Refolding of the Deinococcus Radiodurans phytochrome photosensory module and an extended backbone resonance assignment by solution NMR

Solution NMR reveals the structure and dynamics of biomolecules in solution. In particular, the method can detect changes due to perturbation of the molecules, without limiting effects of frozen particles or crystal environments. Phytochromes are photosensors which control the response to red/far-red light in bacteria, fungi and plants, undergo specific structural changes when photoactivated from the Pr to the Pfr state. While structures of phytochromes have been revealed in both states, the structural mechanism of photoconversion remains incompletely understood. Our previous NMR studies of the entire photosensory core module of the D. radiodurans phytochrome have revealed novel structural changes, but the backbone assignment was incomplete. In particular, a lack of the assignment in the protein core hindered more detailed insight in signaling mechanism. Here, we outline an efficient procedure for the refolding of the three-domain, photosensory core fragment of the D. radiodurans phytochrome in its monomeric form. We find that treatment with guanidinium hydrochloride and subsequent dilution effectively refolds the phytochrome, maintaining its functionality. We characterize the refolded protein with solution NMR spectroscopy newly assigning 27 (44) residues in Pr (Pfr), out of which 12 exhibit notable chemical shift perturbation upon photoactivation. The study presents a functional method for purification and refolding of a multidomain protein and opens the door for further structural and dynamic analysis of phytochromes. Author summary Refolding of proteins is an established method to increase the deuterium-hydrogen exchange of amid bonds in isotopically labeled proteins, which are located deep in the protein core. Yet, the method has to be optimized for each individual protein and in particular for multidomain proteins it is not trivial to find satisfactory experimental conditions. Here we identify a method to refold a D. radiodurans phytochrome construct and characterize the outcome of the procedure using solution NMR and optical spectroscopy. The quick accessibility on whether the refolded phytochrome was functional or not has been obtained from optical spectra, which also made the screening of a number of additives possible. The procedure led to a significant increase in the number of the assigned residues especially in the protein core, close to the photochemically active chromophore, which enables a more detailed investigation of the structure and dynamics throughout the photocycle of the phytochrome.

Refolding of Proteins Expressed as Inclusion Bodies in E. coli

Microbial-based biotherapeutics that are produced in Escherichia coli (E. coli) can be generated intracellularly in the form of inclusion bodies (IBs) or in soluble active form in periplasmic space or extracellularly. Overexpression of these biotherapeutics in E. coli leads to formation of insoluble aggregates called inclusion bodies. These IBs contain misfolded and inactive form of proteins which need to be refolded to obtain a functionally active form of proteins. Here, we discuss refolding of E. coli-based recombinant human granulocyte colony-stimulating factor (GCSF), expressed as IBs, and highlight some of the key features associated with the refolding kinetic reaction.

Co-Expression of Chaperones for Improvement of Soluble Expression and Purification of An Anti-HER2 scFv in Escherichia Coli

Background

Single-chain fragment variable (scFv) is one of the most commonly used antibody fragments. They offer some advantages over full-length antibodies, including better penetration to target tissues. However, their functional production has been a challenge for manufacturers due to the potential misfolding and formation of inclusion bodies. Here we evaluated the soluble expression and purification of molecular chaperone co-expression.

Materials and Methods

E. coli BL21(DE3) cells were co-transformed with the mixture of plasmids pKJE7 and pET22b-scFv by the electroporation method. First, L-arabinose was added to induce the expression of molecular chaperones, and then IPTG was used as an inducer to start the expression of anti-HER2 scFv. The effect of cultivation temperature and IPTG concentration on soluble expression of the protein with or without chaperones was evaluated. The soluble expressed protein was subjected to native purification using the Ni-NTA affinity column.

Results

SDS-PAGE analysis confirmed the successful co-expression of anti-HER2-scFv and DnaK/DnaJ/GrpE chaperones. Co-expression with chaperones and low-temperature cultivation synergistically improved the soluble expression of anti-HER2 scFv. Co-expression with chaperone also exhibited an approximately four-fold increase in the final yield of purified soluble protein.

Conclusion

The combination of co-expression with chaperones and low temperature presented in this work may be useful for the improvement of commercial production of other scFvs in E. coli as functionally bioactive and soluble form.

