1
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Crossley JA, Allen WJ, Watkins DW, Sabir T, Radford SE, Tuma R, Collinson I, Fessl T. Dynamic coupling of fast channel gating with slow ATP-turnover underpins protein transport through the Sec translocon. EMBO J 2024; 43:1-13. [PMID: 38177311 PMCID: PMC10883268 DOI: 10.1038/s44318-023-00004-1] [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: 06/30/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 01/06/2024] Open
Abstract
The Sec translocon is a highly conserved membrane assembly for polypeptide transport across, or into, lipid bilayers. In bacteria, secretion through the core channel complex-SecYEG in the inner membrane-is powered by the cytosolic ATPase SecA. Here, we use single-molecule fluorescence to interrogate the conformational state of SecYEG throughout the ATP hydrolysis cycle of SecA. We show that the SecYEG channel fluctuations between open and closed states are much faster (~20-fold during translocation) than ATP turnover, and that the nucleotide status of SecA modulates the rates of opening and closure. The SecY variant PrlA4, which exhibits faster transport but unaffected ATPase rates, increases the dwell time in the open state, facilitating pre-protein diffusion through the pore and thereby enhancing translocation efficiency. Thus, rapid SecYEG channel dynamics are allosterically coupled to SecA via modulation of the energy landscape, and play an integral part in protein transport. Loose coupling of ATP-turnover by SecA to the dynamic properties of SecYEG is compatible with a Brownian-rachet mechanism of translocation, rather than strict nucleotide-dependent interconversion between different static states of a power stroke.
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Affiliation(s)
- Joel A Crossley
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic
- School of Clinical and Applied Sciences, Leeds Beckett University, Leeds, LS1 3HE, UK
| | - William J Allen
- School of Biochemistry, University of Bristol, Bristol, BS8 1QU, UK
| | - Daniel W Watkins
- School of Biochemistry, University of Bristol, Bristol, BS8 1QU, UK
| | - Tara Sabir
- School of Clinical and Applied Sciences, Leeds Beckett University, Leeds, LS1 3HE, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, BS8 1QU, UK.
| | - Tomas Fessl
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic.
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2
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Pino-Rosa S, Medina-Pascual MJ, Carrasco G, Garrido N, Villalón P, Valiente M, Valdezate S. Focusing on Gordonia Infections: Distribution, Antimicrobial Susceptibilities and Phylogeny. Antibiotics (Basel) 2023; 12:1568. [PMID: 37998770 PMCID: PMC10668661 DOI: 10.3390/antibiotics12111568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023] Open
Abstract
The immunosuppression conditions and the presence of medical devices in patients favor the Gordonia infections. However, the features of this aerobic actinomycete have been little explored. Strains (n = 164) were characterized with 16S rDNA and secA1 genes to define their phylogenetic relationships, and subjected to broth microdilution to profile the antimicrobial susceptibilities of Gordonia species that caused infections in Spain during the 2005-2021 period. Four out of the eleven identified species were responsible for 86.0% of the infections: Gordonia sputi (53.0%), Gordonia bronchialis (18.3%), Gordonia terrae (8.5%) and Gordonia otitidis (6.1%). Respiratory tract infections (61.6%) and bacteremia (21.9%) were the most common infections. The secA1 gene resolved the inconclusive identification, and two major clonal lineages were observed for G. sputi and G. bronchialis. Species showed a wide antimicrobial susceptibility profile. Cefoxitin resistance varies depending on the species, reaching 94.2% for G. sputi and 36.0% for G. terrae. What is noteworthy is the minocycline resistance in G. sputi (11.5%), the clarithromycin resistance in G. bronchialis secA1 lineage II (30.0%) and the amoxicillin-clavulanate and cefepime resistance in G. terrae (21.4% and 42.8%, respectively). G. sputi and G. bronchialis stand out as the prevalent species causing infections in Spain. Resistance against cefoxitin and other antimicrobials should be considered.
