1
|
Blechar J, de Jesus V, Fürtig B, Hengesbach M, Schwalbe H. Shine-Dalgarno Accessibility Governs Ribosome Binding to the Adenine Riboswitch. ACS Chem Biol 2024; 19:607-618. [PMID: 38412235 DOI: 10.1021/acschembio.3c00435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Translational riboswitches located in the 5' UTR of the messenger RNA (mRNA) regulate translation through variation of the accessibility of the ribosome binding site (RBS). These are the result of conformational changes in the riboswitch RNA governed by ligand binding. Here, we use a combination of single-molecule colocalization techniques (Single-Molecule Kinetic Analysis of RNA Transient Structure (SiM-KARTS) and Single-Molecule Kinetic Analysis of Ribosome Binding (SiM-KARB)) and microscale thermophoresis (MST) to investigate the adenine-sensing riboswitch in Vibrio vulnificus, focusing on the changes of accessibility between the ligand-free and ligand-bound states. We show that both methods faithfully report on the accessibility of the RBS within the riboswitch and that both methods identify an increase in accessibility upon adenine binding. Expanding on the regulatory context, we show the impact of the ribosomal protein S1 on the unwinding of the RNA secondary structure, thereby favoring ribosome binding even for the apo state. The determined rate constants suggest that binding of the ribosome is faster than the time required to change from the ON state to the OFF state, a prerequisite for efficient regulation decision.
Collapse
Affiliation(s)
- Julius Blechar
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| |
Collapse
|
2
|
Binding of 30S Ribosome Induces Single-stranded Conformation Within and Downstream of the Expression Platform in a Translational Riboswitch. J Mol Biol 2022; 434:167668. [PMID: 35667471 DOI: 10.1016/j.jmb.2022.167668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/29/2022] [Accepted: 05/31/2022] [Indexed: 11/23/2022]
Abstract
Translational riboswitches are bacterial gene regulatory elements found in the 5'-untranslated region of mRNAs. They operate through a conformational refolding reaction that is triggered by a concentration change of a modulating small molecular ligand. The translation initiation region (TIR) is either released from or incorporated into base pairing interactions through the conformational switch. Hence, initiation of translation is regulated by the accessibility of the Shine-Dalgarno sequence and start codon. Interaction with the 30S ribosome is indispensable for the structural switch between functional OFF and ON states. However, on a molecular level it is still not fully resolved how the ribosome is accommodated near or at the translation initiation region in the context of translational riboswitches. The standby model of translation initiation postulates a binding site where the mRNA enters the ribosome and where it resides until the initiation site becomes unstructured and accessible. We here investigated the adenine-sensing riboswitch from Vibrio vulnificus. By application of a 19F labelling strategy for NMR spectroscopy that utilizes ligation techniques to synthesize differentially 19F labelled riboswitch molecules we show that nucleotides directly downstream of the riboswitch domain are first involved in productive interaction with the 30S ribosomal subunit. Upon the concerted action of ligand and the ribosomal protein rS1 the TIR becomes available and subsequently the 30S ribosome can slide towards the TIR. It will be interesting to see whether this is a general feature in translational riboswitches or if riboswitches exist where this region is structured and represent yet another layer of regulation.
Collapse
|
3
|
Burridge C, Waudby CA, Włodarski T, Cassaignau AME, Cabrita LD, Christodoulou J. Nascent chain dynamics and ribosome interactions within folded ribosome-nascent chain complexes observed by NMR spectroscopy. Chem Sci 2021; 12:13120-13126. [PMID: 34745542 PMCID: PMC8513902 DOI: 10.1039/d1sc04313g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/09/2021] [Indexed: 12/24/2022] Open
Abstract
The folding of many proteins can begin during biosynthesis on the ribosome and can be modulated by the ribosome itself. Such perturbations are generally believed to be mediated through interactions between the nascent chain and the ribosome surface, but despite recent progress in characterising interactions of unfolded states with the ribosome, and their impact on the initiation of co-translational folding, a complete quantitative analysis of interactions across both folded and unfolded states of a nascent chain has yet to be realised. Here we apply solution-state NMR spectroscopy to measure transverse proton relaxation rates for methyl groups in folded ribosome-nascent chain complexes of the FLN5 filamin domain. We observe substantial increases in relaxation rates for the nascent chain relative to the isolated domain, which can be related to changes in effective rotational correlation times using measurements of relaxation and cross-correlated relaxation in the isolated domain. Using this approach, we can identify interactions between the nascent chain and the ribosome surface, driven predominantly by electrostatics, and by measuring the change in these interactions as the subsequent FLN6 domain emerges, we may deduce their impact on the free energy landscapes associated with the co-translational folding process.
Collapse
Affiliation(s)
- Charles Burridge
- Institute of Structural and Molecular Biology, University College London London WC1E 6BT UK
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London London WC1E 6BT UK
| | - Tomasz Włodarski
- Institute of Structural and Molecular Biology, University College London London WC1E 6BT UK
| | - Anaïs M E Cassaignau
- Institute of Structural and Molecular Biology, University College London London WC1E 6BT UK
| | - Lisa D Cabrita
- Institute of Structural and Molecular Biology, University College London London WC1E 6BT UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London London WC1E 6BT UK
| |
Collapse
|
4
|
Switching at the ribosome: riboswitches need rProteins as modulators to regulate translation. Nat Commun 2021; 12:4723. [PMID: 34354064 PMCID: PMC8342710 DOI: 10.1038/s41467-021-25024-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/17/2021] [Indexed: 11/29/2022] Open
Abstract
Translational riboswitches are cis-acting RNA regulators that modulate the expression of genes during translation initiation. Their mechanism is considered as an RNA-only gene-regulatory system inducing a ligand-dependent shift of the population of functional ON- and OFF-states. The interaction of riboswitches with the translation machinery remained unexplored. For the adenine-sensing riboswitch from Vibrio vulnificus we show that ligand binding alone is not sufficient for switching to a translational ON-state but the interaction of the riboswitch with the 30S ribosome is indispensable. Only the synergy of binding of adenine and of 30S ribosome, in particular protein rS1, induces complete opening of the translation initiation region. Our investigation thus unravels the intricate dynamic network involving RNA regulator, ligand inducer and ribosome protein modulator during translation initiation. Translational regulation by riboswitches is an important mechanism for the modulation of gene expression in bacteria. Here the authors show that the ligand-induced allosteric switch in the adenine-sensing riboswitch from V. vulnificus is insufficient and leads only to a partial opening of the ribosome binding site and requires interaction with 30S-bound ribosomal protein S1, which acts as an RNA chaperone.
Collapse
|
5
|
Kharkov BB, Podkorytov IS, Bondarev SA, Belousov MV, Salikov VA, Zhouravleva GA, Skrynnikov NR. The Role of Rotational Motion in Diffusion NMR Experiments on Supramolecular Assemblies: Application to Sup35NM Fibrils. Angew Chem Int Ed Engl 2021; 60:15445-15451. [PMID: 33891789 DOI: 10.1002/anie.202102408] [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: 02/16/2021] [Revised: 04/19/2021] [Indexed: 11/08/2022]
Abstract
Pulsed-field gradient (PFG) NMR is an important tool for characterization of biomolecules and supramolecular assemblies. However, for micrometer-sized objects, such as amyloid fibrils, these experiments become difficult to interpret because in addition to translational diffusion they are also sensitive to rotational diffusion. We have constructed a mathematical theory describing the outcome of PFG NMR experiments on rod-like fibrils. To test its validity, we have studied the fibrils formed by Sup35NM segment of the prion protein Sup35. The interpretation of the PFG NMR data in this system is fully consistent with the evidence from electron microscopy. Contrary to some previously expressed views, the signals originating from disordered regions in the fibrils can be readily differentiated from the similar signals representing small soluble species (e.g. proteolytic fragments). This paves the way for diffusion-sorted NMR experiments on complex amyloidogenic samples.
