>) larvae

Ambient levels of ultraviolet-B radiation (UVB) have a variety of detrimental effects on aquatic organisms. These include death and effects on growth, development, physiology, and behavior. Amphibians show all of these effects. However, the effects vary with species, life history stage, and ecological context. Little is known about the implications of the detrimental effects of UVB on ecological dynamics. Our study was designed to test how UVB may affect predator–prey interactions, an important ecological dynamic. Specifically, we tested the effect of UVB on the susceptibility of Cascades frog (Rana cascadae) larvae to predation by rough-skinned newts (Taricha granulosa). We also further examined the sublethal effects of UVB on growth and development in Cascades frog larvae. We found no direct effect of UVB exposure on survival. However, UVB-exposed frog larvae displayed decreased growth and increased prevalence of deformities. UVB also caused increased susceptibility to predation, but there was a significant treatment–block interaction. UVB increased susceptibility to predation in two out of five blocks of Cascades frogs. The other three blocks did not show an effect of UVB on susceptibility to predation. Our study suggests that UVB can alter susceptibility to predation in at least one amphibian species. UVB-induced alteration of predator–prey interactions could potentially lead to changes at the population, community, and ecosystem levels. Handling editor: K. Martens     

Life history of the bird cherry-oat aphid, Rhopalosiphum padi, on transgenic and non-transformed wheat challenged with Wheat streak mosaic virus

The life history of the bird cherry-oat aphid, Rhopalosiphum padi (L.) (Hemiptera: Aphididae), was studied via laboratory assays on Wheat streak mosaic virus (WSMV)-infected and non-infected transgenic and non-transformed wheat [ Triticum aestivum L. (Poaceae)]. Although R. padi is not a WSMV vector, it is known to colonize WSMV-infected wheat plants. Two transgenic soft white winter wheat genotypes, 366-D03 and 366-D8, that express the WSMV coat protein gene, and the WSMV-susceptible non-transformed cultivar Daws were tested. All genotypes showed disease symptoms when infected with WSMV. Whereas plant height was significantly reduced on virus-infected compared to non-infected plants of all genotypes, virus-infected transgenic plants exhibited lower virus titer and lower disease rating scores than Daws. No significant effects of WSMV infection or genotypes were observed on the length of R. padi nymphal development period, nor on their pre-, and post-reproductive periods. Rhopalosiphum padi reproductive period was significantly longer on Daws infected with WSMV than on non-infected plants of this cultivar. In contrast, there were no significant differences in length of R. padi reproductive period between virus-infected and non-infected transgenic plants within a genotype. Rhopalosiphum padi daily fecundity was significantly lower and adult longevity significantly longer on virus-infected than on non-infected plants of all genotypes. Total aphid fecundity and intrinsic rate of increase were not significantly different among treatments. The percentage of winged aphids that developed was greater on WSMV-infected compared to non-infected plants within a genotype. Results indicate that both virus infection status of plants and wheat genotype influence the life history of R. padi.     

Autocrine activation of adenosine A1 receptors blocks D1A but not D1B dopamine receptor desensitization

Adenosine is known to modulate dopamine responses in several brain areas. Here, we show that tonic activation of adenosine receptors is able to impede desensitization of D1 dopamine receptors. As measured by cAMP accumulation in transfected COS-7 cells, long-term exposure to dopamine agonists promoted desensitization of D1B receptor but not that of D1A receptor. The inability of D1A receptor to desensitize was a result of the adenosine present in culture medium acting through activation of adenosine A1 receptors. Cell incubation with either adenosine deaminase, CGS-15943, a generic adenosine receptor antagonist, or the A1 antagonist DPCPX restored the long-term desensitization time-course of D1A receptors. In Ltk cells stably expressing A1 adenosine receptors and D1A dopamine receptors, pre-treatment of cells with R(-)-PIA, a full A1 receptor agonist, did not significantly inhibit the acute increase in cAMP levels induced by D1 receptor agonists, but blocked desensitization of D1A receptors. However, simultaneous activation of A1 and D1A receptors promoted a delayed D1A receptor desensitization. This suggests that functional interaction between A1 and D1A receptors may depend on the activation kinetics of components regulating D1 receptor responses, acting differentially on D1A and D1B receptors.     

