Discovery of a significant,nontopological preference for antiparallel alignment of helices with parallel regions in sheets

To help elucidate the role of secondary structure packing preferences in protein folding, here we present an analysis of the packing geometry observed between alpha-helices and between alpha-helices and beta-sheets in 1316 diverse, nonredundant protein structures. Finite-length vectors were fit to the alpha-carbon atoms in each of the helices and strands, and the packing angle between the vectors, Omega, was determined at the closest point of approach within each helix-helix or helix-sheet pair. Helix-sheet interactions were found in 391 of the proteins, and the distributions of Omega values were calculated for all the helix-sheet and helix-helix interactions. The packing angle preferences for helix-helix interactions are similar to those previously observed. However, analysis of helix-strand packing preferences uncovered a remarkable tendency for helices to align antiparallel to parallel regions of beta-sheets, independent of the topological constraints or prevalence of beta-alpha-beta motifs in the proteins. This packing angle preference is significantly diminished in helix interactions involving mixed and antiparallel beta-sheets, suggesting a role for helix-sheet dipole alignment in guiding supersecondary structure formation in protein folding. This knowledge of preferred packing angles can be used to guide the engineering of stable protein modules.     

Identification of Mimotope Peptides Which Bind to the Mycotoxin Deoxynivalenol-Specific Monoclonal Antibody

Monoclonal antibody 6F5 (mAb 6F5), which recognizes the mycotoxin deoxynivalenol (DON) (vomitoxin), was used to select for peptides that mimic the mycotoxin by employing a library of filamentous phages that have random 7-mer peptides on their surfaces. Two phage clones selected from the random peptide phage-displayed library coded for the amino acid sequences SWGPFPF and SWGPLPF. These clones were designated DONPEP.2 and DONPEP.12, respectively. The results of a competitive enzyme-linked immunosorbent assay (ELISA) suggested that the two phage displayed peptides bound to mAb 6F5 specifically at the DON binding site. The amino acid sequence of DONPEP.2 plus a structurally flexible linker at the C terminus (SWGPFPFGGGSC) was synthesized and tested to determine its ability to bind to mAb 6F5. This synthetic peptide (designated peptide C430) and DON competed with each other for mAb 6F5 binding. When translationally fused with bacterial alkaline phosphatase, DONPEP.2 bound specifically to mAb 6F5, while the fusion protein retained alkaline phosphatase activity. The potential of using DONPEP.2 as an immunochemical reagent in a DON immunoassay was evaluated with a DON-spiked wheat extract. When peptide C430 was conjugated to bovine serum albumin, it elicited antibody specific to peptide C430 but not to DON in both mice and rabbits. In an in vitro translation system containing rabbit reticulocyte lysate, synthetic peptide C430 did not inhibit protein synthesis but did show antagonism toward DON-induced protein synthesis inhibition. These data suggest that the peptides selected in this study bind to mAb 6F5 and that peptide C430 binds to ribosomes at the same sites as DON.     

Identification of mimotope peptides which bind to the mycotoxin deoxynivalenol-specific monoclonal antibody.

Monoclonal antibody 6F5 (mAb 6F5), which recognizes the mycotoxin deoxynivalenol (DON) (vomitoxin), was used to select for peptides that mimic the mycotoxin by employing a library of filamentous phages that have random 7-mer peptides on their surfaces. Two phage clones selected from the random peptide phage-displayed library coded for the amino acid sequences SWGPFPF and SWGPLPF. These clones were designated DONPEP.2 and DONPEP.12, respectively. The results of a competitive enzyme-linked immunosorbent assay (ELISA) suggested that the two phage displayed peptides bound to mAb 6F5 specifically at the DON binding site. The amino acid sequence of DONPEP.2 plus a structurally flexible linker at the C terminus (SWGPFPFGGGSC) was synthesized and tested to determine its ability to bind to mAb 6F5. This synthetic peptide (designated peptide C430) and DON competed with each other for mAb 6F5 binding. When translationally fused with bacterial alkaline phosphatase, DONPEP.2 bound specifically to mAb 6F5, while the fusion protein retained alkaline phosphatase activity. The potential of using DONPEP.2 as an immunochemical reagent in a DON immunoassay was evaluated with a DON-spiked wheat extract. When peptide C430 was conjugated to bovine serum albumin, it elicited antibody specific to peptide C430 but not to DON in both mice and rabbits. In an in vitro translation system containing rabbit reticulocyte lysate, synthetic peptide C430 did not inhibit protein synthesis but did show antagonism toward DON-induced protein synthesis inhibition. These data suggest that the peptides selected in this study bind to mAb 6F5 and that peptide C430 binds to ribosomes at the same sites as DON.     

FOOD PREFERENCE AND THE EXTENT OF OVERLAP IN SOME INSECTIVOROUS BIRDS, WITH SPECIAL REFERENCE TO THE TYRANNIDAE

Analysis of published records of the food of flycatchers (Tyrannidae), swallows (Hirundinidae) and vireos (Vireonidae) of North America, and terns (Laridae) of the Pacific Ocean showed that size, rather than taxonomic, differences in food appear to be the most important ones for these birds. Although the distribution of insect sizes in nature approaches a two-parameter log-normal distribution, the distributions of the sizes of food items taken by birds show no significant differences from log-normal. Birds of a given feeding type (e.g. flycatchers) show a strong correlation of average prey size with bird body weight, and a significantly less strong correlation with bill characteristics, indicating that body size is a better predictor of prey size than any single bill character. The slopes and/or intercepts of regressions of food size against body weight are different for birds of different foraging type. Values of overlap in food preference are proportional to the similarity of the two species compared, expressed as the ratio of their weights. Because insect taxa differ in size and because the amount of overlap in taxonomic composition of foods is therefore very roughly proportional to the amount of overlap in size, taxonomic differences in food may merely reflect differences in size preferences. Values for overlap in food are greater than for most cases involving spatial niche parameters, indicating space is more easily divided than food, a conclusion supported by the relative rarity of large flycatchers.     

