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Ganjave SD, O'Niel RA, Wangikar PP. Rate of dilution and redox ratio influence the refolding efficiency of recombinant fungal dehydrogenases. Int J Biol Macromol 2023; 250:126163. [PMID: 37549766 DOI: 10.1016/j.ijbiomac.2023.126163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/19/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
Dehydrogenases from fungi are attracting attention as industrial biocatalysts due to their high activity and chiral selectivity. However, these enzymes form insoluble aggregates when overexpressed in E. coli, limiting their industrial application. In the present study, we report the systematic development of a refolding process for selected, industrially relevant fungal dehydrogenases, viz., formate dehydrogenase from Candida boidinii (CbFDH) and formate and alcohol dehydrogenases from Geotrichum candium (GcFDH and GcADH, respectively). We first employed a screen to evaluate the effects of different variables on refolding including the buffer system, additives, and rate of dilution. The extent of refolding was determined by enzyme assays, circular dichroism, and tryptophan fluorescence. Our results showed that glycerol and reducing environment are essential for refolding of these dehydrogenases. Further, slow dilution of solubilized protein over 16 h dramatically improved the recovery of refolded enzymes compared to rapid dilution. The importance of slow dilution was further confirmed in a 10-fold scaled-up refolding trial. Overall, we demonstrate a robust method for refolding of fungal dehydrogenases, thus improving their availability for various biocatalytic applications.
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Affiliation(s)
- Snehal D Ganjave
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Ruchika Annie O'Niel
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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2
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Vallerinteavide Mavelli G, Sadeghi S, Drum CL. Laboratory Scale Production of Complex Proteins Using Charge Complimentary Nanoenvironments. Methods Mol Biol 2023; 2671:403-418. [PMID: 37308658 DOI: 10.1007/978-1-0716-3222-2_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein refolding is a crucial procedure in bacterial recombinant expression. Aggregation and misfolding are the two challenges that can affect the overall yield and specific activity of the folded proteins. We demonstrated the in vitro use of nanoscale "thermostable exoshells" (tES) to encapsulate, fold and release diverse protein substrates. With tES, the soluble yield, functional yield, and specific activity increased from 2-fold to >100-fold when compared to folding in its absence. On average, the soluble yield was determined to be 6.5 mg/100 mg of tES for a set of 12 diverse substrates evaluated. The electrostatic charge complementation between the tES interior and the protein substrate was considered as the primary determinant for functional folding. We thus describe a useful and simple method for in vitro folding that has been evaluated and implemented in our laboratory.
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Affiliation(s)
| | - Samira Sadeghi
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chester Lee Drum
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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3
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Kachhawaha K, Singh S, Joshi K, Nain P, Singh SK. Bioprocessing of recombinant proteins from Escherichia coli inclusion bodies: insights from structure-function relationship for novel applications. Prep Biochem Biotechnol 2022; 53:728-752. [PMID: 36534636 DOI: 10.1080/10826068.2022.2155835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The formation of inclusion bodies (IBs) during expression of recombinant therapeutic proteins using E. coli is a significant hurdle in producing high-quality, safe, and efficacious medicines. The improved understanding of the structure-function relationship of the IBs has resulted in the development of novel biotechnologies that have streamlined the isolation, solubilization, refolding, and purification of the active functional proteins from the bacterial IBs. Together, this overall effort promises to radically improve the scope of experimental biology of therapeutic protein production and expand new prospects in IBs usage. Notably, the IBs are increasingly used for applications in more pristine areas such as drug delivery and material sciences. In this review, we intend to provide a comprehensive picture of the bio-processing of bacterial IBs, including assessing critical gaps that still need to be addressed and potential solutions to overcome them. We expect this review to be a useful resource for those working in the area of protein refolding and therapeutic protein production.
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Affiliation(s)
- Kajal Kachhawaha
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Santanu Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Khyati Joshi
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Priyanka Nain
- Department of Chemical and Bimolecular Engineering, University of Delaware, Newark, DE, USA
| | - Sumit K Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
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4
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Buscajoni L, Martinetz MC, Berkemeyer M, Brocard C. Refolding in the modern biopharmaceutical industry. Biotechnol Adv 2022; 61:108050. [PMID: 36252795 DOI: 10.1016/j.biotechadv.2022.108050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 11/02/2022]
Abstract
Inclusion bodies (IBs) often emerge upon overexpression of recombinant proteins in E. coli. From IBs, refolding is necessary to generate the native protein that can be further purified to obtain pure and active biologicals. This work focusses on refolding as a significant process step during biopharmaceutical manufacturing with an industrial perspective. A theoretical and historical background on protein refolding gives the reader a starting point for further insights into industrial process development. Quality requirements on IBs as starting material for refolding are discussed and further economic and ecological aspects are considered with regards to buffer systems and refolding conditions. A process development roadmap shows the development of a refolding process starting from first exploratory screening rounds to scale-up and implementation in manufacturing plant. Different aspects, with a direct influence on yield, such as the selection of chemicals including pH, ionic strength, additives, etc., and other often neglected aspects, important during scale-up, such as mixing, and gas-fluid interaction, are highlighted with the use of a quality by design (QbD) approach. The benefits of simulation sciences (process simulation and computer fluid dynamics) and process analytical technology (PAT) for seamless process development are emphasized. The work concludes with an outlook on future applications of refolding and highlights open research inquiries.