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Affiliation(s)
| | | | | | | | | | | | - Sylvia Valdezate
- Reference and Research Laboratory for Taxonomy, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain; (S.P.-R.); (M.J.M.-P.); (G.C.); (N.G.); (P.V.); (M.V.)
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3
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Allen WJ, Collinson I. A unifying mechanism for protein transport through the core bacterial Sec machinery. Open Biol 2023; 13:230166. [PMID: 37643640 PMCID: PMC10465204 DOI: 10.1098/rsob.230166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/21/2023] [Indexed: 08/31/2023] Open
Abstract
Encapsulation and compartmentalization are fundamental to the evolution of cellular life, but they also pose a challenge: how to partition the molecules that perform biological functions-the proteins-across impermeable barriers into sub-cellular organelles, and to the outside. The solution lies in the evolution of specialized machines, translocons, found in every biological membrane, which act both as gate and gatekeeper across and into membrane bilayers. Understanding how these translocons operate at the molecular level has been a long-standing ambition of cell biology, and one that is approaching its denouement; particularly in the case of the ubiquitous Sec system. In this review, we highlight the fruits of recent game-changing technical innovations in structural biology, biophysics and biochemistry to present a largely complete mechanism for the bacterial version of the core Sec machinery. We discuss the merits of our model over alternative proposals and identify the remaining open questions. The template laid out by the study of the Sec system will be of immense value for probing the many other translocons found in diverse biological membranes, towards the ultimate goal of altering or impeding their functions for pharmaceutical or biotechnological purposes.
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Affiliation(s)
- William J. Allen
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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4
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Molina JA, Galaz-Davison P, Komives EA, Artsimovitch I, Ramírez-Sarmiento CA. Allosteric couplings upon binding of RfaH to transcription elongation complexes. Nucleic Acids Res 2022; 50:6384-6397. [PMID: 35670666 PMCID: PMC9226497 DOI: 10.1093/nar/gkac453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 05/07/2022] [Accepted: 05/18/2022] [Indexed: 12/03/2022] Open
Abstract
In every domain of life, NusG-like proteins bind to the elongating RNA polymerase (RNAP) to support processive RNA synthesis and to couple transcription to ongoing cellular processes. Structures of factor-bound transcription elongation complexes (TECs) reveal similar contacts to RNAP, consistent with a shared mechanism of action. However, NusG homologs differ in their regulatory roles, modes of recruitment, and effects on RNA synthesis. Some of these differences could be due to conformational changes in RNAP and NusG-like proteins, which cannot be captured in static structures. Here, we employed hydrogen-deuterium exchange mass spectrometry to investigate changes in local and non-local structural dynamics of Escherichia coli NusG and its paralog RfaH, which have opposite effects on expression of xenogenes, upon binding to TEC. We found that NusG and RfaH regions that bind RNAP became solvent-protected in factor-bound TECs, whereas RNAP regions that interact with both factors showed opposite deuterium uptake changes when bound to NusG or RfaH. Additional changes far from the factor-binding site were observed only with RfaH. Our results provide insights into differences in structural dynamics exerted by NusG and RfaH during binding to TEC, which may explain their different functional outcomes and allosteric regulation of transcriptional pausing by RfaH.
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Affiliation(s)
- José Alejandro Molina
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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5
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Allen WJ, Corey RA, Watkins DW, Oliveira ASF, Hards K, Cook GM, Collinson I. Rate-limiting transport of positively charged arginine residues through the Sec-machinery is integral to the mechanism of protein secretion. eLife 2022; 11:e77586. [PMID: 35486093 PMCID: PMC9110029 DOI: 10.7554/elife.77586] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/29/2022] [Indexed: 11/24/2022] Open
Abstract
Transport of proteins across and into membranes is a fundamental biological process with the vast majority being conducted by the ubiquitous Sec machinery. In bacteria, this is usually achieved when the SecY-complex engages the cytosolic ATPase SecA (secretion) or translating ribosomes (insertion). Great strides have been made towards understanding the mechanism of protein translocation. Yet, important questions remain - notably, the nature of the individual steps that constitute transport, and how the proton-motive force (PMF) across the plasma membrane contributes. Here, we apply a recently developed high-resolution protein transport assay to explore these questions. We find that pre-protein transport is limited primarily by the diffusion of arginine residues across the membrane, particularly in the context of bulky hydrophobic sequences. This specific effect of arginine, caused by its positive charge, is mitigated for lysine which can be deprotonated and transported across the membrane in its neutral form. These observations have interesting implications for the mechanism of protein secretion, suggesting a simple mechanism through which the PMF can aid transport by enabling a 'proton ratchet', wherein re-protonation of exiting lysine residues prevents channel re-entry, biasing transport in the outward direction.
