Structure and Disorder in an Unfolded State under Nondenaturing Conditions from Ensemble Models Consistent with a Large Number of Experimental Restraints

Obtaining detailed structural models of disordered states of proteins under nondenaturing conditions is important for a better understanding of both functional intrinsically disordered proteins and unfolded states of folded proteins. Extensive experimental characterization of the drk N-terminal SH3 domain unfolded state has shown that, although it appears to be highly disordered, it possesses significant nonrandom secondary and tertiary structure. In our previous attempts to generate structural models of the unfolded state using the program ENSEMBLE, we were limited by insufficient experimental restraints and conformational sampling. In this study, we have vastly expanded our experimental restraint set to include ¹H-¹⁵N residual dipolar couplings, small-angle X-ray scattering measurements, nitroxide paramagnetic relaxation enhancements, O₂-induced ¹³C paramagnetic shifts, hydrogen-exchange protection factors, and ¹⁵N R₂ data, in addition to the previously used nuclear Overhauser effects, amino terminal Cu²⁺-Ni²⁺ binding paramagnetic relaxation enhancements, J-couplings, chemical shifts, hydrodynamic radius, and solvent accessibility restraints. We have also implemented a new ensemble calculation methodology that uses iterative conformational sampling and seeks to calculate the simplest possible ensemble models. As a result, we can now generate ensembles that are consistent with much larger experimental data sets than was previously possible. Although highly heterogeneous and having broad molecular size distributions, the calculated drk N-terminal SH3 domain unfolded-state ensembles have very different properties than expected for random or statistical coils and possess significant nonnative α-helical structure and both native-like and nonnative tertiary structure.     

Synthesis of tetravalent LacNAc-glycoclusters as high-affinity cross-linker against Erythrina cristagalli agglutinin

Four kinds of tetravalent double-headed glycoclusters [(LacNAc)₄-DHGs] were designed with linkers of varying lengths consisting of alkanedioic carboxyamido groups (C₆, C₁₂, C₁₈ and C₂₄) between two bi-antennary LacNAc-glycosides. These glycoclusters served as high-affinity cross-linking ligands for the LacNAc-binding lectin Erythrina cristagalli agglutinin (ECA). The binding activity and cross-linking between each ligand and ECA were characterized by a hemagglutination inhibition (HI) assay, isothermal titration calorimetry (ITC), a quantitative precipitation assay and dynamic light scattering (DLS). For the precipitation assay and DLS measurement, the synthesized (LacNAc)₄-DHGs were found to be capable of binding and precipitating the ECA as multivalent ligands. ITC analysis indicated the binding of (LacNAc)₄-DHGs was driven by a favorable enthalpy change. Furthermore, the entropy penalty from binding (LacNAc)₄-DHGs clearly decreased in a spacer length-dependent manner. The binding affinities of flexible (LacNAc)₄-DHGs (C₁₈ and C₂₄) with long spacers were found to be more favorable than those of the clusters having short spacers (C₆ and C₁₂). These results were supported by molecular dynamics simulations with explicit water molecules for the tetravalent glycoclusters with ECA. We concluded that the subtle modification in the epitope-presenting scaffolds exerts the significant effect in the recognition efficiency involved in the LacNAc moieties by ECA.     

Temperature dependence of superoxide dismutase activity in plankton

The effect of temperature (from 1 to 37 °C) on in vitro effective superoxide dismutase (SOD) activity of several organisms was investigated and compared. Antarctic plankton, cultures of the alga Nannochloropsis sp., and the cyanobacterium Synechococcus strain WH 7803, and pure bovine erythrocyte SOD was studied. It was found that in all cases SOD activity increased with decreasing temperature within the temperature range assayed, in the Polar as well as the temperate plankton cells. This behavior of SOD is counterintuitive in terms of our experience when looking at enzyme activity or any other chemical reaction. We suggest a theoretical explanation for this apparently odd behavior. The advantage of such behavior is that the same amount of antioxidant will act better under low temperatures when reactive oxygen species (ROS) increase. Moreover, this protective process would act in vivo at a faster pace than the ex novo enzyme synthesis.     

