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Streit JO, Bukvin IV, Chan SHS, Bashir S, Woodburn LF, Włodarski T, Figueiredo AM, Jurkeviciute G, Sidhu HK, Hornby CR, Waudby CA, Cabrita LD, Cassaignau AME, Christodoulou J. The ribosome lowers the entropic penalty of protein folding. Nature 2024; 633:232-239. [PMID: 39112704 PMCID: PMC11374706 DOI: 10.1038/s41586-024-07784-4] [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: 08/10/2023] [Accepted: 07/04/2024] [Indexed: 08/17/2024]
Abstract
Most proteins fold during biosynthesis on the ribosome1, and co-translational folding energetics, pathways and outcomes of many proteins have been found to differ considerably from those in refolding studies2-10. The origin of this folding modulation by the ribosome has remained unknown. Here we have determined atomistic structures of the unfolded state of a model protein on and off the ribosome, which reveal that the ribosome structurally expands the unfolded nascent chain and increases its solvation, resulting in its entropic destabilization relative to the peptide chain in isolation. Quantitative 19F NMR experiments confirm that this destabilization reduces the entropic penalty of folding by up to 30 kcal mol-1 and promotes formation of partially folded intermediates on the ribosome, an observation that extends to other protein domains and is obligate for some proteins to acquire their active conformation. The thermodynamic effects also contribute to the ribosome protecting the nascent chain from mutation-induced unfolding, which suggests a crucial role of the ribosome in supporting protein evolution. By correlating nascent chain structure and dynamics to their folding energetics and post-translational outcomes, our findings establish the physical basis of the distinct thermodynamics of co-translational protein folding.
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Affiliation(s)
- Julian O Streit
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Ivana V Bukvin
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Sammy H S Chan
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK.
| | - Shahzad Bashir
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Lauren F Woodburn
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Tomasz Włodarski
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Angelo Miguel Figueiredo
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Gabija Jurkeviciute
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Haneesh K Sidhu
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Charity R Hornby
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Lisa D Cabrita
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Anaïs M E Cassaignau
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK.
| | - John Christodoulou
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK.
- Department of Biological Sciences, Birkbeck College, London, UK.
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2
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Lenard AJ, Mulder FAA, Madl T. Solvent paramagnetic relaxation enhancement as a versatile method for studying structure and dynamics of biomolecular systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:113-139. [PMID: 36496256 DOI: 10.1016/j.pnmrs.2022.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 06/17/2023]
Abstract
Solvent paramagnetic relaxation enhancement (sPRE) is a versatile nuclear magnetic resonance (NMR)-based method that allows characterization of the structure and dynamics of biomolecular systems through providing quantitative experimental information on solvent accessibility of NMR-active nuclei. Addition of soluble paramagnetic probes to the solution of a biomolecule leads to paramagnetic relaxation enhancement in a concentration-dependent manner. Here we review recent progress in the sPRE-based characterization of structural and dynamic properties of biomolecules and their complexes, and aim to deliver a comprehensive illustration of a growing number of applications of the method to various biological systems. We discuss the physical principles of sPRE measurements and provide an overview of available co-solute paramagnetic probes. We then explore how sPRE, in combination with complementary biophysical techniques, can further advance biomolecular structure determination, identification of interaction surfaces within protein complexes, and probing of conformational changes and low-population transient states, as well as deliver insights into weak, nonspecific, and transient interactions between proteins and co-solutes. In addition, we present examples of how the incorporation of solvent paramagnetic probes can improve the sensitivity of NMR experiments and discuss the prospects of applying sPRE to NMR metabolomics, drug discovery, and the study of intrinsically disordered proteins.
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Affiliation(s)
- Aneta J Lenard
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria.
| | - Frans A A Mulder
- Interdisciplinary Nanoscience Center and Department of Chemistry, University of Aarhus, DK-8000 Aarhus, Denmark; Institute of Biochemistry, Johannes Kepler Universität Linz, 4040 Linz, Austria.