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Affiliation(s)
- William J Allen
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
| | - Robin A Corey
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
| | - Daniel W Watkins
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
| | - A Sofia F Oliveira
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
- School of Chemistry, University of Bristol, University WalkBristolUnited Kingdom
| | - Kiel Hards
- Department of Microbiology and Immunology, University of OtagoDunedinNew Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of OtagoDunedinNew Zealand
| | - Ian Collinson
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
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6
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Wang B, Lane BJ, Kapsalis C, Ault JR, Sobott F, El Mkami H, Calabrese AN, Kalli AC, Pliotas C. Pocket delipidation induced by membrane tension or modification leads to a structurally analogous mechanosensitive channel state. Structure 2022; 30:608-622.e5. [PMID: 34986323 PMCID: PMC9033278 DOI: 10.1016/j.str.2021.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/13/2021] [Accepted: 12/07/2021] [Indexed: 01/06/2023]
Abstract
The mechanosensitive ion channel of large conductance MscL gates in response to membrane tension changes. Lipid removal from transmembrane pockets leads to a concerted structural and functional MscL response, but it remains unknown whether there is a correlation between the tension-mediated state and the state derived by pocket delipidation in the absence of tension. Here, we combined pulsed electron paramagnetic resonance spectroscopy and hydrogen-deuterium exchange mass spectrometry, coupled with molecular dynamics simulations under membrane tension, to investigate the structural changes associated with the distinctively derived states. Whether it is tension- or modification-mediated pocket delipidation, we find that MscL samples a similar expanded subconducting state. This is the final step of the delipidation pathway, but only an intermediate stop on the tension-mediated path, with additional tension triggering further channel opening. Our findings hint at synergistic modes of regulation by lipid molecules in membrane tension-activated mechanosensitive channels.
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Affiliation(s)
- Bolin Wang
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Benjamin J Lane
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Charalampos Kapsalis
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - James R Ault
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Frank Sobott
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Hassane El Mkami
- School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, UK
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Antreas C Kalli
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds LS2 9NL, UK
| | - Christos Pliotas
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK.
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7
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Zhang W, Liu Z, Zhou Y, Lai C, Sun B, He M, Zhai Z, Wang J, Wang Q, Wang X, Wang F, Pan Y. Elucidating the molecular mechanisms of perfluorooctanoic acid-serum protein interactions by structural mass spectrometry. CHEMOSPHERE 2022; 291:132945. [PMID: 34798108 DOI: 10.1016/j.chemosphere.2021.132945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/08/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Perfluorooctanoic acid (PFOA) is a persistent environmental pollutant and will continually accumulate in blood due to its chemical inertness and strong interaction with serum proteins, especially serum albumin (SA), inducing highly adverse health risks. However, the molecular mechanisms of dynamic interactions between PFOA with serum proteins remain unclear, limiting the development of potential therapeutic strategies. Herein, we developed an integrated structural strategy to systematically profile the molecular details of dynamic interactions among PFOA, SA, and β-cyclodextrin (β-CD) by combing native mass spectrometry (nMS), lysine reactivity profiling (LRP), and molecular docking (MD) simulation. The SA site 1, site 2 pockets, and cleft nearby are observed as the primary interaction regions of PFOA. Further, β-CD can disrupt the PFOA combinations with bovine SA regions around sites Lys20, Lys280, Lys350, and Lys431-Lys439, with an overall reversing efficiency of about 26% at an identical concentration to PFOA. The interactome of PFOA with complex human serum proteins is globally profiled with molecular interaction details, including human serum albumin, apolipoprotein A-I, alpha-2-macroglobulin, and complement C3. Our results reveal molecular insights into the detail of the interaction between PFOA and serum proteins, beneficial to understanding PFOA toxicology.
