1
|
Handayani CV, Laksmi FA, Andriani A, Nuryana I, Mubarik NR, Agustriana E, Dewi KS, Purnawan A. Expression of soluble moloney murine leukemia virus-reverse transcriptase in Escherichia coli BL21 star (DE3) using autoinduction system. Mol Biol Rep 2024; 51:628. [PMID: 38717629 DOI: 10.1007/s11033-024-09583-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/23/2024] [Indexed: 06/07/2024]
Abstract
Autoinduction systems in Escherichia coli can control the production of proteins without the addition of a particular inducer. In the present study, we optimized the heterologous expression of Moloney Murine Leukemia Virus derived Reverse Transcriptase (MMLV-RT) in E. coli. Among 4 autoinduction media, media Imperial College resulted the highest MMLV-RT overexpression in E. coli BL21 Star (DE3) with incubation time 96 h. The enzyme was produced most optimum in soluble fraction of lysate cells. The MMLV-RT was then purified using the Immobilized Metal Affinity Chromatography method and had specific activity of 629.4 U/mg. The system resulted lower specific activity and longer incubation of the enzyme than a classical Isopropyl ß-D-1-thiogalactopyranoside (IPTG)-induction system. However, the autoinduction resulted higher yield of the enzyme than the conventional induction (27.8%). Techno Economic Analysis revealed that this method could produce MMLV-RT using autoinduction at half the cost of MMLV-RT production by IPTG-induction. Bioprocessing techniques are necessary to conduct to obtain higher quality of MMLV-RT under autoinduction system.
Collapse
Affiliation(s)
- Christina Vivid Handayani
- Research Center for Applied Microbiology, National Agency for Research and Innovation, Jl. Raya Bogor, Km. 46, Cibinong, Bogor, 16911, Indonesia
- Biotechnology Program, Graduate School, IPB University, Bogor, Indonesia
| | - Fina Amreta Laksmi
- Research Center for Applied Microbiology, National Agency for Research and Innovation, Jl. Raya Bogor, Km. 46, Cibinong, Bogor, 16911, Indonesia.
| | - Ade Andriani
- Research Center for Applied Microbiology, National Agency for Research and Innovation, Jl. Raya Bogor, Km. 46, Cibinong, Bogor, 16911, Indonesia.
| | - Isa Nuryana
- Research Center for Applied Microbiology, National Agency for Research and Innovation, Jl. Raya Bogor, Km. 46, Cibinong, Bogor, 16911, Indonesia
| | - Nisa Rachmania Mubarik
- Department of Biology, Faculty of Mathematic and Natural Science, IPB University, Bogor, Indonesia
| | - Eva Agustriana
- Research Center for Applied Microbiology, National Agency for Research and Innovation, Jl. Raya Bogor, Km. 46, Cibinong, Bogor, 16911, Indonesia
| | - Kartika Sari Dewi
- Research Center for Genetic Engineering, National Agency for Research and Innovation, Jl. Raya Bogor, Km. 46, Cibinong, Bogor, 16911, Indonesia
| | - Awan Purnawan
- Research Center for Applied Microbiology, National Agency for Research and Innovation, Jl. Raya Bogor, Km. 46, Cibinong, Bogor, 16911, Indonesia
| |
Collapse
|
2
|
Construction of a constitutively active type III secretion system for heterologous protein secretion. Appl Microbiol Biotechnol 2023; 107:1785-1800. [PMID: 36786917 DOI: 10.1007/s00253-023-12411-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 02/15/2023]
Abstract
Proteins comprise a multibillion-dollar industry in enzymes and therapeutics, but bacterial protein production can be costly and inefficient. Proteins of interest (POIs) must be extracted from lysed cells and inclusion bodies, purified, and resolubilized, which adds significant time and cost to the protein-manufacturing process. The Salmonella pathogenicity island 1 (SPI-1) type III secretion system (T3SS) has been engineered to address these problems by secreting soluble, active proteins directly into the culture media, reducing the number of purification steps. However, the current best practices method of T3SS pathway activation is not ideal for industrial scaleup. Previously, the T3SS was activated by plasmid-based overexpression of the T3SS transcriptional regulator, hilA, which requires the addition of a small molecule inducer (IPTG) to the culture media. IPTG adds significant cost to production and plasmid-based expression is subject to instability in large-scale fermentation. Here, we modulate the upstream transcriptional regulator, hilD, to activate the T3SS via three distinct methods. In doing so, we develop a toolbox of T3SS activation methods and construct constitutively active T3SS strains capable of secreting a range of heterologous proteins at titers comparable to plasmid-based hilA overexpression. We also explore how each activation method in our toolbox impacts the SPI-1 regulatory cascade and discover an epistatic relationship between T3SS regulators, hilE and the hilD 3' untranslated region (hilD 3'UTR). Together, these findings further our goal of making an industrially competitive protein production strain that reduces the challenges associated with plasmid induction and maintenance. KEY POINTS: • Characterized 3 new type III secretion system (T3SS) activation methods for heterologous protein secretion, including 2 constitutive activation methods. • Eliminated the need for a second plasmid and a small molecule inducer to activate the system, making it more suitable for industrial production. • Discovered new regulatory insights into the SPI-1 T3SS, including an epistatic relationship between regulators hilE and the hilD 3' untranslated region.
Collapse
|
3
|
Naser D, Tarasca MV, Siebeneichler B, Schaefer A, Deol HK, Soule TGB, Almey J, Kelso S, Mishra GG, Simon H, Meiering EM. High-Resolution NMR H/D Exchange of Human Superoxide Dismutase Inclusion Bodies Reveals Significant Native Features Despite Structural Heterogeneity. Angew Chem Int Ed Engl 2022; 61:e202112645. [PMID: 35316563 DOI: 10.1002/anie.202112645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Indexed: 01/16/2023]
Abstract
Protein aggregation is central to aging, disease and biotechnology. While there has been recent progress in defining structural features of cellular protein aggregates, many aspects remain unclear due to heterogeneity of aggregates presenting obstacles to characterization. Here we report high-resolution analysis of cellular inclusion bodies (IBs) of immature human superoxide dismutase (SOD1) mutants using NMR quenched amide hydrogen/deuterium exchange (qHDX), FTIR and Congo red binding. The extent of aggregation is correlated with mutant global stability and, notably, the free energy of native dimer dissociation, indicating contributions of native-like monomer associations to IB formation. This is further manifested by a common pattern of extensive protection against H/D exchange throughout nine mutant SOD1s despite their diverse characteristics. These results reveal multiple aggregation-prone regions in SOD1 and illuminate how aggregation may occur via an ensemble of pathways.