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Affiliation(s)
- Luisa Buscajoni
- Boehringer-Ingelheim RCV GmbH & Co KG, Biopharma Austria, Process Science Downstream Development, Dr. Boehringer-Gasse 5- 11, 1120 Vienna, Austria.
| | - Michael C Martinetz
- Boehringer-Ingelheim RCV GmbH & Co KG, Biopharma Austria, Process Science Downstream Development, Dr. Boehringer-Gasse 5- 11, 1120 Vienna, Austria.
| | - Matthias Berkemeyer
- Boehringer-Ingelheim RCV GmbH & Co KG, Biopharma Austria, Process Science Downstream Development, Dr. Boehringer-Gasse 5- 11, 1120 Vienna, Austria.
| | - Cécile Brocard
- Boehringer-Ingelheim RCV GmbH & Co KG, Biopharma Austria, Process Science Downstream Development, Dr. Boehringer-Gasse 5- 11, 1120 Vienna, Austria.
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A general approach to protein folding using thermostable exoshells. Nat Commun 2021; 12:5720. [PMID: 34588451 PMCID: PMC8481291 DOI: 10.1038/s41467-021-25996-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/07/2021] [Indexed: 02/08/2023] Open
Abstract
In vitro protein folding is a complex process which often results in protein aggregation, low yields and low specific activity. Here we report the use of nanoscale exoshells (tES) to provide complementary nanoenvironments for the folding and release of 12 highly diverse protein substrates ranging from small protein toxins to human albumin, a dimeric protein (alkaline phosphatase), a trimeric ion channel (Omp2a) and the tetrameric tumor suppressor, p53. These proteins represent a unique diversity in size, volume, disulfide linkages, isoelectric point and multi versus monomeric nature of their functional units. Protein encapsulation within tES increased crude soluble yield (3-fold to >100-fold), functional yield (2-fold to >100-fold) and specific activity (3-fold to >100-fold) for all the proteins tested. The average soluble yield was 6.5 mg/100 mg of tES with charge complementation between the tES internal cavity and the protein substrate being the primary determinant of functional folding. Our results confirm the importance of nanoscale electrostatic effects and provide a solution for folding proteins in vitro.
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Komar AA. A Code Within a Code: How Codons Fine-Tune Protein Folding in the Cell. BIOCHEMISTRY (MOSCOW) 2021; 86:976-991. [PMID: 34488574 DOI: 10.1134/s0006297921080083] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genetic code sets the correspondence between the sequence of a given nucleotide triplet in an mRNA molecule, called a codon, and the amino acid that is added to the growing polypeptide chain during protein synthesis. With four bases (A, G, U, and C), there are 64 possible triplet codons: 61 sense codons (encoding amino acids) and 3 nonsense codons (so-called, stop codons that define termination of translation). In most organisms, there are 20 common/standard amino acids used in protein synthesis; thus, the genetic code is redundant with most amino acids (with the exception of Met and Trp) are being encoded by more than one (synonymous) codon. Synonymous codons were initially presumed to have entirely equivalent functions, however, the finding that synonymous codons are not present at equal frequencies in mRNA suggested that the specific codon choice might have functional implications beyond coding for amino acid. Observation of nonequivalent use of codons in mRNAs implied a possibility of the existence of auxiliary information in the genetic code. Indeed, it has been found that genetic code contains several layers of such additional information and that synonymous codons are strategically placed within mRNAs to ensure a particular translation kinetics facilitating and fine-tuning co-translational protein folding in the cell via step-wise/sequential structuring of distinct regions of the polypeptide chain emerging from the ribosome at different points in time. This review summarizes key findings in the field that have identified the role of synonymous codons and their usage in protein folding in the cell.
