Thermodynamics of information transfer between subunits in oligomeric enzymes and kinetic cooperativity. 2. Thermodynamics of kinetic cooperativity

The principles of structural kinetics allow one to define the thermodynamic conditions that are sufficient to generate a certain type of kinetic behavior. If subunits are loosely coupled, that is if no quaternary constraint exists between them, the kinetic behavior of the polymeric enzyme is qualitatively defined by the behavior of an ideal dimer. The nature and the extent of the kinetic cooperativity are defined by the energy of interaction, delta G rho, between two subunits. This energy of interaction is that of an ideal dimer relative to that of the A2 and B2 states. This thermodynamic formulation of a given type of cooperativity holds whatever the degree of polymerization of the enzyme. Under these conditions of loose coupling between subunits, positive kinetic cooperativity cannot be associated with any sigmoidicity of the rate curve. The range of energy coupling where positive kinetic cooperativity must, of necessity, be observed becomes more and more narrow as the number of subunit interactions is increased. This range, however, is independent of the number of subunits. The same situation is not observed for negative cooperativity which appears to be independent of both the number of subunits and the number of subunit interactions. If the subunits are tightly coupled, that is if quaternary constraints exist between them, three thermodynamic parameters, delta G' rho, delta G lambda, delta G mu, are required to define the nature of kinetic cooperativity. delta G' rho is the free energy of an ideal strained dimer relative to that of strained A2 and B2 states. delta G lambda and delta G mu represent the difference of strain energies between conformations A and B and B and B relative to that existing between conformations A and A. One may determine in the parametric space (delta G' rho, delta G lambda, delta G mu) the boundaries between the sufficient conditions that generate a certain type of cooperativity and the lack of these conditions. The kinetic parameters of the rate equation are not all independent. A number of constraint conditions exist between them which depend upon the subunit design of the polymeric enzyme. The existence of these constraint conditions may be diagnostic of a certain type of subunit interactions.     

Microbial hydroxylation of natural drimenic lactones.

Incubation of confertifolin and isodrimenin with Mucor plumbeus, Aspergillus niger or Rhizopus arrhizus gave in good yields the corresponding 3 beta-hydroxy derivatives. From isodrimenin, the known natural 7 alpha-hydroxy derivative (futronolide) was also obtained and its structure was definitely established by X-ray crystallographic study of its acetate derivative.     

Drosophila rab GDI mutants disrupt development but have normal rab membrane extraction

Summary: Rab GTPases are essential for vesicular transport. Rab GDP dissociation inhibitor (GDI) binds to GDP‐bound rabs, removes rabs from acceptor membranes and delivers rabs to donor membranes. We isolated lethal GDI mutations in Drosophila and analyzed their developmental phenotypes. To learn how these mutations affect GDI structure, the crystal structure of Drosophila GDI was determined by molecular replacement to a resolution of 3.0 Å. Two hypomorphic, missense mutations are located in domain II of GDI at highly conserved positions, but not in previously identified sequence conserved regions. The mutant GDIs were tested for ability to extract rabs from membranes and showed wild‐type levels of rab membrane extraction. The two missense alleles showed intragenic complementation, indicating that domain II of GDI may have two separable functions. This study indicates that GDI function is essential for development of a complex, multicellular organism and that puparium formation and pole cell formation are especially dependent on GDI function. genesis 31:17–29, 2001. © 2001 Wiley‐Liss, Inc.     

Pectinase in papermaking: solving retention problems in mechanical pulps bleached with hydrogen peroxide

Treatment with the enzyme pectinase has been reported to lower the cationic demand of thermomechanical pulp (TMP) bleached with alkaline peroxide in the laboratory. We have extended this discovery to bleached TMP produced industrially, and shown that commercial enzyme preparations can treat pulp within 15 min at the temperature and pH values prevalent in paper mills. About half of the cationic demand in the bleached pulp can be destroyed by pectinase. Dynamic drainage jar experiments show that the enzyme treatment improves the effectiveness of several cationic polymers to increase retention of fines and filler particles. It does not increase retention in the absence of retention aids or with nonionic polymers, and does not damage the strength properties of the pulp. Pectinase could be easily incorporated into paper machine stock preparation systems to lower the charges of cationic retention aids needed in furnishes containing peroxide-bleached mechanical pulp.     

