Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment.

Statistical potentials based on pairwise interactions between C alpha atoms are commonly used in protein threading/fold-recognition attempts. Inclusion of higher order interaction is a possible means of improving the specificity of these potentials. Delaunay tessellation of the C alpha-atom representation of protein structure has been suggested as a means of defining multi-body interactions. A large number of parameters are required to define all four-body interactions of 20 amino acid types (20(4) = 160,000). Assuming that residue order within a four-body contact is irrelevant reduces this to a manageable 8,855 parameters, using a nonredundant dataset of 608 protein structures. Three lines of evidence support the significance and utility of the four-body potential for sequence-structure matching. First, compared to the four-body model, all lower-order interaction models (three-body, two-body, one-body) are found statistically inadequate to explain the frequency distribution of residue contacts. Second, coherent patterns of interaction are seen in a graphic presentation of the four-body potential. Many patterns have plausible biophysical explanations and are consistent across sets of residues sharing certain properties (e.g., size, hydrophobicity, or charge). Third, the utility of the multi-body potential is tested on a test set of 12 same-length pairs of proteins of known structure for two protocols: Sequence-recognizes-structure, where a query sequence is threaded (without gap) through the native and a non-native structure; and structure-recognizes-sequence, where a query structure is threaded by its native and another non-native sequence. Using cross-validated training, protein sequences correctly recognized their native structure in all 24 cases. Conversely, structures recognized the native sequence in 23 of 24 cases. Further, the score differences between correct and decoy structures increased significantly using the three- or four-body potential compared to potentials of lower order.     

Determination of the binding frame of the chaperone SecB within the physiological ligand oligopeptide-binding protein.

Chaperone proteins demonstrate the paradoxical ability to bind ligands rapidly and with high affinity but with no apparent sequence specificity. To learn more about this singular property, we have mapped the binding frame of the chaperone SecB from E. coli on the oligopeptide-binding protein. Similar studies performed on the maltose-binding and galactose-binding proteins revealed centrally positioned binding frames of approximately 160 aminoacyl residues. The work described here shows that OppA, which is significantly longer than the previously studied ligands, has a binding frame that covers 460 amino acids, nearly the entire length of the protein. We propose modes of binding to account for the data.     

The X-ray structure of a mutant eye lens beta B2-crystallin with truncated sequence extensions.

beta-Crystallins are oligomeric eye lens proteins that are related to monomeric gamma-crystallins by domain swapping: like gamma-crystallins, they are comprised of two similar domains but they differ in having long sequence extensions. beta B2, a major component of beta-crystallin oligomers, self-associates to a homodimer in solution. In two crystal structures of native beta B2, the protein is a 222-symmetric tetramer of eight domains. It has previously been shown that a mutant of rat beta B2-crystallin, in which the bulk of the N- and C-terminal sequence extensions has been deleted, assembles into dimers and tetramers. Here we present the 3.0 A resolution X-ray structure of the tetramer, beta B2 delta NC1. The mutant tetramer has a very similar set of domain interactions to the native structure. However, the structures differ in the relative orientation of the two sets of four domains. The paired N- and C-terminal domain interface, which is at the heart of the dimer structure, is very similar to the native structure. However, the truncation of the C-terminal extension removes an important tryptophan residue, which prevents the extension from acting as a (non-covalent) linker, as it does in native beta B2. There is a knock-on structural effect that removes a contact between extension and covalent linker, and this appears to cause a small twist in the linker that is amplified into a 20 degrees rotation between sets of paired domains.     

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.     

Domain Evolution in the α-Amylase Family

The available amino acid sequences of the α-amylase family (glycosyl hydrolase family 13) were searched to identify their domain B, a distinct domain that protrudes from the regular catalytic (β/α)₈-barrel between the strand β3 and the helix α3. The isolated domain B sequences were inspected visually and also analyzed by Hydrophobic Cluster Analysis (HCA) to find common features. Sequence analyses and inspection of the few available three-dimensional structures suggest that the secondary structure of domain B varies with the enzyme specificity. Domain B in these different forms, however, may still have evolved from a common ancestor. The largest number of different specificities was found in the group with structural similarity to domain B from Bacillus cereus oligo-1,6-glucosidase that contains an α-helix succeeded by a three-stranded antiparallel β-sheet. These enzymes are α-glucosidase, cyclomaltodextrinase, dextran glucosidase, trehalose-6-phosphate hydrolase, neopullulanase, and a few α-amylases. Domain B of this type was observed also in some mammalian proteins involved in the transport of amino acids. These proteins show remarkable similarity with (β/α)₈-barrel elements throughout the entire sequence of enzymes from the oligo-1,6-glucosidase group. The transport proteins, in turn, resemble the animal 4F2 heavy-chain cell surface antigens, for which the sequences either lack domain B or contain only parts thereof. The similarities are compiled to indicate a possible route of domain evolution in the α-amylase family. Received: 4 December 1996 / Accepted: 13 March 1997     

Variable chemical defence in the checkerspot butterfly Euphydryas gillettii (Lepidoptera: NymphaIidae)

Abstract.