Collapse
Affiliation(s)
- Boris B Kharkov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Ivan S Podkorytov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Mikhail V Belousov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034, St. Petersburg, Russia.,Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St. Petersburg, Russia
| | - Vladislav A Salikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Nikolai R Skrynnikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia.,Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| |
Collapse
|
6
|
Kharkov BB, Podkorytov IS, Bondarev SA, Belousov MV, Salikov VA, Zhouravleva GA, Skrynnikov NR. The Role of Rotational Motion in Diffusion NMR Experiments on Supramolecular Assemblies: Application to Sup35NM Fibrils. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Boris B. Kharkov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
| | - Ivan S. Podkorytov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
| | - Stanislav A. Bondarev
- Department of Genetics and Biotechnology St. Petersburg State University 199034 St. Petersburg Russia
| | - Mikhail V. Belousov
- Department of Genetics and Biotechnology St. Petersburg State University 199034 St. Petersburg Russia
- Laboratory for Proteomics of Supra-Organismal Systems All-Russia Research Institute for Agricultural Microbiology (ARRIAM) 196608 St. Petersburg Russia
| | - Vladislav A. Salikov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology St. Petersburg State University 199034 St. Petersburg Russia
| | - Nikolai R. Skrynnikov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
- Department of Chemistry Purdue University West Lafayette IN 47907 USA
| |
Collapse
|
7
|
Yu J, Ramirez LM, Premo A, Busch DB, Lin Q, Burz DS, Shekhtman A. Ribosome-Amplified Metabolism, RAMBO, Measured by NMR Spectroscopy. Biochemistry 2021; 60:1885-1895. [PMID: 34081430 DOI: 10.1021/acs.biochem.1c00074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
NMR spectroscopy was used to investigate the phenomenon of ribosome-amplified metabolism or RAMBO between pyruvate kinase and ribosomes. Because the concentration of ribosomes increases as the cell grows, ribosome binding interactions may regulate metabolic fluxes by altering the distribution of bound and free enzymes. Pyruvate kinase (PK) catalyzes the last step of glycolysis and represents a major drug target for controlling bacterial infections. The binding of metabolic enzymes to ribosomes creates protein quinary structures with altered catalytic activities. NMR spectroscopy and chemical cross-linking combined with high-resolution mass spectrometry were used to establish that PK binds to ribosome at three independent sites, the L1 stalk, the A site, and the mRNA entry pore. The bioanalytical methodology described characterizes the altered kinetics and confirms the specificity of pyruvate kinase-ribosome interaction, affording an opportunity to investigate the ribosome dependence of metabolic reactions under solution conditions that closely mimic the cytosol. Expanding on the concept of ribosomal heterogeneity, which describes variations in ribosomal constituents that contribute to the specificity of cellular processes, this work firmly establishes the reciprocal process by which ribosome-dependent quinary interactions affect metabolic activity.
Collapse
Affiliation(s)
- JianChao Yu
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Lisa M Ramirez
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Aaron Premo
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Devin B Busch
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Qishan Lin
- RNA Epitranscriptomics & Proteomics Resource, University at Albany, State University of New York, Albany, New York 12222, United States
| | - David S Burz
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| |
Collapse
|
8
|
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.
Collapse
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; , ,
| |
Collapse
|
9
|
Probing the dynamic stalk region of the ribosome using solution NMR. Sci Rep 2019; 9:13528. [PMID: 31537834 PMCID: PMC6753160 DOI: 10.1038/s41598-019-49190-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/31/2019] [Indexed: 11/29/2022] Open
Abstract
We describe an NMR approach based on the measurement of residual dipolar couplings (RDCs) to probe the structural and motional properties of the dynamic regions of the ribosome. Alignment of intact 70S ribosomes in filamentous bacteriophage enabled measurement of RDCs in the mobile C-terminal domain (CTD) of the stalk protein bL12. A structural refinement of this domain using the observed RDCs did not show large changes relative to the isolated protein in the absence of the ribosome, and we also found that alignment of the CTD was almost independent of the presence of the core ribosome particle, indicating that the inter-domain linker has significant flexibility. The nature of this linker was subsequently probed in more detail using a paramagnetic alignment strategy, which revealed partial propagation of alignment between neighbouring domains, providing direct experimental validation of a structural ensemble previously derived from SAXS and NMR relaxation measurements. Our results demonstrate the prospect of better characterising dynamical and functional regions of more challenging macromolecular machines and systems, for example ribosome–nascent chain complexes.
Collapse
|
10
|
Abstract
The large ribosomal subunit has a distinct feature, the stalk, extending outside the ribosome. In bacteria it is called the L12 stalk. The base of the stalk is protein uL10 to which two or three dimers of proteins bL12 bind. In archea and eukarya P1 and P2 proteins constitute the stalk. All these extending proteins, that have a high degree of flexibility due to a hinge between their N- and C-terminal parts, are essential for proper functionalization of some of the translation factors. The role of the stalk proteins has remained enigmatic for decades but is gradually approaching an understanding. In this review we summarise the knowhow about the structure and function of the ribosomal stalk till date starting from the early phase of ribosome research.
Collapse
|
11
|
Local unfolding of the HSP27 monomer regulates chaperone activity. Nat Commun 2019; 10:1068. [PMID: 30842409 PMCID: PMC6403371 DOI: 10.1038/s41467-019-08557-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 12/20/2018] [Indexed: 12/21/2022] Open
Abstract
The small heat-shock protein HSP27 is a redox-sensitive molecular chaperone that is expressed throughout the human body. Here, we describe redox-induced changes to the structure, dynamics, and function of HSP27 and its conserved α-crystallin domain (ACD). While HSP27 assembles into oligomers, we show that the monomers formed upon reduction are highly active chaperones in vitro, but are susceptible to self-aggregation. By using relaxation dispersion and high-pressure nuclear magnetic resonance (NMR) spectroscopy, we observe that the pair of β-strands that mediate dimerisation partially unfold in the monomer. We note that numerous HSP27 mutations associated with inherited neuropathies cluster to this dynamic region. High levels of sequence conservation in ACDs from mammalian sHSPs suggest that the exposed, disordered interface present in free monomers or oligomeric subunits may be a general, functional feature of sHSPs. The small heat-shock protein HSP27 occurs predominantly in oligomeric forms, which makes its structural characterisation challenging. Here the authors employ CPMG and high-pressure NMR with native mass spectrometry and biophysical assays to show that the active monomeric form of HSP27 is substantially disordered and highly chaperone-active.
Collapse
|
12
|
Abstract
Ribosomes are biological nanomachine that synthesise all proteins within a cell. It took decades to reveal the architecture of this essential cellular component. To understand the structure -function relationship of this nanomachine needed the utilisisation of different biochemical, biophysical and structural techniques. Structural studies combined with mutagenesis of the different ribosomal complexes comprising various RNAs and proteins enabled us to understand how this machine works inside a cell. Nowadays quite a number of ribosomal structures were published that confirmed biochemical studies on particular steps of protein synthesis by the ribosome . Four major steps were identified: initiation , elongation, termination and recycling. These steps lead us to the important question how the ribosome function can be regulated. Advances in technology for cryo electron microscopy: sample preparations, image recording, developments in algorithms for image analysis and processing significantly helped in revelation of structural details of the ribosome . We now have a library of ribosome structures from prokaryotes to eukaryotes that enable us to understand the complex mechanics of this nanomachine. As this structural library continues to grow, we gradually improve our understanding of this process and how it can be regulated and how the specific ribosomes can be stalled or activated, or completely disabled. This article provides a comprehensive overview of ribosomal structures that represent structural snapshots of the ribosome at its different functional states. Better understanding rises more particular questions that have to be addressed by determination structures of more complexes.Synopsis: Structural biology of the ribosome.