Collapse
Affiliation(s)
- Dalia Naser
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Michael V Tarasca
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Bruna Siebeneichler
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Anna Schaefer
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Harmeen K Deol
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Tyler G B Soule
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.,Current address: Department of Clinical Neurosciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Johnathan Almey
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Susan Kelso
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.,Current address: Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Gyana G Mishra
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.,Current address: Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Hilary Simon
- Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | | |
Collapse
|
4
|
Naser D, Tarasca MV, Siebeneichler B, Schaefer A, Deol HK, Soule TGB, Almey J, Kelso S, Mishra GG, Simon H, Meiering EM. High‐Resolution NMR H/D Exchange of Human Superoxide Dismutase Inclusion Bodies Reveals Significant Native Features Despite Structural Heterogeneity. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dalia Naser
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
| | - Michael V. Tarasca
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
| | | | - Anna Schaefer
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
| | - Harmeen K. Deol
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
| | - Tyler G. B. Soule
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
- Current address: Department of Clinical Neurosciences University of Calgary Calgary, AB T2N 1N4 Canada
| | - Johnathan Almey
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
| | - Susan Kelso
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
- Current address: Department of Molecular Genetics University of Toronto Toronto, ON M5S 1A1 Canada
| | - Gyana G. Mishra
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
- Current address: Department of Biology University of Waterloo Waterloo, ON N2L 3G1 Canada
| | - Hilary Simon
- Department of Chemistry University of Waterloo Waterloo, ON N2L 3G1 Canada
| | | |
Collapse
|
5
|
Salahuddin P, Khan RH, Furkan M, Uversky VN, Islam Z, Fatima MT. Mechanisms of amyloid proteins aggregation and their inhibition by antibodies, small molecule inhibitors, nano-particles and nano-bodies. Int J Biol Macromol 2021; 186:580-590. [PMID: 34271045 DOI: 10.1016/j.ijbiomac.2021.07.056] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 07/02/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022]
Abstract
Protein misfolding and aggregation can be induced by a wide variety of factors, such as dominant disease-associated mutations, changes in the environmental conditions (pH, temperature, ionic strength, protein concentration, exposure to transition metal ions, exposure to toxins, posttranslational modifications including glycation, phosphorylation, and sulfation). Misfolded intermediates interact with similar intermediates and progressively form dimers, oligomers, protofibrils, and fibrils. In amyloidoses, fibrillar aggregates are deposited in the tissues either as intracellular inclusion or extracellular plaques (amyloid). When such proteinaceous deposit occurs in the neuronal cells, it initiates degeneration of neurons and consequently resulting in the manifestation of various neurodegenerative diseases. Several different types of molecules have been designed and tested both in vitro and in vivo to evaluate their anti-amyloidogenic efficacies. For instance, the native structure of a protein associated with amyloidosis could be stabilized by ligands, antibodies could be used to remove plaques, oligomer-specific antibody A11 could be used to remove oligomers, or prefibrillar aggregates could be removed by affibodies. Keeping the above views in mind, in this review we have discussed protein misfolding and aggregation, mechanisms of protein aggregation, factors responsible for aggregations, and strategies for aggregation inhibition.
Collapse
Affiliation(s)
- Parveen Salahuddin
- DISC, Interdisciplinary Biotechnology Unit, A.M.U., Aligarh 202002, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, A.M.U., Aligarh 202002, India.
| | - Mohammad Furkan
- Interdisciplinary Biotechnology Unit, A.M.U., Aligarh 202002, India
| | - Vladimir N Uversky
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya Str., 7, Pushchino, Moscow region 142290, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Zeyaul Islam
- Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, P.O Box 5825, Doha, Qatar
| | - Munazza Tamkeen Fatima
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, P.O. Box 2713, Doha, Qatar
| |
Collapse
|
6
|
Metzger KF, Padutsch W, Pekarsky A, Kopp J, Voloshin AM, Kühnel H, Maurer M. IGF1 inclusion bodies: A QbD based process approach for efficient USP as well as early DSP unit operations. J Biotechnol 2020; 312:23-34. [DOI: 10.1016/j.jbiotec.2020.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/04/2020] [Accepted: 02/26/2020] [Indexed: 12/20/2022]
|
7
|
Uversky VN, Finkelstein AV. Life in Phases: Intra- and Inter- Molecular Phase Transitions in Protein Solutions. Biomolecules 2019; 9:E842. [PMID: 31817975 PMCID: PMC6995567 DOI: 10.3390/biom9120842] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023] Open
Abstract
Proteins, these evolutionarily-edited biological polymers, are able to undergo intramolecular and intermolecular phase transitions. Spontaneous intramolecular phase transitions define the folding of globular proteins, whereas binding-induced, intra- and inter- molecular phase transitions play a crucial role in the functionality of many intrinsically-disordered proteins. On the other hand, intermolecular phase transitions are the behind-the-scenes players in a diverse set of macrosystemic phenomena taking place in protein solutions, such as new phase nucleation in bulk, on the interface, and on the impurities, protein crystallization, protein aggregation, the formation of amyloid fibrils, and intermolecular liquid-liquid or liquid-gel phase transitions associated with the biogenesis of membraneless organelles in the cells. This review is dedicated to the systematic analysis of the phase behavior of protein molecules and their ensembles, and provides a description of the major physical principles governing intramolecular and intermolecular phase transitions in protein solutions.
Collapse
Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Moscow, Russia
| | - Alexei V. Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow, Russia
- Biology Department, Lomonosov Moscow State University, 119192 Moscow, Russia
- Bioltechnogy Department, Lomonosov Moscow State University, 142290 Pushchino, Moscow, Russia
| |
Collapse
|
8
|
Restrepo-Pineda S, Bando-Campos CG, Valdez-Cruz NA, Trujillo-Roldán MA. Recombinant production of ESAT-6 antigen in thermoinducible Escherichia coli: the role of culture scale and temperature on metabolic response, expression of chaperones, and architecture of inclusion bodies. Cell Stress Chaperones 2019; 24:777-792. [PMID: 31165436 PMCID: PMC6629757 DOI: 10.1007/s12192-019-01006-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 05/01/2019] [Accepted: 05/06/2019] [Indexed: 12/31/2022] Open
Abstract
The heat-inducible expression system has been widely used to produce recombinant proteins in Escherichia coli. However, the rise in temperature affects cell growth, activates the bacterial Heat-Shock Response (HSR), and promotes the formation of insoluble protein aggregates known as inclusion bodies (IBs). In this work, we evaluate the effect of the culture scale (shake flasks and bioreactors) and induction temperature (39 and 42 °C) on the kinetic behavior of thermoinducible recombinant E. coli ATCC 53606 producing rESAT-6 (6-kDa early-secretory antigenic target from Mycobacterium tuberculosis), compared with cultures grown at 30 °C (without induction). Also, the expression of the major E. coli chaperones (DnaK and GroEL) was analyzed. We found that almost twice maximum biomass and rESAT-6 production were obtained in bioreactors (~ 3.29 g/L of biomass and ~ 0.27 g/L of rESAT-6) than in shake flasks (~ 1.41 g/L of biomass and ~ 0.14 g/L of rESAT-6) when induction was carried out at 42 °C, but similar amounts of rESAT-6 were obtained from cultures induced at 39 °C (~ 0.14 g/L). In all thermo-induced conditions, rESAT-6 was trapped in IBs. Furthermore, DnaK was preferably expressed in the soluble fraction, while GroEL was present in IBs. Importantly, IBs formed at 39 °C, in both shake flasks and bioreactors, were more susceptible to degradation by proteinase-K, indicating a lower amyloid content compared to IBs formed at 42 °C. Our work presents evidence that the culture scale and the induction temperature modify the E. coli metabolic response, expression of chaperones, and structure of the IBs during rESAT-6 protein production in a thermoinducible system.
Collapse
Affiliation(s)
- Sara Restrepo-Pineda
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, CP. 04510 Ciudad de México, Mexico
| | - Carlos G. Bando-Campos
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, 04510 Ciudad de México, CP Mexico
| | - Norma A. Valdez-Cruz
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, 04510 Ciudad de México, CP Mexico
| | - Mauricio A. Trujillo-Roldán
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, CP. 04510 Ciudad de México, Mexico
| |
Collapse
|
9
|
In Vitro Digestion with Proteases Producing MHC Class II Ligands. Methods Mol Biol 2019. [PMID: 31147948 DOI: 10.1007/978-1-4939-9450-2_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Proteases generate peptides that bind to MHC class II molecules to interact with a wide diversity of CD4+ T cells. They are expressed in dedicated organelles: endosomes and lysosomes of professional antigen-presenting cells (pAPCs) such as B cells, macrophages, and dendritic cells. The identification of endosomal proteases which produce antigenic peptides is important for example for better vaccination and to prevent autoimmune diseases. Here, we describe a panel of techniques (in vitro digestion assays of protein with recombinant proteases or purified endosomes/lysosomes, T cell stimulation) to monitor the production of MHC class II ligands.
Collapse
|
10
|
Abstract
Production of fuels and chemicals from renewable lignocellulosic feedstocks is a promising alternative to petroleum-derived compounds. Due to the complexity of lignocellulosic feedstocks, microbial conversion of all potential substrates will require substantial metabolic engineering. Non-model microbes offer desirable physiological traits, but also increase the difficulty of heterologous pathway engineering and optimization. The development of modular design principles that allow metabolic pathways to be used in a variety of novel microbes with minimal strain-specific optimization will enable the rapid construction of microbes for commercial production of biofuels and bioproducts. In this review, we discuss variability of lignocellulosic feedstocks, pathways for catabolism of lignocellulose-derived compounds, challenges to heterologous engineering of catabolic pathways, and opportunities to apply modular pathway design. Implementation of these approaches will simplify the process of modifying non-model microbes to convert diverse lignocellulosic feedstocks.
