Georg Schmid

Flux analysis of underdetermined metabolic networks: the quest for the missing constraints

Traditionally, the intracellular fluxes of complex metabolic networks were quantified by isotopic-tracer experiments, but, owing to practical limitations, ‘metabolic-flux balancing is emerging as an alternative. This has become an important tool for the quantitative analysis of the physiology of microorganisms and mammalian cells. It has been successfully applied to finding potential sites for metabolic engineering, determining metabolic capabilities and designing optimal feeding strategies. However, it has the fundamental problem that metabolic networks, and cyclic metabolic pathways in particular, are underdetermined. The search for constraints that can be used to determine fluxes correctly for a range of different conditions is an exciting challenge.

Metabolic flux analysis of hybridoma cells in different culture media using mass balances

The estimation of the intracellular fluxes of mammalian cells using only the mass balances of the relevant metabolites is not possible because the set of linear equations defined by these mass balances is underdetermined. Either additional experimental flux data or additional theoretical constraints are required to find one unique flux distribution out of the solution space that is bound by the mass balances. Here, a method is developed using the latter approach. The uptake and production rates of amino acids, glucose, lactate, O2, CO2, NH4, MAB, and the intracellular amino acid pools have been determined for two different steady‐states. The cellular composition {total protein and protein composition, total lipids and fatty acid distribution, total carbohydrates, DNA and RNA} has been measured to calculate the requirements for biosynthesis. It is shown to be essential to determine the uptake/production rates of ammonia and either carbon dioxide or oxygen. In mammalian cells these are cometabolites of cyclic metabolic pathways. The flux distribution that is found using the Euclidean minimum norm as the additional theoretical constraint and taking either the CO2 or the NAD(P)H mass balance into account is shown to be in agreement with the measured O2 and CO2 metabolic rates.

X-ray structure of junctional adhesion molecule: structural basis for homophilic adhesion via a novel dimerization motif

Junctional adhesion molecules (JAMs) are a family of immunoglobulin‐like single‐span transmembrane molecules that are expressed in endothelial cells, epithelial cells, leukocytes and myocardia. JAM has been suggested to contribute to the adhesive function of tight junctions and to regulate leukocyte trans migration. We describe the crystal structure of the recombinant extracellular part of mouse JAM (rsJAM) at 2.5 Å resolution. rsJAM consists of two immunoglobulin‐like domains that are connected by a conformationally restrained short linker. Two rsJAM molecules form a U‐shaped dimer with highly complementary interactions between the N‐terminal domains. Two salt bridges are formed in a complementary manner by a novel dimerization motif, R(V,I,L)E, which is essential for the formation of rsJAM dimers in solution and common to the known members of the JAM family. Based on the crystal packing and studies with mutant rsJAM, we propose a model for homophilic adhesion of JAM. In this model, U‐shaped JAM dimers are oriented in cis on the cell surface and form a two‐dimensional network by trans‐interactions of their N‐terminal domains with JAM dimers from an opposite cell surface.

Modulating cholesteryl ester transfer protein activity maintains efficient pre-β-HDL formation and increases reverse cholesterol transport

The mechanism by which cholesteryl ester transfer protein (CETP) activity affects HDL metabolism was investigated using agents that selectively target CETP (dalcetrapib, torcetrapib, anacetrapib). In contrast with torcetrapib and anacetrapib, dalcetrapib requires cysteine 13 to decrease CETP activity, measured as transfer of cholesteryl ester (CE) from HDL to LDL, and does not affect transfer of CE from HDL3 to HDL2. Only dalcetrapib induced a conformational change in CETP, when added to human plasma in vitro, also observed in vivo and correlated with CETP activity. CETP-induced pre-β-HDL formation in vitro in human plasma was unchanged by dalcetrapib ≤3 µM and increased at 10 µM. A dose-dependent inhibition of pre-β-HDL formation by torcetrapib and anacetrapib (0.1 to 10 µM) suggested that dalcetrapib modulates CETP activity. In hamsters injected with [3H]cholesterol-labeled autologous macrophages, and given dalcetrapib (100 mg twice daily), torcetrapib [30 mg once daily (QD)], or anacetrapib (30 mg QD), only dalcetrapib significantly increased fecal elimination of both [3H]neutral sterols and [3H]bile acids, whereas all compounds increased plasma HDL-[3H]cholesterol. These data suggest that modulation of CETP activity by dalcetrapib does not inhibit CETP-induced pre-β-HDL formation, which may be required to increase reverse cholesterol transport.

Homophilic Interaction of Junctional Adhesion Molecule

Junctional adhesion molecule (JAM) is an integral membrane protein that belongs to the immunoglobulin superfamily, localizes at tight junctions, and regulates both paracellular permeability and leukocyte transmigration. To investigate molecular determinants of JAM function, the extracellular domain of murine JAM was produced as a recombinant soluble protein (rsJAM) in insect cells. rsJAM consisted in large part of noncovalent homodimers, as assessed by analytical ultracentrifugation. JAM dimers were also detected at the surface of Chinese hamster ovary cells transfected with murine JAM, as evaluated by cross-linking and immunoprecipitation. Furthermore, fluid-phase rsJAM bound dose-dependently solid-phase rsJAM, and such homophilic binding was inhibited by anti-JAM Fab BV11, but not by Fab BV12. Interestingly, Fab BV11 exclusively bound rsJAM dimers (but not monomers) in solution, whereas Fab BV12 bound both dimers and monomers. Finally, we mapped the BV11 and BV12 epitopes to a largely overlapping sequence in proximity of the extracellular amino terminus of JAM. We hypothesize that rsJAM dimerization induces a BV11-positive conformation which in turn is critical for rsJAM homophilic interactions. Dimerization and homophilic binding may contribute to both adhesive function and junctional organization of JAM.