Pressure effects on lipid-protein interactions in (Na+ + K+)-ATPase

The (Na⁺ + K⁺)-stimulated ATPase activity decreases with increasing pressure and a plot of the logarithm of the activity versus pressure shows a change in slope at a defined breakpoint pressure (P_b). The value of P_b increases linearly with increasing temperature. A $\text{d}\text{T}\text{d}\text{P}$ value of 27.7 ± 0.4 (S.D.) K/1000 atm is obtained. This is in very good agreement with the pressure shift for the melting transitions in phospholipids and aliphatic chains. This strongly indicates that an aliphatic chain melting process is involved in the breakpoint in the Arrhenius plot and pressure dependence of (Na⁺ + K⁺)-ATPase. The p-nitrophenyl phosphatase activity of this enzyme also decreases with pressure. In this case the plot of the logarithm of the activity versus pressure is linear without a break-point. The temperature dependence for (Na⁺ + K⁺)-ATPase was also studied in the presence of fluidizing drugs: desipramine and benzylalcohol. The presence of these drugs had no effect on the inflection point in the Arrhenius plot.     

PERSPECTIVE: THE THEORIES OF FISHER AND WRIGHT IN THE CONTEXT OF METAPOPULATIONS: WHEN NATURE DOES MANY SMALL EXPERIMENTS

We critically review the two major theories of adaptive evolution developed early in this century, Wright's shifting balance theory and Fisher's large population size theory, in light of novel findings from field observations, laboratory experiments, and theoretical research conducted over the past 15 years. Ecological studies of metapopulations have established that the processes of local extinction and colonization of demes are relatively common in natural populations of many species and theoretical population genetic models have shown that these ecological processes have genetic consequences within and among local demes. Within demes, random genetic drift converts nonadditive genetic variance into additive genetic variance, increasing, rather than limiting, the potential for adaptation to local environments. For this reason, the genetic differences that arise by drift among demes, can be augmented by local selection. The resulting adaptive differences in gene combinations potentially contribute to the genetic origin of new species. These and other recent findings were not discussed by either Wright or Fisher. For example, although Wright emphasized epistatic genetic variance, he did not discuss the conversion process. Similarly, Fisher did not discuss how the average additive effect of a gene varies among demes across a metapopulation whenever there is epistasis. We discuss the implications of such recent findings for the Wright-Fisher controversy and identify some critical open questions that require additional empirical and theoretical study.     

The relationship between iron status and lead absorption in rats

The absorption of lead from loops of small intestinein situ was investigated in rats in which iron absorption was increased by stimuli varying in type, intensity, or duration. Lead absorption was increased by a short period of severe iron restriction before any change in hematological indices became apparent. A period of hypoxia, which markedly increased iron absorption, did not influence absorption of lead. An extended period of moderate iron restriction resulted in a marked reduction in liver iron stores and increased iron absorption throughout the 17-wk experiment. Under these conditions lead absorption was initially also increased, but after 12 wk, when iron intake had become adequate to meet essential requirements, lead absorption was similar to that in iron-supplemented rats. These results are discussed in the light of evidence for a receptor-mediated absorption process for iron.     

Phospholipid metabolism under muscarinic cholinergic stimulation exhibits brain asymmetry

In order to characterize some of the lateralized biochemical events promoted in brain upon massive neurotransmitter release, the labeling of lipids under specific stimulation of the muscarinic acetylcholine receptor (mAChR) has been studied in synaptosomes obtained from right and left cerebral cortex (RCC and LCC respectively). Synaptosomes were incubated with [³²P]phosphate in the absence and in the presence of the cholinergic agonist carbamoylcholine and the muscarinic antagonist atropine. Binding of the agonist to the mAChR promoted an enhanced labeling of polyphosphoinositides, such effect being considerably more pronounced in the LCC than in the RCC. The differences observed could be due to a higher mAChR-elicited activity of phospholipase C in the RCC than in the LCC. The results show that mAChR stimulation activates the turnover of inosítol lipids to a different extent in the two hemispheres, indicating either an uneven distribution of the receptor in brain and/or dissimilarities in the degree of coupling of the mAChR with its corresponding transmembrane signaling system in each hemicortex.     

Rewiring yeast metabolism to synthesize products beyond ethanol

Saccharomyces cerevisiae, Baker's yeast, is the industrial workhorse for producing ethanol and the subject of substantial metabolic engineering research in both industry and academia. S. cerevisiae has been used to demonstrate production of a wide range of chemical products from glucose. However, in many cases, the demonstrations report titers and yields that fall below thresholds for industrial feasibility. Ethanol synthesis is a central part of S. cerevisiae metabolism, and redirecting flux to other products remains a barrier to industrialize strains for producing other molecules. Removing ethanol producing pathways leads to poor fitness, such as impaired growth on glucose. Here, we review metabolic engineering efforts aimed at restoring growth in non-ethanol producing strains with emphasis on relieving glucose repression associated with the Crabtree effect and rewiring metabolism to provide access to critical cellular building blocks. Substantial progress has been made in the past decade, but many opportunities for improvement remain.