Systematic Investigation of Insulin Fibrillation on a Chip

A microfluidic protein aggregation device (microPAD) that allows the user to perform a series of protein incubations with various concentrations of two reagents is demonstrated. The microfluidic device consists of 64 incubation chambers to perform individual incubations of the protein at 64 specific conditions. Parallel processes of metering reagents, stepwise concentration gradient generation, and mixing are achieved simultaneously by pneumatic valves. Fibrillation of bovine insulin was selected to test the device. The effect of insulin and sodium chloride (NaCl) concentration on the formation of fibrillar structures was studied by observing the growth rate of partially folded protein, using the fluorescent marker Thioflavin-T. Moreover, dual gradients of different NaCl and hydrochloric acid (HCl) concentrations were formed, to investigate their interactive roles in the formation of insulin fibrils and spherulites. The chip-system provides a bird’s eye view on protein aggregation, including an overview of the factors that affect the process and their interactions. This microfluidic platform is potentially useful for rapid analysis of the fibrillation of proteins associated with many misfolding-based diseases, such as quantitative and qualitative studies on amyloid growth.

Modeling, simulation, and employing dilution-dialysis microfluidic chip (DDMC) for heightening proteins refolding efficiency

Miniaturized systems based on the principles of microfluidics are widely used in various fields, such as biochemical and biomedical applications. Systematic design processes are demanded the proper use of these microfluidic devices based on mathematical simulations. Aggregated proteins (e.g., inclusion bodies) in solution with chaotropic agents (such as urea) at high concentration in combination with reducing agents are denatured. Refolding methods to achieve the native proteins from inclusion bodies of recombinant protein relying on denaturant dilution or dialysis approaches for suppressing protein aggregation is very important in the industrial field. In this paper, a modeling approach is introduced and employed that enables a compact and cost-effective method for on-chip refolding process. The innovative aspect of the presented refolding method is incorporation dialysis and dilution. Dilution-dialysis microfluidic chip (DDMC) increases productivity folding of proteins with the gradual reduction of the amount of urea. It has shown the potential of DDMC for performing refolding of protein trials. The principles of the microfluidic device detailed in this paper are to produce protein on the dilution with slow mixing through diffusion of a denatured protein solution and stepwise dialysis of a refolding buffer flowing together and the flow regime is creeping flow. The operation of DDMC was modeled in two dimensions. This system simulated by COMSOL Multiphysics Modeling Software. The simulation results for a microfluidic refolding chip showed that DDMC was deemed to be perfectly suitable for control decreasing urea in the fluid model. The DDMC was validated through an experimental study. According to the results, refolding efficiency of denaturant Hen egg white lysozyme (HEWL) (EC 3.2.1.17) used as a model protein was improved. Regard to the remaining activity test, it was increased from 42.6 in simple dilution to 93.7 using DDMC.

A Systematic Protein Refolding Screen Method using the DGR Approach Reveals that Time and Secondary TSA are Essential Variables

Refolding of proteins derived from inclusion bodies is very promising as it can provide a reliable source of target proteins of high purity. However, inclusion body-based protein production is often limited by the lack of techniques for the detection of correctly refolded protein. Thus, the selection of the refolding conditions is mostly achieved using trial and error approaches and is thus a time-consuming process. In this study, we use the latest developments in the differential scanning fluorimetry guided refolding approach as an analytical method to detect correctly refolded protein. We describe a systematic buffer screen that contains a 96-well primary pH-refolding screen in conjunction with a secondary additive screen. Our research demonstrates that this approach could be applied for determining refolding conditions for several proteins. In addition, it revealed which “helper” molecules, such as arginine and additives are essential. Four different proteins: HA-RBD, MDM2, IL-17A and PD-L1 were used to validate our refolding approach. Our systematic protocol evaluates the impact of the “helper” molecules, the pH, buffer system and time on the protein refolding process in a high-throughput fashion. Finally, we demonstrate that refolding time and a secondary thermal shift assay buffer screen are critical factors for improving refolding efficiency.

Protein recovery from inclusion bodies of Escherichia coli using mild solubilization process

Formation of inclusion bodies in bacterial hosts poses a major challenge for large scale recovery of bioactive proteins. The process of obtaining bioactive protein from inclusion bodies is labor intensive and the yields of recombinant protein are often low. Here we review the developments in the field that are targeted at improving the yield, as well as quality of the recombinant protein by optimizing the individual steps of the process, especially solubilization of the inclusion bodies and refolding of the solubilized protein. Mild solubilization methods have been discussed which are based on the understanding of the fact that protein molecules in inclusion body aggregates have native-like structure. These methods solubilize the inclusion body aggregates while preserving the native-like protein structure. Subsequent protein refolding and purification results in high recovery of bioactive protein. Other parameters which influence the overall recovery of bioactive protein from inclusion bodies have also been discussed. A schematic model describing the utility of mild solubilization methods for high throughput recovery of bioactive protein has also been presented.

