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Liebermann DG, Jungwirth J, Riven I, Barak Y, Levy D, Horovitz A, Haran G. From Microstates to Macrostates in the Conformational Dynamics of GroEL: A Single-Molecule Förster Resonance Energy Transfer Study. J Phys Chem Lett 2023:6513-6521. [PMID: 37440608 PMCID: PMC10388350 DOI: 10.1021/acs.jpclett.3c01281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
The chaperonin GroEL is a multisubunit molecular machine that assists in protein folding in the Escherichia coli cytosol. Past studies have shown that GroEL undergoes large allosteric conformational changes during its reaction cycle. Here, we report single-molecule Förster resonance energy transfer measurements that directly probe the conformational transitions of one subunit within GroEL and its single-ring variant under equilibrium conditions. We find that four microstates span the conformational manifold of the protein and interconvert on the submillisecond time scale. A unique set of relative populations of these microstates, termed a macrostate, is obtained by varying solution conditions, e.g., adding different nucleotides or the cochaperone GroES. Strikingly, ATP titration studies demonstrate that the partition between the apo and ATP-ligated conformational macrostates traces a sigmoidal response with a Hill coefficient similar to that obtained in bulk experiments of ATP hydrolysis. These coinciding results from bulk measurements for an entire ring and single-molecule measurements for a single subunit provide new evidence for the concerted allosteric transition of all seven subunits.
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Abstract
Understanding and exploiting molecular mechanisms in biology is central to chemical biology. Chemical biology studies of biological macromolecules are now in a perfect continuum with molecular level and nanomolecular level mechanistic studies involving whole organisms. The potential opportunity presented by such studies is the design and creation of genuine precision active pharmaceutical ingredients (APIs; including DNA, siRNA, smaller-molecule bioactives) that demonstrate exceptional levels of disease target specificity and selectivity. This article covers the best of my personal and collaborative academic research work using an organic chemistry and chemical biology approach towards understanding biological molecular recognition processes, work that appears to be leading to the generation of novel precision APIs with genuine potential for the treatments of major chronic diseases that afflict globally.
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Huang F, Shen L, Wang J, Qu A, Yang H, Zhang Z, An Y, Shi L. Effect of the Surface Charge of Artificial Chaperones on the Refolding of Thermally Denatured Lysozymes. ACS APPLIED MATERIALS & INTERFACES 2016; 8:3669-3678. [PMID: 26570996 DOI: 10.1021/acsami.5b08843] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Artificial chaperones are of great interest in fighting protein misfolding and aggregation for the protection of protein bioactivity. A comprehensive understanding of the interaction between artificial chaperones and proteins is critical for the effective utilization of these materials in biomedicine. In this work, we fabricated three kinds of artificial chaperones with different surface charges based on mixed-shell polymeric micelles (MSPMs), and investigated their protective effect for lysozymes under thermal stress. It was found that MSPMs with different surface charges showed distinct chaperone-like behavior, and the neutral MSPM with PEG shell and PMEO2MA hydrophobic domain at high temperature is superior to the negatively and positively charged one, because of the excessive electrostatic interactions between the protein and charged MSPMs. The results may benefit to optimize this kind of artificial chaperone with enhanced properties and expand their application in the future.
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Affiliation(s)
- Fan Huang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Nankai University , Tianjin 300071, China
| | - Liangliang Shen
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Nankai University , Tianjin 300071, China
| | - Jianzu Wang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Nankai University , Tianjin 300071, China
| | - Aoting Qu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Nankai University , Tianjin 300071, China
| | - Huiru Yang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Nankai University , Tianjin 300071, China
| | - Zhenkun Zhang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Nankai University , Tianjin 300071, China
| | - Yingli An
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Nankai University , Tianjin 300071, China
| | - Linqi Shi
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Nankai University , Tianjin 300071, China
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Miller AD. Sense–antisense (complementary) peptide interactions and the proteomic code; potential opportunities in biology and pharmaceutical science. Expert Opin Biol Ther 2015; 15:245-67. [DOI: 10.1517/14712598.2015.983069] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Feng Y, Zhang M, Zhang L, Zhang T, Ding J, Zhuang Y, Wang X, Yang Z. An automatic refolding apparatus for preparative-scale protein production. PLoS One 2012; 7:e45891. [PMID: 23029296 PMCID: PMC3459974 DOI: 10.1371/journal.pone.0045891] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 08/27/2012] [Indexed: 11/18/2022] Open
Abstract
Protein refolding is an important process to recover active recombinant proteins from inclusion bodies. Refolding by simple dilution, dialysis and on-column refolding methods are the most common techniques reported in the literature. However, the refolding process is time-consuming and laborious due to the variability of the behavior of each protein and requires a great deal of trial-and-error to achieve success. Hence, there is a need for automation to make the whole process as convenient as possible. In this study, we invented an automatic apparatus that integrated three refolding techniques: varying dilution, dialysis and on-column refolding. We demonstrated the effectiveness of this technology by varying the flow rates of the dilution buffer into the denatured protein and testing different refolding methods. We carried out different refolding methods on this apparatus: a combination of dilution and dialysis for human stromal cell-derived factor 1 (SDF-1/CXCL12) and thioredoxin fused-human artemin protein (Trx-ARTN); dilution refolding for thioredoxin fused-human insulin-like growth factor I protein (Trx-IGF1) and enhanced fluorescent protein (EGFP); and on-column refolding for bovine serum albumin (BSA). The protein refolding processes of these five proteins were preliminarily optimized using the slowly descending denaturants (or additives) method. Using this strategy of decreasing denaturants concentration, the efficiency of protein refolding was found to produce higher quantities of native protein. The standard refolding apparatus configuration can support different operations for different applications; it is not limited to simple dilution, dialysis and on-column refolding techniques. Refolding by slowly decreasing denaturants concentration, followed by concentration or purification on-column, may be a useful strategy for rapid and efficient recovery of active proteins from inclusion bodies. An automatic refolding apparatus employing this flexible strategy may provide a powerful tool for preparative scale protein production.