Collapse
Affiliation(s)
- Abid Javed
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London, WC1E 7HX, UK
| | - Elena V Orlova
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London, WC1E 7HX, UK.
| |
Collapse
|
13
|
Zhang Y, Launay H, Schramm A, Lebrun R, Gontero B. Exploring intrinsically disordered proteins in Chlamydomonas reinhardtii. Sci Rep 2018; 8:6805. [PMID: 29717210 PMCID: PMC5931566 DOI: 10.1038/s41598-018-24772-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/26/2018] [Indexed: 11/14/2022] Open
Abstract
The content of intrinsically disordered protein (IDP) is related to organism complexity, evolution, and regulation. In the Plantae, despite their high complexity, experimental investigation of IDP content is lacking. We identified by mass spectrometry 682 heat-resistant proteins from the green alga, Chlamydomonas reinhardtii. Using a phosphoproteome database, we found that 331 of these proteins are targets of phosphorylation. We analyzed the flexibility propensity of the heat-resistant proteins and their specific features as well as those of predicted IDPs from the same organism. Their mean percentage of disorder was about 20%. Most of the IDPs (~70%) were addressed to other compartments than mitochondrion and chloroplast. Their amino acid composition was biased compared to other classic IDPs. Their molecular functions were diverse; the predominant ones were nucleic acid binding and unfolded protein binding and the less abundant one was catalytic activity. The most represented proteins were ribosomal proteins, proteins associated to flagella, chaperones and histones. We also found CP12, the only experimental IDP from C. reinhardtii that is referenced in disordered protein database. This is the first experimental investigation of IDPs in C. reinhardtii that also combines in silico analysis.
Collapse
Affiliation(s)
- Yizhi Zhang
- Aix Marseille Univ, CNRS, BIP, UMR 7281, IMM, 31 Chemin J. Aiguier, 13402, Marseille, Cedex 20, France
| | - Hélène Launay
- Aix Marseille Univ, CNRS, BIP, UMR 7281, IMM, 31 Chemin J. Aiguier, 13402, Marseille, Cedex 20, France
| | | | - Régine Lebrun
- Plate-forme Protéomique, Marseille Protéomique (MaP), IBiSA labeled, IMM, FR 3479, CNRS, B.P. 71, 13402, Marseille, Cedex 20, France
| | - Brigitte Gontero
- Aix Marseille Univ, CNRS, BIP, UMR 7281, IMM, 31 Chemin J. Aiguier, 13402, Marseille, Cedex 20, France.
| |
Collapse
|
14
|
Onset of disorder and protein aggregation due to oxidation-induced intermolecular disulfide bonds: case study of RRM2 domain from TDP-43. Sci Rep 2017; 7:11161. [PMID: 28894122 PMCID: PMC5593996 DOI: 10.1038/s41598-017-10574-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/09/2017] [Indexed: 12/13/2022] Open
Abstract
We have investigated the behavior of second RNA-recognition motif (RRM2) of neuropathological protein TDP43 under the effect of oxidative stress as modeled in vitro. Toward this end we have used the specially adapted version of H/D exchange experiment, NMR relaxation and diffusion measurements, dynamic light scattering, controlled proteolysis, gel electrophoresis, site-directed mutagenesis and microsecond MD simulations. Under oxidizing conditions RRM2 forms disulfide-bonded dimers that experience unfolding and then assemble into aggregate particles (APs). These particles are strongly disordered, highly inhomogeneous and susceptible to proteolysis; some of them withstand the dithiothreitol treatment. They can recruit/release monomeric RRM2 through thiol-disulfide exchange reactions. By using a combination of dynamic light scattering and NMR diffusion data we were able to approximate the size distribution function for the APs. The key to the observed aggregation behavior is the diminished ability of disulfide-bonded RRM2 dimers to refold and their increased propensity to misfold, which makes them vulnerable to large thermal fluctuations. The emerging picture provides detailed insight on how oxidative stress can contribute to neurodegenerative disease, with unfolding, aggregation, and proteolytic cleavage as different facets of the process.
Collapse
|
15
|
Malki I, Cantrelle FX, Sottejeau Y, Lippens G, Lambert JC, Landrieu I. Regulation of the interaction between the neuronal BIN1 isoform 1 and Tau proteins - role of the SH3 domain. FEBS J 2017; 284:3218-3229. [PMID: 28755476 DOI: 10.1111/febs.14185] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 06/25/2017] [Accepted: 07/25/2017] [Indexed: 12/16/2022]
Abstract
Bridging integrator 1 (bin1) gene is a genetic determinant of Alzheimer's disease (AD) and has been reported to modulate Alzheimer's pathogenesis through pathway(s) involving Tau. The functional impact of Tau/BIN1 interaction as well as the molecular details of this interaction are still not fully resolved. As a consequence, how BIN1 through its interaction with Tau affects AD risk is also still not determined. To progress in this understanding, interaction of Tau with two BIN1 isoforms was investigated using Nuclear Magnetic Resonance spectroscopy. 1 H, 15 N spectra showed that the C-terminal SH3 domain of BIN1 isoform 1 (BIN1Iso1) is not mobile in solution but locked with the core of the protein. In contrast, the SH3 domain of BIN1 isoform 9 (BIN1Iso9) behaves as an independent mobile domain. This reveals an equilibrium between close and open conformations for the SH3 domain. Interestingly, a 334-376 peptide from the clathrin and AP-2-binding domain (CLAP) domain of BIN1Iso1, which contains a SH3-binding site, is able to compete with BIN1-SH3 intramolecular interaction. For both BIN1 isoforms, the SH3 domain can interact with Tau(210-240) sequence. Tau(210-240) peptide can indeed displace the intramolecular interaction of the BIN1-SH3 of BIN1Iso1 and form a complex with the released domain. The measured Kd were in agreement with a stronger affinity of Tau peptide. Both CLAP and Tau peptides occupied the same surface on the BIN1-SH3 domain, showing that their interaction is mutually exclusive. These results emphasize an additional level of complexity in the regulation of the interaction between BIN1 and Tau dependent of the BIN1 isoforms.
Collapse
Affiliation(s)
- Idir Malki
- Lille University, CNRS UMR8576, Lille, France
| | | | - Yoann Sottejeau
- Lille University, INSERM UMR1167, Pasteur Institute of Lille, Lille, France
| | - Guy Lippens
- Lille University, CNRS UMR8576, Lille, France
| | | | | |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Deckert A, Waudby CA, Wlodarski T, Wentink AS, Wang X, Kirkpatrick JP, Paton JFS, Camilloni C, Kukic P, Dobson CM, Vendruscolo M, Cabrita LD, Christodoulou J. Structural characterization of the interaction of α-synuclein nascent chains with the ribosomal surface and trigger factor. Proc Natl Acad Sci U S A 2016; 113:5012-7. [PMID: 27092002 PMCID: PMC4983817 DOI: 10.1073/pnas.1519124113] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ribosome is increasingly becoming recognized as a key hub for integrating quality control processes associated with protein biosynthesis and cotranslational folding (CTF). The molecular mechanisms by which these processes take place, however, remain largely unknown, in particular in the case of intrinsically disordered proteins (IDPs). To address this question, we studied at a residue-specific level the structure and dynamics of ribosome-nascent chain complexes (RNCs) of α-synuclein (αSyn), an IDP associated with Parkinson's disease (PD). Using solution-state nuclear magnetic resonance (NMR) spectroscopy and coarse-grained molecular dynamics (MD) simulations, we find that, although the nascent chain (NC) has a highly disordered conformation, its N-terminal region shows resonance broadening consistent with interactions involving specific regions of the ribosome surface. We also investigated the effects of the ribosome-associated molecular chaperone trigger factor (TF) on αSyn structure and dynamics using resonance broadening to define a footprint of the TF-RNC interactions. We have used these data to construct structural models that suggest specific ways by which emerging NCs can interact with the biosynthesis and quality control machinery.