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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3
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Abstract
Folding of polypeptides begins during their synthesis on ribosomes. This process has evolved as a means for the cell to maintain proteostasis, by mitigating the risk of protein misfolding and aggregation. The capacity to now depict this cellular feat at increasingly higher resolution is providing insight into the mechanistic determinants that promote successful folding. Emerging from these studies is the intimate interplay between protein translation and folding, and within this the ribosome particle is the key player. Its unique structural properties provide a specialized scaffold against which nascent polypeptides can begin to form structure in a highly coordinated, co-translational manner. Here, we examine how, as a macromolecular machine, the ribosome modulates the intrinsic dynamic properties of emerging nascent polypeptide chains and guides them toward their biologically active structures.
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Affiliation(s)
- Anaïs M E Cassaignau
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 7HX, United Kingdom; , ,
| | - Lisa D Cabrita
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 7HX, United Kingdom; , ,
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 7HX, United Kingdom; , ,
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4
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Waudby CA, Burridge C, Christodoulou J. Optimal design of adaptively sampled NMR experiments for measurement of methyl group dynamics with application to a ribosome-nascent chain complex. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 326:106937. [PMID: 33706222 PMCID: PMC7613274 DOI: 10.1016/j.jmr.2021.106937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/25/2021] [Accepted: 02/05/2021] [Indexed: 05/14/2023]
Abstract
NMR measurements of cross-correlated nuclear spin relaxation provide powerful probes of polypeptide dynamics and rotational diffusion, free from contributions due to chemical exchange or interactions with external spins. Here, we report on the development of a sensitivity-optimized pulse sequence for the analysis of the differential relaxation of transitions within isolated 13CH3 spin systems, in order to characterise rotational diffusion and side chain order through the product S2τc. We describe the application of optimal design theory to implement a real-time 'on-the-fly' adaptive sampling scheme that maximizes the accuracy of the measured parameters. The increase in sensitivity obtained using this approach enables quantitative measurements of rotational diffusion within folded states of translationally-arrested ribosome-nascent chain complexes of the FLN5 filamin domain, and can be used to place strong limits on interactions between the domain and the ribosome surface.
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Affiliation(s)
- Christopher A Waudby
- Department of Structural and Molecular Biology, UCL, Gower St, London WC1E 6BT, UK.
| | - Charles Burridge
- Department of Structural and Molecular Biology, UCL, Gower St, London WC1E 6BT, UK
| | - John Christodoulou
- Department of Structural and Molecular Biology, UCL, Gower St, London WC1E 6BT, UK.
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5
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Cassaignau AME, Włodarski T, Chan SHS, Woodburn LF, Bukvin IV, Streit JO, Cabrita LD, Waudby CA, Christodoulou J. Interactions between nascent proteins and the ribosome surface inhibit co-translational folding. Nat Chem 2021; 13:1214-1220. [PMID: 34650236 PMCID: PMC8627912 DOI: 10.1038/s41557-021-00796-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/24/2021] [Indexed: 11/19/2022]
Abstract
Most proteins begin to fold during biosynthesis on the ribosome. It has been suggested that interactions between the emerging polypeptide and the ribosome surface might allow the ribosome itself to modulate co-translational folding. Here we combine protein engineering and NMR spectroscopy to characterize a series of interactions between the ribosome surface and unfolded nascent chains of the immunoglobulin-like FLN5 filamin domain. The strongest interactions are found for a C-terminal segment that is essential for folding, and we demonstrate quantitative agreement between the strength of this interaction and the energetics of the co-translational folding process itself. Mutations in this region that reduce the extent of binding result in a shift in the co-translational folding equilibrium towards the native state. Our results therefore demonstrate that a competition between folding and binding provides a simple, dynamic mechanism for the modulation of co-translational folding by the ribosome.
