1
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Wales TE, Pajak A, Roeselová A, Shivakumaraswamy S, Howell S, Kjær S, Hartl FU, Engen JR, Balchin D. Resolving chaperone-assisted protein folding on the ribosome at the peptide level. Nat Struct Mol Biol 2024:10.1038/s41594-024-01355-x. [PMID: 38987455 DOI: 10.1038/s41594-024-01355-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 06/17/2024] [Indexed: 07/12/2024]
Abstract
Protein folding in vivo begins during synthesis on the ribosome and is modulated by molecular chaperones that engage the nascent polypeptide. How these features of protein biogenesis influence the maturation pathway of nascent proteins is incompletely understood. Here, we use hydrogen-deuterium exchange mass spectrometry to define, at peptide resolution, the cotranslational chaperone-assisted folding pathway of Escherichia coli dihydrofolate reductase. The nascent polypeptide folds along an unanticipated pathway through structured intermediates not populated during refolding from denaturant. Association with the ribosome allows these intermediates to form, as otherwise destabilizing carboxy-terminal sequences remain confined in the ribosome exit tunnel. Trigger factor binds partially folded states without disrupting their structure, and the nascent chain is poised to complete folding immediately upon emergence of the C terminus from the exit tunnel. By mapping interactions between the nascent chain and ribosomal proteins, we trace the path of the emerging polypeptide during synthesis. Our work reveals new mechanisms by which cellular factors shape the conformational search for the native state.
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Affiliation(s)
- Thomas E Wales
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, USA
| | - Aleksandra Pajak
- Protein Biogenesis Laboratory, The Francis Crick Institute, London, UK
| | - Alžběta Roeselová
- Protein Biogenesis Laboratory, The Francis Crick Institute, London, UK
| | | | - Steven Howell
- Proteomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Svend Kjær
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, USA.
| | - David Balchin
- Protein Biogenesis Laboratory, The Francis Crick Institute, London, UK.
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2
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Cárdenas-Guerra RE, Montes-Flores O, Nava-Pintor EE, Reséndiz-Cardiel G, Flores-Pucheta CI, Rodríguez-Gavaldón YI, Arroyo R, Bottazzi ME, Hotez PJ, Ortega-López J. Chagasin from Trypanosoma cruzi as a molecular scaffold to express epitopes of TSA-1 as soluble recombinant chimeras. Protein Expr Purif 2024; 218:106458. [PMID: 38423156 DOI: 10.1016/j.pep.2024.106458] [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: 09/05/2023] [Revised: 02/13/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
Trypanosoma cruzi is the causative agent of Chagas disease, a global public health problem. New therapeutic drugs and biologics are needed. The TSA-1 recombinant protein of T. cruzi is one such promising antigen for developing a therapeutic vaccine. However, it is overexpressed in E. coli as inclusion bodies, requiring an additional refolding step. As an alternative, in this study, we propose the endogenous cysteine protease inhibitor chagasin as a molecular scaffold to generate chimeric proteins. These proteins will contain combinations of two of the five conserved epitopes (E1 to E5) of TSA-1 in the L4 and L6 chagasin loops. Twenty chimeras (Q1-Q20) were designed, and their solubility was predicted using bioinformatics tools. Nine chimeras with different degrees of solubility were selected and expressed in E. coli BL21 (DE3). Western blot assays with anti-6x-His and anti-chagasin antibodies confirmed the expression of soluble recombinant chimeras. Both theoretically and experimentally, the Q12 (E5-E3) chimera was the most soluble, and the Q20 (E4-E5) the most insoluble protein. Q4 (E5-E1) and Q8 (E5-E2) chimeras were classified as proteins with medium solubility that exhibited the highest yield in the soluble fraction. Notably, Q4 has a yield of 239 mg/L, well above the yield of recombinant chagasin (16.5 mg/L) expressed in a soluble form. The expression of the Q4 chimera was scaled up to a 7 L fermenter obtaining a yield of 490 mg/L. These data show that chagasin can serve as a molecular scaffold for the expression of TSA-1 epitopes in the form of soluble chimeras.