Collapse
|
11
|
Ghaeidamini M, Kharat AN, Haertlé T, Ahmad F, Saboury AA. β-Cyclodextrin-Modified Magnetic Nanoparticles Immobilized on Sepharose Surface Provide an Effective Matrix for Protein Refolding. J Phys Chem B 2018; 122:9907-9919. [PMID: 30299940 DOI: 10.1021/acs.jpcb.8b07226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In this article, we propose an impressive and facile strategy to improve protein refolding using solid phase artificial molecular chaperones consisting of the surface-functionalized magnetic nanoparticles. Specifically, monotosyl-β-cyclodextrin connected to the surface of 3-aminopropyltriethoxysilane (APES)-modified magnetic nanoparticles is immobilized on the sepharose surface to promote interaction with exposed hydrophobic surfaces of partially folded (intermediates) and unfolded states of proteins. Their efficiencies were investigated by circular dichroism spectroscopy and photoluminescence spectroscopy of the protein. Although the mechanism of this method is based on principles of hydrophobic chromatography, this system is not only purging the native protein from inactive inclusion bodies but also improving the protein refolding process. We chose β-cyclodextrin (β-CD) considering multiple reports in the literature about its efficiency in protein refolding and its biocompatibility. To increase the surface area/volume ratio of the sepharose surface by nanoparticles, more β-CD molecules are connected to the sepharose surface to make a better interaction with proteins. We suppose that proteins are isolated in the nanospace created by bound cyclodextrins on the resin surface so intermolecular interactions are reduced. The architecture of nanoparticles was characterized by Fourier transform infrared spectra, X-ray diffraction, scanning electron microscopy images, energy dispersive X-ray spectroscopy, nuclear magnetic resonance (1H NMR and 13C NMR), and dynamic light scattering.
Collapse
Affiliation(s)
- Marziyeh Ghaeidamini
- School of Chemistry, University Collage of Science , University of Tehran , Tehran , Iran
| | - Ali N Kharat
- School of Chemistry, University Collage of Science , University of Tehran , Tehran , Iran
| | - Thomas Haertlé
- Department of Animal Nutrition , Poznan University of Life Sciences , 60-637 Poznan , Poland.,Biopolymers, Interactions, Assemblies, UR 1268 , Institut National de la Recherche Agronomique , 44000 Nantes , France.,Institute of Biochemistry and Biophysics , University of Tehran , Tehran , Iran
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi 110025 , India
| | - Ali A Saboury
- Institute of Biochemistry and Biophysics , University of Tehran , Tehran , Iran
| |
Collapse
|
12
|
Sarr M, Kronqvist N, Chen G, Aleksis R, Purhonen P, Hebert H, Jaudzems K, Rising A, Johansson J. A spidroin-derived solubility tag enables controlled aggregation of a designed amyloid protein. FEBS J 2018; 285:1873-1885. [PMID: 29604175 DOI: 10.1111/febs.14451] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/08/2018] [Accepted: 03/26/2018] [Indexed: 12/31/2022]
Abstract
Amyloidogenesis is associated with more than 30 diseases, but the molecular mechanisms involved in cell toxicity and fibril formation remain largely unknown. The inherent tendency of amyloid-forming proteins to aggregate renders expression, purification, and experimental studies challenging. NT* is a solubility tag derived from a spider silk protein that was recently introduced for the production of several aggregation-prone peptides and proteins at high yields. Herein, we investigate whether fusion to NT* can prevent amyloid fibril formation and enable controlled aggregation for experimental studies. As an example of an amyloidogenic protein, we chose the de novo-designed polypeptide β17. The fusion protein NT*-β17 was recombinantly expressed in Escherichia coli to produce high amounts of soluble and mostly monomeric protein. Structural analysis showed that β17 is kept in a largely unstructured conformation in fusion with NT*. After proteolytic release, β17 adopts a β-sheet conformation in a pH- and salt-dependent manner and assembles into amyloid-like fibrils. The ability of NT* to prevent premature aggregation and to enable structural studies of prefibrillar states may facilitate investigation of proteins involved in amyloid diseases.
Collapse
Affiliation(s)
- Médoune Sarr
- Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Huddinge, Sweden
| | - Nina Kronqvist
- Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Huddinge, Sweden
| | - Gefei Chen
- Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Huddinge, Sweden
| | - Rihards Aleksis
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Pasi Purhonen
- Department of Biosciences and Nutrition, Karolinska Institutet, and School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Huddinge, Sweden
| | - Hans Hebert
- Department of Biosciences and Nutrition, Karolinska Institutet, and School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Huddinge, Sweden
| | - Kristaps Jaudzems
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Anna Rising
- Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Huddinge, Sweden.,Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Johansson
- Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Huddinge, Sweden
| |
Collapse
|
13
|
Hoffmann D, Ebrahimi M, Gerlach D, Salzig D, Czermak P. Reassessment of inclusion body-based production as a versatile opportunity for difficult-to-express recombinant proteins. Crit Rev Biotechnol 2017; 38:729-744. [DOI: 10.1080/07388551.2017.1398134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Daniel Hoffmann
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Mehrdad Ebrahimi
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Doreen Gerlach
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Project group Bioresources, Giessen, Germany
| | - Denise Salzig
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Peter Czermak
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Project group Bioresources, Giessen, Germany
- Faculty of Biology and Chemistry, Justus Liebig University, Giessen, Germany
- Department of Chemical Engineering, Kansas State University, Manhattan, KS, USA
| |
Collapse
|
14
|
Carreón YJP, González-Gutiérrez J, Pérez-Camacho MI, Mercado-Uribe H. Patterns produced by dried droplets of protein binary mixtures suspended in water. Colloids Surf B Biointerfaces 2017; 161:103-110. [PMID: 29055238 DOI: 10.1016/j.colsurfb.2017.10.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 12/31/2022]
Abstract
Patterns formed by the evaporation of a drop containing biological molecules have provided meaningful information about certain pathologies. In this context, several works propose the study of protein solutions as a model to understand the formation of deposits of biological fluids. Generally, dry droplets of proteins in a saline solution create complex aggregates. Here, we present an experimental study on the formation of patterns produced by the evaporation of droplet suspensions containing a protein binary mixture. We explore the structural aspect of such deposits by using optical and atomic force microscopy. We found that salt is unnecessary for the formation of complex structures such as crystal clusters, dendritic and undulated branches, and interlocked chains. Such structural features allow us to differentiate among protein binary mixtures. Finally, we discuss the potential use of this finding to reveal the presence of a protein suspensions, the folded and unfolded state of a protein, as well as their structural changes.
Collapse
|
15
|
Mukherjee J, Gupta MN. Protein aggregates: Forms, functions and applications. Int J Biol Macromol 2017; 97:778-789. [DOI: 10.1016/j.ijbiomac.2016.11.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 11/02/2016] [Accepted: 11/05/2016] [Indexed: 11/15/2022]
|
16
|
Effects of ionic strength on inclusion body refolding at high concentration. Protein Expr Purif 2017; 130:100-106. [DOI: 10.1016/j.pep.2016.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 10/11/2016] [Accepted: 10/13/2016] [Indexed: 02/01/2023]
|
17
|
Salahuddin P, Siddiqi MK, Khan S, Abdelhameed AS, Khan RH. Mechanisms of protein misfolding: Novel therapeutic approaches to protein-misfolding diseases. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.06.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
18
|
Sadavarte R, Filipe CDM, Ghosh R. Recovery of functionally-active protein from inclusion bodies using a thermal-cycling method. Biotechnol Prog 2016; 33:133-139. [PMID: 27690284 DOI: 10.1002/btpr.2376] [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: 04/01/2016] [Revised: 09/27/2016] [Indexed: 11/05/2022]
Abstract
Heterologous overexpression of genes in Escherichia coli has made it possible to obtain high titers of recombinant proteins. However, this can result in the formation of aggregated protein particles known as 'inclusion bodies'. Protein sequestered as inclusion body is inactive and needs to be converted back to its functional form by refolding using appropriate techniques. In the current study inclusion bodies of the enzyme aminoglycoside nucleotidyl transferase (or ANT(2″)-Ia) were first solubilized in urea and subsequently subjected to thermal cycling under controlled conditions as part of the refolding strategy. Thermal cycling led to disaggregation of the individual protein chains and simultaneously refolding the released protein molecules to their native state. The optimum condition was identified as 10-80°C thermal cycling at 3°C s-1 for 2 h. Enzyme activity measurements showed that thermal cycling under optimized conditions resulted in 257% activity recovery when compared with nonrefolded protein. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:133-139, 2017.