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Affiliation(s)
- Anaïs M. E. Cassaignau
- grid.83440.3b0000000121901201Institute of Structural and Molecular Biology, University College London, London, UK
| | - Tomasz Włodarski
- grid.83440.3b0000000121901201Institute of Structural and Molecular Biology, University College London, London, UK
| | - Sammy H. S. Chan
- grid.83440.3b0000000121901201Institute of Structural and Molecular Biology, University College London, London, UK
| | - Lauren F. Woodburn
- grid.83440.3b0000000121901201Institute of Structural and Molecular Biology, University College London, London, UK
| | - Ivana V. Bukvin
- grid.83440.3b0000000121901201Institute of Structural and Molecular Biology, University College London, London, UK
| | - Julian O. Streit
- grid.83440.3b0000000121901201Institute of Structural and Molecular Biology, University College London, London, UK
| | - Lisa D. Cabrita
- grid.83440.3b0000000121901201Institute of Structural and Molecular Biology, University College London, London, UK
| | - Christopher A. Waudby
- grid.83440.3b0000000121901201Institute of Structural and Molecular Biology, University College London, London, UK
| | - John Christodoulou
- grid.83440.3b0000000121901201Institute of Structural and Molecular Biology, University College London, London, UK ,grid.4464.20000 0001 2161 2573Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
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6
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Obtaining Hydrodynamic Radii of Intrinsically Disordered Protein Ensembles by Pulsed Field Gradient NMR Measurements. Methods Mol Biol 2020; 2141:285-302. [PMID: 32696363 DOI: 10.1007/978-1-0716-0524-0_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
In the disordered state, a protein exhibits a high degree of structural freedom, in both space and time. For an ensemble of disordered or unfolded proteins, this means that the ensemble comprises a high diversity of structures, ranging from compact collapsed states to fully extended polypeptide chains. In addition, each chain is highly dynamic and undergoes conformational changes and local dynamics on both fast and slow timescales. The size properties of disordered proteins are thus best described as ensemble averages. A straightforward measure of the size is the hydrodynamic radius, RH, of the ensemble. Since the disordered state is conformationally fluid, the observed RH does not refer to a particular shape or fold. Instead, it should be interpreted as a measure for the average compaction of the structural ensemble. In addition to characterizing the disordered ensemble itself, RH can be used to, with good precision, monitor changes in the ensemble size properties upon functional interactions of the disordered protein, e.g., dimerization, ligand binding, and folding pathways. Here, we present a step-by-step protocol for diffusion measurements using pulsed field gradient nuclear magnetic resonance (PFG NMR) spectroscopy. We describe how to calibrate the magnetic field gradient and offer different schemes for sample preparation. Finally, we describe how to obtain RH directly from the diffusion coefficient as well as from using an internal standard as a reference.
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7
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Combined smFRET and NMR analysis of riboswitch structural dynamics. Methods 2019; 153:22-34. [DOI: 10.1016/j.ymeth.2018.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 12/13/2022] Open
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8
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Javed A, Christodoulou J, Cabrita LD, Orlova EV. The ribosome and its role in protein folding: looking through a magnifying glass. Acta Crystallogr D Struct Biol 2017; 73:509-521. [PMID: 28580913 PMCID: PMC5458493 DOI: 10.1107/s2059798317007446] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/19/2017] [Indexed: 11/21/2022] Open
Abstract
Protein folding, a process that underpins cellular activity, begins co-translationally on the ribosome. During translation, a newly synthesized polypeptide chain enters the ribosomal exit tunnel and actively interacts with the ribosome elements - the r-proteins and rRNA that line the tunnel - prior to emerging into the cellular milieu. While understanding of the structure and function of the ribosome has advanced significantly, little is known about the process of folding of the emerging nascent chain (NC). Advances in cryo-electron microscopy are enabling visualization of NCs within the exit tunnel, allowing early glimpses of the interplay between the NC and the ribosome. Once it has emerged from the exit tunnel into the cytosol, the NC (still attached to its parent ribosome) can acquire a range of conformations, which can be characterized by NMR spectroscopy. Using experimental restraints within molecular-dynamics simulations, the ensemble of NC structures can be described. In order to delineate the process of co-translational protein folding, a hybrid structural biology approach is foreseeable, potentially offering a complete atomic description of protein folding as it occurs on the ribosome.
