Crystal Contact Engineering Enables Efficient Capture and Purification of an Oxidoreductase by Technical Crystallization

Technical crystallization is an attractive method to purify recombinant proteins. However, it is rarely applied due to the limited crystallizability of many proteins. To overcome this limitation, single amino acid exchanges are rationally introduced to enhance intermolecular interactions at the crystal contacts of the industrially relevant biocatalyst Lactobacillus brevis alcohol dehydrogenase (LbADH). The wildtype (WT) and the best crystallizing and enzymatically active LbADH mutants K32A, D54F, Q126H, and T102E are produced with Escherichia coli and subsequently crystallized from cell lysate in stirred mL-crystallizers. Notwithstanding the high host cell protein (HCP) concentrations in the lysate, all mutants crystallize significantly faster than the WT. Combinations of mutations result in double mutants with faster crystallization kinetics than the respective single mutants, demonstrating a synergetic effect. The almost entire depletion of the soluble LbADH fraction at crystallization equilibrium is observed, proving high yields. The HCP concentration is reduced to below 0.5% after crystal dissolution and recrystallization, and thus a 100-fold HCP reduction is achieved after two successive crystallization steps. The combination of fast kinetics, high yields, and high target protein purity highlights the potential of crystal contact engineering to transform technical crystallization into an efficient protein capture and purification step in biotechnological downstream processes.

Improved packing of preparative biochromatography columns by mechanical vibration

The bioprocessing industry relies on packed-bed column chromatography as its primary separation process to attain the required high product purities and fulfill the strict requirements from regulatory bodies. Conventional column packing methods rely on flow packing and/or mechanical compression. In this work, the application of ultrasound and mechanical vibration during packing was studied with respect to packing density and homogeneity. We investigated two widely used biochromatography media, incompressible ceramic hydroxyapatite, and compressible polymethacrylate-based particles, packed in a laboratory-scale column with an inner diameter of 50 mm. It was shown that ultrasonic irradiation led to reduced particle segregation during sedimentation of a homogenized slurry of polymethacrylate particles. However, the application of ultrasound did not lead to an improved microstructure of already packed columns due to the low volumetric energy input (~152 W/L) caused by high acoustic reflection losses. In contrast, the application of pneumatic mechanical vibration led to considerable improvements. Flow-decoupled axial linear vibration was most suitable at a volumetric force output of ~1,190 N/L. In the case of the ceramic hydroxyapatite particles, a 13% further decrease of the packing height was achieved and the reduced height equivalent to a theoretical plate (rHETP) was decreased by 44%. For the polymethacrylate particles, a 18% further packing consolidation was achieved and the rHETP was reduced by 25%. Hence, it was shown that applying mechanical vibration resulted in more efficiently packed columns. The application of vibration furthermore is potentially suitable for in situ elimination of flow channels near the column wall.

Neutron and X-ray crystal structures of Lactobacillus brevis alcohol dehydrogenase reveal new insights into hydrogen-bonding pathways

Lactobacillus brevis alcohol dehydrogenase (LbADH) is a well studied homotetrameric enzyme which catalyzes the enantioselective reduction of prochiral ketones to the corresponding secondary alcohols. LbADH is stable and enzymatically active at elevated temperatures and accepts a broad range of substrates, making it a valuable tool in industrial biocatalysis. Here, the expression, purification and crystallization of LbADH to generate large, single crystals with a volume of up to 1 mm3 suitable for neutron diffraction studies are described. Neutron diffraction data were collected from an H/D-exchanged LbADH crystal using the BIODIFF instrument at the Heinz Maier-Leibnitz Zentrum (MLZ), Garching, Germany to a resolution dmin of 2.15 Å in 16 days. This allowed the first neutron crystal structure of LbADH to be determined. The neutron structure revealed new details of the hydrogen-bonding network originating from the ion-binding site of LbADH and provided new insights into the reasons why divalent magnesium (Mg2+) or manganese (Mn2+) ions are necessary for its activity. X-ray diffraction data were obtained from the same crystal at the European Synchrotron Radiation Facility (ESRF), Grenoble, France to a resolution dmin of 1.48 Å. The high-resolution X-ray structure suggested partial occupancy of Mn2+ and Mg2+ at the ion-binding site. This is supported by the different binding affinity of Mn2+ and Mg2+ to the tetrameric structure calculated via free-energy molecular-dynamics simulations.