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Affiliation(s)
- Wenxiang Zhang
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, China; CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Ye Zhou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Can Lai
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Binwen Sun
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min He
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ziyang Zhai
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Jian Wang
- The Second Hospital of Dalian Medical University, Dalian, 116023, China
| | - Qi Wang
- The Second Hospital of Dalian Medical University, Dalian, 116023, China
| | - Xian Wang
- Key Laboratory of Analytical Chemistry of State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, 430074, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, China.
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8
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Krishnamurthy S, Sardis MF, Eleftheriadis N, Chatzi KE, Smit JH, Karathanou K, Gouridis G, Portaliou AG, Bondar AN, Karamanou S, Economou A. Preproteins couple the intrinsic dynamics of SecA to its ATPase cycle to translocate via a catch and release mechanism. Cell Rep 2022; 38:110346. [PMID: 35139375 DOI: 10.1016/j.celrep.2022.110346] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/22/2021] [Accepted: 01/12/2022] [Indexed: 12/11/2022] Open
Abstract
Protein machines undergo conformational motions to interact with and manipulate polymeric substrates. The Sec translocase promiscuously recognizes, becomes activated, and secretes >500 non-folded preprotein clients across bacterial cytoplasmic membranes. Here, we reveal that the intrinsic dynamics of the translocase ATPase, SecA, and of preproteins combine to achieve translocation. SecA possesses an intrinsically dynamic preprotein clamp attached to an equally dynamic ATPase motor. Alternating motor conformations are finely controlled by the γ-phosphate of ATP, while ADP causes motor stalling, independently of clamp motions. Functional preproteins physically bridge these independent dynamics. Their signal peptides promote clamp closing; their mature domain overcomes the rate-limiting ADP release. While repeated ATP cycles shift the motor between unique states, multiple conformationally frustrated prongs in the clamp repeatedly "catch and release" trapped preprotein segments until translocation completion. This universal mechanism allows any preprotein to promiscuously recognize the translocase, usurp its intrinsic dynamics, and become secreted.
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Affiliation(s)
- Srinath Krishnamurthy
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Marios-Frantzeskos Sardis
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Nikolaos Eleftheriadis
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Katerina E Chatzi
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Jochem H Smit
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Konstantina Karathanou
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Arnimallee 14, 14195 Berlin, Germany
| | - Giorgos Gouridis
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium; Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands; Structural Biology Division, Institute of Molecular Biology and Biotechnology (IMBB-FORTH), Nikolaou Plastira 100, Heraklion, Crete, Greece
| | - Athina G Portaliou
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Arnimallee 14, 14195 Berlin, Germany; University of Bucharest, Faculty of Physics, Atomiștilor 405, 077125 Măgurele, Romania; Forschungszentrum Jülich, Institute of Computational Biomedicine, IAS-5/INM-9, Wilhelm-Johnen Straße, 5428 Jülich, Germany
| | - Spyridoula Karamanou
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Anastassios Economou
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium.
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9
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Chen W, Komives EA. Open, engage, bind, translocate: The multi-level dynamics of bacterial protein translocation. Structure 2021; 29:781-782. [PMID: 34358463 DOI: 10.1016/j.str.2021.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The bacterial Sec translocase transports unfolded proteins across membranes. In this issue of Structure, Krishnamurthy et al. (2021) report a nexus of conformational dynamics in the translocase motor protein, SecA. Their findings shed light on the Sec activation mechanism and suggest a general role for multi-level dynamics in protein functions.