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Affiliation(s)
- Anton A Komar
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA. .,Department of Biochemistry and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA.,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.,DAPCEL, Inc., Cleveland, OH 44106, USA
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7
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Bacterial Inclusion Bodies: A Treasure Trove of Bioactive Proteins. Trends Biotechnol 2020; 38:474-486. [DOI: 10.1016/j.tibtech.2019.12.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/29/2019] [Accepted: 12/06/2019] [Indexed: 12/24/2022]
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de la Cruz JJ, Villanueva-Lizama L, Dzul-Huchim V, Ramírez-Sierra MJ, Martinez-Vega P, Rosado-Vallado M, Ortega-Lopez J, Flores-Pucheta CI, Gillespie P, Zhan B, Bottazzi ME, Hotez PJ, Dumonteil E. Production of recombinant TSA-1 and evaluation of its potential for the immuno-therapeutic control of Trypanosoma cruzi infection in mice. Hum Vaccin Immunother 2018; 15:210-219. [PMID: 30192702 PMCID: PMC6363145 DOI: 10.1080/21645515.2018.1520581] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A therapeutic vaccine for human Chagas disease (American trypanosomiasis caused by Trypanosoma cruzi) is under development based on the success of vaccinating mice with DNA constructs expressing the antigens Tc24 and Tc-TSA-1. However, because DNA and nucleic acid vaccines produce less than optimal responses in humans, our strategy relies on administering a recombinant protein-based vaccine, together with adjuvants that promote Th1-type immunity. Here we describe a process for the purification and refolding of recombinant TSA-1 expressed in Escherichia coli. The overall yield (20–25%) and endotoxin level of the purified recombinant TSA-1 (rTSA-1) is suitable for pilot scale production of the antigen for use in phase 1 clinical trials. Mice infected with T. cruzi were treated with rTSA-1, either alone or with Toll-like receptor 4 (TLR-4) agonist adjuvants including monophosphoryl lipid A (MPLA), glucopyranosyl lipid A (GLA, IDRI), and E6020 (EISEI, Inc). TSA-1 with the TLR-4 agonists was effective at reducing parasitemia relative to rTSA-1 alone, although it was difficult to discern a therapeutic effect compared to treatment with TLR-4 agonists alone. However, rTSA-1 with a 10 ug dose of MPLA optimized reductions in cardiac tissue inflammation, which were significantly reduced compared to MPLA alone. It also elicited the lowest parasite burden and the highest levels of TSA-1-specific IFN-gamma levels and IFN-gamma/IL-4 ratios. These results warrant the further evaluation of rTSA-1 in combination with rTc24 in order to maximize the therapeutic effect of vaccine-linked chemotherapy in both mice and non-human primates before advancing to clinical development.
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Affiliation(s)
- Juan Jose de la Cruz
- a Laboratorio de Parasitología, Centro de Investigaciones Regionales Dr. Hideyo Noguchi , Universidad Autónoma de Yucatán , Mérida , Yucatán , México
| | - Liliana Villanueva-Lizama
- a Laboratorio de Parasitología, Centro de Investigaciones Regionales Dr. Hideyo Noguchi , Universidad Autónoma de Yucatán , Mérida , Yucatán , México
| | - Victor Dzul-Huchim
- a Laboratorio de Parasitología, Centro de Investigaciones Regionales Dr. Hideyo Noguchi , Universidad Autónoma de Yucatán , Mérida , Yucatán , México
| | - María-Jesus Ramírez-Sierra
- a Laboratorio de Parasitología, Centro de Investigaciones Regionales Dr. Hideyo Noguchi , Universidad Autónoma de Yucatán , Mérida , Yucatán , México
| | - Pedro Martinez-Vega
- a Laboratorio de Parasitología, Centro de Investigaciones Regionales Dr. Hideyo Noguchi , Universidad Autónoma de Yucatán , Mérida , Yucatán , México
| | - Miguel Rosado-Vallado
- a Laboratorio de Parasitología, Centro de Investigaciones Regionales Dr. Hideyo Noguchi , Universidad Autónoma de Yucatán , Mérida , Yucatán , México
| | - Jaime Ortega-Lopez
- b Departamento de Biotecnología y Bioingeniería , CINVESTAV-IPN , Ciudad de México , México
| | | | - Portia Gillespie
- c Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics and Molecular Virology and Microbiology , National School of Tropical Medicine, Baylor College of Medicine , Houston , TX , USA
| | - Bin Zhan
- c Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics and Molecular Virology and Microbiology , National School of Tropical Medicine, Baylor College of Medicine , Houston , TX , USA
| | - Maria Elena Bottazzi
- c Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics and Molecular Virology and Microbiology , National School of Tropical Medicine, Baylor College of Medicine , Houston , TX , USA
| | - Peter J Hotez
- c Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics and Molecular Virology and Microbiology , National School of Tropical Medicine, Baylor College of Medicine , Houston , TX , USA
| | - Eric Dumonteil
- d Department of Tropical Medicine , Vector-Borne and Infectious Disease Research Center, School of Public Health and Tropical Medicine, Tulane University , New Orleans , LA , USA
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