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Affiliation(s)
- Yanye Feng
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, China
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ming Zhang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Linlin Zhang
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ting Zhang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Jianfeng Ding
- Department of R&D, Novoprotein Scientific Inc, Shanghai, China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Xiaoning Wang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, China
- * E-mail: (XW); (ZY)
| | - Zhong Yang
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
- * E-mail: (XW); (ZY)
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Sabate R, de Groot NS, Ventura S. Protein folding and aggregation in bacteria. Cell Mol Life Sci 2010; 67:2695-715. [PMID: 20358253 PMCID: PMC11115605 DOI: 10.1007/s00018-010-0344-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 02/19/2010] [Accepted: 03/05/2010] [Indexed: 01/31/2023]
Abstract
Proteins might experience many conformational changes and interactions during their lifetimes, from their synthesis at ribosomes to their controlled degradation. Because, in most cases, only folded proteins are functional, protein folding in bacteria is tightly controlled genetically, transcriptionally, and at the protein sequence level. In addition, important cellular machinery assists the folding of polypeptides to avoid misfolding and ensure the attainment of functional structures. When these redundant protective strategies are overcome, misfolded polypeptides are recruited into insoluble inclusion bodies. The protein embedded in these intracellular deposits might display different conformations including functional and beta-sheet-rich structures. The latter assemblies are similar to the amyloid fibrils characteristic of several human neurodegenerative diseases. Interestingly, bacteria exploit the same structural principles for functional properties such as adhesion or cytotoxicity. Overall, this review illustrates how prokaryotic organisms might provide the bedrock on which to understand the complexity of protein folding and aggregation in the cell.
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Affiliation(s)
- Raimon Sabate
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Natalia S. de Groot
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Salvador Ventura
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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De M, Rotello VM. Synthetic "chaperones": nanoparticle-mediated refolding of thermally denatured proteins. Chem Commun (Camb) 2008:3504-6. [PMID: 18654694 PMCID: PMC2646367 DOI: 10.1039/b805242e] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thermally denatured chymotrypsin, lysozyme and papain are substantially refolded towards their native conformation by gold nanoparticle bearing dicarboxylate sidechains.
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Affiliation(s)
- Mrinmoy De
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, MA 01003, USA. E-mail:
| | - Vincent M. Rotello
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, MA 01003, USA. E-mail:
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Multhoff G, De Maio A. Stress down south: meeting report of the fifth International Workshop on the Molecular Biology of Stress Responses. Cell Stress Chaperones 2006; 11:108-15. [PMID: 16817316 PMCID: PMC1484512 DOI: 10.1379/csc-203.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Gabriele Multhoff
- Department of Hematology/Oncology, University Hospital Regensburg, 93053 Regensburg, Germany.
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Jones H, Dalmaris J, Wright M, Steinke JHG, Miller AD. Hydrogel polymer appears to mimic the performance of the GroEL/GroES molecular chaperone machine. Org Biomol Chem 2006; 4:2568-74. [PMID: 16791320 DOI: 10.1039/b603915d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Controlled protein folding/refolding remains a substantial challenge to the biotechnology industry. Robust and adaptable artificial polymer molecular chaperones could make important contributions towards solving this problem. Taking inspiration from the mechanism of the GroEL/GroES molecular chaperone machine, we report the preparation and testing of a selection of cross-linked thermo-responsive hydrogels, one of which is shown to assist quantitative refolding of a stringent unfolded protein substrate (mitochondrial malate dehydrogenase [mMDH]) during temperature cycling between hydrophobic and hydrophilic states. To our knowledge, this is the first hydrogel-only artificial polymer molecular chaperone to be derived, which is also potentially a generic artificial polymer molecular chaperone for use in a folding bioreactor.
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Affiliation(s)
- Huw Jones
- Imperial College Genetic Therapies Centre, Department of Chemistry, Flowers Building, Imperial College London, UK
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