The Høylandet area – patterns and processes of a pristine boreal-subalpine ecosystem – a synopsis

The research activities on soil–freshwaterinteractions and freshwater biotic structure andprocesses in the Høylandet area during the years 1986–89are presented in this issue ofHydrobiologia. The 9 papers cover a range of topicsfrom physiochemical gradients and processes in soilsand freshwaters to selected aspects of freshwaterbiotic community structure and temporal variability.This synopsis aims (a) to present an overview of majorfindings, (b) to interpret the results in the contextof air pollution effects and (c) to outlinesuggestions for future research activities inHøylandet. The area has a sub-oceanic climate varyingfrom 1100 to 2200 mm of precipitation normallyoriginating from unpolluted airmasses from the NorthAtlantic. It is chemically dominated by sea salts, haslow concentrations and low deposition of mineralacids. The catchment geology is variable and complexand consists mainly of various granites and gneisses.The soils are undisturbed ancient soils,primarily iron podzols associated with forests, orintact histosols with strong organic characterassociated with mires, often quite acidic.They are sensitive because occurrence of predominantlyinsoluble unstable Al-complexes may leach out ifexposed to anthropogenically acidified soil drainagewater and turn up as toxic inorganic aqueous Al insurface runoff. Small amounts of locally generatednitrogen compounds are mostly retained in thecatchment. The water qualities of these Høylandetsites are run by inputs of sea salts, hydrologicalprocesses including dilution of the base flow, orlateral surface or overland flow and in-catchmentprocesses. Relative to affected areas, it appears thatthe inputs and catchment processes are in balance,i.e., that the inputs of strong acid anions, hydrogenions and sea salts are equilibrated by internalweathering and other processes and integrated withinapparently intact biogeochemical cycles. The overallresult is that these soils remain a net source ofalkalinity to the runoff. These results are confirmedby regional studies of water quality both at low andhigh flow which show that the humus and ionic contentof the water decreased with elevation, headwatersbeing more dominated by sea salts and dilutionprocesses. Excess sulphate concentrations are low, andfew if any sites appear anthropogenically acidified,the most acid pHs reflecting presence of natural weakorganic acids.The resulting surface water quality allows a diverseaquatic fauna and flora with representatives of manyacid-sensitive groups. The fish fauna consists ofself-reproducing salmonid populations with normaldemography and ecological interactions. Despite highin-lake mortality, both brown trout and Arctic charrexhibited normal age-class compositions, with noindication of the recruitment failure or highpost-spawning mortality commonly observed inacid-stressed situations. The zooplankton and benthos in the lakesare inhabited by populations of several acid sensitivespecies, like Daphnia spp and Gammaruslacustris, and with dominance of mayfly species ofthe genus Baetis in the stream fauna. Thediatom flora includes many species which are rare orabsent in acidified waters. The observed gradients indiversity and biomass seem dominated by localenvironmental conditions which reflect natural ratherthan man-made processes. The pristine nature of thearea also emerges from the paleoecological studies inLake Røyrtjønna which show that the low acidity ofthis lake evironment has persisted from preindustrialtill present times. Suggestion for future researchactivities in Høylandet are outlined.     

Atomistic mechanisms of huntingtin N‐terminal fragment insertion on a phospholipid bilayer revealed by molecular dynamics simulations

