Experimental optimization of protein refolding with a genetic algorithm

Advances in monitoring and control of refolding kinetics combining PAT and modeling

Overexpression of recombinant proteins in Escherichia coli results in misfolded and non-active protein aggregates in the cytoplasm, so-called inclusion bodies (IB). In recent years, a change in the mindset regarding IBs could be observed: IBs are no longer considered an unwanted waste product, but a valid alternative to produce a product with high yield, purity, and stability in short process times. However, solubilization of IBs and subsequent refolding is necessary to obtain a correctly folded and active product. This protein refolding process is a crucial downstream unit operation-commonly done as a dilution in batch or fed-batch mode. Drawbacks of the state-of-the-art include the following: the large volume of buffers and capacities of refolding tanks, issues with uniform mixing, challenging analytics at low protein concentrations, reaction kinetics in non-usable aggregates, and generally low re-folding yields. There is no generic platform procedure available and a lack of robust control strategies. The introduction of Quality by Design (QbD) is the method-of-choice to provide a controlled and reproducible refolding environment. However, reliable online monitoring techniques to describe the refolding kinetics in real-time are scarce. In our view, only monitoring and control of re-folding kinetics can ensure a productive, scalable, and versatile platform technology for re-folding processes. For this review, we screened the current literature for a combination of online process analytical technology (PAT) and modeling techniques to ensure a controlled refolding process. Based on our research, we propose an integrated approach based on the idea that all aspects that cannot be monitored directly are estimated via digital twins and used in real-time for process control. KEY POINTS: • Monitoring and a thorough understanding of refolding kinetics are essential for model-based control of refolding processes. • The introduction of Quality by Design combining Process Analytical Technology and modeling ensures a robust platform for inclusion body refolding.

Optimization of process conditions for mammalian fed-batch cell culture in automated micro-bioreactor system using genetic algorithm

Recombinant proteins produced by mammalian cell culture technology represent an important segment of therapeutic molecules. Development of their manufacturing processes is a time- and resource-consuming task. A wide array of process conditions, e.g. physico-chemical parameters, medium composition, feeding strategy, needs to be optimized to design a commercially feasible process with the desired productivity and product characteristics. Traditionally, statistical experimental designs, i.e. design-of-experiments methodology, have been used for such optimizations. However, statistical design approach has several limitations related to high dimensionality of the explored parameter space originating from the complexity of the mammalian cell culture processes. An alternative is therefore desired to overcome these limitations. In this study, we have successfully used a simple genetic algorithm as a method of experimental design for optimization of mammalian cell culture processes for two recombinant cell lines, one expressing a monoclonal antibody and one an Fc-fusion protein. Harnessing the automation capability of a robotically driven micro-bioreactor system to execute the genetic algorithm-derived experiments, a set of 14 process parameters was optimized within 132 experiments per cell line (six generations of 22 experiments), showing the feasibility of this approach as an alternative to classical statistical experimental designs.

The ambivalent effect of Fe3O4 nanoparticles on the urea-induced unfolding and dilution-based refolding of lysozyme

Due to the numerous biological applications of magnetite (Fe₃O₄) nanoparticles (MNPs), it is essential to identify the influence of these nanoparticles on basic biological processes. Therefore, in this research, the effect of MNPs on the structure and activity of hen egg white lysozyme (HEWL) (EC 3.2.1.1) as a model protein was examined using tryptophan intrinsic fluorescence, UV/Vis, and circular dichroism spectroscopy. Moreover, enzyme activities were analyzed by a turbidometric approach in the presence of MNPs at concentrations providing MNPs/HEWL ratios in the range of 0.04-1.25. As-synthesized MNPS were characterized by Fourier transform infrared spectroscopy, x-ray diffraction, scanning electron microscopy, transmission electron microscopy, vibrating sample magnetometry and the zeta potential of MNPs was measured to be -29 mV. The goal of this work was investigating the ordering or disordering effect of MNPs on protein structure at ratios lower or higher than 0.918 as concentration ratio of threshold (CRT), respectively, in order to answer the question: 'How can the denaturation and refolding of a model protein (HEWL) be affected by MNPs?' As has been reported recently, the protein folding, helicity, and half-life were improved at <CRT to make the protein more ordered and conversely, HEWL was unfolded, and the helicity and half-life were decreased at >CRT to make the protein more disordered upon interaction with MNPs. The disordering effect of urea at >CRT and even at <CRT in the denaturation buffer (urea 6 M) increased and at <CRT the MNPs can provide a significant improvement in the refolding of the unfolded urea treated protein. These observations provide a new perspective on the growing applications of MNPs in biotechnology and biomedicine.

Integrated refolding techniques for Schistosoma japonicum MTH1 overexpressed as inclusion bodies in Escherichia coli

The full-length cDNA of MTH1in Schistosoma japonicum was previously isolated. However, insoluble protein expression in Escherichia coli is the biggest bottleneck limiting biological and biophysical studies. Protein aggregation could not be significantly prevented using solubilization or refolding techniques, and denatured MTH1 protein could not be refolded to the native monomer form. Hence, integrating several refolding techniques within the protein refolding process of MTH1, a large amount of active MTH1 was obtained for protein crystallization. We primarily utilized the two-step-denaturing and refolding method and the protein refolding screening technique, as well as the continuous dialysis method. First, we identified the refolding buffer composition that allowed for successful refolding to overcome protein precipitation. Next, we used the two-step-denaturing and refolding method and the continuous dialysis method to suppress protein aggregation. In the end, we obtained 15 mg of active MTH1 monomer with 95% purity from 0.5l medium. Integrated refolding techniques proved to be excellent for obtaining the native monomer of S. japonicum MTH1 from inclusion bodies, paving the way for future biological and biophysical studies.