• 1 Like other checkerspots, Euphydryas gillettii butterflies may contain the defensive chemicals, iridoid glycosides, which are sequestered from their hostplants during larval feeding.
• 2 We analysed the iridoid glycoside content of E.gillettii adults from two different populations, Warm Lake, Idaho, and Granite Creek, Wyoming, that have different patterns of hostplant use.
• 3 Gas chromatographic analysis of thirty butterflies from the Wyoming population showed that they contained a mean of 1.27 (±0.19 SE) % dry weight iridoid glycosides. Notably, 20% of these butterflies contained no detectable iridoid glycosides.
• 4 In contrast, nineteen butterflies from the Idaho population contained a mean of 3.89 (±0.38 SE) % dry weight iridoid glycosides, and all butterflies contained iridoid glycosides.
• 5 These results illustrate how the chemical defence of herbivorous insects varies according to differential use of potential hostplants.

     

Effects of temperature on phenological synchrony and altitudinal distribution of jumping plant lice (Hemiptera: Psylloidea) on dwarf willow (Salix lapponum) in Norway

Summary.

• 1 The geographical distributions of three species of jumping plant lice (psyllids) along an altitudinal transect (988–1300 m a.s.l.) in southern Norway were restricted within the range of their host plant Salix lapponum. One species, Cacopsylla propinqua, occurred at all sampling locations between 988 and 1222 m, whereas C.palmeni was confined to higher altitudes (1153–1222 m) and C.brunneipennis was more abundant at lower altitudes (988–1101 m).
• 2 C.brunneipennis and C.palmeni developed only on female catkins. Development times of catkins and psyllids were similar (approximately 50 days) and successful psyllid development depended on close phenological synchrony with catkins.
• 3 Thermal requirements for development of female catkins were greater at low altitude (988 m) compared with higher altitude (1222 m), showing local adaptation of S.lapponum to altitude. In general, thermal requirements of psyllids were less than those of catkins at the same location. C.brunneipennis had higher thermal requirements than C.palmeni.
• 4 Field experiments, using polythene enclosures to elevate temperatures at two sites at different altitudes (by 0.6–1.4 deg. C), showed that insects had an enhanced relative rate of development under elevated temperatures compared with their host plants.
• 5 Indices of phenological synchrony were calculated from thermal requirements of psyllids and catkins. Under elevated temperatures, phenological synchrony decreased at both sites. This resulted in the subsequent development of smaller adult insects at low altitude, although at higher altitude, insects developing under elevated temperatures were larger and had a higher survival rate compared with controls.
• 6 Effects of temperature on phenological synchrony may explain the limits to the geographical range of psyllids. The consequences of climate change on psyllid populations will depend on the effects of decreased phenological synchrony on insect development and this may differ within the insect's geographical range.

     

Direct and indirect effects of plant genetic variation on enemy impact

Abstract.

• 1 The Tritrophic and Enemy Impact concepts predict that natural enemy impact varies: (a) among plant genotypes and (b) may depend on the abundance of heterospecific herbivores, respectively. I tested these predictions using three herbivore species on potted, cloned genotypes of Salik sericea Marshall in a common garden experiment.
• 2 Densities of the leaf miner (Phyllonorycter salicifoliella (Chambers)) and two leaf galling sawflies (Phyllocolpa nigrita (Marlatt) and Phyllocolpa eleanorae Smith and Fritz) varied significantly among willow clones, indicating genetic variation in resistance.
• 3 Survival and natural enemy impact caused by egg and larval parasitoids and/or unknown predators differed significantly among willow clones for each of the three herbivore species, indicating genetic variation in survival and enemy impact.
• 4 Survival of Phyllonorycter was negatively density-dependent among clones.
• 5 Survival of Phyllonorycter and Phyllocolpa eleanorae were positively correlated with densities of heterospecific herbivores among clones and parasitism of these species were negatively correlated with densities of the same heterospecific herbivores among clones.
• 6 At least for Phyllonorycter this positive correlation may suggest either facilitation of survival between herbivore species, which do not share natural enemies, or an apparent interaction caused by host plant genetic variation.
• 7 Among clones, egg parasitism of Phyllocolpa eleanorae was weakly positively correlated with density of Phyllocolpa nigrita. Since these species share the same Trichogramma egg parasitoid, this interaction could support the hypothesis of apparent competition.

     

Ecomorphological adaptations to bioluminescence in Porichthys notatus

Synopsis The midshipman fish, Porichthys notatus, is a visually active nocturnal predator. It must acquire exogenous sources of luciferin to remain luminescent and feeds on a variety of luminescent prey. Its ecomorphological adaptations for nocturnal predation were examined by observing predation on zooplankton illuminated by dinoflagellates. Its visual sensitivity is well adapted for detection of its own luminescence and its prey's luminescence. P. notatus can detect the luminescence of dinoflagellates and use this indirect light to increase predation on nonluminescent prey. Flash frequency and duration modulated predation rates. The interval between flash onset and strike initiation regulated strike success. High prey concentration decreased predation success due to increased optical and mechanosensory noise. Other ecomorphological adaptations of this predator to its special photic environment include a pigmented digestive tract, duplex retina with the capacity to discriminate emission spectra, contractible pupil, and the potential to counter illuminate. These morphological adaptations combined with an ambush predator style allow effective predation while minimizing exposure risk.