Collapse
Affiliation(s)
- Annika Deckert
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom; Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom; Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Tomasz Wlodarski
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom; Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Anne S Wentink
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom; Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Xiaolin Wang
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom; Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - John P Kirkpatrick
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom; Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Jack F S Paton
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom; Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Predrag Kukic
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Lisa D Cabrita
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom; Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom;
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom; Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom;
| |
Collapse
|
19
|
A structural ensemble of a ribosome-nascent chain complex during cotranslational protein folding. Nat Struct Mol Biol 2016; 23:278-285. [PMID: 26926436 PMCID: PMC5405865 DOI: 10.1038/nsmb.3182] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 02/02/2016] [Indexed: 12/18/2022]
Abstract
Although detailed pictures of ribosome structures are emerging, little is known about the structural and cotranslational folding properties of nascent polypeptide chains at the atomic level. Here we used solution-state NMR spectroscopy to define a structural ensemble of a ribosome-nascent chain complex (RNC) formed during protein biosynthesis in Escherichia coli, in which a pair of immunoglobulin-like domains adopts a folded N-terminal domain (FLN5) and a disordered but compact C-terminal domain (FLN6). To study how FLN5 acquires its native structure cotranslationally, we progressively shortened the RNC constructs. We found that the ribosome modulates the folding process, because the complete sequence of FLN5 emerged well beyond the tunnel before acquiring native structure, whereas FLN5 in isolation folded spontaneously, even when truncated. This finding suggests that regulating structure acquisition during biosynthesis can reduce the probability of misfolding, particularly of homologous domains.
Collapse
|
20
|
Chan SHS, Waudby CA, Cassaignau AME, Cabrita LD, Christodoulou J. Increasing the sensitivity of NMR diffusion measurements by paramagnetic longitudinal relaxation enhancement, with application to ribosome-nascent chain complexes. JOURNAL OF BIOMOLECULAR NMR 2015; 63:151-163. [PMID: 26253948 PMCID: PMC4924603 DOI: 10.1007/s10858-015-9968-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 07/13/2015] [Indexed: 05/27/2023]
Abstract
The translational diffusion of macromolecules can be examined non-invasively by stimulated echo (STE) NMR experiments to accurately determine their molecular sizes. These measurements can be important probes of intermolecular interactions and protein folding and unfolding, and are crucial in monitoring the integrity of large macromolecular assemblies such as ribosome-nascent chain complexes (RNCs). However, NMR studies of these complexes can be severely constrained by their slow tumbling, low solubility (with maximum concentrations of up to 10 μM), and short lifetimes resulting in weak signal, and therefore continuing improvements in experimental sensitivity are essential. Here we explore the use of the paramagnetic longitudinal relaxation enhancement (PLRE) agent NiDO2A on the sensitivity of (15)N XSTE and SORDID heteronuclear STE experiments, which can be used to monitor the integrity of these unstable complexes. We exploit the dependence of the PLRE effect on the gyromagnetic ratio and electronic relaxation time to accelerate recovery of (1)H magnetization without adversely affecting storage on N z during diffusion delays or introducing significant transverse relaxation line broadening. By applying the longitudinal relaxation-optimized SORDID pulse sequence together with NiDO2A to 70S Escherichia coli ribosomes and RNCs, NMR diffusion sensitivity enhancements of up to 4.5-fold relative to XSTE are achieved, alongside ~1.9-fold improvements in two-dimensional NMR sensitivity, without compromising the sample integrity. We anticipate these results will significantly advance the use of NMR to probe dynamic regions of ribosomes and other large, unstable macromolecular assemblies.
Collapse
Affiliation(s)
- Sammy H S Chan
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 6BT, UK
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 6BT, UK
| | - Anaïs M E Cassaignau
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 6BT, UK
| | - Lisa D Cabrita
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 6BT, UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 6BT, UK
| |
Collapse
|
21
|
Baldwin AJ, Egan DL, Warren F, Barker PD, Dobson CM, Butterworth PJ, Ellis PR. Investigating the mechanisms of amylolysis of starch granules by solution-state NMR. Biomacromolecules 2015; 16:1614-21. [PMID: 25815624 PMCID: PMC4429494 DOI: 10.1021/acs.biomac.5b00190] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/26/2015] [Indexed: 11/30/2022]
Abstract
Starch is a prominent component of the human diet and is hydrolyzed by α-amylase post-ingestion. Probing the mechanism of this process has proven challenging, due to the intrinsic heterogeneity of individual starch granules. By means of solution-state NMR, we demonstrate that flexible polysaccharide chains protruding from the solvent-exposed surfaces of waxy rice starch granules are highly mobile and that during hydrothermal treatment, when the granules swell, the number of flexible residues on the exposed surfaces increases by a factor of 15. Moreover, we show that these flexible chains are the primary substrates for α-amylase, being cleaved in the initial stages of hydrolysis. These findings allow us to conclude that the quantity of flexible α-glucan chains protruding from the granule surface will greatly influence the rate of energy acquisition from digestion of starch.
Collapse
Affiliation(s)
- Andrew J. Baldwin
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
| | - Danielle L. Egan
- Biopolymers
Group, Diabetes and Nutritional Sciences Division, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, United
Kingdom
| | - Fredrick
J. Warren
- Biopolymers
Group, Diabetes and Nutritional Sciences Division, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, United
Kingdom
| | - Paul D. Barker
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
| | - Christopher M. Dobson
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
| | - Peter J. Butterworth
- Biopolymers
Group, Diabetes and Nutritional Sciences Division, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, United
Kingdom
| | - Peter R. Ellis
- Biopolymers
Group, Diabetes and Nutritional Sciences Division, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, United
Kingdom
| |
Collapse
|
22
|
Barbet-Massin E, Huang CT, Daebel V, Hsu STD, Reif B. Ortsaufgelöste Festkörper-NMR-Studien am “Trigger-Faktor” im Komplex mit der großen ribosomalen 50S-Untereinheit. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409393] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
23
|
Barbet-Massin E, Huang CT, Daebel V, Hsu STD, Reif B. Site-Specific Solid-State NMR Studies of “Trigger Factor” in Complex with the Large Ribosomal Subunit 50S. Angew Chem Int Ed Engl 2015; 54:4367-9. [DOI: 10.1002/anie.201409393] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 01/09/2015] [Indexed: 02/01/2023]
|
24
|
Park SJ. NMR Study of larger proteins using isotope labeling. JOURNAL OF THE KOREAN MAGNETIC RESONANCE SOCIETY 2014. [DOI: 10.6564/jkmrs.2014.18.2.047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
25
|
Gigant B, Landrieu I, Fauquant C, Barbier P, Huvent I, Wieruszeski JM, Knossow M, Lippens G. Mechanism of Tau-promoted microtubule assembly as probed by NMR spectroscopy. J Am Chem Soc 2014; 136:12615-23. [PMID: 25162583 DOI: 10.1021/ja504864m] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Determining the molecular mechanism of the neuronal Tau protein in the tubulin heterodimer assembly has been a challenge owing to the dynamic character of the complex and the large size of microtubules. We use here defined constructs comprising one or two tubulin heterodimers to characterize their association with a functional fragment of Tau, named TauF4. TauF4 binds with high affinities to the tubulin heterodimer complexes, but NMR spectroscopy shows that it remains highly dynamic, partly because of the interaction with the acidic C-terminal tails of the tubulin monomers. When bound to a single tubulin heterodimer, TauF4 is characterized by an overhanging peptide corresponding to the first of the four microtubule binding repeats of Tau. This peptide becomes immobilized in the complex with two longitudinally associated tubulin heterodimers. The longitudinal associations are favored by the fragment and contribute to Tau's functional role in microtubule assembly.
Collapse
Affiliation(s)
- Benoît Gigant
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, Centre National de la Recherche Scientifique , 91198 Gif sur Yvette, France
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Waudby CA, Launay H, Cabrita LD, Christodoulou J. Protein folding on the ribosome studied using NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 74:57-75. [PMID: 24083462 PMCID: PMC3991860 DOI: 10.1016/j.pnmrs.2013.07.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 07/17/2013] [Accepted: 07/17/2013] [Indexed: 05/11/2023]
Abstract
NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome-nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity.
