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Mendoza C, Hanegan C, Sperry A, Vargas L, Case T, Bikman B, Mizrachi D. Insulin receptor-inspired soluble insulin binder. Eur J Cell Biol 2023; 102:151293. [PMID: 36739671 DOI: 10.1016/j.ejcb.2023.151293] [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: 06/16/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
The insulin receptor (IR) is a 320 kDa membrane receptor tyrosine kinase mediating the pleiotropic actions of insulin, leading to phosphorylation of several intracellular substrates including serine/threonine-protein kinase (AKT1), and IR autophosphorylation. Structural details of the IR have been recently revealed. A high-binding insulin site, L1 (Kd =2 nM), consists of two distant domains in the primary sequence of the IR. Our design simplified the L1 binding site and transformed it into a soluble insulin binder (sIB). The sIB, a 17 kDa protein, binds insulin with 38 nM affinity. The sIB competes with IR for insulin and reduces by more than 50% phosphorylation of AKT1 in HEK 293 T cells, with similar effects on IR autophosphorylation. The sIB represents a new tool for research of insulin binding and signaling properties.
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Affiliation(s)
- Christopher Mendoza
- Cell Biology and Physiology, College of Life Sciences, Brigham Young University, Provo, UT, United States
| | - Cameron Hanegan
- Cell Biology and Physiology, College of Life Sciences, Brigham Young University, Provo, UT, United States
| | - Alek Sperry
- Mechanical Engineering, College of Engineering, Brigham Young University, Provo, UT, United States
| | - Logan Vargas
- Cell Biology and Physiology, College of Life Sciences, Brigham Young University, Provo, UT, United States
| | - Trevor Case
- Cell Biology and Physiology, College of Life Sciences, Brigham Young University, Provo, UT, United States
| | - Benjamin Bikman
- Cell Biology and Physiology, College of Life Sciences, Brigham Young University, Provo, UT, United States
| | - Dario Mizrachi
- Cell Biology and Physiology, College of Life Sciences, Brigham Young University, Provo, UT, United States.
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Winter DL, Lebhar H, McCluskey JB, Glover DJ. A versatile multimodal chromatography strategy to rapidly purify protein nanostructures assembled in cell lysates. J Nanobiotechnology 2023; 21:66. [PMID: 36829140 PMCID: PMC9960191 DOI: 10.1186/s12951-023-01817-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/14/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Protein nanostructures produced through the self-assembly of individual subunits are attractive scaffolds to attach and position functional molecules for applications in biomaterials, metabolic engineering, tissue engineering, and a plethora of nanomaterials. However, the assembly of multicomponent protein nanomaterials is generally a laborious process that requires each protein component to be separately expressed and purified prior to assembly. Moreover, excess components not incorporated into the final assembly must be removed from the solution and thereby necessitate additional processing steps. RESULTS We developed an efficient approach to purify functionalized protein nanostructures directly from bacterial lysates through a type of multimodal chromatography (MMC) that combines size-exclusion, hydrophilic interaction, and ion exchange to separate recombinant protein assemblies from excess free subunits and bacterial proteins. We employed the ultrastable filamentous protein gamma-prefoldin as a material scaffold that can be functionalized with a variety of protein domains through SpyTag/SpyCatcher conjugation chemistry. The purification of recombinant gamma-prefoldin filaments from bacterial lysates using MMC was tested across a wide range of salt concentrations and pH, demonstrating that the MMC resin is robust, however the optimal choice of salt species, salt concentration, and pH is likely dependent on the protein nanostructure to be purified. In addition, we show that pre-processing of the samples with tangential flow filtration to remove nucleotides and metabolites improves resin capacity, and that post-processing with Triton X-114 phase partitioning is useful to remove lipids and any remaining lipid-associated protein. Subsequently, functionalized protein filaments were purified from bacterial lysates using MMC and shown to be free of unincorporated subunits. The assembly and purification of protein filaments with varying amounts of functionalization was confirmed using polyacrylamide gel electrophoresis, Förster resonance energy transfer, and transmission electron microscopy. Finally, we compared our MMC workflow to anion exchange chromatography with the purification of encapsulin nanocompartments containing a fluorescent protein as a cargo, demonstrating the versatility of the protocol and that the purity of the assembly is comparable to more traditional procedures. CONCLUSIONS We envision that the use of MMC will increase the throughput of protein nanostructure prototyping as well as enable the upscaling of the bioproduction of protein nanodevices.