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Affiliation(s)
- Wei Chen
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
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10
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A nexus of intrinsic dynamics underlies translocase priming. Structure 2021; 29:846-858.e7. [PMID: 33852897 DOI: 10.1016/j.str.2021.03.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/06/2021] [Accepted: 03/25/2021] [Indexed: 11/22/2022]
Abstract
The cytoplasmic ATPase SecA and the membrane-embedded SecYEG channel assemble to form the Sec translocase. How this interaction primes and catalytically activates the translocase remains unclear. We show that priming exploits a nexus of intrinsic dynamics in SecA. Using atomistic simulations, smFRET, and HDX-MS, we reveal multiple dynamic islands that cross-talk with domain and quaternary motions. These dynamic elements are functionally important and conserved. Central to the nexus is a slender stem through which rotation of the preprotein clamp of SecA is biased by ATPase domain motions between open and closed clamping states. An H-bonded framework covering most of SecA enables multi-tier dynamics and conformational alterations with minimal energy input. As a result, cognate ligands select preexisting conformations and alter local dynamics to regulate catalytic activity and clamp motions. These events prime the translocase for high-affinity reception of non-folded preprotein clients. Dynamics nexuses are likely universal and essential in multi-liganded proteins.
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11
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Refined measurement of SecA-driven protein secretion reveals that translocation is indirectly coupled to ATP turnover. Proc Natl Acad Sci U S A 2020; 117:31808-31816. [PMID: 33257538 DOI: 10.1073/pnas.2010906117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The universally conserved Sec system is the primary method cells utilize to transport proteins across membranes. Until recently, measuring the activity-a prerequisite for understanding how biological systems work-has been limited to discontinuous protein transport assays with poor time resolution or reported by large, nonnatural tags that perturb the process. The development of an assay based on a split superbright luciferase (NanoLuc) changed this. Here, we exploit this technology to unpick the steps that constitute posttranslational protein transport in bacteria. Under the conditions deployed, the transport of a model preprotein substrate (proSpy) occurs at 200 amino acids (aa) per minute, with SecA able to dissociate and rebind during transport. Prior to that, there is no evidence for a distinct, rate-limiting initiation event. Kinetic modeling suggests that SecA-driven transport activity is best described by a series of large (∼30 aa) steps, each coupled to hundreds of ATP hydrolysis events. The features we describe are consistent with a nondeterministic motor mechanism, such as a Brownian ratchet.
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12
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Structural predictions of the functions of membrane proteins from HDX-MS. Biochem Soc Trans 2020; 48:971-979. [PMID: 32597490 PMCID: PMC7329338 DOI: 10.1042/bst20190880] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 11/17/2022]
Abstract
HDX-MS has emerged as a powerful tool to interrogate the structure and dynamics of proteins and their complexes. Recent advances in the methodology and instrumentation have enabled the application of HDX-MS to membrane proteins. Such targets are challenging to investigate with conventional strategies. Developing new tools are therefore pertinent for improving our fundamental knowledge of how membrane proteins function in the cell. Importantly, investigating this central class of biomolecules within their native lipid environment remains a challenge but also a key goal ahead. In this short review, we outline recent progresses in dissecting the conformational mechanisms of membrane proteins using HDX-MS. We further describe how the use of computational strategies can aid the interpretation of experimental data and enable visualisation of otherwise intractable membrane protein states. This unique integration of experiments with computations holds significant potential for future applications.