Collapse
|
27
|
NMR spectroscopy on domain dynamics in biomacromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 112:58-117. [DOI: 10.1016/j.pbiomolbio.2013.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 12/22/2022]
|
28
|
Gelis I, Vitzthum V, Dhimole N, Caporini MA, Schedlbauer A, Carnevale D, Connell SR, Fucini P, Bodenhausen G. Solid-state NMR enhanced by dynamic nuclear polarization as a novel tool for ribosome structural biology. JOURNAL OF BIOMOLECULAR NMR 2013; 56:85-93. [PMID: 23689811 DOI: 10.1007/s10858-013-9721-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 03/07/2013] [Indexed: 06/02/2023]
Abstract
The impact of Nuclear Magnetic Resonance (NMR) on studies of large macromolecular complexes hinges on improvements in sensitivity and resolution. Dynamic nuclear polarization (DNP) in the solid state can offer improved sensitivity, provided sample preparation is optimized to preserve spectral resolution. For a few nanomoles of intact ribosomes and an 800 kDa ribosomal complex we demonstrate that the combination of DNP and magic-angle spinning NMR (MAS-NMR) allows one to overcome current sensitivity limitations so that homo- and heteronuclear (13)C and (15)N NMR correlation spectra can be recorded. Ribosome particles, directly pelleted and frozen into an NMR rotor, yield DNP signal enhancements on the order of ~25-fold and spectra that exhibit narrow linewidths, suitable for obtaining site-specific information. We anticipate that the same approach is applicable to other high molecular weight complexes.
Collapse
Affiliation(s)
- Ioannis Gelis
- Buchmann Institute for Molecular Life Sciences, Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Salvatella X. Structural aspects of amyloid formation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:73-101. [PMID: 23663966 DOI: 10.1016/b978-0-12-386931-9.00004-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Amyloid fibrils are highly organized and generally insoluble protein aggregates rich in β secondary structure that can be formed by a wide range of sequences. They have been the object of intense scrutiny because their formation has been associated with a number of neurodegenerative disorders such as Alzheimer's, Parkinson's, Huntington's, and Creutzfeldt-Jakob's diseases. As a consequence of these efforts, much is now known about the properties of proteins that render them prone to form amyloid fibrils, about the mechanism of fibrillation, about the molecular structures of the fibrils, and about the forces that stabilize them. The relationship between the structural properties of the monomeric protein and those of the corresponding aggregate has been, in particular, intensively studied. In this chapter, we will provide an account of current knowledge on this intriguing relationship and provide the reader with key references about this topic.
Collapse
|
30
|
Rundqvist L, Tengel T, Zdunek J, Björn E, Schleucher J, Alcocer MJC, Larsson G. Solution structure, copper binding and backbone dynamics of recombinant Ber e 1-the major allergen from Brazil nut. PLoS One 2012; 7:e46435. [PMID: 23056307 PMCID: PMC3464261 DOI: 10.1371/journal.pone.0046435] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 08/29/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The 2S albumin Ber e 1 is the major allergen in Brazil nuts. Previous findings indicated that the protein alone does not cause an allergenic response in mice, but the addition of components from a Brazil nut lipid fraction were required. Structural details of Ber e 1 may contribute to the understanding of the allergenic properties of the protein and its potential interaction partners. METHODOLOGY/PRINCIPAL FINDINGS The solution structure of recombinant Ber e 1 was solved using NMR spectroscopy and measurements of the protein back bone dynamics at a residue-specific level were extracted using (15)N-spin relaxation. A hydrophobic cavity was identified in the structure of Ber e 1. Using the paramagnetic relaxation enhancement property of Cu(2+) in conjunction with NMR, it was shown that Ber e 1 is able to specifically interact with the divalent copper ion and the binding site was modeled into the structure. The IgE binding region as well as the copper binding site show increased dynamics on both fast ps-ns timescale as well as slower µs-ms timescale. CONCLUSIONS/SIGNIFICANCE The overall fold of Ber e 1 is similar to other 2S albumins, but the hydrophobic cavity resembles that of a homologous non-specific lipid transfer protein. Ber e 1 is the first 2S albumin shown to interact with Cu(2+) ions. This Cu(2+) binding has minimal effect on the electrostatic potential on the surface of the protein, but the charge distribution within the hydrophobic cavity is significantly altered. As the hydrophobic cavity is likely to be involved in a putative lipid interaction the Cu(2+) can in turn affect the interaction that is essential to provoke an allergenic response.
Collapse
Affiliation(s)
- Louise Rundqvist
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Tobias Tengel
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Janusz Zdunek
- Protein Constructor Developers Company, Umeå, Sweden
| | - Erik Björn
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Jürgen Schleucher
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Marcos J. C. Alcocer
- Department of Nutritional Sciences, University of Nottingham, Loughborough, United Kingdom
| | - Göran Larsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- * E-mail:
| |
Collapse
|
31
|
Zhang D, Liu G, Xue J, Lou J, Nierhaus KH, Gong W, Qin Y. Common chaperone activity in the G-domain of trGTPase protects L11-L12 interaction on the ribosome. Nucleic Acids Res 2012; 40:10851-65. [PMID: 22965132 PMCID: PMC3505967 DOI: 10.1093/nar/gks833] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Translational GTPases (trGTPases) regulate all phases of protein synthesis. An early event in the interaction of a trGTPase with the ribosome is the contact of the G-domain with the C-terminal domain (CTD) of ribosomal protein L12 (L12-CTD) and subsequently interacts with the N-terminal domain of L11 (L11-NTD). However, the structural and functional relationships between L12-CTD and L11-NTD remain unclear. Here, we performed mutagenesis, biochemical and structural studies to identify the interactions between L11-NTD and L12-CTD. Mutagenesis of conserved residues in the interaction site revealed their role in the docking of trGTPases. During docking, loop62 of L11-NTD protrudes into a cleft in L12-CTD, leading to an open conformation of this domain and exposure of hydrophobic core. This unfavorable situation for L12-CTD stability is resolved by a chaperone-like activity of the contacting G-domain. Our results suggest that all trGTPases-regardless of their different specific functions-use a common mechanism for stabilizing the L11-NTD•L12-CTD interactions.
Collapse
Affiliation(s)
- Dandan Zhang
- Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | | | | | | | | | | | | |
Collapse
|
32
|
Waudby CA, Mantle MD, Cabrita LD, Gladden LF, Dobson CM, Christodoulou J. Rapid Distinction of Intracellular and Extracellular Proteins Using NMR Diffusion Measurements. J Am Chem Soc 2012; 134:11312-5. [DOI: 10.1021/ja304912c] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Christopher A. Waudby
- Institute of Structural and
Molecular Biology, University College London and Birkbeck College, Gower Street, London WC1E 6BT, U.K
| | - Mick D. Mantle
- Department of Chemical Engineering
and Biotechnology, University of Cambridge, Pembroke Street, Cambridge CB2 3RA, U.K
| | - Lisa D. Cabrita
- Institute of Structural and
Molecular Biology, University College London and Birkbeck College, Gower Street, London WC1E 6BT, U.K
| | - Lynn F. Gladden
- Department of Chemical Engineering
and Biotechnology, University of Cambridge, Pembroke Street, Cambridge CB2 3RA, U.K
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge
CB2 1EW, U.K
| | - John Christodoulou
- Institute of Structural and
Molecular Biology, University College London and Birkbeck College, Gower Street, London WC1E 6BT, U.K
| |
Collapse
|
33
|
Deroo S, Hyung SJ, Marcoux J, Gordiyenko Y, Koripella RK, Sanyal S, Robinson CV. Mechanism and rates of exchange of L7/L12 between ribosomes and the effects of binding EF-G. ACS Chem Biol 2012; 7:1120-7. [PMID: 22489843 PMCID: PMC4058753 DOI: 10.1021/cb300081s] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The ribosomal stalk complex binds and recruits translation factors to the ribosome during protein biosynthesis. In Escherichia coli the stalk is composed of protein L10 and four copies of L7/L12. Despite the crucial role of the stalk, mechanistic details of L7/L12 subunit exchange are not established. By incubating isotopically labeled intact ribosomes with their unlabeled counterparts we monitored the exchange of the labile stalk proteins by recording mass spectra as a function of time. On the basis of kinetic analysis, we proposed a mechanism whereby exchange proceeds via L7/L12 monomers and dimers. We also compared exchange of L7/L12 from free ribosomes with exchange from ribosomes in complex with elongation factor G (EF-G), trapped in the posttranslocational state by fusidic acid. Results showed that binding of EF-G reduces the L7/L12 exchange reaction of monomers by ~27% and of dimers by ~47% compared with exchange from free ribosomes. This is consistent with a model in which binding of EF-G does not modify interactions between the L7/L12 monomers but rather one of the four monomers, and as a result one of the two dimers, become anchored to the ribosome-EF-G complex preventing their free exchange. Overall therefore our results not only provide mechanistic insight into the exchange of L7/L12 monomers and dimers and the effects of EF-G binding but also have implications for modulating stability in response to environmental and functional stimuli within the cell.