Collapse
Affiliation(s)
- Rahul Sadavarte
- Dept. of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L7, Canada
| | - Carlos D M Filipe
- Dept. of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L7, Canada
| | - Raja Ghosh
- Dept. of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L7, Canada
| |
Collapse
|
19
|
Li Y, Chen F, Li Z, Li C, Zhang Y. Identification and Functional Characterization of Sesquiterpene Synthases from Xanthium strumarium. PLANT & CELL PHYSIOLOGY 2016; 57:630-41. [PMID: 26858282 DOI: 10.1093/pcp/pcw019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/18/2016] [Indexed: 05/16/2023]
Abstract
Xanthium strumarium synthesizes various pharmacologically active sesquiterpenes. The molecular characterization of sesquiterpene biosynthesis in X. strumarium has not been reported so far. In this study, the cDNAs coding for three sesquiterpene synthases (designated as XsTPS1, XsTPS2 and XsTPS3) were isolated using the X. strumarium transcriptome that we recently constructed. XsTPS1, XsTPS2 and XsTPS3 were revealed to have primary activities forming germacrene D, guaia-4,6-diene and germacrene A, respectively, by either ectopic expression in yeast cells or purified recombinant protein-based in vitro assays. Quantitative real-time PCRs and metabolite analysis for the different plant parts showed that the transcript abundance of XsTPS1-XsTPS3 is consistent with the accumulation pattern of their enzymatic products, supporting their biochemical functions in vivo. In particular, we discovered that none of the XsTPS2 product, guaia-4,6-diene, can be detected in one of the X. strumarium cultivars used in this study (it was named the Hubei-cultivar), in which a natural deletion of two A bases in the XsTPS2 cDNA disrupts its activity, which further confirmed the proposed biochemical role of XsTPS2 in X. strumarium in vivo.
Collapse
Affiliation(s)
- Yuanjun Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Science, Wuhan 430074, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangfang Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Science, Wuhan 430074, China
| | - Zhenqiu Li
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Changfu Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Science, Wuhan 430074, China
| | - Yansheng Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Science, Wuhan 430074, China
| |
Collapse
|
20
|
Kenry K, Loh KP, Lim CT. Selective concentration-dependent manipulation of intrinsic fluorescence of plasma proteins by graphene oxide nanosheets. RSC Adv 2016. [DOI: 10.1039/c6ra04978h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We investigate the molecular interactions between graphene oxide (GO) and blood plasma proteins, in particular, the influence of GO on the intrinsic fluorescence of these proteins.
Collapse
Affiliation(s)
- Kenry Kenry
- NUS Graduate School for Integrative Sciences and Engineering
- National University of Singapore
- Singapore 117456
- Singapore
- Centre for Advanced 2D Materials and Graphene Research Centre
| | - Kian Ping Loh
- Centre for Advanced 2D Materials and Graphene Research Centre
- National University of Singapore
- Singapore 117543
- Singapore
- Department of Chemistry
| | - Chwee Teck Lim
- Centre for Advanced 2D Materials and Graphene Research Centre
- National University of Singapore
- Singapore 117543
- Singapore
- Department of Biomedical Engineering
| |
Collapse
|
21
|
Ryś S, Muca R, Kołodziej M, Piątkowski W, Dürauer A, Jungbauer A, Antos D. Design and optimization of protein refolding with crossflow ultrafiltration. Chem Eng Sci 2015. [DOI: 10.1016/j.ces.2015.03.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
22
|
Gharanlar J, Hosseinkhani S, Sajedi RH, Yaghmaei P. The Effect of Surface Charge Saturation on Heat-induced Aggregation of Firefly Luciferase. Photochem Photobiol 2015; 91:1156-64. [PMID: 25989897 DOI: 10.1111/php.12467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/27/2015] [Indexed: 10/23/2022]
Abstract
We present here the effect of firefly luciferase surface charge saturation and the presence of some additives on its thermal-induced aggregation. Three mutants of firefly luciferase prepared by introduction of surface Arg residues named as 2R, 3R and 5R have two, three and five additional arginine residues substituted at their surface compared to native luciferase; respectively. Turbidimetric study of heat-induced aggregation indicates that all three mutants were reproducibly aggregated at higher rates relative to wild type in spite of their higher thermostability. Among them, 2R had most evaluated propensity to heat-induced aggregation. Therefore, the hydrophilization followed by appearing of more substituted arginine residues with positive charge on the firefly luciferase surface was not reduced its thermal aggregation. Nevertheless, at the same condition in the presence of charged amino acids, e.g. Arg, Lys and Glu, as well as a hydrophobic amino acid, e.g. Val, the heat-induced aggregation of wild type and mutants of firefly luciferases was markedly decelerated than those in the absence of additives. On the basis of obtained results it seems, relinquishment of variety in charge of amino acid side chains, they via local interactions with proteins cause to decrease rate and extent of their thermal aggregation.
Collapse
Affiliation(s)
- Jamileh Gharanlar
- Department of Biology, Faculty of Basic Sciences, Tehran Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Parichehr Yaghmaei
- Department of Biology, Faculty of Basic Sciences, Tehran Science and Research Branch, Islamic Azad University, Tehran, Iran
| |
Collapse
|
23
|
Bak A, Leung D, Barrett SE, Forster S, Minnihan EC, Leithead AW, Cunningham J, Toussaint N, Crocker LS. Physicochemical and formulation developability assessment for therapeutic peptide delivery--a primer. AAPS JOURNAL 2014; 17:144-55. [PMID: 25398427 DOI: 10.1208/s12248-014-9688-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 10/09/2014] [Indexed: 12/12/2022]
Abstract
Peptides are an important class of endogenous ligands that regulate key biological cascades. As such, peptides represent a promising therapeutic class with the potential to alleviate many severe disease states. Despite their therapeutic potential, peptides frequently pose drug delivery challenges to scientists. This review introduces the physicochemical, biophysical, biopharmaceutical, and formulation developability aspects of peptides pertinent to the drug discovery-to-development interface. It introduces the relevance of these properties with respect to the delivery modalities available for peptide pharmaceuticals, with the parenteral route being the most prevalent route of administration. This review also presents characterization strategies for oral delivery of peptides with the aim of illuminating developability issues with the drug candidate. A brief overview of other routes of administration, including inhaled, transdermal, and intranasal routes, is provided as these routes are generally preferred by patients over injectables. Finally, this review presents formulation techniques to mitigate some of the developability obstacles associated with peptide delivery. The authors emphasize opportunities for the thoughtful application of pharmaceutical science to the development of peptide drugs and to the general advancement of this promising class of pharmaceuticals.
