Simulating temperature-dependent ecological processes at the sub-continental scale: male gypsy moth flight phenology as an example

 We simulated male gypsy moth flight phenology for the location of 1371 weather stations east of 100° W longitude and north of 35° N latitude in North America. The output of these simulations, based on average weather conditions from 1961 to 1990, was submitted to two map-interpolation methods: multiple regression and universal kriging. Multiple regression was found to be as accurate as universal kriging and demands less computing power. A map of the date of peak male gypsy moth flight was generated by universal kriging. This map itself constitutes a useful pest-management planning tool; in addition, the map delineates the potential range of the gypsy moth based on its seasonality at the northern edge of its current distribution in eastern North America. The simulation and map-interpolation methods described in this paper thus constitute an interesting approach to the study and monitoring of the ecological impacts of climate change and shifts in land-use patterns at the sub-continental level. Received: 26 May 1998 / Accepted: 6 July 1998     

Building self-avoiding lattice models of proteins using a self-consistent field optimization

We present an algorithm to build self-avoiding lattice models of chain molecules with low RMS deviation from their actual 3D structures. To find the optimal coordinates for the lattice chain model, we minimize a function that consists of three terms: (1) the sum of squared deviations of link coordinates on a lattice from their off-lattice values, (2) the sum of “short-range” terms, penalizing violation of chain connectivity, and (3) the sum of “long-range” repulsive terms, penalizing chain self-intersections. We treat this function as a chain molecule “energy” and minimize it using self-consistent field (SCF) theory to represent the pairwise link repulsions as 3D fields acting on the links. The statistical mechanics of chain molecules enables computation of the chain distribution in this field on the lattice. The field is refined by iteration to become self-consistent with the chain distribution, then dynamic programming is used to find the optimal lattice model as the “lowest-energy” chain pathway in this SCF. We have tested the method on one of the coarsest (and most difficult) lattices used for model building on proteins of all structural types and show that the method is adequate for building self-avoiding models of proteins with low RMS deviations from the actual structures. © 1996 Wiley-Liss, Inc.     

Chiral aminophosphonate eluent for enantiomeric analysis of amino acids

An aqueous solution of the (+)-monoethyl ester of N-(l′-hydroxymethyl-)propyl-α-aminobenzylphosphonic acid has been proposed as a suitable chiral eluent for enantiomeric analysis of amino acids by ligand-exchange chromatography. Asymmetric synthesis of the chiral selector using (−)-(R)-2-aminobutan-1-ol as a starting reactant is described. The dependence of the parameters of separation of valine enantiomers on concentration of the complexing ion, pH, and temperature has been investigated. It is shown that the order in which enantiomers are eluted from a column depends on the concentration of the complexing ion and pH. © 1996 Wiley-Liss, Inc.     

Molecular determinants of FGF-21 activity-synergy and cross-talk with PPARgamma signaling

Fibroblast growth factor (FGF)-21 is a novel regulator of insulin-independent glucose transport in 3T3-L1 adipocytes and has glucose and triglyceride lowering effects in rodent models of diabetes. The precise mechanisms whereby FGF-21 regulates metabolism remain to be determined. Here we describe the early signaling events triggered by FGF-21 treatment of 3T3-L1 adipocytes and reveal a functional interplay between FGF-21 and peroxisome proliferator-activated receptor gamma (PPARgamma) pathways that leads to a marked stimulation of glucose transport. While the early actions of FGF-21 on 3T3-L1 adipocytes involve rapid accumulation of intracellular calcium and phosphorylation of Akt, GSK-3, p70(S6K), SHP-2, MEK1/2, and Stat3, continuous treatment for 72 h induces an increase in PPARgamma protein expression. Moreover, chronic activation of the PPARgamma pathway in 3T3-L1 adipocytes with the PPARgamma agonist and anti-diabetic agent, rosiglitazone (BRL 49653), enhances FGF-21 action to induce tyrosine phosphorylation of FGF receptor-2. Strikingly, treatment of cells with FGF-21 and rosiglitazone in combination leads to a pronounced increase in expression of the GLUT1 glucose transporter and a marked synergy in stimulation of glucose transport. Together these results reveal a novel synergy between two regulators of glucose homeostasis, FGF-21 and PPARgamma, and further define FGF-21 mechanism of action.     

Structure of Escherichia coli ribose-5-phosphate isomerase: a ubiquitous enzyme of the pentose phosphate pathway and the Calvin cycle

Ribose-5-phosphate isomerase A (RpiA; EC 5.3.1.6) interconverts ribose-5-phosphate and ribulose-5-phosphate. This enzyme plays essential roles in carbohydrate anabolism and catabolism; it is ubiquitous and highly conserved. The structure of RpiA from Escherichia coli was solved by multiwavelength anomalous diffraction (MAD) phasing, and refined to 1.5 A resolution (R factor 22.4%, R(free) 23.7%). RpiA exhibits an alpha/beta/(alpha/beta)/beta/alpha fold, some portions of which are similar to proteins of the alcohol dehydrogenase family. The two subunits of the dimer in the asymmetric unit have different conformations, representing the opening/closing of a cleft. Active site residues were identified in the cleft using sequence conservation, as well as the structure of a complex with the inhibitor arabinose-5-phosphate at 1.25 A resolution. A mechanism for acid-base catalysis is proposed.     