Collapse
Affiliation(s)
- Stéphanie Deroo
- University of Oxford, Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
| | - Suk-Joon Hyung
- University of Michigan, Department of Chemistry, 930 N. University, Ann Arbor, MI 48109-1055, USA
| | - Julien Marcoux
- University of Oxford, Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
| | - Yuliya Gordiyenko
- University of Oxford, Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
| | - Ravi Kiran Koripella
- Uppsala University, Department of Cell and Molecular Biology, BMC, Box-596, S-75 124 Uppsala, Sweden
| | - Suparna Sanyal
- Uppsala University, Department of Cell and Molecular Biology, BMC, Box-596, S-75 124 Uppsala, Sweden
| | - Carol V. Robinson
- University of Oxford, Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
| |
Collapse
|
34
|
Catron B, Caruso JA, Limbach PA. Selective detection of peptide-oligonucleotide heteroconjugates utilizing capillary HPLC-ICPMS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1053-1061. [PMID: 22451333 PMCID: PMC3348256 DOI: 10.1007/s13361-012-0366-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 12/06/2011] [Accepted: 02/18/2012] [Indexed: 05/31/2023]
Abstract
A method for the selective detection and quantification of peptide:oligonucleotide heteroconjugates, such as those generated by protein:nucleic acid cross-links, using capillary reversed-phase high performance liquid chromatography (cap-RPHPLC) coupled with inductively coupled plasma mass spectrometry detection (ICPMS) is described. The selective detection of phosphorus as (31)P(+), the only natural isotope, in peptide-oligonucleotide heteroconjugates is enabled by the elemental detection capabilities of the ICPMS. Mobile phase conditions that allow separation of heteroconjugates while maintaining ICPMS compatibility were investigated. We found that trifluoroacetic acid (TFA) mobile phases, used in conventional peptide separations, and hexafluoroisopropanol/triethylamine (HFIP/TEA) mobile phases, used in conventional oligonucleotide separations, both are compatible with ICPMS and enable heteroconjugate separation. The TFA-based separations yielded limits of detection (LOD) of ~40 ppb phosphorus, which is nearly seven times lower than the LOD for HFIP/TEA-based separations. Using the TFA mobile phase, 1-2 pmol of a model heteroconjugate were routinely separated and detected by this optimized capLC-ICPMS method.
Collapse
Affiliation(s)
- Brittany Catron
- University of Cincinnati/Agilent Technologies Metallomics Center of the Americas, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221-0172, USA
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, OH 45221-0172, USA
| | - Joseph A. Caruso
- University of Cincinnati/Agilent Technologies Metallomics Center of the Americas, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221-0172, USA
| | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, OH 45221-0172, USA
| |
Collapse
|
35
|
Ribosome purification approaches for studying interactions of regulatory proteins and RNAs with the ribosome. Methods Mol Biol 2012; 905:273-89. [PMID: 22736011 PMCID: PMC4607317 DOI: 10.1007/978-1-61779-949-5_18] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Ribosomes are large complexes of RNA and protein that perform the essential task of protein synthesis in the cell. Ribosomes also serve as the initiation point for several translation-associated functions. To perform these tasks efficiently, ribosomes interact with a myriad of nonribosomal proteins and RNAs. Given that most of these interactions are transient, purification of the interacting factors in complex with the ribosome can be a challenging undertaking. Here, we review methods commonly used to isolate ribosomes and study ribosome-associated factors. We also discuss crucial parameters for designing and executing ribosome association studies. Finally, we present a detailed protocol for reporter based enrichment assays that are employed to selectively isolate ribosomes translating a particular message of interest. These protocols can be used to study a wide range of ribosome-associated functions.
Collapse
|
36
|
Mandava CS, Peisker K, Ederth J, Kumar R, Ge X, Szaflarski W, Sanyal S. Bacterial ribosome requires multiple L12 dimers for efficient initiation and elongation of protein synthesis involving IF2 and EF-G. Nucleic Acids Res 2011; 40:2054-64. [PMID: 22102582 PMCID: PMC3299993 DOI: 10.1093/nar/gkr1031] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ribosomal stalk in bacteria is composed of four or six copies of L12 proteins arranged in dimers that bind to the adjacent sites on protein L10, spanning 10 amino acids each from the L10 C-terminus. To study why multiple L12 dimers are required on the ribosome, we created a chromosomally engineered Escherichia coli strain, JE105, in which the peripheral L12 dimer binding site was deleted. Thus JE105 harbors ribosomes with only a single L12 dimer. Compared to MG1655, the parental strain with two L12 dimers, JE105 showed significant growth defect suggesting suboptimal function of the ribosomes with one L12 dimer. When tested in a cell-free reconstituted transcription–translation assay the synthesis of a full-length protein, firefly luciferase, was notably slower with JE105 70S ribosomes and 50S subunits. Further, in vitro analysis by fast kinetics revealed that single L12 dimer ribosomes from JE105 are defective in two major steps of translation, namely initiation and elongation involving translational GTPases IF2 and EF-G. Varying number of L12 dimers on the ribosome can be a mechanism in bacteria for modulating the rate of translation in response to growth condition.
Collapse
Affiliation(s)
- Chandra Sekhar Mandava
- Department of Cell and Molecular Biology, Uppsala University, BMC, Box-596, SE-751 24 Uppsala, Sweden
| | | | | | | | | | | | | |
Collapse
|
37
|
An HflX-type GTPase from Sulfolobus solfataricus binds to the 50S ribosomal subunit in all nucleotide-bound states. J Bacteriol 2011; 193:2861-7. [PMID: 21478358 DOI: 10.1128/jb.01552-10] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
HflX GTPases are found in all three domains of life, the Bacteria, Archaea, and Eukarya. HflX from Escherichia coli has been shown to bind to the 50S ribosomal subunit in a nucleotide-dependent manner, and this interaction strongly stimulates its GTPase activity. We recently determined the structure of an HflX ortholog from the archaeon Sulfolobus solfataricus (SsoHflX). It revealed the presence of a novel HflX domain that might function in RNA binding and is linked to a canonical G domain. This domain arrangement is common to all archaeal, bacterial, and eukaryotic HflX GTPases. This paper shows that the archaeal SsoHflX, like its bacterial orthologs, binds to the 50S ribosomal subunit. This interaction does not depend on the presence of guanine nucleotides. The HflX domain is sufficient for ribosome interaction. Binding appears to be restricted to free 50S ribosomal subunits and does not occur with 70S ribosomes engaged in translation. The fingerprint (1)H-(15)N heteronuclear correlation nuclear magnetic resonance (NMR) spectrum of SsoHflX reveals a large number of well-resolved resonances that are broadened upon binding to the 50S ribosomal subunit. The GTPase activity of SsoHflX is stimulated by crude fractions of 50S ribosomal subunits, but this effect is lost with further high-salt purification of the 50S ribosomal subunits, suggesting that the stimulation depends on an extrinsic factor bound to the 50S ribosomal subunit. Our results reveal common properties but also marked differences between archaeal and bacterial HflX proteins.