Protein flexibility using constraints from molecular dynamics simulations

Proteins are held together in the native state by hydrophobic interactions, hydrogen bonds and interactions with the surrounding water, whose strength as well as spatial and temporal distribution affects protein flexibility and hence function. We study these effects using 10 ns molecular dynamics simulations of pure water and of two proteins, the glutamate receptor ligand binding domain and barnase. We find that most of the noncovalent interactions flicker on and off over typically nanoseconds, and so we can obtain good statistics from the molecular dynamics simulations. Based on this information, a topological network of rigid bonds corresponding to a protein structure with covalent and noncovalent bonds is constructed, with account being taken of the influence of the flickering hydrogen bonds. We define the duty cycle for the noncovalent interactions as the percentage of time a given interaction is present, which we use as an input to investigate flexibility/rigidity patterns, in the algorithm FIRST which constructs and analyses topological networks.     

Constrained geometric simulation of diffusive motion in proteins

We describe a new computational method, FRODA (framework rigidity optimized dynamic algorithm), for exploring the internal mobility of proteins. The rigid regions in the protein are first determined, and then replaced by ghost templates which are used to guide the movements of the atoms in the protein. Using random moves, the available conformational phase space of a 100 residue protein can be well explored in approximately 10-100 min of computer time using a single processor. All of the covalent, hydrophobic and hydrogen bond constraints are maintained, and van der Waals overlaps are avoided, throughout the simulation. We illustrate the results of a FRODA simulation on barnase, and show that good agreement is obtained with nuclear magnetic resonance experiments. We additionally show how FRODA can be used to find a pathway from one conformation to another. This directed dynamics is illustrated with the protein dihydrofolate reductase.     

A revision of the West Indian species of Lepanthes (Orchidaceae). III. Cuba

A study of herbarium material ofLepanthes indicates that there are at least 18 species on Cuba. The history of the collections and publications on the genus from the island is summarized, and a detailed key to the species is given. One new combination is proposed (L. blepharophylla) and the following species are described as new:L. acunae,L. dressleri,L. cubensis,L. grisebachiana,L. obliquiloba, andL. occidentalis, of which three are from western provinces and two have been associated with inappropriate names.L. mandibularis Reichb. f. is tentatively considered a synonym ofL. chrysostigma Lindl. although the type ofL. mandibularis could not be found. The range of variation included under the nameL. fulva Lindl. suggests that more than one species is involved.     

SELECTIVE PREDATION BY TWO SWIFTS AND A SWALLOW IN CENTRAL AMERICA

Samples of flying insects were made at three sites and during dry and wet seasons in Costa Rica and at two sites during the wet season in Panama. Compared with these were the diets of three aerially foraging birds: the Band-rumped Swift Chaetura spinicauda and Rough-winged Swallow Stelgidopteryx ruficollis in Costa Rica and the Short-tailed Swift Chaetura brachyura in Panama. Among insects flying, Diptera accounted for between 52 and 75%, with smaller numbers of Hymenoptera (mean = 15%) and Coleoptera (10%). In bird stomach contents, however, Hymenoptera predominated (59–81%), Coleoptera were less common (mean = 18.5%) and Diptera least common (3.4%) of the three orders. The discrepancy between diets and samples of flying insects could not be accounted for solely on the basis of differential digestion. The composition of the swift and swallow diets was similar; there were no significant seasonal differences in the taxonomic composition of the diet of Chaetura spinicauda. Size distributions of beetle prey fitted log-normal distributions in every case. Mean size of prey was significantly larger than that of insects available in all comparisons. Although there was no seasonal difference in the mean size of prey of Chaetura spinicauda, the variance in prey size, used as a measure of niche width, was significantly larger in the wet than in the dry season. Although insect densities may be higher, foraging time is reduced and the wet season is likely the worse season. This result therefore supports Emlen's hypothesis of narrower niches under optimal conditions and broader niches under suboptimal conditions. For increasing altitude above ground published data show a decrease in the density of insects flying, a decrease in the proportions of taxa favoured by the birds, and a significant decrease in the mean size of beetles. None of these trends can explain the differences between the birds' diets and the samples of flying insects. Preference of prey by these birds is concluded not to be a function of prey size alone, but to involve interaction among prey size, ease of capture, and local density. Because of different flight abilities, insect taxa will differ in ease of capture and, consequently, in mean size preferred by the predator, as well as proportions in the diet. This factor favours Hymenoptera and Coleoptera over Diptera as prey. Local concentrations of winged ants, bees and social wasps, and fig wasps make these prey differentially easy to exploit and explain the preference of Hymenoptera over Coleoptera. Large species of swifts are hypothesized to be the evolutionary consequence of the tendency of aerially foraging birds to exploit local concentrations of single prey species.