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Yang Q, Zhou X, Lou B, Zheng N, Chen J, Yang G. An F OF 1-ATPase motor-embedded chromatophore as a nanorobot for overcoming biological barriers and targeting acidic tumor sites. Acta Biomater 2024; 179:207-219. [PMID: 38513724 DOI: 10.1016/j.actbio.2024.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 03/23/2024]
Abstract
Despite the booming progress of anticancer nanomedicines in the past two decades, precise tumor-targetability and sufficient tumor-accumulation are less successful and still require further research. To tackle this challenge, herein we present a biomolecular motor (FOF1-ATPase)-embedded chromatophore as nanorobot to efficiently overcome biological barriers, and thoroughly investigate its chemotactic motility, tumor-accumulation ability and endocytosis. Chromatophores embedded with FOF1-ATPase motors were firstly extracted from Thermus thermophilus, then their properties were fully characterized. Specifically, two microfluidic platforms (laminar flow microchip and tumor microenvironment (TME) microchip) were designed and developed to fully investigate the motility, tumor-accumulation ability and endocytosis of the chromatophore nanorobot (CN). The results from the laminar flow microchip indicated that the obtained CN possessed the strongly positive chemotaxis towards protons. And the TME microchip experiments verified that the CN had a desirable tumor-accumulation ability. Cellular uptake experiments demonstrated that the CN efficiently promoted the endocytosis of the fluorescence DiO into the HT-29 cells. And the in vivo studies revealed that the intravenously administered CN exhibited vigorous tumor-targetability and accumulation ability as well as highly efficient antitumor efficacy. All the results suggested that FOF1-ATPase motors-embedded CN could be promising nanomachines with powerful self-propulsion for overcoming physiological barriers and tumor-targeted drug delivery. STATEMENT OF SIGNIFICANCE: In this study, we demonstrated that FOF1-ATPase-embedded chromatophore nanorobots exhibit a strong proton chemotaxis, which not only plays a key role in tumor-targetability and accumulation, but also promotes tumor tissue penetration and internalization. The results of in vitro and in vivo studies indicated that drug-loaded chromatophore nanorobots are capable to simultaneously accomplish tumor-targeting, accumulation, penetration and internalization for enhanced tumor therapy. Our study provides a fundamental basis for further study on FOF1-ATPase-embedded chromatophore as tumor-targeting drug delivery systems that have promising clinical applications. It offers a new and more efficient delivery vehicle for cancer related therapeutics.
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Affiliation(s)
- Qingliang Yang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Xuhui Zhou
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Bang Lou
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Ning Zheng
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Jiale Chen
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Gensheng Yang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.
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2
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Nesterov SV, Yaguzhinsky LS. Directed proton transfer from F o to F 1 extends the multifaceted proton functions in ATP synthase. Biophys Rev 2023; 15:859-873. [PMID: 37975013 PMCID: PMC10643803 DOI: 10.1007/s12551-023-01132-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/30/2023] [Indexed: 11/19/2023] Open
Abstract
The role of protons in ATP synthase is typically considered to be energy storage in the form of an electrochemical potential, as well as an operating element proving rotation. However, this review emphasizes that protons also act as activators of conformational changes in F1 and as direct participants in phosphorylation reaction. The protons transferred through Fo do not immediately leave to the bulk aqueous phase, but instead provide for the formation of a pH gradient between acidifying Fo and alkalizing F1. It facilitates a directed inter-subunit proton transfer to F1, where they are used in the ATP synthesis reaction. This ensures that the enzyme activity is not limited by a lack of protons in the alkaline mitochondrial matrix or chloroplast stroma. Up to one hundred protons bind to the carboxyl groups of the F1 subunit, altering the electrical interactions between the amino acids of the enzyme. This removes the inhibition of ATP synthase caused by the electrostatic attraction of charged amino acids of the stator and rotor and also makes the enzyme more prone to conformational changes. Protonation occurs during ATP synthesis initiation and during phosphorylation, while deprotonation blocks the rotation inhibiting both synthesis and hydrolysis. Thus, protons participate in the functioning of all main components of ATP synthase molecular machine making it effectively a proton-driven electric machine. The review highlights the key role of protons as a coupling factor in ATP synthase with multifaceted functions, including charge and energy transport, torque generation, facilitation of conformational changes, and participation in the ATP synthesis reaction.
