Crystallization and x-ray diffraction studies of a phosphate-binding protein involved in active transport in Escherichia coli

We have obtained single crystals of a phosphate-binding protein (Mr = 34,400) that serves as initial receptor in osmotic shock-sensitive active transport in Escherichia coli. The crystals, suitable for high resolution crystallographic analysis, belong to the space group P2(1)2(1)2(1). The unit cell has dimensions of a = 41.97, b = 64.66, and c = 124.6 A and contains four protein molecules. Including this phosphate-binding protein, there are now a total of six different binding protein structures currently under investigation in our laboratory, the others being those specific for L-arabinose, D-galactose, D-maltose, sulfate, or leucine/isoleucine/valine.     

Crystal structure of human annexin I at 2.5 A resolution.

cDNA coding for N-terminally truncated human annexin I, a member of the family of Ca(2+)-dependent phospholipid binding proteins, has been cloned and expressed in Escherichia coli. The expressed protein is biologically active, and has been purified and crystallized in space group P2(1)2(1)2(1) with cell dimensions a = 139.36 A, b = 67.50 A, and c = 42.11 A. The crystal structure has been determined by molecular replacement at 3.0 A resolution using the annexin V core structure as the search model. The average backbone deviation between these two structures is 2.34 A. The structure has been refined to an R-factor of 17.7% at 2.5 A resolution. Six calcium sites have been identified in the annexin I structure. Each is located in the loop region of the helix-loop-helix motif. Two of the six calcium sites in annexin I are not occupied in the annexin V structure. The superpositions of the corresponding loop regions in the four domains show that the calcium binding loops in annexin I can be divided into two classes: type II and type III. Both classes are different from the well-known EF-hand motif (type I).     

A highly conserved nuclear gene for low-level phylogenetics: elongation factor-1 alpha recovers morphology-based tree for heliothine moths

Molecular systematists need increased access to nuclear genes. Highly conserved, low copy number protein-encoding nuclear genes have attractive features for phylogenetic inference but have heretofore been applied mostly to very ancient divergences. By virtue of their synonymous substitutions, such genes should contain a wealth of information about lower-level taxonomic relationships as well, with the advantage that amino acid conservatism makes both alignment and primer definition straightforward. We tested this postulate for the elongation factor-1 alpha (EF-1 alpha) gene in the noctuid moth subfamily Heliothinae, which has probably diversified since the middle Tertiary. We sequenced 1,240 bp in 18 taxa representing heliothine groupings strongly supported by previous morphological and allozyme studies. The single most parsimonious gene tree and the neighbor-joining tree for all nucleotides show almost complete concordance with the morphological tree. Homoplasy and pairwise divergence levels are low, transition/transversion ratios are high, and phylogenetic information is spread evenly across gene regions. The EF-1 alpha gene and presumably other highly conserved genes hold much promise for phylogenetics of Tertiary age eukaryote groups.      

Increased purine nucleotide cycle activity associated with dietary zinc deficiency

Rat muscle 5′-AMP aminohydrolase (EC 3.5.4.6), adenylosuccinate synthetase (EC 6.3.4.4), and adenylosuccinate lyase (EC 4.3.2.2) activities were elevated 50–60% in zinc-deficient weanling rats when compared with restricted-fed zinc supplemental control rats. In addition, the activities of these enzymes were increased by 50–100% when zinc-deficient rats were compared with $\text{ad libitum}$-fed controls. There was no significant difference in total muscle protein or total muscle zinc among the three groups of animals. This increased activity of the purine nucleotide cycle may be responsible for the recently observed increase in blood ammonia in zinc-deficient rats when compared to controls.     

Chick embryo fibroblasts produce two forms of hyaluronidase

Cultured chick embryo fibroblasts derived from skin and skeletal muscle exhibit hyaluronidase activity both associated with the cell layer and secreted into the medium. Although both forms of the enzyme have a number of similar characteristics (R.W. Orkin and B.P. Toole, 1980, J. Biol. CHem. 255), they differ in thermal stability at neutral pH and in behavior on ion-exchange chromatography. Both forms of the enzyme are equally stable at acidic pH for long intervals, but the cell-associated hyaluronidase is significantly less stable than the secreted froms at neutral pH and at temperatures more than or equal to 30 degrees C. Neither the presence of proteases nor inhibitors of hyaluronidase appear to be involved in the cell-asspcoated enzyme. Chromatography of the two forms of hyaluronidase on carboxymethyl cellulose reveals that most (60-90 percent) of the secreted form of the enzyme elutes at a lower ionic strength than the cell- associated enzyme. Treatment of the secreted form of hyaluronidase with neuraminidase shifts its elution profile on carboxymethyl cellulose toward that of the cell-associated form, and also decreases its thermal stability at neutral pH. In contrast, treatment of the secreted form of hyaluronidase with alkaline phosphatase has no detectable effect. These data suggest that the secreted hyaluronidase differs from the cellular form in possessing additional sialic acid residues which endow the former with increased stability in the extracellular milieu.     