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Affiliation(s)
- Daniel L. Winter
- grid.1005.40000 0004 4902 0432School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Hélène Lebhar
- grid.1005.40000 0004 4902 0432Recombinant Products Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
| | - Joshua B. McCluskey
- grid.1005.40000 0004 4902 0432School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Dominic J. Glover
- grid.1005.40000 0004 4902 0432School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
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Reineke TM. Bioconjugate Chemistry: Enabling Innovation and Fostering Community at the Nexus of Synthetic and Biological Research. Bioconjug Chem 2023; 34:1-2. [PMID: 36563340 DOI: 10.1021/acs.bioconjchem.2c00591] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Theresa M Reineke
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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DiRusso CJ, Dashtiahangar M, Gilmore TD. Scaffold proteins as dynamic integrators of biological processes. J Biol Chem 2022; 298:102628. [PMID: 36273588 PMCID: PMC9672449 DOI: 10.1016/j.jbc.2022.102628] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 11/15/2022] Open
Abstract
Scaffold proteins act as molecular hubs for the docking of multiple proteins to organize efficient functional units for signaling cascades. Over 300 human proteins have been characterized as scaffolds, acting in a variety of signaling pathways. While the term scaffold implies a static, supportive platform, it is now clear that scaffolds are not simply inert docking stations but can undergo conformational changes that affect their dependent signaling pathways. In this review, we catalog scaffold proteins that have been shown to undergo actionable conformational changes, with a focus on the role that conformational change plays in the activity of the classic yeast scaffold STE5, as well as three human scaffold proteins (KSR, NEMO, SHANK3) that are integral to well-known signaling pathways (RAS, NF-κB, postsynaptic density). We also discuss scaffold protein conformational changes vis-à-vis liquid-liquid phase separation. Changes in scaffold structure have also been implicated in human disease, and we discuss how aberrant conformational changes may be involved in disease-related dysregulation of scaffold and signaling functions. Finally, we discuss how understanding these conformational dynamics will provide insight into the flexibility of signaling cascades and may enhance our ability to treat scaffold-associated diseases.
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Hazegh Nikroo A, Lemmens LJM, Wezeman T, Ottmann C, Merkx M, Brunsveld L. Switchable Control of Scaffold Protein Activity via Engineered Phosphoregulated Autoinhibition. ACS Synth Biol 2022; 11:2464-2472. [PMID: 35765959 PMCID: PMC9295147 DOI: 10.1021/acssynbio.2c00122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
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Scaffold proteins
operate as organizing hubs to enable high-fidelity
signaling, fulfilling crucial roles in the regulation of cellular
processes. Bottom-up construction of controllable scaffolding platforms
is attractive for the implementation of regulatory processes in synthetic
biology. Here, we present a modular and switchable synthetic scaffolding
system, integrating scaffold-mediated signaling with switchable kinase/phosphatase
input control. Phosphorylation-responsive inhibitory peptide motifs
were fused to 14-3-3 proteins to generate dimeric protein scaffolds
with appended regulatory peptide motifs. The availability of the scaffold
for intermolecular partner protein binding could be lowered up to
35-fold upon phosphorylation of the autoinhibition motifs, as demonstrated
using three different kinases. In addition, a hetero-bivalent autoinhibitory
platform design allowed for dual-kinase input regulation of scaffold
activity. Reversibility of the regulatory platform was illustrated
through phosphatase-controlled abrogation of autoinhibition, resulting
in full recovery of 14-3-3 scaffold activity.
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Affiliation(s)
- Arjan Hazegh Nikroo
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, Eindhoven, 5612AZ Arizona, The Netherlands
| | - Lenne J M Lemmens
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, Eindhoven, 5612AZ Arizona, The Netherlands
| | - Tim Wezeman
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, Eindhoven, 5612AZ Arizona, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, Eindhoven, 5612AZ Arizona, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, Eindhoven, 5612AZ Arizona, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, Eindhoven, 5612AZ Arizona, The Netherlands
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Rocha RA, Speight RE, Scott C. Engineering Enzyme Properties for Improved Biocatalytic Processes in Batch and Continuous Flow. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.1c00424] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Raquel A. Rocha
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
- CSIRO Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
| | - Robert E. Speight
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Colin Scott
- CSIRO Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
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Yan G, Li X, Yang J, Li Z, Hou J, Rao B, Hu Y, Ma L, Wang Y. Cost-Effective Production of ATP and S-Adenosylmethionine Using Engineered Multidomain Scaffold Proteins. Biomolecules 2021; 11:biom11111706. [PMID: 34827704 PMCID: PMC8616028 DOI: 10.3390/biom11111706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/18/2021] [Accepted: 10/18/2021] [Indexed: 12/27/2022] Open
Abstract
Adenosine triphosphate (ATP) and S-adenosyl-L-methionine (SAM) are important intermediates that are widely present in living organisms. Large-scale preparation and application of ATP or SAM is limited by expensive raw materials. To lower the production costs for ATP/SAM, in this study we used strategies applying engineered multidomain scaffold proteins to synthesize ATP and SAM. An artificial scaffold protein containing CBM3 domain, IM proteins and CL-labeled proteins was assembled to form complex 1 for catalytic reactions to increase ATP production. The ATP synthesis system produced approximately 25 g/L of ATP with approximately 15 g/L of ADP and 5 g/L of AMP using 12.5 g/L of adenosine and 40 g/L of sodium hexametaphosphate reaction at 35 °C and a pH of 8.5 for 6 h. Based on the above ATP synthesis system, two CL-labeled methionine adenosyltransferases (CL9-MAT4 and CL9-MAT5) were applied to construct scaffold protein complex 2 to achieve SAM synthesis. Approximately 25 μg of MAT4 in a reaction system with 0.3 M MgCl2 catalyzed at 20 °C and a pH of 8 catalyzed 0.5 g/L of l-Met to produce approximately 0.9 g/L of SAM. Approximately 25 μg of MAT5 in a reaction system with 0.7 M MgCl2 catalyzed at 35 °C and a pH of 8 catalyzed 0.5 g/L of l-Met to produce approximately 1.2 g/L of SAM. Here, we showed that low-cost substrates can be efficiently converted into high-value additional ATP and SAM via multi-enzyme catalytic reactions by engineered multidomain scaffold proteins.
