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Golub M, Pieper J. Recent Progress in Solution Structure Studies of Photosynthetic Proteins Using Small-Angle Scattering Methods. Molecules 2023; 28:7414. [PMID: 37959833 PMCID: PMC10650700 DOI: 10.3390/molecules28217414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Utilized for gaining structural insights, small-angle neutron and X-ray scattering techniques (SANS and SAXS, respectively) enable an examination of biomolecules, including photosynthetic pigment-protein complexes, in solution at physiological temperatures. These methods can be seen as instrumental bridges between the high-resolution structural information achieved by crystallography or cryo-electron microscopy and functional explorations conducted in a solution state. The review starts with a comprehensive overview about the fundamental principles and applications of SANS and SAXS, with a particular focus on the recent advancements permitting to enhance the efficiency of these techniques in photosynthesis research. Among the recent developments discussed are: (i) the advent of novel modeling tools whereby a direct connection between SANS and SAXS data and high-resolution structures is created; (ii) the employment of selective deuteration, which is utilized to enhance spatial selectivity and contrast matching; (iii) the potential symbioses with molecular dynamics simulations; and (iv) the amalgamations with functional studies that are conducted to unearth structure-function relationships. Finally, reference is made to time-resolved SANS/SAXS experiments, which enable the monitoring of large-scale structural transformations of proteins in a real-time framework.
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Affiliation(s)
| | - Jörg Pieper
- Institute of Physics, University of Tartu, Wilhelm Ostwald Str. 1, 50411 Tartu, Estonia;
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2
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Krüger G, Kirkpatrick J, Mahieu E, Franzetti B, Gabel F, Carlomagno T. A real-time analysis of GFP unfolding by the AAA+ unfoldase PAN. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 350:107431. [PMID: 37058954 DOI: 10.1016/j.jmr.2023.107431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 05/10/2023]
Abstract
Protein quality control systems are essential to maintain a healthy proteome. They often consist of an unfoldase unit, typically an AAA+ ATPase, coupled with a protease unit. In all kingdoms of life, they function to eliminate misfolded proteins, and thus prevent that their aggregates do harm to the cell, and to rapidly regulate protein levels in the presence of environmental changes. Despite the huge progress made in the past two decades in understanding the mechanism of function of protein degradation systems, the fate of the substrate during the unfolding and proteolytic processes remains poorly understood. Here we exploit an NMR-based approach to monitor GFP processing by the archaeal PAN unfoldase and the PAN-20S degradation system in real time. We find that PAN-dependent unfolding of GFP does not involve the release of partially-folded GFP molecules resulting from futile unfolding attempts. In contrast, once stably engaged with PAN, GFP molecules are efficiently transferred to the proteolytic chamber of the 20S subunit, despite the only weak affinity of PAN for the 20S subunit in the absence of substrate. This is essential to guarantee that unfolded but not proteolyzed proteins are not released into solution, where they would form toxic aggregates. The results of our studies are in good agreement with previous results derived from real-time small-angle-neutron-scattering experiments and have the advantage of allowing the investigation of substrates and products at amino-acid resolution.
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Affiliation(s)
- Georg Krüger
- Institute of Organic Chemistry and Centre of Biomolecular Drug Design, Leibniz University Hannover, Schneiderberg 38, D-30167 Hannover, Germany
| | - John Kirkpatrick
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, United Kingdom
| | - Emilie Mahieu
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Bruno Franzetti
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Frank Gabel
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Teresa Carlomagno
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, United Kingdom.
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Observing protein degradation in solution by the PAN-20S proteasome complex: Astate-of-the-art example of bio-macromolecular TR-SANS. Methods Enzymol 2022; 678:97-120. [PMID: 36641218 DOI: 10.1016/bs.mie.2022.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the present book chapter we illustrate the state-of-the-art of time-resolved small-angle neutron scattering (TR-SANS) by a concrete example of a dynamic bio-macromolecular system, i.e., regulated protein degradation by the archaeal PAN-20S proteasome complex. We present the specific and unique structural information that can be obtained by this approach, in combination with bio-macromolecular deuteration and online spectrophotometric measurements of a fluorescent substrate (GFP). The complementarity with atomic-resolution structural biology techniques (SAXS, NMR, crystallography and cryo-EM) and with the advent of atomic structure prediction are discussed, as well as the respective limitations and future perspectives.