Simulation of the dynamic packing behavior of preparative chromatography columns via discrete particle modeling

Preparative packed-bed chromatography using polymer-based, compressible, porous resins is a powerful method for purification of macromolecular bioproducts. During operation, a complex, hysteretic, thus, history-dependent packed bed behavior is often observed but theoretical understanding of the causes is limited. Therefore, a rigorous modeling approach of the chromatography column on the particle scale has been made which takes into account interparticle micromechanics and fluid-particle interactions for the first time. A three-dimensional deterministic model was created by applying Computational Fluid Dynamics (CFD) coupled with the Discrete Element Method (DEM). The column packing behavior during either flow or mechanical compression was investigated in-silico and in laboratory experiments. A pronounced axial compression-relaxation profile was identified that differed for both compression strategies. Void spaces were clearly visible in the packed bed after compression. It was assumed that the observed bed inhomogeneity was because of a force-chain network at the particle scale. The simulation satisfactorily reproduced the measured behavior regarding packing compression as well as pressure-flow dependency. Furthermore, the particle Young's modulus and particle-wall friction as well as interparticle friction were identified as crucial parameters affecting packing dynamics. It was concluded that compaction of the chromatographic bed is rather because of particle rearrangement than particle deformation. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 32:363-371, 2016.

Large-scale crystallization of proteins for purification and formulation

Since about 170 years, salts were used to create supersaturated solutions and crystallize proteins. The dehydrating effect of salts as well as their kosmotropic or chaotropic character was revealed. Even the suitability of organic solvents for crystallization was already recognized. Interestingly, what was performed during the early times is still practiced today. A lot of effort was put into understanding the underlying physico-chemical interaction mechanisms leading to protein crystallization. However, it was understood that already the solvation of proteins is a highly complex process not to mention the intricate interrelation of electrostatic and hydrophobic interactions taking place. Although many basic questions are still unanswered, preparative protein crystallization was attempted as illustrated in the presented case studies. Due to the highly variable nature of crystallization, individual design of the crystallization process is needed in every single case. It was shown that preparative crystallization from impure protein solutions as a capture step is possible after applying adequate pre-treatment procedures like precipitation or extraction. Protein crystallization can replace one or more chromatography steps. It was further shown that crystallization can serve as an attractive alternative means for formulation of therapeutic proteins. Crystalline proteins can offer enhanced purity and enable highly concentrated doses of the active ingredient. Easy scalability of the proposed protein crystallization processes was shown using the maximum local energy dissipation as a suitable scale-up criterion. Molecular modeling and target-oriented protein engineering may allow protein crystallization to become part of a platform purification process in the near future.

Modeling of transient flow through a viscoelastic preparative chromatography packing

The common method for purification of macromolecular bioproducts is preparative packed-bed chromatography using polymer-based, compressible, viscoelastic resins. Because of a downstream processing bottleneck, the chromatography equipment is often operated at its hydrodynamic limit. In this case, the resins may exhibit a complex behavior which results in compression-relaxation hystereses. Up to now, no modeling approach of transient flow through a chromatography packing has been made considering the viscoelasticity of the resins. The aim of the present work was to develop a novel model and compare model calculations with experimental data of two agarose-based resins. Fluid flow and bed permeability were modeled by Darcy's law and the Kozeny-Carman equation, respectively. Fluid flow was coupled to solid matrix stress via an axial force balance and a continuity equation of a deformable packing. Viscoelasticity was considered according to a Kelvin-Voigt material. The coupled equations were solved with a finite difference scheme using a deformable mesh. The model boundary conditions were preset transient pressure drop functions which resemble simulated load/elution/equilibration cycles. Calculations using a homogeneous model (assuming constant variables along the column height) gave a fair agreement with experimental data with regard to predicted flow rate, bed height, and compression-relaxation hysteresis for symmetric as well as asymmetric pressure drop functions. Calculations using an inhomogeneous model gave profiles of the bed porosity as a function of the bed height. In addition, the influence of medium wall support and intraparticle porosity was illustrated. The inhomogeneous model provides insights that so far are not easily experimentally accessible.