Microfluidic chips with multi-junctions: an advanced tool in recovering proteins from inclusion bodies

Active recombinant proteins are used for studying the biological functions of genes and for the development of therapeutic drugs. Overexpression of recombinant proteins in bacteria often results in the formation of inclusion bodies, which are protein aggregates with non-native conformations. Protein refolding is an important process for obtaining active recombinant proteins from inclusion bodies. However, the conventional refolding method of dialysis or dilution is time-consuming and recovered active protein yields are often low, and a cumbersome trial-and-error process is required to achieve success. To circumvent these difficulties, we used controllable diffusion through laminar flow in microchannels to regulate the denaturant concentration. This method largely aims at reducing protein aggregation during the refolding procedure. This Commentary introduces the principles of the protein refolding method using microfluidic chips and the advantage of our results as a tool for rapid and efficient recovery of active recombinant proteins from inclusion bodies.

Expression, production, and renaturation of a functional single-chain variable antibody fragment (scFv) against human ICAM-1

Intercellular adhesion molecule-1 (ICAM-1) is an important factor in the progression of inflammatory responses in vivo. To develop a new anti-inflammatory drug to block the biological activity of ICAM-1, we produced a monoclonal antibody (Ka=4.19×10⁻⁸ M) against human ICAM-1. The anti-ICAM-1 single-chain variable antibody fragment (scFv) was expressed at a high level as inclusion bodies in Escherichia coli. We refolded the scFv (Ka=2.35×10⁻⁷ M) by ion-exchange chromatography, dialysis, and dilution. The results showed that column chromatography refolding by high-performance Q Sepharose had remarkable advantages over conventional dilution and dialysis methods. Furthermore, the anti-ICAM-1 scFv yield of about 60 mg/L was higher with this method. The purity of the final product was greater than 90%, as shown by denaturing gel electrophoresis. Enzyme-linked immunosorbent assay, cell culture, and animal experiments were used to assess the immunological properties and biological activities of the renatured scFv.

Refolding techniques for recovering biologically active recombinant proteins from inclusion bodies

Biologically active proteins are useful for studying the biological functions of genes and for the development of therapeutic drugs and biomaterials in a biotechnology industry. Overexpression of recombinant proteins in bacteria, such as Escherichia coli, often results in the formation of inclusion bodies, which are protein aggregates with non-native conformations. As inclusion bodies contain relatively pure and intact proteins, protein refolding is an important process to obtain active recombinant proteins from inclusion bodies. However, conventional refolding methods, such as dialysis and dilution, are time consuming and, often, recovered yields of active proteins are low, and a trial-and-error process is required to achieve success. Recently, several approaches have been reported to refold these aggregated proteins into an active form. The strategies largely aim at reducing protein aggregation during the refolding procedure. This review focuses on protein refolding techniques using chemical additives and laminar flow in microfluidic chips for the efficient recovery of active proteins from inclusion bodies.

Membrane-assisted online renaturation for automated microfluidic lectin blotting

Aberrant glycosylation plays a pivotal role in a diverse set of diseases, including cancer. A microfluidic lectin blotting platform is introduced to enable and expedite the identification of protein glycosylation based on protein size and affinity for specific lectins. The integrated multistage assay eliminates manual intervention steps required for slab-gel lectin blotting, increases total assay throughput, limits reagent and sample consumption, and is completed using one instrument. The assay comprises non-reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) followed by online post-sizing SDS filtration and lectin-based affinity blotting. Important functionality is conferred through both device and assay advances that enable integration of nanoporous membranes flanking a central microchamber to create sub-nanoliter volume compartments that trap SDS-protein complexes and allow electrophoretic SDS removal with buffer exchange. Recapitulation of protein binding for lectin was optimized through quantitative assessment of SDS-treated green fluorescent protein. Immunoglobulin A1 aberrantly glycosylated with galactose-deficient O-glycans was probed in ~6 min using ~3 μL of sample. This new microfluidic lectin blotting platform provides a rapid and automated assay for the assessment of aberrant glycosylation.