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13
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Hansen K, Politis A. Improving Peptide Fragmentation for Hydrogen-Deuterium Exchange Mass Spectrometry Using a Time-Dependent Collision Energy Calculator. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:996-999. [PMID: 32141743 DOI: 10.1021/jasms.9b00133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is becoming a popular technique for interrogating biological systems. In recent years, advancements have been made to increase peptide coverage for proteins that resist digestion such as antibodies and membrane proteins. These methods commonly include using alternative digestion enzymes or longer chromatographic gradients, which may be expensive or time-consuming to implement. Here, we recommend an efficient proteomics-based approach to increase peptide confidence and coverage. A major filtering parameter for peptides in HDX is the number of product ions detected; this is a result of the collision energy (CE) applied within the MS. A traditional linear ramp achieves optimal CE for only short periods of time. More product ions will be created and detected if optimal CE can be achieved for a longer period of time. As a result, the coverage, redundancy, and data confidence are all increased. We achieved this by implementing a mobility-dependent CE look up table (LUT) which increases the CE as a function of mobility. We developed a program to calculate the optimal CE for a set of peptides and MS settings based on initial reference samples. We demonstrated the utility of the CE LUT on three protein samples including the soluble phosphorylase B, IgG2, and the membrane-stabilized AcrB. We showed that applying a CE LUT provided 8.5-50% more peptides compared to a linear CE ramp. The results demonstrate that a time-dependent CE LUT is a quick and inexpensive method to increase data confidence and peptide abundance for HDX-MS experiments.
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Affiliation(s)
- Kjetil Hansen
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, U.K
| | - Argyris Politis
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, U.K
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Martens C, Politis A. A glimpse into the molecular mechanism of integral membrane proteins through hydrogen-deuterium exchange mass spectrometry. Protein Sci 2020; 29:1285-1301. [PMID: 32170968 PMCID: PMC7255514 DOI: 10.1002/pro.3853] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/11/2020] [Accepted: 03/11/2020] [Indexed: 01/07/2023]
Abstract
Integral membrane proteins (IMPs) control countless fundamental biological processes and constitute the majority of drug targets. For this reason, uncovering their molecular mechanism of action has long been an intense field of research. They are, however, notoriously difficult to work with, mainly due to their localization within the heterogeneous of environment of the biological membrane and the instability once extracted from the lipid bilayer. High‐resolution structures have unveiled many mechanistic aspects of IMPs but also revealed that the elucidation of static pictures has limitations. Hydrogen–deuterium exchange coupled to mass spectrometry (HDX‐MS) has recently emerged as a powerful biophysical tool for interrogating the conformational dynamics of proteins and their interactions with ligands. Its versatility has proven particularly useful to reveal mechanistic aspects of challenging classes of proteins such as IMPs. This review recapitulates the accomplishments of HDX‐MS as it has matured into an essential tool for membrane protein structural biologists.
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Affiliation(s)
- Chloe Martens
- Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
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Ahdash Z, Pyle E, Allen WJ, Corey RA, Collinson I, Politis A. HDX-MS reveals nucleotide-dependent, anti-correlated opening and closure of SecA and SecY channels of the bacterial translocon. eLife 2019; 8:47402. [PMID: 31290743 PMCID: PMC6639072 DOI: 10.7554/elife.47402] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/09/2019] [Indexed: 01/28/2023] Open
Abstract
The bacterial Sec translocon is a multi-protein complex responsible for translocating diverse proteins across the plasma membrane. For post-translational protein translocation, the Sec-channel – SecYEG – associates with the motor protein SecA to mediate the ATP-dependent transport of pre-proteins across the membrane. Previously, a diffusional-based Brownian ratchet mechanism for protein secretion has been proposed; the structural dynamics required to facilitate this mechanism remain unknown. Here, we employ hydrogen-deuterium exchange mass spectrometry (HDX-MS) to reveal striking nucleotide-dependent conformational changes in the Sec protein-channel from Escherichia coli. In addition to the ATP-dependent opening of SecY, reported previously, we observe a counteracting, and ATP-dependent, constriction of SecA around the pre-protein. ATP binding causes SecY to open and SecA to close; while, ADP produced by hydrolysis, has the opposite effect. This alternating behaviour could help impose the directionality of the Brownian ratchet for protein transport through the Sec machinery.
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Affiliation(s)
- Zainab Ahdash
- Department of Chemistry, King's College London, London, United Kingdom
| | - Euan Pyle
- Department of Chemistry, King's College London, London, United Kingdom.,Department of Chemistry, Imperial College London, London, United Kingdom
| | | | - Robin A Corey
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Argyris Politis
- Department of Chemistry, King's College London, London, United Kingdom
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