Emergence and biological complexity

Biological networks possess an organization that expresses their potential information. A function, I(X:Y)N, called mutual information of integration, define, on a quantitative basis, three types of organization. If I(X:Y)N=0, the properties of the global system XY can be reduced to the properties of its component sub-systems X and Y. Hence, XY is not a real system displaying collective properties but the mere collection of X and Y. Its properties are the properties of the sub-systems X and Y. If I(X:Y)N>0, the system is integrated. Although it behaves as a coherent whole, it does not possess many collective properties. Last, if I(X:Y)N<0, the system possesses emergent collective properties and can be considered complex for it possesses many collective properties that cannot be predicted from the independent study of component sub-systems X and Y. In a biological system, the emergence of information usually means the emergence of a novel function. This is probably what is occurring with enzymes. If a protein binds two ligands able to interact, and if the condition above is fulfilled, then the protein behaves as an enzyme able to allow a catalytic reaction between the two reagents.     

Preliminary observations on the spawning conditions of the European amphioxus (Branchiostoma lanceolatum) in captivity

Members of the subphylum Cephalochordata, which include the genus Branchiostoma (i.e. amphioxus), represent the closest living invertebrate relatives of the vertebrates. To date, developmental studies have been carried out on three amphioxus species (the European Branchiostoma lanceolatum, the East Asian B. belcheri, and Floridian-Caribbean B. floridae). In most instances, adult animals have been collected from the field during their ripe season and allowed (or stimulated) to spawn in the laboratory. In any given year, dates of laboratory pawning have been limited by two factors. First, natural populations of these three most studied species of amphioxus are ripe, at most, for only a couple of months each year and, second, even when apparently ripe, animals spawn only at unpredictable intervals of every several days. This limited supply of living material hinders the development of amphioxus as a model system because this limitation makes it more difficult to work out protocols for new laboratory techniques. Therefore we are developing laboratory methods for increasing the number of amphioxus spawning dates per year. The present study found that a Mediterranean population of B. lanceolatum living near the Franco-Spanish border spawned naturally at the end of May and again at the end of June in 2003. Re-feeding experiments in the laboratory demonstrated that the gonads emptied at the end of May refilled with gametes by the end of June. We also found that animals with large gonads (both, obtained from the field and kept and fed at the laboratory during several weeks) could be induced to spawn in the laboratory out of phase with the field population if they were temperature shocked (spawning occurred 36 hours after a sustained increase in water temperature from 19 degrees C to 25 degrees C).     

Biomass-diversity responses and spatial dependencies in disturbed tallgrass prairies

Monotonic, hump-shaped and zero-correlation productivity-diversity relationships have been found to date in many ecosystems. This diversity of responses has puzzled ecologists in their search for general principles on ecosystem functioning. Some state that the scale of observation is crucial in defining this relationship. We have developed a spatial model of tallgrass prairies where biomass and litter dynamics are defined by uncoupled difference equations. In this system, we periodically apply prescribed fire as a disturbance that propagates through neighboring cells. The model shows percolation thresholds at points where small-scale spatial heterogeneity and large-scale, global correlation coexist, resulting in power-law distributions in available areas for non-dominant species. These points maximize the biomass-diversity relationship. Our results suggest that spatial dependencies and the disturbance heterogeneity hypothesis are the cornerstone processes accounting for unimodality in productivity-diversity relationships.     

Genome‐wide association study for jumping performances in French sport horses

A genome‐wide association study was performed to identify single nucleotide polymorphisms (SNPs) associated with jumping performances of warmbloods in France. The 999 horses included in the study for jumping performances were sport horses [mostly Selle Français (68%), Anglo‐Arabians (13%) and horses from the other European studbooks]. Horses were genotyped using the Illumina EquineSNP50 BeadChip. Of the 54 602 SNPs available on this chip, 44 424 were retained after quality testing. Phenotypes were obtained by deregressing official breeding values for jumping competitions to use all available information, that is, the performances of each horse as well as those of its relatives. Two models were used to test the effects of the genotypes on deregressed phenotypes: a single‐marker mixed model and a haplotype‐based mixed model (significant: P < 1E‐05; suggestive: P < 1E‐04). Both models included a polygenic effect to take into account familial structures. For jumping performances, one suggestive quantitative trait locus (QTL) located on chromosome 1 (BIEC2_31196 and BIEC2_31198) was detected with both models. This QTL explains 0.7% of the phenotypic variance. RYR2, a gene encoding a major calcium channel in cardiac muscle in humans and mice, is located 0.55 Mb from this potential QTL.