Collapse
Affiliation(s)
- Annette Bak
- Discovery Pharmaceutical Sciences, Merck & Co, Kenilworth, New Jersey, USA,
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
|
25
|
Serebryany E, King JA. The βγ-crystallins: native state stability and pathways to aggregation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 115:32-41. [PMID: 24835736 DOI: 10.1016/j.pbiomolbio.2014.05.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 04/30/2014] [Accepted: 05/02/2014] [Indexed: 01/26/2023]
Abstract
The βγ-crystallins are among the most stable and long-lived proteins in the human body. With increasing age, however, they transform to high molecular weight light-scattering aggregates, resulting in cataracts. This occurs despite the presence in the lens of high concentrations of the a-crystallin chaperones. Aggregation of crystallins can be induced in vitro by a variety of stresses, including acidic pH, ultraviolet light, oxidative damage, heating or freezing, and specific amino acid substitutions. Accumulating evidence points to the existence of specific biochemical pathways of protein: protein interaction and polymerization. We review the methods used for studying crystallin stability and aggregation and discuss the sometimes counterintuitive relationships between factors that favor native state stability and those that favor non-native aggregation. We discuss the behavior of βγ-crystallins in mixtures and their chaperone ability; the consequences of missense mutations and covalent damage to the side-chains; and the evolutionary strategies that have shaped these proteins. Efforts are ongoing to reveal the nature of cataractous crystallin aggregates and understand the mechanisms of aggregation in the context of key models of protein polymerization: amyloid, native-state, and domain-swapped. Such mechanistic understanding is likely to be of value for the development of therapeutic interventions and draw attention to unanswered questions about the relationship between a protein's native state stability and its transformation to an aggregated state.
Collapse
Affiliation(s)
- Eugene Serebryany
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jonathan A King
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States.
| |
Collapse
|
26
|
Der BS, Kluwe C, Miklos AE, Jacak R, Lyskov S, Gray JJ, Georgiou G, Ellington AD, Kuhlman B. Alternative computational protocols for supercharging protein surfaces for reversible unfolding and retention of stability. PLoS One 2013; 8:e64363. [PMID: 23741319 PMCID: PMC3669367 DOI: 10.1371/journal.pone.0064363] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/11/2013] [Indexed: 12/29/2022] Open
Abstract
Reengineering protein surfaces to exhibit high net charge, referred to as “supercharging”, can improve reversibility of unfolding by preventing aggregation of partially unfolded states. Incorporation of charged side chains should be optimized while considering structural and energetic consequences, as numerous mutations and accumulation of like-charges can also destabilize the native state. A previously demonstrated approach deterministically mutates flexible polar residues (amino acids DERKNQ) with the fewest average neighboring atoms per side chain atom (AvNAPSA). Our approach uses Rosetta-based energy calculations to choose the surface mutations. Both protocols are available for use through the ROSIE web server. The automated Rosetta and AvNAPSA approaches for supercharging choose dissimilar mutations, raising an interesting division in surface charging strategy. Rosetta-supercharged variants of GFP (RscG) ranging from −11 to −61 and +7 to +58 were experimentally tested, and for comparison, we re-tested the previously developed AvNAPSA-supercharged variants of GFP (AscG) with +36 and −30 net charge. Mid-charge variants demonstrated ∼3-fold improvement in refolding with retention of stability. However, as we pushed to higher net charges, expression and soluble yield decreased, indicating that net charge or mutational load may be limiting factors. Interestingly, the two different approaches resulted in GFP variants with similar refolding properties. Our results show that there are multiple sets of residues that can be mutated to successfully supercharge a protein, and combining alternative supercharge protocols with experimental testing can be an effective approach for charge-based improvement to refolding.
Collapse
Affiliation(s)
- Bryan S. Der
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Christien Kluwe
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Aleksandr E. Miklos
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
- Applied Research Laboratories, University of Texas at Austin, Austin, Texas, United States of America
| | - Ron Jacak
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sergey Lyskov
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - George Georgiou
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Andrew D. Ellington
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
- Applied Research Laboratories, University of Texas at Austin, Austin, Texas, United States of America
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
| |
Collapse
|
27
|
Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, Gray JJ, Das R. Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). PLoS One 2013; 8:e63906. [PMID: 23717507 PMCID: PMC3661552 DOI: 10.1371/journal.pone.0063906] [Citation(s) in RCA: 275] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 04/04/2013] [Indexed: 11/21/2022] Open
Abstract
The Rosetta molecular modeling software package provides experimentally tested and rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, nucleic acids, and a growing number of non-natural polymers. Despite its free availability to academic users and improving documentation, use of Rosetta has largely remained confined to developers and their immediate collaborators due to the code's difficulty of use, the requirement for large computational resources, and the unavailability of servers for most of the Rosetta applications. Here, we present a unified web framework for Rosetta applications called ROSIE (Rosetta Online Server that Includes Everyone). ROSIE provides (a) a common user interface for Rosetta protocols, (b) a stable application programming interface for developers to add additional protocols, (c) a flexible back-end to allow leveraging of computer cluster resources shared by RosettaCommons member institutions, and (d) centralized administration by the RosettaCommons to ensure continuous maintenance. This paper describes the ROSIE server infrastructure, a step-by-step 'serverification' protocol for use by Rosetta developers, and the deployment of the first nine ROSIE applications by six separate developer teams: Docking, RNA de novo, ERRASER, Antibody, Sequence Tolerance, Supercharge, Beta peptide design, NCBB design, and VIP redesign. As illustrated by the number and diversity of these applications, ROSIE offers a general and speedy paradigm for serverification of Rosetta applications that incurs negligible cost to developers and lowers barriers to Rosetta use for the broader biological community. ROSIE is available at http://rosie.rosettacommons.org.
Collapse
Affiliation(s)
- Sergey Lyskov
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Fang-Chieh Chou
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
| | - Shane Ó. Conchúir
- California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Bryan S. Der
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kevin Drew
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - Daisuke Kuroda
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jianqing Xu
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Brian D. Weitzner
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - P. Douglas Renfrew
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - Parin Sripakdeevong
- Biophysics Program, Stanford University, Stanford, California, United States of America
| | - Benjamin Borgo
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - James J. Havranek
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Tanja Kortemme
- California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Graduate Group in Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Richard Bonneau
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
- Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
- Program in Molecular Biophysics, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Physics, Stanford University, Stanford, California, United States of America
| |
Collapse
|
28
|
Tohmé M, Maschalidi S, Manoury B. In vitro digestion with proteases producing MHC class II ligands. Methods Mol Biol 2013; 960:509-515. [PMID: 23329510 DOI: 10.1007/978-1-62703-218-6_37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Proteases generate peptides that bind to MHC class II molecules to interact with a wide diversity of CD4(+) T cells. They are expressed in dedicated organelles: endosomes and lysosomes of professional antigen presenting cells (pAPCs) such as B cells, macrophages, and dendritic cells. The identification of endosomal proteases which produce antigenic peptides is important, for example, for better vaccination and to prevent autoimmune diseases. Here, we describe a panel of technics (in vitro digestion assays of protein with recombinant proteases or purified endosomes/lysosomes, T cell stimulation) to monitor the production of MHC class II ligands.
Collapse
Affiliation(s)
- Mira Tohmé
- Sorbonne Paris Cité, Faculté de médecine René Descartes, INSERM U1013 and Université Paris Descartes, Paris, France
| | - Sophia Maschalidi
- Sorbonne Paris Cité, Faculté de médecine René Descartes, INSERM U1013 and Université Paris Descartes, Paris, France
| | - Bénédicte Manoury
- Sorbonne Paris Cité, Faculté de médecine René Descartes, INSERM U1013 and Université Paris Descartes, Paris, France.
| |
Collapse
|
29
|
Ji F, Jung J, Koharudin LMI, Gronenborn AM. The human W42R γD-crystallin mutant structure provides a link between congenital and age-related cataracts. J Biol Chem 2012; 288:99-109. [PMID: 23124202 DOI: 10.1074/jbc.m112.416354] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Some mutants of human γD-crystallin are closely linked to congenital cataracts, although the detailed molecular mechanisms of mutant-associated cataract formation are generally not known. Here we report on a recently discovered γD-crystallin mutant (W42R) that has been linked to autosomal dominant, congenital cataracts in a Chinese family. The mutant protein is much less soluble and stable than wild-type γD-crystallin. We solved the crystal structure of W42R at 1.7 Å resolution, which revealed only minor differences from the wild-type structure. Interestingly, the W42R variant is highly susceptible to protease digestion, suggesting the presence of a small population of partially unfolded protein. This partially unfolded species was confirmed and quantified by NMR spectroscopy. Hydrogen/deuterium exchange experiments revealed chemical exchange between the folded and unfolded species. Exposure of wild-type γD-crystallin to UV caused damage to the N-terminal domain of the protein, resulting in very similar proteolytic susceptibility as observed for the W42R mutant. Altogether, our combined data allowed us to propose a model for W42R pathogenesis, with the W42R mutant serving as a mimic for photodamaged γD-crystallin involved in age-related cataract.
