NFkappaB selectivity of estrogen receptor ligands revealed by comparative crystallographic analyses

Our understanding of how steroid hormones regulate physiological functions has been significantly advanced by structural biology approaches. However, progress has been hampered by misfolding of the ligand binding domains in heterologous expression systems and by conformational flexibility that interferes with crystallization. Here, we show that protein folding problems that are common to steroid hormone receptors are circumvented by mutations that stabilize well-characterized conformations of the receptor. We use this approach to present the structure of an apo steroid receptor that reveals a ligand-accessible channel allowing soaking of preformed crystals. Furthermore, crystallization of different pharmacological classes of compounds allowed us to define the structural basis of NFkappaB-selective signaling through the estrogen receptor, thus revealing a unique conformation of the receptor that allows selective suppression of inflammatory gene expression. The ability to crystallize many receptor-ligand complexes with distinct pharmacophores allows one to define structural features of signaling specificity that would not be apparent in a single structure.     

Analytical Results for Individual and Group Selection of Any Intensity

The idea of evolutionary game theory is to relate the payoff of a game to reproductive success (= fitness). An underlying assumption in most models is that fitness is a linear function of the payoff. For stochastic evolutionary dynamics in finite populations, this leads to analytical results in the limit of weak selection, where the game has a small effect on overall fitness. But this linear function makes the analysis of strong selection difficult. Here, we show that analytical results can be obtained for any intensity of selection, if fitness is defined as an exponential function of payoff. This approach also works for group selection (= multi-level selection). We discuss the difference between our approach and that of inclusive fitness theory.     

Elevated numbers of Fc gamma RIIIA+ (CD16+) effector CD8 T cells with NK cell-like function in chronic hepatitis C virus infection

CTL are crucial in the defense against viral infections. In the course of investigating peripheral blood and intrahepatic CD8 T cells in patients with chronic hepatitis C virus (HCV) infection, we observed a significant population of CD8 T cells expressing the FcgammaRIIIA (CD16) receptor. This observation led us to characterize these cells with respect to their phenotype and function in a cohort of patients with chronic HCV infection as well as in healthy blood donors. On average, 10% of peripheral blood CD8 T cells from HCV-infected patients expressed CD16 compared with only a few percent in healthy donors. CD16(+) CD8 T cells displayed a late-stage effector phenotype with high levels of perforin. These cells exhibited a restricted TCR profile suggesting underlying clonal expansion. Stimulation of CD16 on CD8 T cells evoked a vigorous response similar to that of CD16 stimulation in NK cells. Our data suggest that CD8 T cells, during chronic HCV infection in humans, continue to differentiate beyond defined stages of terminal effector cells, acquiring CD16 and NK cell-like functional properties.     

Impact of IgG Fc‐Oligosaccharides on Recombinant Monoclonal Antibody Structure,Stability, Safety,and Efficacy

Glycosylation of the conserved asparagine residue in the CH2 domain is the most common posttranslational modification of recombinant monoclonal antibodies. Ideally, a consistent oligosaccharide profile should be maintained from early clinical material to commercial material for the development of recombinant monoclonal therapeutics, though variation in the profile is a typical result of process changes. The risk of oligosaccharide variation posed to further development is required to be thoroughly evaluated based on its impact on antibody structure, stability, efficacy and safety. The variation should be controlled within a range so that there is no detrimental impact on safety and efficacy and thus allowing the use of early phase safety and efficacy data to support project advancement to later phase. This review article focuses on the current scientific understanding of the commonly observed oligosaccharides found in recombinant monoclonal antibodies and their impact on structure, stability and biological functions, which are the basis to evaluate safety and efficacy. It also provides a brief discussion on critical quality attribute (CQA) assessment with regard to oligosaccharides based on the mechanism of action (MOA). © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1173–1181, 2017     

Habitat suitability,corridors and dispersal barriers for large carnivores in Poland

Carnivores are often particularly sensitive to landscape fragmentation. Ecological corridors may help to connect local populations, ensuring gene flow and retaining viable meta-populations. We aimed to establish habitat suitability models for two large carnivores in Poland, the grey wolf Canis lupus Linnaeus, 1758 and the Eurasian lynx Lynx lynx Linnaeus, 1758, based on ecological niche factor analysis (ENFA). Secondly, we calculated least cost paths (LCPs) based on cost values obtained from ENFA. Thirdly, we determined structures that might act as barriers, thus diminishing the value of the corridor unless appropriate conservation measures are taken. We compared some of the results with actual dispersal data of four lynx in eastern Poland. Results indicate that both species are highly marginalised. Less habitat that is currently available in Poland is suitable for lynx than for wolves. We determined a total of 76 LCPs. Comparison of these theoretical corridors with actual dispersal routes suggests that the traits of calculated LCPs are mostly within the range of those of real routes. We highlight a variety of features that might act as barriers, such as major roads (including planned highways), urbanized areas, and large un-forested areas. We give suggestions where concerted conservation efforts (eg wildlife passages) might be particularly well-directed.     