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Affiliation(s)
- Semen V. Nesterov
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, 123182 Moscow, Russia
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Lev S. Yaguzhinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Belozersky Research Institute for Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
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3
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Direct observation of stepping rotation of V-ATPase reveals rigid component in coupling between V o and V 1 motors. Proc Natl Acad Sci U S A 2022; 119:e2210204119. [PMID: 36215468 PMCID: PMC9586324 DOI: 10.1073/pnas.2210204119] [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] [Indexed: 11/30/2022] Open
Abstract
V-ATPases are ion pumps consisting of two rotary motor proteins, Vo and V1, that actively transport ions across the cell membrane using the chemical energy of ATP. To understand how V-ATPases transduce the energy in the presence of a structural symmetry mismatch between Vo and V1, we simultaneously visualized the rotational pauses and forward and backward steps of Vo and V1 coupled with ion transport and ATP hydrolysis reactions, respectively. Our results suggest that V-ATPases with multiple peripheral stalks are more rigidly coupled than F-ATPases that have only one peripheral stalk and work as ATP synthases. Our high-speed/high-precision single-molecule imaging of rotary ATPases in action will pave the way for a comprehensive understanding of their energy transduction mechanisms. V-ATPases are rotary motor proteins that convert the chemical energy of ATP into the electrochemical potential of ions across cell membranes. V-ATPases consist of two rotary motors, Vo and V1, and Enterococcus hirae V-ATPase (EhVoV1) actively transports Na+ in Vo (EhVo) by using torque generated by ATP hydrolysis in V1 (EhV1). Here, we observed ATP-driven stepping rotation of detergent-solubilized EhVoV1 wild-type, aE634A, and BR350K mutants under various Na+ and ATP concentrations ([Na+] and [ATP], respectively) by using a 40-nm gold nanoparticle as a low-load probe. When [Na+] was low and [ATP] was high, under the condition that only Na+ binding to EhVo is rate limiting, wild-type and aE634A exhibited 10 pausing positions reflecting 10-fold symmetry of the EhVo rotor and almost no backward steps. Duration time before the forward steps was inversely proportional to [Na+], confirming that Na+ binding triggers the steps. When both [ATP] and [Na+] were low, under the condition that both Na+ and ATP bindings are rate limiting, aE634A exhibited 13 pausing positions reflecting 10- and 3-fold symmetries of EhVo and EhV1, respectively. The distribution of duration time before the forward step was fitted well by the sum of two exponential decay functions with distinct time constants. Furthermore, occasional backward steps smaller than 36° were observed. Small backward steps were also observed during three long ATP cleavage pauses of BR350K. These results indicate that EhVo and EhV1 do not share pausing positions, Na+ and ATP bindings occur at different angles, and the coupling between EhVo and EhV1 has a rigid component.
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4
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Imaging Minimal Bacteria at the Nanoscale: a Reliable and Versatile Process to Perform Single-Molecule Localization Microscopy in Mycoplasmas. Microbiol Spectr 2022; 10:e0064522. [PMID: 35638916 PMCID: PMC9241803 DOI: 10.1128/spectrum.00645-22] [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] [Indexed: 11/24/2022] Open
Abstract
Mycoplasmas are the smallest free-living organisms. These bacteria are important models for both fundamental and synthetic biology, owing to their highly reduced genomes. They are also relevant in the medical and veterinary fields, as they are pathogenic to both humans and most livestock species. Mycoplasma cells have minute sizes, often in the 300- to 800-nm range. As these dimensions are close to the diffraction limit of visible light, fluorescence imaging in mycoplasmas is often poorly informative. Recently developed superresolution imaging techniques can break this diffraction limit, improving the imaging resolution by an order of magnitude and offering a new nanoscale vision of the organization of these bacteria. These techniques have, however, not been applied to mycoplasmas before. Here, we describe an efficient and reliable protocol to perform single-molecule localization microscopy (SMLM) imaging in mycoplasmas. We provide a polyvalent transposon-based system to express the photoconvertible fluorescent protein mEos3.2, enabling photo-activated localization microscopy (PALM) in most Mycoplasma species. We also describe the application of direct stochastic optical reconstruction microscopy (dSTORM). We showcase the potential of these techniques by studying the subcellular localization of two proteins of interest. Our work highlights the benefits of state-of-the-art microscopy techniques for mycoplasmology and provides an incentive to further the development of SMLM strategies to study these organisms in the future. IMPORTANCE Mycoplasmas are important models in biology, as well as highly problematic pathogens in the medical and veterinary fields. The very small sizes of these bacteria, well below a micron, limits the usefulness of traditional fluorescence imaging methods, as their resolution limit is similar to the dimensions of the cells. Here, to bypass this issue, we established a set of state-of-the-art superresolution microscopy techniques in a wide range of Mycoplasma species. We describe two strategies: PALM, based on the expression of a specific photoconvertible fluorescent protein, and dSTORM, based on fluorophore-coupled antibody labeling. With these methods, we successfully performed single-molecule imaging of proteins of interest at the surface of the cells and in the cytoplasm, at lateral resolutions well below 50 nm. Our work paves the way toward a better understanding of mycoplasma biology through imaging of subcellular structures at the nanometer scale.