Collapse
Affiliation(s)
- Fangling Ji
- School of Life Science and Biotechnology, Dalian University of Technology, Lingong Road, Dalian 116024, China
| | | | | | | |
Collapse
|
30
|
Kawaji S, Gumber S, Whittington RJ. Evaluation of the immunogenicity of Mycobacterium avium subsp. paratuberculosis (MAP) stress-associated recombinant proteins. Vet Microbiol 2012; 155:298-309. [DOI: 10.1016/j.vetmic.2011.08.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/16/2011] [Accepted: 08/19/2011] [Indexed: 12/09/2022]
|
31
|
Cloning, expression, purification, and characterization of a glutamate-specific endopeptidase from Bacillus licheniformis. Protein Expr Purif 2012; 82:138-43. [PMID: 22202650 DOI: 10.1016/j.pep.2011.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 12/05/2011] [Accepted: 12/06/2011] [Indexed: 11/17/2022]
|
32
|
Sanz-Barrio R, Millán AFS, Corral-Martínez P, Seguí-Simarro JM, Farran I. Tobacco plastidial thioredoxins as modulators of recombinant protein production in transgenic chloroplasts. PLANT BIOTECHNOLOGY JOURNAL 2011; 9:639-50. [PMID: 21426478 DOI: 10.1111/j.1467-7652.2011.00608.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Thioredoxins (Trxs) are small ubiquitous disulphide proteins widely known to enhance expression and solubility of recombinant proteins in microbial expression systems. Given the common evolutionary heritage of chloroplasts and bacteria, we attempted to analyse whether plastid Trxs could also act as modulators of recombinant protein expression in transgenic chloroplasts. For that purpose, two tobacco Trxs (m and f) with different phylogenetic origins were assessed. Using plastid transformation, we assayed two strategies: the fusion and the co-expression of Trxs with human serum albumin (HSA), which was previously observed to form large protein bodies in tobacco chloroplasts. Our results indicate that both Trxs behave similarly as regards HSA accumulation, although they act differently when fused or co-expressed with HSA. Trxs-HSA fusions markedly increased the final yield of HSA (up to 26% of total protein) when compared with control lines that only expressed HSA; this increase was mainly caused by higher HSA stability of the fused proteins. However, the fusion strategy failed to prevent the formation of protein bodies within chloroplasts. On the other hand, the co-expression constructs gave rise to an absence of large protein bodies although no more soluble HSA was accumulated. In these plants, electron micrographs showed HSA and Trxs co-localization in small protein bodies with fibrillar texture, suggesting a possible influence of Trxs on HSA solubilization. Moreover, the in vitro chaperone activity of Trx m and f was demonstrated, which supports the hypothesis of a direct relationship between Trx presence and HSA aggregates solubilization in plants co-expressing both proteins.
Collapse
Affiliation(s)
- Ruth Sanz-Barrio
- Instituto de Agrobiotecnología (UPNA-CSIC-Gobierno de Navarra), Pamplona, Spain
| | | | | | | | | |
Collapse
|
33
|
Mahler B, Doddapaneni K, Kleckner I, Yuan C, Wistow G, Wu Z. Characterization of a transient unfolding intermediate in a core mutant of γS-crystallin. J Mol Biol 2010; 405:840-50. [PMID: 21108948 DOI: 10.1016/j.jmb.2010.11.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 10/15/2010] [Accepted: 11/01/2010] [Indexed: 10/18/2022]
Abstract
In many age-related and neurological diseases, formerly native proteins aggregate via formation of a partially unfolded intermediate. γS-Crystallin is a highly stable structural protein of the eye lens. In the mouse Opj cataract, a non-conservative F9S mutation in the N-terminal domain core of γS allows the adoption of a native fold but renders the protein susceptible to temperature- and concentration-dependent aggregation, including fibril formation. Hydrogen/deuterium exchange and denaturant unfolding studies of this mutant protein (Opj) have suggested the existence of a partially unfolded intermediate in its aggregation pathway. Here, we used NMR and fluorescence spectroscopy to obtain evidence for this intermediate. In 3.5 M urea, Opj forms a stable and partially unfolded entity that is characterized by an unstructured N-terminal domain and a largely intact C-terminal domain. Under physiologically relevant conditions, Carr-Purcell-Meiboom-Gill T(2)-relaxation dispersion experiments showed that the N-terminal domain residues were in conformational exchange with a loosely structured intermediate with a population of 1-2%, which increased with temperature. This provides direct evidence for a model in which proteins of native fold can explore an intermediate state with an increased propensity for formation of aggregates, such as fibrils. For the crystallins, this shows how inherited sequence variants or environmentally induced modifications can destabilize a well-folded protein, allowing the formation of intermediates able to act as nucleation sites for aggregation and the accumulation of light-scattering centers in the cataractous lens.
Collapse
Affiliation(s)
- Bryon Mahler
- Biochemistry Department, Ohio State University, Columbus, OH 43210, USA
| | | | | | | | | | | |
Collapse
|
34
|
Kudou M, Yumioka R, Ejima D, Arakawa T, Tsumoto K. A novel protein refolding system using lauroyl-l-glutamate as a solubilizing detergent and arginine as a folding assisting agent. Protein Expr Purif 2010; 75:46-54. [PMID: 20817098 DOI: 10.1016/j.pep.2010.08.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 08/23/2010] [Accepted: 08/26/2010] [Indexed: 11/26/2022]
Abstract
More than 50 detergents, including acylated amino acid derivatives, were screened for their ability to solubilize and refold recombinant proteins expressed as inclusion bodies. Two model proteins, human interleukin-6 and microbial transglutaminase, were solubilized by these detergents and the solubilized proteins were rapidly diluted for testing their solubilization and refolding effectiveness. Long chain-acylated amino acid derivatives having dicarboxylic acid moieties were found to be superior to others under the conditions tested. In particular, lauroyl-l-glutamate (C12-l-Glu) showed the highest recovery of the native proteins. The effectiveness of dilution refolding was greatly improved by adding aggregation suppressive arginine into the refolding solvents. To gain understanding how this detergent works, interactions between detergents and proteins were examined using spectroscopic and native gel electrophoretic analyses, showing ideal properties for C12-l-Glu as a solubilzing agent, i.e. highly reversible nature of the detergent binding to the model globular proteins and of the conformational changes. These properties most likely have contributed to the effective protein solubilzation and refolding of inclusion bodies using C12-l-Glu and arginine.
Collapse
Affiliation(s)
- Motonori Kudou
- Department of Medical Genome Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Japan
| | | | | | | | | |
Collapse
|
35
|
Acosta-Sampson L, King J. Partially folded aggregation intermediates of human gammaD-, gammaC-, and gammaS-crystallin are recognized and bound by human alphaB-crystallin chaperone. J Mol Biol 2010; 401:134-52. [PMID: 20621668 DOI: 10.1016/j.jmb.2010.05.067] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Revised: 05/20/2010] [Accepted: 05/26/2010] [Indexed: 11/16/2022]
Abstract
Human gamma-crystallins are long-lived, unusually stable proteins of the eye lens exhibiting duplicated, double Greek key domains. The lens also contains high concentrations of the small heat shock chaperone alpha-crystallin, which suppresses aggregation of model substrates in vitro. Mature-onset cataract is believed to represent an aggregated state of partially unfolded and covalently damaged crystallins. Nonetheless, the lack of cell or tissue culture for anucleate lens fibers and the insoluble state of cataract proteins have made it difficult to identify the conformation of the human gamma-crystallin substrate species recognized by human alpha-crystallin. The three major human lens monomeric gamma-crystallins, gammaD, gammaC, and gammaS, all refold in vitro in the absence of chaperones, on dilution from denaturant into buffer. However, off-pathway aggregation of the partially folded intermediates competes with productive refolding. Incubation with human alphaB-crystallin chaperone during refolding suppressed the aggregation pathways of the three human gamma-crystallin proteins. The chaperone did not dissociate or refold the aggregated chains under these conditions. The alphaB-crystallin oligomers formed long-lived stable complexes with their gammaD-crystallin substrates. Using alpha-crystallin chaperone variants lacking tryptophans, we obtained fluorescence spectra of the chaperone-substrate complex. Binding of substrate gamma-crystallins with two or three of the four buried tryptophans replaced by phenylalanines showed that the bound substrate remained in a partially folded state with neither domain native-like. These in vitro results provide support for protein unfolding/protein aggregation models for cataract, with alpha-crystallin suppressing aggregation of damaged or unfolded proteins through early adulthood but becoming saturated with advancing age.