A mathematical biothermal model of the california sea lion

The thermal behavior of the California sea lion is modeled by a set of seventeen simultaneous partial differential equations. Numerical solution of these equations yields temperature profiles in the sea lion that closely reproduce experimental data obtained with the animals at rest in air. The model predicts that exercise is necessary to maintain body temperature while immersed in very cold water (0°C) but that very efficient heat conservation occurs during diving because of bradycardia, limited circulation, and absence of respiration.     

Sex‐specific evolution of relative leg size in Drosophila prolongata results from changes in the intersegmental coordination of tissue growth

Evolution of relative organ size is the most prolific source of morphological diversity, yet the underlying molecular mechanisms that modify growth control are largely unknown. Models where organ proportions have undergone recent evolutionary changes hold the greatest promise for understanding this process. Uniquely among Drosophila species, Drosophila prolongata displays a dramatic, male‐specific increase in the size of its forelegs relative to other legs. By comparing leg development between males and females of D. prolongata and its closest relative Drosophila carrolli, we show that the exaggerated male forelegs are produced by a sex‐ and segment‐specific increase in mitosis during the final larval instar. Intersegmental compensatory control, where smaller leg primordia grow at a faster rate, is observed in both species and sexes. However, the equilibrium growth rates that determine the final relative proportion between the first and second legs have shifted in male D. prolongata compared both to conspecific females and to D. carrolli. We suggest that the observed developmental changes that produce new adult proportions reflect an interplay between conserved growth coordination mechanisms and evolving organ‐specific growth targets.     

Survey of black howler (<Emphasis Type="Italic">Alouatta pigra</Emphasis>) and spider (<Emphasis Type="Italic">Ateles geoffroyi</Emphasis>) monkeys in the Mayan sites of Calakmul and Yaxchilán,Mexico and Tikal,Guatemala

Surveys of populations of spider and howler monkeys were conducted at the Mayan sites of Calakmul and Yaxchilán, Mexico and Tikal, Guatemala. The forests in which these sites are found are part of the largest landmass of tropical rain forests present in Mesoamerica, encompassing about 4 million ha. Triangulation of monkey vocalization combined with ground surveys was used to determine the presence of howler and spider monkey groups. Howler monkey mean troop size at these sites varied from 6.6±2.1 individuals in Yaxchilán to 7.5±1.9 in Calakmul to 8.7±2.2 in Tikal. Density estimates varied from 12.8 individuals/km² in Yaxchilán to 15.2 individuals/km² in Calakmul to 17.8 individuals/km² in Tikal. Mean spider monkey subgroup size varied from 4.7±2.6 individuals in Tikal to 5.6±3.0 individuals in Yaxchilán to 7.7±3.8 individuals in Calakmul. Spider monkey density varied from 17.0 individuals/km² in Yaxchilán to 17.2 individuals/km² in Calakmul to 56.4 individuals/km² in Tikal. All sightings of both howler and spider monkeys at the three sites were in undisturbed rain forest vegetation and spider monkeys in general were more frequently sighted at higher tree heights than howlers. We discuss the value of further acquiring data on howler and spider monkey populations existing in extensive forest tracts and on the conservation value for both primate species of the forests surrounding the Mayan ruins found in this area of Mesoamerica.     

Structural and functional characterization of pi bulges and other short intrahelical deformations

We data-mined the Protein Data Bank for short intrahelical deformations, including pi bulges. These are defined as a contiguous stretch of intrahelical residues deviating from the standard alpha-helical i-->i-4 hydrogen bonding pattern, bilaterally flanked by at least one alpha-helical turn resulting in a helix kink of less than 40 degrees. We find that such motifs exist in 4.7% of a PDB subset filtered by quality metrics (resolution <2.5 A, R-factor <0.25, sequence identity <35%). These are typically characterized by at least one i-->i-5 main chain hydrogen bond, with energetically favorable main chain dihedral angles, followed by a variable number of main chain carbonyl groups that do not accept intrahelical main chain hydrogen bonds. Their stabilization commonly occurs via hydrogen bonding to water molecules or polar groups. Numerous deformations are implicated in basic yet vital functional roles, commonly as ligand binding site contributors.