Protein crystallization in stirred systems--scale-up via the maximum local energy dissipation

Macromolecular bioproducts like therapeutic proteins have usually been crystallized with µL-scale vapor diffusion experiments for structure determination by X-ray diffraction. Little systematic know-how exists for technical-scale protein crystallization in stirred vessels. In this study, the Fab-fragment of the therapeutic antibody Canakinumab was successfully crystallized in a stirred-tank reactor on a 6 mL-scale. A four times faster onset of crystallization of the Fab-fragment was observed compared to the non-agitated 10 µL-scale. Further studies on a liter-scale with lysozyme confirmed this effect. A 10 times faster onset of crystallization was observed in this case at an optimum stirrer speed. Commonly suggested scale-up criteria (i.e., minimum stirrer speed to keep the protein crystals in suspension or constant impeller tip speed) were shown not to be successful. Therefore, the criterion of constant maximum local energy dissipation was applied for scale-up of the stirred crystallization process for the first time. The maximum local energy dissipation was estimated by measuring the drop size distribution of an oil/surfactant/water emulsion in stirred-tank reactors on a 6 mL-, 100 mL-, and 1 L-scale. A comparable crystallization behavior was achieved in all stirred-tank reactors when the maximum local energy dissipation was kept constant for scale-up. A maximum local energy dissipation of 2.2 W kg(-1) was identified to be the optimum for lysozyme crystallization at all scales under study.

Ethnicity as a predictor of graft longevity and recipient mortality in heart transplantation

BACKGROUND

There is a dearth of data about the effect of donor and recipient ethnicity on survival and rejection rate after clinical heart transplantation, although the subject had been partly studied before. We compared the mortality and rejection rate among different ethnic groups at our institution.

METHODS

In retrospect, 525 consecutive donors provided cardiac allografts to adult and pediatric patients undergoing orthotropic heart transplantation at a single, urban US medical center between 2000 and 2005. Donors and recipients were categorized according to ethnicity: African American, Asian, Caucasian, Hispanic, and Others (Indian, Mediterranean/Arabic, Afghans). Donor and recipient ethnicity-as an independent factor and the interaction between them-were examined as a risk factor for mortality and rejection after heart transplantation. Mean follow-up period was 3.2+/-1.9 years (range, 0.1 to 6.6). All recipients received triple immunosuppression consisting of a calcineurin inhibitor, an antiproliferative agent, and steroids. No patients received induction immunotherapy. The end points of the study were early and late mortality, rejection rate, and rejection-free survival time.

RESULTS

The overall mortality was 17.3% (91 patients). Recipient mortality rate according to donor race was: African American, 23.1%; Asian, 11.1%; Caucasian, 18.7%; and Hispanic, 14.6%. No statistical significance was found, although the mortality differences presented. Recipient mortality with regard to recipients ethnicity was: African American, 22.2%; Asian, 6.3%; Caucasian, 18%; Hispanic, 18.9%; and others 40% (P=.048). Donor-recipient race match was not found as a risk factor influencing mortality as the matched group mortality was 17.5% comparing with the mismatched group mortality of 17.8% (P=.874). The overall rejection rate was 3.8% (20 rejection events). Rejection rate according donor race was: African American, 7.7%; Asian, 10.7%; Caucasian, 4%; and Hispanic, 1.3% (P=.027). Rejection rate with respect to recipients ethnicity was: African American, 0; Asian, 3.2%; Caucasian, 4.4%; Hispanic, 2.7%; and others, 20% with no statistical significance (P=.236). Donor recipient race match was not found as a risk factor influencing rejection rate (P=.58).