Prediction of the Metabolic Activity of a Mixed Bacillus Culture during the Biodegradation of Wastewater from the Potato Industry

The advantages of the analysis of electrical impedance changes for the prediction of the metabolic activity of mixed Bacillus cultures used for high temperature industrial wastewater utilization are demonstrated. The primary aim of this study was to investigate the possibilities of a fast assessment of the biodegradative capabilities of microorganisms, their requirements regarding the medium composition as well as the inhibiting effect of high‐strength (i.e., highly concentrated) wastewaters on microbial growth. Four mixed Bacillus cultures were cultivated at 45 and 55 °C on two kinds of wastewater from the potato starch industry. The course of changes in the electrical impedance during the cultivation of the bacteria in the examined wastewaters was described by the mathematical Gompertz model. Three kinetics parameters (maximum rate of impedance changes, I_max; the time necessary to reach, I_max, T_I; and the duration of the lag phase, λ) were proposed for the statistical analysis of the bacterial metabolic activity. The temperature of the biodegradation process and the type and strength of the wastewater significantly influenced the microbial metabolic activity of the mixed bacterial cultures used. Monitoring of the impedance changes, caused by microbial metabolism, and its proposed mathematical specification allowed for predicting the dynamics of the microbiological degradation of wastewater and estimating the inhibiting effects of these media on the microorganisms.     

Thermodynamic linked-function analysis of Mg(2+)-activated yeast pyruvate kinase.

Yeast pyruvate kinase (YPK) is regulated by intermediates of the glycolytic pathway [e.g., phosphoenolpyruvate (PEP), fructose 1,6-bisphosphate (FBP), and citrate] and by the ATP charge of the cell. Recent kinetic and thermodynamic data with Mn(2+)-activated YPK show that Mn(2+) mediates the allosteric communication between the substrate, PEP, and the allosteric effector, FBP [Mesecar, A., and Nowak, T. (1997) Biochemistry 36, 6792, 6803]. These results indicate that divalent cations modulate multiligand interactions, and hence cooperativity with YPK. The nature of multiligand interactions on YPK was investigated in the presence of the physiological divalent activator Mg(2+). The binding interactions of PEP, Mg(2+), and FBP were monitored by fluorescence spectroscopy. The binding data were subject to thermodynamic linked-function analysis to determine the magnitudes of the multiligand interactions governing the allosteric activation of YPK. The two ligand coupling free energies between PEP and Mg(2+), PEP and FBP, and FBP and Mg(2+) are 0.88, -0.38, and -0.75 kcal/mol, respectively. The two-ligand coupling free energies between PEP and Mn(2+) and FBP and Mn(2+) are more negative than those with Mg(2+) as the cation. This indicates that the interactions between the divalent cation and PEP with YPK are different for Mg(2+) and Mn(2+) and that the interaction is not simply electrostatic in nature, as originally hypothesized. The magnitude of the heterotropic interaction between the metal and FBP is similar with Mg(2+) and Mn(2+). The simultaneous binding of Mg(2+), PEP, and FBP to YPK is favored by 3.21 kcal/mol compared to independent binding. This complex is destabilized by 3.30 kcal/mol relative to the analogous YPK-Mn(2+)-PEP-FDP complex. Interpretation of K(d) values when cooperative binding occurs must be done with care as these are not simple thermodynamic constants. These data demonstrate that the divalent metal, which activates phosphoryl transfer in YPK, plays a key role in modulating the various multiligand interactions that define the overall allosteric properties of the enzyme.     

Kinetic linked-function analysis of the multiligand interactions on Mg(2+)-activated yeast pyruvate kinase.

The multiligand interactions governing the allosteric response of Mg(2+)-activated yeast pyruvate kinase (YPK) during steady-state turnover were quantitated by kinetic linked-function analysis. The substrate, PEP, the enzyme-bound divalent metal, Mg(2+), and the allosteric effector, FBP, positively influence each other's interaction with the enzyme in the presence of saturating concentrations of the second substrate, MgADP. The presence of Mg(2+) enhances the interaction of PEP and of FBP with YPK by -2.0 and -1.0 kcal/mol, respectively. The simultaneous interaction of PEP, Mg(2+), and FBP with YPK is favored by -4.1 kcal/mol over the sum of their independent binding free energies. The coupling free energies measured for Mg(2+)-activated YPK are weaker than the corresponding coupling free energies measured for Mn(2+)-activated YPK [Mesecar, A., and Nowak, T. (1997) Biochemistry 36, 6792, 6803], but are consistent with results of thermodynamic measurements with the Mg(2+)-YPK complex [Bollenbach, T. J., and Nowak, T. (2001) Biochemistry 36, 13088-13096]. A comparison of ligand binding data measured by kinetic and thermodynamic linked-function analyses reveals that the MgADP complex modulates both the binding of the other three ligands and the two- and three-ligand coupling interactions between the other three ligands. Enzyme-bound Mg(2+) does not influence the homotropic cooperativity in PEP binding to YPK. It is the MgADP complex that induces homotropic cooperativity in PEP binding. It is the enzyme-bound Mn(2+) that induces homotropic binding of PEP with Mn(2+)-activated YPK. These results lend support to the hypothesis that divalent metals modulate the interactions of ligands on YPK and that divalent metals play a role in regulation of the glycolytic pathway.