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Krueger S. Small-angle neutron scattering contrast variation studies of biological complexes: Challenges and triumphs. Curr Opin Struct Biol 2022; 74:102375. [PMID: 35490650 PMCID: PMC10988784 DOI: 10.1016/j.sbi.2022.102375] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/09/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022]
Abstract
Small-angle neutron scattering (SANS) has been a beneficial tool for studying the structure of biological macromolecules in solution for several decades. Continued improvements in sample preparation techniques, including deuterium labeling, neutron instrumentation and complementary techniques such as small-angle x-ray scattering (SAXS), cryo-EM, NMR and x-ray crystallography, along with the availability of more powerful structure prediction algorithms and computational resources has made SANS more important than ever as a means to obtain unique information on the structure of biological complexes in solution. In particular, the contrast variation (CV) technique, which requires a large commitment in both sample preparation and measurement time, has become more practical with the advent of these improved resources. Here, challenges and recent triumphs as well as future prospects are discussed.
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Affiliation(s)
- Susan Krueger
- NIST Center for Neutron Research, NIST, Gaithersburg, MD, 20899, USA.
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Hogrel G, Marino-Puertas L, Laurent S, Ibrahim Z, Covès J, Girard E, Gabel F, Fenel D, Daugeron MC, Clouet-d'Orval B, Basta T, Flament D, Franzetti B. Characterization of a small tRNA-binding protein that interacts with the archaeal proteasome complex. Mol Microbiol 2022; 118:16-29. [PMID: 35615908 PMCID: PMC9540759 DOI: 10.1111/mmi.14948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 11/27/2022]
Abstract
The proteasome system allows the elimination of functional or structurally impaired proteins. This includes the degradation of nascent peptides. In Archaea, how the proteasome complex interacts with the translational machinery remains to be described. Here, we characterised a small orphan protein, Q9UZY3 (Uniprot ID) conserved in Thermococcales. The protein was identified in native pull-down experiments using the proteasome regulatory complex (PAN) as bait. X-ray crystallography and SAXS experiments revealed that the protein is monomeric and adopts a β-barrel core structure with an Oligonucleotide/oligosaccharide-Binding (OB) fold, typically found in translation elongation factors. Mobility shift experiment showed that Q9UZY3 displays tRNA binding properties. Pull-downs, co-immunoprecipitation and ITC studies revealed that Q9UZY3 interacts in vitro with PAN. Native pull-downs and proteomic analysis using different versions of Q9UZY3 showed that the protein interacts with the assembled PAN-20S proteasome machinery in Pyrococcus abyssi cellular extracts. The protein was therefore named Pbp11, for Proteasome Binding Protein of 11 kDa. Interestingly, the interaction network of Pbp11 also includes ribosomal proteins, tRNA processing enzymes and exosome subunits dependent on Pbp11's N-terminal domain that was found to be essential for tRNA binding. Together these data suggest that Pbp11 participates in an interface between the proteasome and the translational machinery.
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Affiliation(s)
- Gaëlle Hogrel
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France.,University of St Andrews, St Andrews, UK
| | | | - Sébastien Laurent
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Ziad Ibrahim
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France.,University of Leicester, Leicester, UK
| | - Jacques Covès
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Eric Girard
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Frank Gabel
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Daphna Fenel
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Marie-Claire Daugeron
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Béatrice Clouet-d'Orval
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
| | - Tamara Basta
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Didier Flament
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
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Martel A, Gabel F. Time-resolved small-angle neutron scattering (TR-SANS) for structural biology of dynamic systems: Principles, recent developments, and practical guidelines. Methods Enzymol 2022; 677:263-290. [DOI: 10.1016/bs.mie.2022.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Tian W, Maresh ME, Trader DJ. Approaches to Evaluate the Impact of a Small-Molecule Binder to a Noncatalytic Site of the Proteasome. Chembiochem 2021; 22:1961-1965. [PMID: 33617657 DOI: 10.1002/cbic.202100023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/11/2021] [Indexed: 11/11/2022]
Abstract
Proteasome activity is crucial for cell survival and proliferation. In recent years, small molecules have been discovered that can affect the catalytic activity of the proteasome. Rather than targeting the active sites of the proteasome, it might be possible to affect ubiquitin-dependent degradation of proteins by limiting the association of the 19S regulatory particle (19S RP) with the 20S core particle (20S CP) of the proteasome. We recently described the discovery of TXS-8, a peptoid that binds to Rpn-6. Rpn-6 is a proteasome-associated protein that makes critical contacts with the 19S RP and the 20S CP. Herein, we present a general workflow to evaluate the impact of a small-molecule binder on proteasome activity by using TXS-8 as an example. This workflow contains three steps in which specific probes or overexpressed proteins in cells are used to determine whether the hydrolysis activity of the proteasome is affected. Although, in our case, TXS-8 did not affect proteasome activity, our workflow is highly amenable to studying a variety of small-molecule-proteasome subunit interactions.
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Affiliation(s)
- Wenzhi Tian
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Marianne E Maresh
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Darci J Trader
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, 47907, USA
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