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Affiliation(s)
- Rosa Elena Cárdenas-Guerra
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, CP 07360, Mexico City, Mexico
| | - Octavio Montes-Flores
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, CP 07360, Mexico City, Mexico
| | - Edgar Ezequiel Nava-Pintor
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, CP 07360, Mexico City, Mexico
| | - Gerardo Reséndiz-Cardiel
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, CP 07360, Mexico City, Mexico
| | - Claudia Ivonne Flores-Pucheta
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, CP 07360, Mexico City, Mexico
| | - Yasmín Irene Rodríguez-Gavaldón
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, CP 07360, Mexico City, Mexico
| | - Rossana Arroyo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, CP 07360, Mexico City, Mexico
| | - Maria Elena Bottazzi
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics and Molecular Virology and Microbiology, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Peter J Hotez
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics and Molecular Virology and Microbiology, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jaime Ortega-López
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, CP 07360, Mexico City, Mexico.
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3
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Rajasekaran N, Kaiser CM. Navigating the complexities of multi-domain protein folding. Curr Opin Struct Biol 2024; 86:102790. [PMID: 38432063 DOI: 10.1016/j.sbi.2024.102790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/11/2024] [Accepted: 02/12/2024] [Indexed: 03/05/2024]
Abstract
Proteome complexity has expanded tremendously over evolutionary time, enabling biological diversification. Much of this complexity is achieved by combining a limited set of structural units into long polypeptides. This widely used evolutionary strategy poses challenges for folding of the resulting multi-domain proteins. As a consequence, their folding differs from that of small single-domain proteins, which generally fold quickly and reversibly. Co-translational processes and chaperone interactions are important aspects of multi-domain protein folding. In this review, we discuss some of the recent experimental progress toward understanding these processes.
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Affiliation(s)
| | - Christian M Kaiser
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States; Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands.
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4
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Chen X, Kaiser CM. AP profiling resolves co-translational folding pathway and chaperone interactions in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555749. [PMID: 37693575 PMCID: PMC10491307 DOI: 10.1101/2023.09.01.555749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Natural proteins have evolved to fold robustly along specific pathways. Folding begins during synthesis, guided by interactions of the nascent protein with the ribosome and molecular chaperones. However, the timing and progression of co-translational folding remain largely elusive, in part because the process is difficult to measure in the natural environment of the cytosol. We developed a high-throughput method to quantify co-translational folding in live cells that we term Arrest Peptide profiling (AP profiling). We employed AP profiling to delineate co-translational folding for a set of GTPase domains with very similar structures, defining how topology shapes folding pathways. Genetic ablation of major nascent chain-binding chaperones resulted in localized folding changes that suggest how functional redundancies among chaperones are achieved by distinct interactions with the nascent protein. Collectively, our studies provide a window into cellular folding pathways of complex proteins and pave the way for systematic studies on nascent protein folding at unprecedented resolution and throughput.
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Affiliation(s)
- Xiuqi Chen
- CMDB Graduate Program, Johns Hopkins University, Baltimore, MD, United States
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
- Present address: Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Christian M. Kaiser
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States
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5
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Rajasekaran N, Kaiser CM. Co-Translational Folding of Multi-Domain Proteins. Front Mol Biosci 2022; 9:869027. [PMID: 35517860 PMCID: PMC9065291 DOI: 10.3389/fmolb.2022.869027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/21/2022] [Indexed: 12/24/2022] Open
Abstract
The majority of proteins in nature are composed of multiple domains connected in a single polypeptide. How these long sequences fold into functional structures without forming toxic misfolds or aggregates is poorly understood. Their folding is inextricably linked to protein synthesis and interactions with cellular machinery, making mechanistic studies challenging. Recent progress has revealed critical features of multi-domain protein folding in isolation and in the context of translation by the ribosome. In this review, we discuss challenges and progress in understanding multi-domain protein folding, and highlight how molecular interactions shape folding and misfolding pathways. With the development of new approaches and model systems, the stage is now set for mechanistically exploring the folding of large multi-domain proteins.