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Affiliation(s)
- Guangbo Yan
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China; (G.Y.); (X.L.); (J.Y.); (Z.L.); (J.H.); (L.M.)
| | - Xia Li
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China; (G.Y.); (X.L.); (J.Y.); (Z.L.); (J.H.); (L.M.)
| | - Jun Yang
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China; (G.Y.); (X.L.); (J.Y.); (Z.L.); (J.H.); (L.M.)
| | - Zhongchen Li
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China; (G.Y.); (X.L.); (J.Y.); (Z.L.); (J.H.); (L.M.)
| | - Jia Hou
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China; (G.Y.); (X.L.); (J.Y.); (Z.L.); (J.H.); (L.M.)
| | - Ben Rao
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Biopesticide Branch of Hubei Innovation Centre of Agricultural Science and Technology, Wuhan 430064, China;
| | - Yong Hu
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratoy of Industrial Microbiology, National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Research Center of Food Fermentation Engineering and Technology, Hubei University of Technology, Wuhan 430062, China;
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China; (G.Y.); (X.L.); (J.Y.); (Z.L.); (J.H.); (L.M.)
| | - Yaping Wang
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China; (G.Y.); (X.L.); (J.Y.); (Z.L.); (J.H.); (L.M.)
- Correspondence:
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Liu Y, Huang Y, Lu R, Xin F, Liu G. Synthetic biology applications of the yeast mating signal pathway. Trends Biotechnol 2021; 40:620-631. [PMID: 34666896 DOI: 10.1016/j.tibtech.2021.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 12/18/2022]
Abstract
Cell fusion is a fundamental biological process that is involved in the development of most eukaryotic organisms. During the fusion process in Saccharomyces cerevisiae, cells respond to pheromones to trigger the MAPK (mitogen-activated protein kinase) cascade to initiate mating, followed by polarization, cell-wall remodeling, membrane fusion, and karyogamy. We highlight the applications of the yeast mating signal pathway in promoter engineering for tuning the expression of output genes, as well as in metabolic engineering for decoupling growth and metabolism, biosensors for sensitive detection and signal amplification, genetic circuits for programmable biological functionalities, and artificial consortia for cell-cell communication. Strategies such as exploiting rational engineering of modular circuits and optimizing the reproductive pathway to precisely maneuver physiological events have implications for scientific research and industrial development.
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Affiliation(s)
- Ying Liu
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Yuxin Huang
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Ran Lu
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Fengxue Xin
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Guannan Liu
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China; Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, Nanjing Tech University, Jiangsu Province, China.
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Towards robust Pseudomonas cell factories to harbour novel biosynthetic pathways. Essays Biochem 2021; 65:319-336. [PMID: 34223620 PMCID: PMC8314020 DOI: 10.1042/ebc20200173] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/01/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023]
Abstract
Biotechnological production in bacteria enables access to numerous valuable chemical compounds. Nowadays, advanced molecular genetic toolsets, enzyme engineering as well as the combinatorial use of biocatalysts, pathways, and circuits even bring new-to-nature compounds within reach. However, the associated substrates and biosynthetic products often cause severe chemical stress to the bacterial hosts. Species of the Pseudomonas clade thus represent especially valuable chassis as they are endowed with multiple stress response mechanisms, which allow them to cope with a variety of harmful chemicals. A built-in cell envelope stress response enables fast adaptations that sustain membrane integrity under adverse conditions. Further, effective export machineries can prevent intracellular accumulation of diverse harmful compounds. Finally, toxic chemicals such as reactive aldehydes can be eliminated by oxidation and stress-induced damage can be recovered. Exploiting and engineering these features will be essential to support an effective production of natural compounds and new chemicals. In this article, we therefore discuss major resistance strategies of Pseudomonads along with approaches pursued for their targeted exploitation and engineering in a biotechnological context. We further highlight strategies for the identification of yet unknown tolerance-associated genes and their utilisation for engineering next-generation chassis and finally discuss effective measures for pathway fine-tuning to establish stable cell factories for the effective production of natural compounds and novel biochemicals.
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