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5
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Marciniak A, Chodnicki P, Hossain KA, Slabonska J, Czub J. Determinants of Directionality and Efficiency of the ATP Synthase F o Motor at Atomic Resolution. J Phys Chem Lett 2022; 13:387-392. [PMID: 34985899 PMCID: PMC8762653 DOI: 10.1021/acs.jpclett.1c03358] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/03/2022] [Indexed: 05/27/2023]
Abstract
Fo subcomplex of ATP synthase is a membrane-embedded rotary motor that converts proton motive force into mechanical energy. Despite a rapid increase in the number of high-resolution structures, the mechanism of tight coupling between proton transport and motion of the rotary c-ring remains elusive. Here, using extensive all-atom free energy simulations, we show how the motor's directionality naturally arises from the interplay between intraprotein interactions and energetics of protonation of the c-ring. Notably, our calculations reveal that the strictly conserved arginine in the a-subunit (R176) serves as a jack-of-all-trades: it dictates the direction of rotation, controls the protonation state of the proton-release site, and separates the two proton-access half-channels. Therefore, arginine is necessary to avoid slippage between the proton flux and the mechanical output and guarantees highly efficient energy conversion. We also provide mechanistic explanations for the reported defective mutations of R176, reconciling the structural information on the Fo motor with previous functional and single-molecule data.
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Affiliation(s)
- Antoni Marciniak
- Department
of Physical Chemistry, Gdansk University
of Technology, Narutowicza St 11/12, 80-233 Gdansk, Poland
| | - Pawel Chodnicki
- Department
of Physical Chemistry, Gdansk University
of Technology, Narutowicza St 11/12, 80-233 Gdansk, Poland
| | - Kazi A Hossain
- Department
of Physical Chemistry, Gdansk University
of Technology, Narutowicza St 11/12, 80-233 Gdansk, Poland
| | - Joanna Slabonska
- Department
of Physical Chemistry, Gdansk University
of Technology, Narutowicza St 11/12, 80-233 Gdansk, Poland
| | - Jacek Czub
- Department
of Physical Chemistry, Gdansk University
of Technology, Narutowicza St 11/12, 80-233 Gdansk, Poland
- BioTechMed
Center, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland
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6
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Nesterov SV, Chesnokov YM, Kamyshinsky RA, Yaguzhinsky LS, Vasilov RG. Determining the Structure and Location of the ATP Synthase in the Membranes of Rat’s Heart Mitochondria Using Cryoelectron Tomography. ACTA ACUST UNITED AC 2020. [DOI: 10.1134/s1995078020010139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Essential Role of the ε Subunit for Reversible Chemo-Mechanical Coupling in F 1-ATPase. Biophys J 2019; 114:178-187. [PMID: 29320685 DOI: 10.1016/j.bpj.2017.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/31/2017] [Accepted: 11/06/2017] [Indexed: 11/22/2022] Open
Abstract
F1-ATPase is a rotary motor protein driven by ATP hydrolysis. Among molecular motors, F1 exhibits unique high reversibility in chemo-mechanical coupling, synthesizing ATP from ADP and inorganic phosphate upon forcible rotor reversal. The ε subunit enhances ATP synthesis coupling efficiency to > 70% upon rotation reversal. However, the detailed mechanism has remained elusive. In this study, we performed stall-and-release experiments to elucidate how the ε subunit modulates ATP association/dissociation and hydrolysis/synthesis process kinetics and thermodynamics, key reaction steps for efficient ATP synthesis. The ε subunit significantly accelerated the rates of ATP dissociation and synthesis by two- to fivefold, whereas those of ATP binding and hydrolysis were not enhanced. Numerical analysis based on the determined kinetic parameters quantitatively reproduced previous findings of two- to fivefold coupling efficiency improvement by the ε subunit at the condition exhibiting the maximum ATP synthesis activity, a physiological role of F1-ATPase. Furthermore, fundamentally similar results were obtained upon ε subunit C-terminal domain truncation, suggesting that the N-terminal domain is responsible for the rate enhancement.