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Affiliation(s)
| | - Christian M. Kaiser
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States,Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States,*Correspondence: Christian M. Kaiser,
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6
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Sharma A, Balda S, Capalash N, Sharma P. Engineering multifunctional enzymes for agro-biomass utilization. BIORESOURCE TECHNOLOGY 2022; 347:126706. [PMID: 35033642 DOI: 10.1016/j.biortech.2022.126706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
Lignocellulosic biomass is a plentiful renewable resource that can be converted into a wide range of high-value-added industrial products. However, the complexity of its structural integrity is one of the major constraints and requires combinations of different fibrolytic enzymes for the cost-effective, industrially and environmentally feasible transformation. An interesting approach is constructing multifunctional enzymes, either in a single polypeptide or by joining multiple domains with linkers and performing diverse reactions simultaneously, in a single host. The production of such chimera proteins multiplies the advantages of different enzymatic reactions in a single setup, in lesser time, at lower production cost and with desirable and improved catalytic activities. This review embodies the various domain-tailoring and extracellular secretion strategies, possible solutions to their challenges, and efforts to experimentally connect different catalytic activities in a single host, as well as their applications.
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Affiliation(s)
- Aarjoo Sharma
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Sanjeev Balda
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Neena Capalash
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Prince Sharma
- Department of Microbiology, Panjab University, Chandigarh, India.
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7
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Sorokina I, Mushegian AR, Koonin EV. Is Protein Folding a Thermodynamically Unfavorable, Active, Energy-Dependent Process? Int J Mol Sci 2022; 23:521. [PMID: 35008947 PMCID: PMC8745595 DOI: 10.3390/ijms23010521] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 02/04/2023] Open
Abstract
The prevailing current view of protein folding is the thermodynamic hypothesis, under which the native folded conformation of a protein corresponds to the global minimum of Gibbs free energy G. We question this concept and show that the empirical evidence behind the thermodynamic hypothesis of folding is far from strong. Furthermore, physical theory-based approaches to the prediction of protein folds and their folding pathways so far have invariably failed except for some very small proteins, despite decades of intensive theory development and the enormous increase of computer power. The recent spectacular successes in protein structure prediction owe to evolutionary modeling of amino acid sequence substitutions enhanced by deep learning methods, but even these breakthroughs provide no information on the protein folding mechanisms and pathways. We discuss an alternative view of protein folding, under which the native state of most proteins does not occupy the global free energy minimum, but rather, a local minimum on a fluctuating free energy landscape. We further argue that ΔG of folding is likely to be positive for the majority of proteins, which therefore fold into their native conformations only through interactions with the energy-dependent molecular machinery of living cells, in particular, the translation system and chaperones. Accordingly, protein folding should be modeled as it occurs in vivo, that is, as a non-equilibrium, active, energy-dependent process.
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Affiliation(s)
| | - Arcady R. Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, VA 22314, USA;
- Clare Hall College, University of Cambridge, Cambridge CB3 9AL, UK
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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8
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Kelly C, Gage MJ. Protein Unfolding: Denaturant vs. Force. Biomedicines 2021; 9:biomedicines9101395. [PMID: 34680512 PMCID: PMC8533514 DOI: 10.3390/biomedicines9101395] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/20/2021] [Accepted: 09/28/2021] [Indexed: 11/16/2022] Open
Abstract
While protein refolding has been studied for over 50 years since the pioneering work of Christian Anfinsen, there have been a limited number of studies correlating results between chemical, thermal, and mechanical unfolding. The limited knowledge of the relationship between these processes makes it challenging to compare results between studies if different refolding methods were applied. Our current work compares the energetic barriers and folding rates derived from chemical, thermal, and mechanical experiments using an immunoglobulin-like domain from the muscle protein titin as a model system. This domain, I83, has high solubility and low stability relative to other Ig domains in titin, though its stability can be modulated by calcium. Our experiments demonstrated that the free energy of refolding was equivalent with all three techniques, but the refolding rates exhibited differences, with mechanical refolding having slightly faster rates. This suggests that results from equilibrium-based measurements can be compared directly but care should be given comparing refolding kinetics derived from refolding experiments that used different unfolding methods.
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Affiliation(s)
- Colleen Kelly
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA 01854, USA;
| | - Matthew J. Gage
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA 01854, USA;
- UMass Movement Center (UMOVE), University of Massachusetts Lowell, Lowell, MA 01854, USA
- Correspondence:
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