The huntingtin protein is characterized by a segment of consecutive glutamines (Q_N) that is responsible for its fibrillation. As with other amyloid proteins, misfolding of huntingtin is related to Huntington's disease through pathways that can involve interactions with phospholipid membranes. Experimental results suggest that the N‐terminal 17‐amino‐acid sequence (htt^NT) positioned just before the Q_N region is important for the binding of huntingtin to membranes. Through all‐atom explicit solvent molecular dynamics simulations, we unveil the structure and dynamics of the htt^NTQ_N fragment on a phospholipid membrane at the atomic level. We observe that the insertion dynamics of this peptide can be described by four main steps—approach, reorganization, anchoring, and insertion—that are very diverse at the atomic level. On the membrane, the htt^NT peptide forms a stable α‐helix essentially parallel to the membrane with its nonpolar side‐chains—mainly Leu‐4, Leu‐7, Phe‐11 and Leu‐14—positioned in the hydrophobic core of the membrane. Salt‐bridges involving Glu‐5, Glu‐12, Lys‐6, and Lys‐15, as well as hydrogen bonds involving Thr‐3 and Ser‐13 with the phospholipids also stabilize the structure and orientation of the htt^NT peptide. These observations do not significantly change upon adding the Q_N region whose role is rather to provide, through its hydrogen bonds with the phospholipids' head group, a stable scaffold facilitating the partitioning of the htt^NT region in the membrane. Moreover, by staying accessible to the solvent, the amyloidogenic Q_N region could also play a key role for the oligomerization of htt^NTQ_N on phospholipid membranes. Proteins 2014; 82:1409–1427. © 2014 Wiley Periodicals, Inc.     

Ecological and evolutionary consequences of spatial and temporal variation in pre-dispersal seed predation

Pre-dispersal seed predation may have important effects on population dynamics and trait evolution in plants. In this review, we first present a conceptual framework of the strength of pre-dispersal seed predation and its variation in space and time. We consider the interaction between plants and their seed predators to be “strong” when it affects plant population dynamics or causes changes in plant trait–fitness relationships, and “weak” when it has no such effects, and propose ways of how to adequately assess these effects. Second, we review the ecological literature between 1991 and 2005 to evaluate documented effects of pre-dispersal seed predation on plants and draw five major conclusions. (1) Pre-dispersal seed predation rates are usually low but sometimes high, and show a considerable variation in space and time. (2) Direct evidence suggests that pre-dispersal seed predation can have a significant effect on recruitment and plant population growth rate. Accumulating evidence of seed-limited recruitment suggests that such effects are common. (3) Pre-dispersal seed predation affects selection on several plant traits, such as flowering phenology and flower number, which are usually interpreted mainly in the context of plant–pollinator interactions. (4) The patterns of variation in the interactions between plants and pre-dispersal seed predators suggest that geographic selection mosaics may be common. (5) Although there are numerous studies estimating seed predation, there are still rather few studies that have aimed at examining the interaction explicitly in terms of effects on plant population dynamics and trait selection. From these we know that seed predators can have important, and often variable, effects on plant population dynamics and trait evolution. However, it still remains to assess how important they are across study systems and relative to other aspects of the plant's biotic and abiotic environment.     

Effects of protein-protein interactions on electron transfer: docking and electron transfer calculations for complexes between flavodoxin and c-type cytochromes

 Theoretical studies of protein-protein association and electron transfer were performed on the binary systems formed by Desulfovibrio vulgaris Hildenborough (D. v. H.) flavodoxin and D. v. H. cytochrome c ₅₅₃ and by flavodoxin and horse heart cytochrome c. Initial structures for the complexes were obtained by rigid-body docking and were refined by MD to allow for molecular flexibility. The structures thus obtained were analysed in terms of their relative stability through the calculation of excess energies. Electrostatic, van der Waals and solvation energy terms showed all to have significant contributions to the stability of complexes. In the best association solutions found for both cytochromes, these bind to different zones of flavodoxin. The binding site of flavodoxin observed for cytochrome c is in accordance with earlier works [27]. The various association modes found were characterised in terms of electron transfer using the Pathways model. For complexes between flavodoxin and horse heart cytochrome c, some correlation was observed between electron tunnelling coupling factors and conformation energy; the best conformation found for electron transfer corresponded also to the best one in terms of energy. For complexes between flavodoxin and cytochrome c ₅₅₃ this was not the case and a lower correlation was observed between electron tunnelling coupling factors and excess energies. These results are in accordance with the differences in the experimental dependence of electron transfer rates with ionic strength observed between these two cases. Received: 29 December 1998 / Accepted: 22 March 1999