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Herling TW, Cassaignau AME, Wentink AS, Peter QAE, Kumar PC, Kartanas T, Schneider MM, Cabrita LD, Christodoulou J, Knowles TPJ. Thermodynamic profiles for cotranslational trigger factor substrate recognition. SCIENCE ADVANCES 2024; 10:eadn4824. [PMID: 38985872 PMCID: PMC11235164 DOI: 10.1126/sciadv.adn4824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
Abstract
Molecular chaperones are central to the maintenance of proteostasis in living cells. A key member of this protein family is trigger factor (TF), which acts throughout the protein life cycle and has a ubiquitous role as the first chaperone encountered by proteins during synthesis. However, our understanding of how TF achieves favorable interactions with such a diverse substrate base remains limited. Here, we use microfluidics to reveal the thermodynamic determinants of this process. We find that TF binding to empty 70S ribosomes is enthalpy-driven, with micromolar affinity, while nanomolar affinity is achieved through a favorable entropic contribution for both intrinsically disordered and folding-competent nascent chains. These findings suggest a general mechanism for cotranslational TF function, which relies on occupation of the exposed TF-substrate binding groove rather than specific complementarity between chaperone and nascent chain. These insights add to our wider understanding of how proteins can achieve broad substrate specificity.
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Affiliation(s)
- Therese W. Herling
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Anaïs M. E. Cassaignau
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1 6BT, UK
| | - Anne S. Wentink
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1 6BT, UK
| | - Quentin A. E. Peter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Pavan C. Kumar
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Tadas Kartanas
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Matthias M. Schneider
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Lisa D. Cabrita
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1 6BT, UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1 6BT, UK
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
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Choudhury M, Dhara A, Kumar M. Trigger Factor in Association with the ClpP1P2 Heterocomplex of Leptospira Promotes Protease/Peptidase Activity. ACS OMEGA 2021; 6:1400-1409. [PMID: 33490799 PMCID: PMC7818586 DOI: 10.1021/acsomega.0c05057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/28/2020] [Indexed: 05/07/2023]
Abstract
The genomic analysis of Leptospira reveals a trigger factor (TF) encoding gene (tig) to be colocalized along with the clpP1 and clpX. The TF is a crouching dragon-like protein known to be a ribosome-associated chaperone that is involved in cotranslational protein folding in bacteria in an ATP-independent mode. In Leptospira, tig is localized upstream of the clpP1 with a short (4 bp) overlap. In the present study, we document the distinctive role of Leptospira TF (LinTF) in the caseinolytic protease (ClpP) system. The recombinant LinTF (rLinTF) was found to improve the peptidase or protease activity of the ClpP1P2 heterocomplex and ClpXP1P2 complex, respectively, on model substrates. In addition, on supplementation of rLinTF to rClpP1P2 bound to its physiological ATPase chaperone ClpX or the antibiotic analogue acyldepsipeptide (ADEP), an augmentation in the activity of ClpP1P2 was observed. These studies underscore the novel role of LinTF in aiding the caseinolytic protease activity of Leptospira. Supplementation of rLinTF to a peptidase assay of rClpP1P2 conditionally in the presence of a salt (sodium citrate) with high Hofmeister strength led us to speculate that rLinTF may have a role in the assembly of multimeric proteins. The deletion of one of the arms (arm-2) of the LinTF structure from the carboxy terminal domain indicated a reduction in its capacity to stimulate rClpP1P2 activity. Thus, the C-terminal domain of LinTF may have a role in the assembly of multimeric ClpP protein, leading to enhancement of ClpP activity.
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Affiliation(s)
| | | | - Manish Kumar
- . Phone: +91-361-258-2230. Fax: +91-361-258-2249
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Ghosh S, Lalani R, Maiti K, Banerjee S, Patel V, Bhowmick S, Misra A. Optimization and efficacy study of synergistic vincristine coloaded liposomal doxorubicin against breast and lung cancer. Nanomedicine (Lond) 2020; 15:2585-2607. [DOI: 10.2217/nnm-2020-0169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aim: To improve the efficacy of poly-ethylene glycol (PEG)ylated liposomes coloaded with doxorubicin and vincristine against triple-negative breast cancer (TNBC) and non-small-cell lung cancer (NSCLC). Methods: The combinatorial index of the drugs was established using the Chou-Talalay method in MDA-MB-231 and A549 cell lines. The most effective ratio was co-encapsulated in factorial design optimized nanoliposomes which were characterized for similarity to clinical standard and evaluated in vitro and in vivo for therapeutic efficacy. Results & conclusion: The formulation exhibited more than 95% co-encapsulation, a size of 95.74 ± 2.65 nm and zeta potential of -9.17 ± 1.19 mV while having no significant differences in physicochemical and biochemical characteristics as compared with the clinical standard. Efficacy evaluation studies showed significantly improved cytotoxicity and tumor regression compared with liposomal doxorubicin indicating improvement in efficacy against TNBC and NSCLC.