Collapse
|
38
|
Structure and Dynamics of Ribosomal Protein L12: An Ensemble Model Based on SAXS and NMR Relaxation. Biophys J 2010; 98:2374-82. [PMID: 20483347 DOI: 10.1016/j.bpj.2010.02.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 01/28/2010] [Accepted: 02/04/2010] [Indexed: 11/20/2022] Open
Abstract
Ribosomal protein L12 is a two-domain protein that forms dimers mediated by its N-terminal domains. A 20-residue linker separates the N- and C-terminal domains. This linker results in a three-lobe topology with significant flexibility, known to be critical for efficient translation. Here we present an ensemble model of spatial distributions and correlation times for the domain reorientations of L12 that reconciles experimental data from small-angle x-ray scattering and nuclear magnetic resonance. We generated an ensemble of L12 conformations in which the structure of each domain is fixed but the domain orientations are variable. The ensemble reproduces the small-angle x-ray scattering data and the optimized correlation times of its reorientational eigenmodes fit the (15)N relaxation data. The ensemble model reveals intrinsic conformational properties of L12 that help explain its function on the ribosome. The two C-terminal domains sample a large volume and extend further away from the ribosome anchor than expected for a random-chain linker, indicating that the flexible linker has residual order. Furthermore, the distances between each C-terminal domain and the anchor are anticorrelated, indicating that one of them is more retracted on average. We speculate that these properties promote the function of L12 to recruit translation factors and control their activity on the ribosome.
Collapse
|
39
|
Weinreis SA, Ellis JP, Cavagnero S. Dynamic fluorescence depolarization: a powerful tool to explore protein folding on the ribosome. Methods 2010; 52:57-73. [PMID: 20685617 PMCID: PMC2934862 DOI: 10.1016/j.ymeth.2010.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 05/28/2010] [Accepted: 06/01/2010] [Indexed: 11/25/2022] Open
Abstract
Protein folding is a fundamental biological process of great significance for cell function and life-related processes. Surprisingly, very little is presently known about how proteins fold in vivo. The influence of the cellular environment is of paramount importance, as molecular chaperones, the ribosome, and the crowded medium affect both folding pathways and potentially even equilibrium structures. Studying protein folding in physiologically relevant environments, however, poses a number of technical challenges due to slow tumbling rates, low concentrations and potentially non-homogenous populations. Early work in this area relied on biological assays based on antibody recognition, proteolysis, and activity studies. More recently, it has been possible to directly observe the structure and dynamics of nascent polypeptides at high resolution by spectroscopic and microscopic techniques. The fluorescence depolarization decay of nascent polypeptides labeled with a small extrinsic fluorophore is a particularly powerful tool to gain insights into the dynamics of newly synthesized proteins. The fluorophore label senses both its own local mobility and the motions of the macromolecule to which it is attached. Fluorescence anisotropy decays can be measured both in the time and frequency domains. The latter mode of data collection is extremely convenient to capture the nanosecond motions in ribosome-bound nascent proteins, indicative of the development of independent structure and folding on the ribosome. In this review, we discuss the theory of fluorescence depolarization and its exciting applications to the study of the dynamics of nascent proteins in the cellular environment.
Collapse
Affiliation(s)
- Sarah A. Weinreis
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
| | | | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
| |
Collapse
|
40
|
Cabrita L, Dobson CM, Christodoulou J. Early Nascent Chain Folding Events on the Ribosome. Isr J Chem 2010. [DOI: 10.1002/ijch.201000015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
41
|
Gordiyenko Y, Videler H, Zhou M, McKay AR, Fucini P, Biegel E, Müller V, Robinson CV. Mass spectrometry defines the stoichiometry of ribosomal stalk complexes across the phylogenetic tree. Mol Cell Proteomics 2010; 9:1774-83. [PMID: 20467040 DOI: 10.1074/mcp.m000072-mcp201] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ribosomal stalk complex plays a crucial role in delivering translation factors to the catalytic site of the ribosome. It has a very similar architecture in all cells, although the protein components in bacteria are unrelated to those in archaea and eukaryotes. Here we used mass spectrometry to investigate ribosomal stalk complexes from bacteria, eukaryotes, and archaea in situ on the ribosome. Specifically we targeted ribosomes with different optimal growth temperatures. Our results showed that for the mesophilic bacterial ribosomes we investigated the stalk complexes are exclusively pentameric or entirely heptameric in the case of thermophilic bacteria, whereas we observed only pentameric stalk complexes in eukaryotic species. We also found the surprising result that for mesophilic archaea, Methanococcus vannielii, Methanococcus maripaludis, and Methanosarcina barkeri, both pentameric and heptameric stoichiometries are present simultaneously within a population of ribosomes. Moreover the ratio of pentameric to heptameric stalk complexes changed during the course of cell growth. We consider these differences in stoichiometry within ribosomal stalk complexes in the context of convergent evolution.
Collapse
Affiliation(s)
- Yuliya Gordiyenko
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Probing ribosome-nascent chain complexes produced in vivo by NMR spectroscopy. Proc Natl Acad Sci U S A 2009; 106:22239-44. [PMID: 20018739 DOI: 10.1073/pnas.0903750106] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The means by which a polypeptide chain acquires its unique 3-D structure is a fundamental question in biology. During its synthesis on the ribosome, a nascent chain (NC) emerges vectorially and will begin to fold in a cotranslational fashion. The complex environment of the cell, coupled with the gradual emergence of the ribosome-tethered NC during its synthesis, imposes conformational restraints on its folding landscape that differ from those placed on an isolated protein when stimulated to fold following denaturation in solution. To begin to examine cotranslational folding as it would occur within a cell, we produce highly selective, isotopically labeled NCs bound to isotopically silent ribosomes in vivo. We then apply NMR spectroscopy to study, at a residue specific level, the conformation of NCs consisting of different fractional lengths of the polypeptide chain corresponding to a given protein. This combined approach provides a powerful means of generating a series of snapshots of the folding of the NC as it emerges from the ribosome. Application of this strategy to the NMR analysis of the progressive synthesis of an Ig-like domain reveals the existence of a partially folded ribosome-bound species that is likely to represent an intermediate species populated during the cotranslational folding process.
Collapse
|
43
|
Naganuma T, Nomura N, Yao M, Mochizuki M, Uchiumi T, Tanaka I. Structural basis for translation factor recruitment to the eukaryotic/archaeal ribosomes. J Biol Chem 2009; 285:4747-56. [PMID: 20007716 DOI: 10.1074/jbc.m109.068098] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The archaeal ribosomal stalk complex has been shown to have an apparently conserved functional structure with eukaryotic pentameric stalk complex; it provides access to eukaryotic elongation factors at levels comparable to that of the eukaryotic stalk. The crystal structure of the archaeal heptameric (P0(P1)(2)(P1)(2)(P1)(2)) stalk complex shows that the rRNA anchor protein P0 consists of an N-terminal rRNA-anchoring domain followed by three separated spine helices on which three P1 dimers bind. Based on the structure, we have generated P0 mutants depleted of any binding site(s) for P1 dimer(s). Factor-dependent GTPase assay of such mutants suggested that the first P1 dimer has higher activity than the others. Furthermore, we constructed a model of the archaeal 50 S with stalk complex by superposing the rRNA-anchoring domain of P0 on the archaeal 50 S. This model indicates that the C termini of P1 dimers where translation factors bind are all localized to the region between the stalk base of the 50 S and P0 spine helices. Together with the mutational experiments we infer that the functional significance of multiple copies of P1 is in creating a factor pool within a limited space near the stalk base of the ribosome.