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Affiliation(s)
- Abid Javed
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England
- Institute of Structural and Molecular Biology, University College London (UCL), Gower Street, London WC1E 6BT, England
| | - John Christodoulou
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England
- Institute of Structural and Molecular Biology, University College London (UCL), Gower Street, London WC1E 6BT, England
| | - Lisa D. Cabrita
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England
- Institute of Structural and Molecular Biology, University College London (UCL), Gower Street, London WC1E 6BT, England
| | - Elena V. Orlova
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England
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9
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Hawk LML, Gee CT, Urick AK, Hu H, Pomerantz WCK. Paramagnetic relaxation enhancement for protein-observed 19F NMR as an enabling approach for efficient fragment screening. RSC Adv 2016; 6:95715-95721. [PMID: 28496971 PMCID: PMC5421645 DOI: 10.1039/c6ra21226c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Protein-observed 19F (PrOF) NMR is an emerging tool for ligand discovery. To optimize the efficiency of PrOF NMR experiments, paramagnetic relaxation enhancement through the addition of chelated Ni(II) was used to shorten longitudinal relaxation time without causing significant line broadening. Thus enhancing relaxation time leads to shorter experiments without perturbing the binding of low- or high-affinity ligands. This method allows for time-efficient screening of potential ligands for a wide variety of proteins in the growing field of fragment-based ligand discovery.
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Affiliation(s)
- Laura M L Hawk
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
| | - Clifford T Gee
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
| | - Andrew K Urick
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, United States
| | - Haitao Hu
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
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10
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Cassaignau AME, Launay HMM, Karyadi ME, Wang X, Waudby CA, Deckert A, Robertson AL, Christodoulou J, Cabrita LD. A strategy for co-translational folding studies of ribosome-bound nascent chain complexes using NMR spectroscopy. Nat Protoc 2016; 11:1492-507. [PMID: 27466710 DOI: 10.1038/nprot.2016.101] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
During biosynthesis on the ribosome, an elongating nascent polypeptide chain can begin to fold, in a process that is central to all living systems. Detailed structural studies of co-translational protein folding are now beginning to emerge; such studies were previously limited, at least in part, by the inherently dynamic nature of emerging nascent chains, which precluded most structural techniques. NMR spectroscopy is able to provide atomic-resolution information for ribosome-nascent chain complexes (RNCs), but it requires large quantities (≥10 mg) of homogeneous, isotopically labeled RNCs. Further challenges include limited sample working concentration and stability of the RNC sample (which contribute to weak NMR signals) and resonance broadening caused by attachment to the large (2.4-MDa) ribosomal complex. Here, we present a strategy to generate isotopically labeled RNCs in Escherichia coli that are suitable for NMR studies. Uniform translational arrest of the nascent chains is achieved using a stalling motif, and isotopically labeled RNCs are produced at high yield using high-cell-density E. coli growth conditions. Homogeneous RNCs are isolated by combining metal affinity chromatography (to isolate ribosome-bound species) with sucrose density centrifugation (to recover intact 70S monosomes). Sensitivity-optimized NMR spectroscopy is then applied to the RNCs, combined with a suite of parallel NMR and biochemical analyses to cross-validate their integrity, including RNC-optimized NMR diffusion measurements to report on ribosome attachment in situ. Comparative NMR studies of RNCs with the analogous isolated proteins permit a high-resolution description of the structure and dynamics of a nascent chain during its progressive biosynthesis on the ribosome.
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Affiliation(s)
- Anaïs M E Cassaignau
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, University of London, London, UK
| | - Hélène M M Launay
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, University of London, London, UK
| | - Maria-Evangelia Karyadi
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, University of London, London, UK
| | - Xiaolin Wang
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, University of London, London, UK
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, University of London, London, UK
| | - Annika Deckert
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, University of London, London, UK
| | - Amy L Robertson
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, University of London, London, UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, University of London, London, UK
| | - Lisa D Cabrita
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, University of London, London, UK
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