Vertical distribution and composition of phytoplankton under the influence of an upper mixed layer

The vertical distribution of phytoplankton is of fundamental importance for the dynamics and structure of aquatic communities. Here, using an advection-reaction-diffusion model, we investigate the distribution and competition of phytoplankton species in a water column, in which inverse resource gradients of light and a nutrient can limit growth of the biomass. This problem poses a challenge for ecologists, as the location of a production layer is not fixed, but rather depends on many internal parameters and environmental factors. In particular, we study the influence of an upper mixed layer (UML) in this system and show that it leads to a variety of dynamic effects: (i) Our model predicts alternative density profiles with a maximum of biomass either within or below the UML, thereby the system may be bistable or the relaxation from an unstable state may require a long-lasting transition. (ii) Reduced mixing in the deep layer can induce oscillations of the biomass; we show that a UML can sustain these oscillations even if the diffusivity is less than the critical mixing for a sinking phytoplankton population. (iii) A UML can strongly modify the outcome of competition between different phytoplankton species, yielding bistability both in the spatial distribution and in the species composition. (iv) A light limited species can obtain a competitive advantage if the diffusivity in the deep layers is reduced below a critical value. This yields a subtle competitive exclusion effect, where the oscillatory states in the deep layers are displaced by steady solutions in the UML. Finally, we present a novel graphical approach for deducing the competition outcome and for the analysis of the role of a UML in aquatic systems.     

Dynamic mechanism of nick recognition by DNA ligase.

DNA ligases are the enzymes responsible for the repair of single-stranded and double-stranded nicks in dsDNA. DNA ligases are structurally similar, possibly sharing a common molecular mechanism of nick recognition and ligation catalysis. This mechanism remains unclear, in part because the structure of ligase in complex with dsDNA has yet to be solved. DNA ligases share common structural elements with DNA polymerases, which have been cocrystallized with dsDNA. Based on the observed DNA polymerase-dsDNA interactions, we propose a mechanism for recognition of a single-stranded nick by DNA ligase. According to this mechanism, ligase induces a B-to-A DNA helix transition of the enzyme-bound dsDNA motif, which results in DNA contraction, bending and unwinding. For non-nicked dsDNA, this transition is reversible, leading to dissociation of the enzyme. For a nicked dsDNA substrate, the contraction of the enzyme-bound DNA motif (a) triggers an opened-closed conformational change of the enzyme, and (b) forces the motif to accommodate the strained A/B-form hybrid conformation, in which the nicked strand tends to retain a B-type helix, while the non-nicked strand tends to form a shortened A-type helix. We propose that this conformation is the catalytically competent transition state, which leads to the formation of the DNA-AMP intermediate and to the subsequent sealing of the nick.     

Integrating structure,bioinformatics, and enzymology to discover function: BioH,a new carboxylesterase from Escherichia coli

Structural proteomics projects are generating three-dimensional structures of novel, uncharacterized proteins at an increasing rate. However, structure alone is often insufficient to deduce the specific biochemical function of a protein. Here we determined the function for a protein using a strategy that integrates structural and bioinformatics data with parallel experimental screening for enzymatic activity. BioH is involved in biotin biosynthesis in Escherichia coli and had no previously known biochemical function. The crystal structure of BioH was determined at 1.7 A resolution. An automated procedure was used to compare the structure of BioH with structural templates from a variety of different enzyme active sites. This screen identified a catalytic triad (Ser82, His235, and Asp207) with a configuration similar to that of the catalytic triad of hydrolases. Analysis of BioH with a panel of hydrolase assays revealed a carboxylesterase activity with a preference for short acyl chain substrates. The combined use of structural bioinformatics with experimental screens for detecting enzyme activity could greatly enhance the rate at which function is determined from structure.     

Studying aminoglycoside modification by the acetyltransferase class of resistance-causing enzymes via microarray

Aminoglycosides are broad-spectrum antibacterials to which some bacteria have acquired resistance. The most common mode of resistance to aminoglycosides is enzymatic modification of the drug by different classes of enzymes including acetyltransferases (AACs). Thus, the modification of aminoglycosides by AAC(2′) from Mycobacterium tuberculosis and AAC(3) from Escherichia coli was studied using aminoglycoside microarrays. Results show that both enzymes modify their substrates displayed on an array surface in a manner that mimics their relative levels of modification in solution. Because aminoglycosides that are modified by resistance-causing enzymes have reduced affinities for binding their therapeutic target, the bacterial rRNA aminoacyl-tRNA site (A-site), arrays were probed for binding to a fluorescently labeled oligonucleotide mimic of the A-site after modification. A decrease in binding was observed when aminoglycosides were modified by AAC(3). In contrast, a decrease in binding of the A-site is not observed when aminoglycosides are modified by AAC(2′). Interestingly, these effects mirror the biological functions of the enzymes: the AAC(3) used in this study is known to confer aminoglycoside resistance, while the AAC(2′) is chromosomally encoded and unlikely to play a role in resistance. These studies lay a direct foundation for studying resistance to aminoglycosides and can also have more broad applications in identifying and studying non-aminoglycoside carbohydrates or proteins as substrates for acetyltransferase enzymes.