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8
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Sielaff H, Yanagisawa S, Frasch WD, Junge W, Börsch M. Structural Asymmetry and Kinetic Limping of Single Rotary F-ATP Synthases. Molecules 2019; 24:E504. [PMID: 30704145 PMCID: PMC6384691 DOI: 10.3390/molecules24030504] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/12/2022] Open
Abstract
F-ATP synthases use proton flow through the FO domain to synthesize ATP in the F₁ domain. In Escherichia coli, the enzyme consists of rotor subunits γεc10 and stator subunits (αβ)₃δab₂. Subunits c10 or (αβ)₃ alone are rotationally symmetric. However, symmetry is broken by the b₂ homodimer, which together with subunit δa, forms a single eccentric stalk connecting the membrane embedded FO domain with the soluble F₁ domain, and the central rotating and curved stalk composed of subunit γε. Although each of the three catalytic binding sites in (αβ)₃ catalyzes the same set of partial reactions in the time average, they might not be fully equivalent at any moment, because the structural symmetry is broken by contact with b₂δ in F₁ and with b₂a in FO. We monitored the enzyme's rotary progression during ATP hydrolysis by three single-molecule techniques: fluorescence video-microscopy with attached actin filaments, Förster resonance energy transfer between pairs of fluorescence probes, and a polarization assay using gold nanorods. We found that one dwell in the three-stepped rotary progression lasting longer than the other two by a factor of up to 1.6. This effect of the structural asymmetry is small due to the internal elastic coupling.
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Affiliation(s)
- Hendrik Sielaff
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany.
| | - Seiga Yanagisawa
- School of Life Sciences, Arizona State University, Tempe, Arizona, AZ 85287, USA.
| | - Wayne D Frasch
- School of Life Sciences, Arizona State University, Tempe, Arizona, AZ 85287, USA.
| | - Wolfgang Junge
- Department of Biology & Chemistry, University of Osnabrück, 49076 Osnabrück, Germany.
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany.
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9
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Abstract
Emerging microtechnologies are aimed at developing a microsystem with densely packed array structure, i.e., an array with a femtoliter reaction chamber, for highly sensitive and quantitative biological assays. Here, we describe a novel femtoliter chamber array system (arrayed lipid bilayer chambers, ALBiC) that contains approximately a million femtoliter chambers, each sealed with a phospholipid bilayer membrane with extremely high efficiency (>90%). This novel platform enables detection of membrane transporter activity at the single-molecule level and thus expands the applicability of femtoliter chamber arrays to highly sensitive assays of transporters.
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10
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Sielaff H, Duncan TM, Börsch M. The regulatory subunit ε in Escherichia coli F OF 1-ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:775-788. [PMID: 29932911 DOI: 10.1016/j.bbabio.2018.06.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/13/2018] [Accepted: 06/14/2018] [Indexed: 11/16/2022]
Abstract
F-type ATP synthases are extraordinary multisubunit proteins that operate as nanomotors. The Escherichia coli (E. coli) enzyme uses the proton motive force (pmf) across the bacterial plasma membrane to drive rotation of the central rotor subunits within a stator subunit complex. Through this mechanical rotation, the rotor coordinates three nucleotide binding sites that sequentially catalyze the synthesis of ATP. Moreover, the enzyme can hydrolyze ATP to turn the rotor in the opposite direction and generate pmf. The direction of net catalysis, i.e. synthesis or hydrolysis of ATP, depends on the cell's bioenergetic conditions. Different control mechanisms have been found for ATP synthases in mitochondria, chloroplasts and bacteria. This review discusses the auto-inhibitory behavior of subunit ε found in FOF1-ATP synthases of many bacteria. We focus on E. coli FOF1-ATP synthase, with insights into the regulatory mechanism of subunit ε arising from structural and biochemical studies complemented by single-molecule microscopy experiments.