Collapse
Affiliation(s)
- Ligia Acosta-Sampson
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 68-330, Cambridge, MA 02139, USA
| | | |
Collapse
|
36
|
Beta-cyclodextrin-bonded silica assists alkaline phosphatase and carbonic anhydrase refolding in a solid phase assisted refolding approach. Process Biochem 2010. [DOI: 10.1016/j.procbio.2009.09.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
37
|
Listwan P, Pédelacq JD, Lockard M, Bell C, Terwilliger TC, Waldo GS. The optimization of in vitro high-throughput chemical lysis of Escherichia coli. Application to ACP domain of the polyketide synthase ppsC from Mycobacterium tuberculosis. ACTA ACUST UNITED AC 2010; 11:41-9. [PMID: 20069378 PMCID: PMC2855807 DOI: 10.1007/s10969-009-9077-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Accepted: 12/30/2009] [Indexed: 11/26/2022]
Abstract
Protein production in Escherichia coli involves high-level expression in a culture, followed by harvesting of the cells and finally their disruption, or lysis, to release the expressed proteins. We compare three high-throughput chemical lysis methods to sonication, using a robotic platform and methodologies developed in our laboratory [1]. Under the same expression conditions, all lysis methods varied in the degree of released soluble proteins. With a set of 96 test proteins, we used our split GFP to quantify the soluble and insoluble protein fractions after lysis. Both the amount of soluble protein and the percentage recovered in the soluble fraction using SoluLyse were well correlated with sonication. Two other methods, Bugbuster and lysozyme, did not correlate well with sonication. Considering the effects of lysis methods on protein solubility is especially important when accurate protein solubility measurements are needed, for example, when testing adjuvants, growth media, temperature, or when establishing the effects of truncation or sequence variation on protein stability.
Collapse
Affiliation(s)
- Pawel Listwan
- Bioscience Division, MS-M888, Los Alamos National Laboratory, Bikini Atoll Rd, SM30, Los Alamos, NM 87545, USA.
| | | | | | | | | | | |
Collapse
|
38
|
Rational Design of Multiple TB Antigens TB10.4 and TB10.4-Ag85B as Subunit Vaccine Candidates Against Mycobacterium Tuberculosis. Pharm Res 2009; 27:224-34. [DOI: 10.1007/s11095-009-9995-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Accepted: 10/12/2009] [Indexed: 10/20/2022]
|
39
|
Matsuoka T, Hamada H, Matsumoto K, Shiraki K. Indispensable structure of solution additives to prevent inactivation of lysozyme for heating and refolding. Biotechnol Prog 2009; 25:1515-24. [DOI: 10.1002/btpr.245] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
40
|
Kang MS, Okuyama M, Mori H, Kimura A. The first alpha-1,3-glucosidase from bacterial origin belonging to glycoside hydrolase family 31. Biochimie 2009; 91:1434-42. [PMID: 19683032 DOI: 10.1016/j.biochi.2009.07.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 07/31/2009] [Indexed: 01/26/2023]
Abstract
Genome analysis of Lactobacillus johnsonii NCC533 has been recently completed. One of its annotated genes, lj0569, encodes the protein having the conserved domain of glycoside hydrolase family 31. Its homolog gene (ljag31) in L. johnsonii NBRC13952 was cloned and expressed using an Escherichia coli expression system, resulting in poor production of recombinant LJAG31 protein due to inclusion body formation. Production of soluble recombinant LJAG31 was improved with high concentration of NaCl in medium, possible endogenous chaperone induction by benzyl alcohol, and over-expression of GroES-GroEL chaperones. Recombinant LJAG31 was an alpha-glucosidase with broad substrate specificity toward both homogeneous and heterogeneous substrates. This enzyme displayed higher specificity (in terms of k(cat)/K(m)) toward nigerose, maltulose, and kojibiose than other natural substrates having an alpha-glucosidic linkage at the non-reducing end, which suggests that these sugars are candidates for prebiotics contributing to the growth of L. johnsonii. To our knowledge, LJAG31 is the first bacterial alpha-1,3-glucosidase to be characterized with a high k(cat)/K(m) value for nigerose [alpha-d-Glcp-(1 --> 3)-d-Glcp]. Transglucosylation of 4-nitrophenyl alpha-d-glucopyranoside produced two 4-nitrophenyl disaccharides (4-nitrophenyl alpha-nigeroside and 4-nitrophenyl alpha-isomaltoside). These hydrolysis and transglucosylation properties of LJAG31 are different from those of mold (Acremonium implicatum) alpha-1,3-glucosidase of glycoside hydrolase family 31.
Collapse
Affiliation(s)
- Min-Sun Kang
- Division of Applied Bioscience, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan.
| | | | | | | |
Collapse
|
41
|
Madar DJ, Patel AS, Lees WJ. Comparison of the oxidative folding of lysozyme at a high protein concentration using aromatic thiols versus glutathione. J Biotechnol 2009; 142:214-9. [PMID: 19477205 DOI: 10.1016/j.jbiotec.2009.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 05/11/2009] [Accepted: 05/19/2009] [Indexed: 10/20/2022]
Abstract
The production of proteins using recombinant DNA technology often requires the use of in vitro protein folding. In order to facilitate in vitro protein folding, a redox buffer is added to the protein folding mixture. The redox buffer is composed of a small molecule disulfide and/or a small molecule thiol. Recently, redox buffers containing aromatic thiols have been shown to be an improvement over traditional redox buffers such as glutathione. For in vitro protein folding to be relevant to protein production on a larger scale, high protein concentrations are required to avoid large volumes of folding buffer. Therefore, we investigated the in vitro folding of lysozyme at 1 mg/mL instead of the traditional 0.1 mg/mL. Aromatic thiols and aromatic disulfides were compared directly with glutathione and glutathione disulfide, the most commonly used redox buffer. Folding experiments at pH 7 using aromatic thiols increased the yield by 20-40% and the folding rate constants by as much as 11 times relative to glutathione. At pH 8, improvements in yields of up to 25% and up to a 7-fold increase in folding rate constants were demonstrated. The effect of aromatic disulfide concentration was also investigated.
Collapse
Affiliation(s)
- David J Madar
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | | |
Collapse
|
42
|
Pinsach J, de Mas C, López-Santín J, Striedner G, Bayer K. Influence of process temperature on recombinant enzyme activity in Escherichia coli fed-batch cultures. Enzyme Microb Technol 2008. [DOI: 10.1016/j.enzmictec.2008.08.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
43
|
Mapping the putative binding site for uPA protein in Esophageal Cancer-Related Gene 2 by heteronuclear NMR method. Arch Biochem Biophys 2008; 479:153-7. [DOI: 10.1016/j.abb.2008.08.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Revised: 08/25/2008] [Accepted: 08/25/2008] [Indexed: 11/23/2022]
|
44
|
|
45
|
Refolding of endostatin from inclusion bodies using high hydrostatic pressure. Anal Biochem 2008; 379:32-9. [DOI: 10.1016/j.ab.2008.04.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Revised: 04/08/2008] [Accepted: 04/14/2008] [Indexed: 11/20/2022]
|
46
|
McCoy J, Lavallie E. Expression and purification of thioredoxin fusion proteins. ACTA ACUST UNITED AC 2008; Chapter 16:Unit16.8. [PMID: 18265135 DOI: 10.1002/0471142727.mb1608s28] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This unit describes a gene fusion expression system that uses thioredoxin, the product of the Escherichia coli trxA gene, as the fusion partner. The system is particularly useful for high-level production of soluble fusion proteins in the E. coli cytoplasm; in many cases heterologous proteins produced as thioredoxin fusion proteins are correctly folded and display full biological activity. Protein fusions to His-patch Trx can usually be purified in a single step from cell lysates. Additional protocols describe E. coli cell lysis using a French pressure cell and fractionation, osmotic release of thioredoxin fusion proteins from the E. coli cytoplasm, and heat treatment to purify some thioredoxin fusion proteins.