Collapse
Affiliation(s)
- Takao Naganuma
- Faculty of Advanced Life Science, Hokkaido University, Kita-ku, Kita-10, Nishi-8, Sapporo, 060-0810, Japan
| | | | | | | | | | | |
Collapse
|
44
|
Hsu STD, Cabrita LD, Fucini P, Christodoulou J, Dobson CM. Probing side-chain dynamics of a ribosome-bound nascent chain using methyl NMR spectroscopy. J Am Chem Soc 2009; 131:8366-7. [PMID: 19492839 DOI: 10.1021/ja902778n] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report here the use of methyl NMR spectroscopy with a selective-excitation pulsing scheme to extract structural information about a ribosome-bound nascent chain, a complex with a molecular weight of more than 2 MDa and a sample concentration in the micromolar range. The carbon chemical shifts of methyl groups are particularly sensitive to the development of the tertiary structure of a protein it folds, and crucially for systems that are at the limit of acceptable signal-to-noise-ratios, methyl group spectroscopy has higher sensitivity than does backbone amide group-based NMR spectroscopy. Comparison of the side-chain methyl correlations of the ribosome-bound nascent chain to previously obtained backbone amide correlations reveals dynamical perturbations within the hydrophobic core of the folded domain, which are attributed to motional restriction of the nascent chain as a result of ribosome attachment. Methyl NMR spectroscopy therefore provides improved spectral quality and complementary structural information to that of the amide groups and hence promises to provide a greatly enhanced understanding of the molecular basis of cotranslational folding at atomic resolution.
Collapse
Affiliation(s)
- Shang-Te Danny Hsu
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | | | | | | | | |
Collapse
|
45
|
Wilhelm K, Darinskas A, Noppe W, Duchardt E, Mok KH, Vukojević V, Schleucher J, Morozova-Roche LA. Protein oligomerization induced by oleic acid at the solid-liquid interface - equine lysozyme cytotoxic complexes. FEBS J 2009; 276:3975-89. [DOI: 10.1111/j.1742-4658.2009.07107.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
46
|
Hsu STD, Bertoncini CW, Dobson CM. Use of protonless NMR spectroscopy to alleviate the loss of information resulting from exchange-broadening. J Am Chem Soc 2009; 131:7222-3. [PMID: 19432443 DOI: 10.1021/ja902307q] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We report here the use of protonless NMR spectroscopy to extract structural information under biologically relevant conditions when conventional proton-detection NMR spectroscopy fails due to the loss of labile proton resonances. By direct (13)C detection, correlations between nonlabile nuclei of a given biomolecule can be determined with high resolution, which becomes particularly useful when the system of interests is sensitive to solvent exchange at elevated temperatures, such as intrinsically disordered proteins. Human alpha-synuclein, which is associated with Parkinson's disease, is used as a model system to illustrate the usefulness of protonless NMR spectroscopy in recovering hitherto missing spectral information.
Collapse
Affiliation(s)
- Shang-Te Danny Hsu
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
| | | | | |
Collapse
|
47
|
Rutkowska A, Beerbaum M, Rajagopalan N, Fiaux J, Schmieder P, Kramer G, Oschkinat H, Bukau B. Large-scale purification of ribosome-nascent chain complexes for biochemical and structural studies. FEBS Lett 2009; 583:2407-13. [DOI: 10.1016/j.febslet.2009.06.041] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 06/17/2009] [Accepted: 06/22/2009] [Indexed: 10/20/2022]
|
48
|
Miyoshi T, Nomura T, Uchiumi T. Engineering and characterization of the ribosomal L10.L12 stalk complex. A structural element responsible for high turnover of the elongation factor G-dependent GTPase. J Biol Chem 2008; 284:85-92. [PMID: 18936095 DOI: 10.1074/jbc.m806024200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ribosomal stalk protein L12 is essential for events dependent on the GTP-binding translation factors. It has been recently shown that ribosomes from Thermus thermophilus contain a heptameric complex L10.(L12)2.(L12)2.(L12)2, rather than the conventional pentameric complex L10.(L12)2.(L12)2. Here we describe the reconstitution of the heptameric complex from purified L10 and L12 and the characterization of its role in elongation factor G-dependent GTPase activity using a hybrid system with Escherichia coli ribosomes. The T. thermophilus heptameric complex resulted in a 2.5-fold higher activity than the E. coli pentameric complex. The structural element of the T. thermophilus complex responsible for the higher activity was investigated using a chimeric L10 protein (Ec-Tt-L10), in which the C-terminal L12-binding site in E. coli L10 was replaced with the same region from T. thermophilus, and two chimeric L12 proteins: Ec-Tt-L12, in which the E. coli N-terminal domain was fused with the T. thermophilus C-terminal domain, and Tt.Ec-L12, in which the T. thermophilus N-terminal domain was fused with the E. coli C-terminal domain. High GTPase turnover was observed with the pentameric chimeric complex formed from E. coli L10 and Ec-Tt-L12 but not with the heptameric complex formed from Ec-Tt-L10 and Tt.Ec-L12. This suggested that the C-terminal region of T. thermophilus L12, rather than the heptameric nature of the complex, was responsible for the high GTPase turnover. Further analyses with other chimeric L12 proteins identified helix alpha6 as the region most likely to contain the responsible element.
Collapse
Affiliation(s)
- Tomohiro Miyoshi
- Department of Biology, Faculty of Science, Niigata University, Niigata 950-2181, Japan and the Institute of High Polymer Research, Faculty of Textile Science and Technology, Shinshu University, Ueda 386-8567, Japan
| | - Takaomi Nomura
- Department of Biology, Faculty of Science, Niigata University, Niigata 950-2181, Japan and the Institute of High Polymer Research, Faculty of Textile Science and Technology, Shinshu University, Ueda 386-8567, Japan
| | - Toshio Uchiumi
- Department of Biology, Faculty of Science, Niigata University, Niigata 950-2181, Japan and the Institute of High Polymer Research, Faculty of Textile Science and Technology, Shinshu University, Ueda 386-8567, Japan.
| |
Collapse
|
49
|
Abstract
The assignment of specific ribosomal functions to individual ribosomal proteins is difficult due to the enormous cooperativity of the ribosome; however, important roles for distinct ribosomal proteins are becoming evident. Although rRNA has a major role in certain aspects of ribosomal function, such as decoding and peptidyl-transferase activity, ribosomal proteins are nevertheless essential for the assembly and optimal functioning of the ribosome. This is particularly true in the context of interactions at the entrance pore for mRNA, for the translation-factor binding site and at the tunnel exit, where both chaperones and complexes associated with protein transport through membranes bind.
Collapse
|
50
|
Korostelev A, Ermolenko DN, Noller HF. Structural dynamics of the ribosome. Curr Opin Chem Biol 2008; 12:674-83. [PMID: 18848900 DOI: 10.1016/j.cbpa.2008.08.037] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 08/23/2008] [Indexed: 01/01/2023]
Abstract
Protein synthesis is inherently a dynamic process, requiring both small-scale and large-scale movements of tRNA and mRNA. It has long been suspected that these movements might be coupled to conformational changes in the ribosome, and in its RNA moieties in particular. Recently, the nature of ribosome structural dynamics has begun to emerge from a combination of approaches, most notably cryo-EM, X-ray crystallography, and FRET. Ribosome movement occurs both on a grand scale, as in the intersubunit rotational movements that are coupled to tRNA-mRNA translocation, and in intricate localized rearrangements such as those that accompany codon-anticodon recognition and peptide bond formation. In spite of much progress, our understanding of the mechanics of translation is now beset with countless new questions, reflecting the vast molecular architecture of the ribosome itself.
Collapse
Affiliation(s)
- Andrei Korostelev
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | | | | |
Collapse
|