CONCLUSIONS

Recipients' ethnicity was found as a significant risk factor for mortality. Rejection rate were found higher among the African American donors and significantly lower in the Hispanic donors. Significantly lower mortality rate was found among Asian recipients. Donor-recipient race match did not influence the mortality or rejection rate.

Advanced protein crystallization using water-soluble ionic liquids as crystallization additives

The application of five water-soluble, halogen-free, alkylammonium-based ionic liquids (ILs) as additives for advanced crystallization of lysozyme was investigated. Their biocompatibility was determined by long-term measurement of the overall mean relative enzyme activities. These were maximally reduced by about 10-15% when up to 200 g IL l(-1) was added. Sitting-drop vapor diffusion crystallization experiments revealed that the addition of some of the ILs led to less crystal polymorphism and precipitation was avoided reliably even at larger NaCl concentrations. The addition of ILs tended to result in larger crystals. The kinetics of lysozyme crystallization were significantly enhanced using ILs as crystallization additives, e.g. by a factor of 5.5 when 100 g ethanolammonium formate l(-1 )was added. ILs with "soft" anions, such as formate or glycolate, were superior to ILs with "hard" anions, like nitrate.

Enabling technologies: fermentation and downstream processing

Efficient parallel tools for bioprocess design, consequent application of the concepts for metabolic process analysis as well as innovative downstream processing techniques are enabling technologies for new industrial bioprocesses from an engineering point of view. Basic principles, state-of-the-art techniques and cutting-edge technologies are briefly reviewed. Emphasis is on parallel bioreactors for bioprocess design, biochemical systems characterization and metabolic control analysis, as well as on preparative chromatography, affinity filtration and protein crystallization on a process scale.

Development of a Transient Segregated Mathematical Model of the Semicontinuous Microbial Production Process of Dihydroxyacetone

For the mathematical description of the semicontinuous two-stage repeated-fed-batch fermentation of dihydroxyacetone (DHA), a novel segregated model incorporating transient growth rates was developed. The fermentation process was carried out in two stages. A viable, not irreversibly product-inhibited culture was maintained in the first reactor stage until a predetermined DHA threshold value was reached. In the second reactor stage, high final product concentrations of up to 220 g L(-1) were reached while the culture was irreversibly product-inhibited. The experimentally observed changes of the physiological state of the culture due to product inhibition were taken into account by introducing a segregation into the mathematical model. It was shown that the state of the cells was dependent on the current environment and on the previous history. This phenomenon was considered in the model by utilizing delay time equations for the specific rates of growth on the primary and the secondary substrate. A comparison with reproducible measurements gave a good correlation between computation and experiment. The mathematical model was validated using independent own experimental data. A comparison with a stationary and nonsegregated model demonstrated the essential improvements of the novel model. It was deduced from the model calculations that high product formation rates of 3.3-3.5 g L(-1) h(-1) as well as high final DHA concentrations of 196-215 g L(-1) can be obtained with a residual broth volume in the first reactor stage of 2% and a DHA threshold value in the range of 100-110 g L(-1).

Study of the inhibitory effect of the product dihydroxyacetone on Gluconobacter oxydans in a semi-continuous two-stage repeated-fed-batch process

The influence of the product inhibition by dihydroxyacetone (DHA) on Gluconobacter oxydans for a novel semi-continuous two-stage repeated-fed-batch process was examined quantitatively. It was shown that the culture was able to grow up to a DHA concentration of 80 kg m(-3) without any influence of product inhibition. The regeneration capability of the reversibly product inhibited culture from a laboratory-scale bioreactor system was observed up to a DHA concentration of about 160 kg m(-3). At higher DHA concentrations, the culture was irreversibly product inhibited. However, due to the robust membrane-bound glycerol dehydrogenase of G. oxydans, product formation was still active for a prolonged period of time. The reachable maximum final DHA concentration was as high as 220 kg m(-3). The lag phases for growth increased exponentially with increasing DHA threshold values of the first reactor stage. These results correlated well with fluorescence in situ hybridization (FISH) measurements confirming that the number of active cells decreased exponentially with increasing DHA concentrations.