Collapse
Affiliation(s)
- J McCoy
- Genetics Institute, Cambridge, Massachusetts, USA
| | | |
Collapse
|
47
|
Vlugt-Wensink KDF, Meijer YJ, van Steenbergen MJ, Verrijk R, Jiskoot W, Crommelin DJA, Hennink WE. Effect of excipients on the encapsulation efficiency and release of human growth hormone from dextran microspheres. Eur J Pharm Biopharm 2007; 67:589-96. [PMID: 17540550 DOI: 10.1016/j.ejpb.2007.04.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2006] [Revised: 04/09/2007] [Accepted: 04/12/2007] [Indexed: 10/23/2022]
Abstract
The possibility was investigated to modulate the encapsulation efficiency and release of human growth hormone (hGH) from hydroxyl ethyl methacrylated dextran (dex-HEMA) hydrogel microspheres by using excipients. Microspheres were prepared by polymerization of dex-HEMA in an aqueous two-phase system of this polymer and PEG with or without excipients (Tween 80, pluronic F68, sucrose, NaCl, urea or methionine). High hGH encapsulation efficiencies (50-70%) were obtained for microspheres prepared without excipients and with Tween 80, NaCl or methionine. Substantially lower encapsulation efficiencies (27% and 19%, respectively) were obtained for microspheres prepared in the presence of sucrose and urea, which was attributed to the more favoured partitioning of hGH over the PEG-phase due to higher hydrophobicity of the (partly) denatured hGH. Likely, differences in precipitate size of the encapsulated hGH resulted in different release profiles between microspheres prepared without excipients (biphasic release: 2 days delay time followed by 6 days release) and the release profile for microspheres prepared with Tween 80, pluronic F68, sucrose, NaCl and urea (release over a period of 6-8 days (without a delay time)). Microspheres prepared with methionine showed a concentration-dependent delay time varying from 0 to 2 days followed by almost zero-order release over 6 days, attributed to the effect of methionine on the polymerization of dex-HEMA. Especially, Tween 80 and methionine are attractive excipients since hGH was encapsulated in high yield (60-70%) and the protein was released from the microspheres mainly in its monomeric form without a delay time and with an almost zero-order release over 6-8 days.
Collapse
|
48
|
Maeda R, Ado K, Takeda N, Taniguchi Y. Promotion of insulin aggregation by protein disulfide isomerase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:1619-27. [PMID: 17920002 DOI: 10.1016/j.bbapap.2007.08.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2007] [Revised: 07/31/2007] [Accepted: 08/21/2007] [Indexed: 10/22/2022]
Abstract
We examined the aggregation of insulin as a result of reduction of disulfide bonds catalyzed by protein disulfide isomerase (PDI) using various techniques. We demonstrated the kinetic correlation between PDI-catalyzed insulin reduction and the aggregate formation, the relationship between aggregation and amyloid formation, and the structural information on the secondary structure of the aggregates. The initial rate of PDI-catalyzed reduction of insulin, apparent rate constants of aggregate growth for sigmoidal features, and lag times were obtained by changing the PDI concentration, temperature, and insulin concentration. In situ kinetics were studied using the dyes; thioflavin T (ThT) and Congo red (CR) in addition to turbidimetry with the insulin reduction by PDI. The ThT and CR binding assay revealed sigmoidal kinetics, and the spectrum of binding CR showed a red shift against time, suggesting an orderly formation of insulin aggregates. The secondary structure of the PDI-promoted insulin aggregates showed antiparallel beta-sheet conformation by FT-IR measurement.
Collapse
Affiliation(s)
- Ryosuke Maeda
- Department of Materials Science and Chemical Engineering, Kitakyushu National College of Technology, 5-20-1 Shii, Kokuraminami-ku, Kitakyushu, Fukuoka 802-0985, Japan
| | | | | | | |
Collapse
|
49
|
Zaveckas M, Zvirbliene A, Zvirblis G, Chmieliauskaite V, Bumelis V, Pesliakas H. Effect of surface histidine mutations and their number on the partitioning and refolding of recombinant human granulocyte-colony stimulating factor (Cys17Ser) in aqueous two-phase systems containing chelated metal ions. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 852:409-19. [PMID: 17339136 DOI: 10.1016/j.jchromb.2007.01.051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Revised: 01/13/2007] [Accepted: 01/29/2007] [Indexed: 10/23/2022]
Abstract
High-level expression of recombinant proteins in Escherichia coli frequently leads to the formation of insoluble protein aggregates, termed inclusion bodies. In order to recover a native protein from inclusion bodies, various protein refolding techniques have been developed. Column-based refolding methods and refolding in aqueous two-phase systems are often an attractive alternative to dilution refolding due to simultaneous purification and improved refolding yields. In this work, the effect of surface histidine mutations and their number on the partitioning and refolding of recombinant human granulocyte-colony stimulating factor Cys17Ser variant (rhG-CSF (C17S)) from solubilized inclusion bodies in aqueous two-phase systems polyethylene glycol (PEG)-dextran, containing metal ions, chelated by dye Light Resistant Yellow 2KT (LR Yellow 2KT)-PEG derivative, was investigated. Human G-CSF is a growth factor that regulates the production of mature neutrophilic granulocytes from the precursor cells. Initially, the role of His156 and His170 residues in the interaction of rhG-CSF (C17S) with Cu(II), Ni(II) and Hg(II) ions, chelated by LR Yellow 2KT-PEG, was investigated at pH 7.0 by means of affinity partitioning of purified, correctly folded rhG-CSF (C17S) mutants. It was determined that both His156 and His170 mutations reduced the affinity of rhG-CSF (C17S) for chelated Cu(II) ions at pH 7.0. His170 mutation significantly reduced the affinity of protein for chelated Ni(II) ions. However, histidine mutations had only a small effect on the affinity of protein for Hg(II) ions. The influence of His156 and His170 mutations on the refolding of rhG-CSF (C17S) from solubilized inclusion bodies in aqueous two-phase systems PEG-dextran, containing chelated Ni(II) and Hg(II) ions, was investigated. Reversible interaction of protein mutants with chelated metal ions was used for refolding in aqueous two-phase systems. Both histidine mutations resulted in a significant decrease of protein refolding efficiency in two-phase systems containing chelated Ni(II) ions, while in the presence of chelated Hg(II) ions their effect on protein refolding was negligible. Refolding studies of rhG-CSF variants with different number of histidine mutations revealed that a direct correlation exists between the number of surface histidine residues and refolding efficiency of rhG-CSF variant in two-phase systems containing chelated Ni(II) ions. This method of protein refolding in aqueous two-phase systems containing chelated metal ions should be applicable to other recombinant proteins that contain accessible histidine residues.
Collapse
|
50
|
Thuy Le AT, Schumann W. A novel cold-inducible expression system for Bacillus subtilis. Protein Expr Purif 2007; 53:264-9. [PMID: 17307364 DOI: 10.1016/j.pep.2006.12.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2006] [Revised: 12/19/2006] [Accepted: 12/22/2006] [Indexed: 11/21/2022]
Abstract
Production of recombinant proteins at low temperatures is one strategy to prevent formation of protein aggregates and the use of an expensive inducer such as IPTG. We report on the construction of two expression vectors both containing the cold-inducible des promoter of Bacillus subtilis, where one allows intra- and the other extracellular synthesis of recombinant proteins. Production of recombinant proteins started within the first 30min after temperature downshock to 25 degrees C and continued for about 5h.
Collapse
Affiliation(s)
- Ai Thi Thuy Le
- Institute of Genetics, Universität Bayreuth, D-95440 Bayreuth, Germany
| | | |
Collapse
|