Structure of the Acid-sensing ion channel 1 in complex with the gating modifier Psalmotoxin 1.

Venom-derived peptide toxins can modify the gating characteristics of excitatory channels in neurons. How they bind and interfere with the flow of ions without directly blocking the ion permeation pathway remains elusive. Here we report the crystal structure of the trimeric chicken Acid-sensing ion channel 1 in complex with the highly selective gating modifier Psalmotoxin 1 at 3.0u2009Å resolution. The structure reveals the molecular interactions of three toxin molecules binding at the proton-sensitive acidic pockets of Acid-sensing ion channel 1 and electron density consistent with a cation trapped in the central vestibule above the ion pathway. A hydrophobic patch and a basic cluster are the key structural elements of Psalmotoxin 1 binding, locking two separate regulatory regions in their relative, desensitized-like arrangement. Our results provide a general concept for gating modifier toxin binding suggesting that both surface motifs are required to modify the gating characteristics of an ion channel.

On-line monitoring of infected Sf-9 insect cell cultures by scanning permittivity measurements and comparison with off-line biovolume measurements

Two infected Sf-9 cell cultures were monitored on-line by multi-frequency permittivity measurements using the Fogale BIOMASS SYSTEM® and by applying different off-line methods (CASY®1, Vi-CELL™, packed cell volume) to measure the biovolume and the mean diameter of the cell population. During the growth phase and the early infection phase the measured permittivity at the working frequency correlated well with the different off-line methods for the biovolume. We found a value of 0.67xa0pFxa0cm−1 permittivity per unit of total biovolume (CASY) (μLxa0mL−1). After the maximum value in the permittivity was reached, i.e. when the viability of the cultures decreased significantly, we observed different time courses for the biovolume depending on the applied method. The differences were compared and could be explained by the underlying measurement principles. Furthermore, the characteristic frequency (fC) was calculated from the on-line scanning permittivity measurements. The fC may provide an indication of changes in cell diameter and membrane properties especially after infection and could also be an indicator for the onset of the virus production phase. The changes in fC were qualitatively explained by the underlying equation that is correlating fC and the properties of the cell population (cell diameter, intracellular conductivity and capacitance per membrane area).

Insect cell cultivation: growth and kinetics

The complete strategy for maximizing the yield of recombinant proteins from insect cell culture must include an optimization of the culture conditions during the growth phase as well as during the subsequent infection phase. The growth of host cells like Spodoptera frugiperda (Sf9 and Sf21) and Trichoplusia ni (BTI-Tn-5Bl-4) to cell densities of ca. 10 × 10E6 cells mlO1 in batch cultures has so far been achieved. Already today some groups have reported even higher viable cell concentrations (>10 × 10E6 cells mlO1) using nutrient feeding strategies. There will be further improvements in this area. However, probably more important will be the characterization of the optimal physiological state that the cells? at high densities? have to be in at the time of infection so as to maintain the same (or reach even higher) specific productivities than in low-density infections.

Monitoring hybridoma metabolism in continuous suspension culture at the intracellular level. I : Steady-state responses to different glutamine feed concentrations

A model mouse hybridoma cell line was grown in continuous culture experiments in a serum-free low-protein lipid-free medium. The steady-state responses of cell numbers, extra- and intracellular metabolite concentrations, substrate and (by) product consumption/production rates, and yield coefficients were investigated as a function of step changes in the glutamine concentration of the feed medium. In addition to the commonly performed analysis of metabolites in culture supernatants, we prepared perchloric acid extracts of cells and determined the amount and the composition of intracellular amino acids and organic acids. Significant differences were found with respect to intracellular metabolite pools for cells growing at nearly identical specific growth rates. To our knowledge this is the first time that data on the intracellular concentrations (pools) of amino acids and Krebs cycle intermediates are reported in the literature that were obtained under carefully defined culture conditions such as those attained in continuous culture experiments.

Activity of glutamate dehydrogenase is increased in ammonia-stressed hybridoma cells.

The effect of added ammonia on the intracellular fluxes in hybridoma cells was investigated by metabolic-flux balancing techniques. It was found that, in ammonia-stressed hybridoma cells, the glutamate-dehydrogenase flux is in the reverse direction compared to control cells. This demonstrates that hybridoma cells are able to prevent the accumulation of ammonia by converting ammonia and alpha-ketoglutarate into glutamate. The additional glutamate that is produced by this flux, as compared to the control culture, is converted by the reactions catalyzed by alanine aminotransferase (45% of the extra glutamate) and aspartate aminotransferase (37%), and a small amount is used for the biosynthesis of proline (6%). The remaining 12% of the extra glutamate is secreted into the culture medium. The data suggest that glutamate dehydrogenase is a potential target for metabolic engineering to prevent ammonia accumulation in high-cell-density culture.