Biofilm population dynamics in a trickle-bed bioreactor used for the biodegradation of aromatic hydrocarbons from waste gas under transient conditions

The dynamics of a multispecies biofilm population in a laboratory-scale trickle-bed bioreactor for the treatment of waste gas was examined. The model pollutant was a VOC-mixture of polyalkylated benzenes called Solvesso 100. Fluorescence in-situ hybridization (FISH) was applied in order to characterise the population composition. The bioreactor was operated under transient conditions by applying pollutant concentration shifts and a starvation phase. Only about 10% of the biofilm mass were cells, the rest consisted of extracellular polymeric substances (EPS). The average fraction of Solvesso 100-degrading cells during pollutant supply periods was less than 10%. About 60% of the cells were saprophytes and about 30% were inactive cells. During pollutant concentration shift experiments, the bioreactor performance adapted within a few hours. The biofilm population exhibited a dependency upon the direction of the shifts. The population reacted within days after a shift-down and within weeks after a shift-up. The pollutant-degraders reacted significantly faster compared to the other cells. During the long-term starvation phase, a shift of the population composition took place. However, this change of composition as well as the degree of metabolic activity was completely reversible. A direct correlation between the biodegradation rate of the bioreactor and the number of pollutant-degrading cells present in the biofilm could not be obtained due to insufficient experimental evidence.

Optimization of the microbial synthesis of dihydroxyacetone from glycerol with Gluconobacter oxydans

An optimized repeated-fed-batch fermentation process for the synthesis of dihydroxyacetone (DHA) from glycerol utilizing Gluconobacter oxydans is presented. Cleaning, sterilization, and inoculation procedures could be reduced significantly compared to the conventional fed-batch process. A stringent requirement was that the product concentration was kept below a critical threshold level at all times in order to avoid irreversible product inhibition of the cells. On the basis of experimentally validated model calculations, a threshold value of about 60 kg x m(-3) DHA was obtained. The innovative bioreactor system consisted of a stirred tank reactor combined with a packed trickle-bed column. In the packed column, active cells could be retained by in situ immobilization on a hydrophilized Ralu-ring carrier material. Within 17 days, the productivity of the process could be increased by 75% to about 2.8 kg x m(-3) h(-1). However, it was observed that the maximum achievable productivity had not been reached yet.

Bacterial community dynamics during start-up of a trickle-bed bioreactor degrading aromatic compounds

This study was performed with a laboratory-scale fixed-bed bioreactor degrading a mixture of aromatic compounds (Solvesso100). The starter culture for the bioreactor was prepared in a fermentor with a wastewater sample of a care painting facility as the inoculum and Solvesso100 as the sole carbon source. The bacterial community dynamics in the fermentor and the bioreactor were examined by a conventional isolation procedure and in situ hybridization with fluorescently labeled rRNA-targeted oligonucleotides. Two significant shifts in the bacterial community structure could be demonstrated. The original inoculum from the wastewater of the car factory was rich in proteobacteria of the alpha and beta subclasses, while the final fermentor enrichment was dominated by bacteria closely related to Pseudomonas putida or Pseudomonas mendocina, which both belong to the gamma subclass of the class Proteobacteria. A second significant shift was observed when the fermentor culture was transferred as inoculum to the trickle-bed bioreactor. The community structure in the bioreactor gradually returned to a higher complexity, with the dominance of beta and alpha subclass proteobacteria, whereas the gamma subclass proteobacteria sharply declined. Obviously, the preceded pollutant adaptant did not lead to a significant enrichment of bacteria that finally dominated in the trickle-bed bioreactor. In the course of experiments, three new 16S as well as 23S rRNA-targeted probes for beta subclass proteobacteria were designed, probe SUBU1237 for the genera Burkholderia and Sutterella, probe ALBO34a for the genera Alcaligenes and Bordetella, and probe Bcv13b for Burkholderia cepacia and Burkholderia vietnamiensis. Bacteria hybridizing with the probe Bcv13b represented the main Solvesso100-degrading population in the reactor.