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Affiliation(s)
- Saikat Ghosh
- Department of Pharmaceutics, Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat - 390001, India
- Formulation Research & Development Department, Sun Pharmaceutical Industries Ltd, Vadodara, Gujarat-390012, India
| | - Rohan Lalani
- Department of Pharmaceutics, Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat - 390001, India
| | - Kuntal Maiti
- Formulation Research & Development Department, Sun Pharmaceutical Industries Ltd, Vadodara, Gujarat-390012, India
| | - Shubhadeep Banerjee
- Formulation Research & Development Department, Sun Pharmaceutical Industries Ltd, Vadodara, Gujarat-390012, India
| | - Vivek Patel
- Department of Pharmaceutics, Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat - 390001, India
| | - Subhas Bhowmick
- Department of Pharmaceutics, Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat - 390001, India
- Formulation Research & Development Department, Sun Pharmaceutical Industries Ltd, Vadodara, Gujarat-390012, India
| | - Ambikanandan Misra
- Department of Pharmaceutics, Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat - 390001, India
- Pharmaceutical Research, Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM's NMIMS University, VL Mehta Road, Vile Parle (W), Mumbai, Maharashtra - 400 056, Maharashtra India
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Morgado L, Burmann BM, Sharpe T, Mazur A, Hiller S. The dynamic dimer structure of the chaperone Trigger Factor. Nat Commun 2017; 8:1992. [PMID: 29222465 PMCID: PMC5722895 DOI: 10.1038/s41467-017-02196-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 11/12/2017] [Indexed: 11/09/2022] Open
Abstract
The chaperone Trigger Factor (TF) from Escherichia coli forms a dimer at cellular concentrations. While the monomer structure of TF is well known, the spatial arrangement of this dimeric chaperone storage form has remained unclear. Here, we determine its structure by a combination of high-resolution NMR spectroscopy and biophysical methods. TF forms a symmetric head-to-tail dimer, where the ribosome binding domain is in contact with the substrate binding domain, while the peptidyl-prolyl isomerase domain contributes only slightly to the dimer affinity. The dimer structure is highly dynamic, with the two ribosome binding domains populating a conformational ensemble in the center. These dynamics result from intermolecular in trans interactions of the TF client-binding site with the ribosome binding domain, which is conformationally frustrated in the absence of the ribosome. The avidity in the dimer structure explains how the dimeric state of TF can be monomerized also by weakly interacting clients.
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Affiliation(s)
- Leonor Morgado
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland
| | - Björn M Burmann
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland.,Department of Chemistry and Molecular Biology, Wallenberg Centre of Molecular and Translational Medicine, University of Gothenburg, 405 30, Göteborg, Sweden
| | - Timothy Sharpe
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland
| | - Adam Mazur
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland.
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Ries F, Carius Y, Rohr M, Gries K, Keller S, Lancaster CRD, Willmund F. Structural and molecular comparison of bacterial and eukaryotic trigger factors. Sci Rep 2017; 7:10680. [PMID: 28878399 PMCID: PMC5587573 DOI: 10.1038/s41598-017-10625-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 08/11/2017] [Indexed: 12/04/2022] Open
Abstract
A considerably small fraction of approximately 60–100 proteins of all chloroplast proteins are encoded by the plastid genome. Many of these proteins are major subunits of complexes with central functions within plastids. In comparison with other subcellular compartments and bacteria, many steps of chloroplast protein biogenesis are not well understood. We report here on the first study of chloroplast-localised trigger factor. In bacteria, this molecular chaperone is known to associate with translating ribosomes to facilitate the folding of newly synthesized proteins. Chloroplast trigger factors of the unicellular green algae Chlamydomonas reinhardtii and the vascular land plant Arabidopsis thaliana were characterized by biophysical and structural methods and compared to the Escherichia coli isoform. We show that chloroplast trigger factor is mainly monomeric and displays only moderate stability against thermal unfolding even under mild heat-stress conditions. The global shape and conformation of these proteins were determined in solution by small-angle X-ray scattering and subsequent ab initio modelling. As observed for bacteria, plastidic trigger factors have a dragon-like structure, albeit with slightly altered domain arrangement and flexibility. This structural conservation despite low amino acid sequence homology illustrates a remarkable evolutionary robustness of chaperone conformations across various kingdoms of life.
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Affiliation(s)
- Fabian Ries
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Erwin-Schrödinger-Str. 70, 67663, Kaiserslautern, Germany
| | - Yvonne Carius
- Department of Structural Biology, Saarland University, Center of Human and Molecular Biology (ZHMB), Faculty of Medicine Building 60, 66421, Homburg, Germany
| | - Marina Rohr
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Erwin-Schrödinger-Str. 70, 67663, Kaiserslautern, Germany
| | - Karin Gries
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Erwin-Schrödinger-Str. 70, 67663, Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - C Roy D Lancaster
- Department of Structural Biology, Saarland University, Center of Human and Molecular Biology (ZHMB), Faculty of Medicine Building 60, 66421, Homburg, Germany.
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Erwin-Schrödinger-Str. 70, 67663, Kaiserslautern, Germany.
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