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Affiliation(s)
- Hendrik Sielaff
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Thomas M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
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11
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Iino R, Iida T, Nakamura A, Saita EI, You H, Sako Y. Single-molecule imaging and manipulation of biomolecular machines and systems. Biochim Biophys Acta Gen Subj 2017; 1862:241-252. [PMID: 28789884 DOI: 10.1016/j.bbagen.2017.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/23/2017] [Accepted: 08/03/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND Biological molecular machines support various activities and behaviors of cells, such as energy production, signal transduction, growth, differentiation, and migration. SCOPE OF REVIEW We provide an overview of single-molecule imaging methods involving both small and large probes used to monitor the dynamic motions of molecular machines in vitro (purified proteins) and in living cells, and single-molecule manipulation methods used to measure the forces, mechanical properties and responses of biomolecules. We also introduce several examples of single-molecule analysis, focusing primarily on motor proteins and signal transduction systems. MAJOR CONCLUSIONS Single-molecule analysis is a powerful approach to unveil the operational mechanisms both of individual molecular machines and of systems consisting of many molecular machines. GENERAL SIGNIFICANCE Quantitative, high-resolution single-molecule analyses of biomolecular systems at the various hierarchies of life will help to answer our fundamental question: "What is life?" This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Ryota Iino
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan.
| | - Tatsuya Iida
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan
| | - Akihiko Nakamura
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan
| | - Ei-Ichiro Saita
- Information Processing Biology Unit, Okinawa Institute of Science and Technology Graduate University, Japan
| | - Huijuan You
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, China.
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12
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Noji H, Ueno H, McMillan DGG. Catalytic robustness and torque generation of the F 1-ATPase. Biophys Rev 2017; 9:103-118. [PMID: 28424741 PMCID: PMC5380711 DOI: 10.1007/s12551-017-0262-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/13/2017] [Indexed: 12/28/2022] Open
Abstract
The F1-ATPase is the catalytic portion of the FoF1 ATP synthase and acts as a rotary molecular motor when it hydrolyzes ATP. Two decades have passed since the single-molecule rotation assay of F1-ATPase was established. Although several fundamental issues remain elusive, basic properties of F-type ATPases as motor proteins have been well characterized, and a large part of the reaction scheme has been revealed by the combination of extensive structural, biochemical, biophysical, and theoretical studies. This review is intended to provide a concise summary of the fundamental features of F1-ATPases, by use of the well-described model F1 from the thermophilic Bacillus PS3 (TF1). In the last part of this review, we focus on the robustness of the rotary catalysis of F1-ATPase to provide a perspective on the re-designing of novel molecular machines.
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Affiliation(s)
- Hiroyuki Noji
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo, 113-8656 Japan
| | - Hiroshi Ueno
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo, 113-8656 Japan
| | - Duncan G. G. McMillan
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo, 113-8656 Japan
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13
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Czub J, Wieczór M, Prokopowicz B, Grubmüller H. Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F 1-ATPase. J Am Chem Soc 2017; 139:4025-4034. [PMID: 28253614 DOI: 10.1021/jacs.6b11708] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
F1-ATPase is a highly efficient molecular motor that can synthesize ATP driven by a mechanical torque. Its ability to function reversibly in either direction requires tight mechanochemical coupling between the catalytic domain and the rotating central shaft, as well as temporal control of substrate binding and product release. Despite great efforts and significant progress, the molecular details of this synchronized and fine-tuned energy conversion mechanism are not fully understood. Here, we use extensive molecular dynamics simulations to reconcile recent single-molecule experiments with structural data and provide a consistent thermodynamic, kinetic and mechanistic description of the main rotary substep in the synthetic cycle of mammalian ATP synthase. The calculated free energy profiles capture a discrete pattern in the rotation of the central γ-shaft, with a metastable intermediate located-consistently with recent experimental findings-at 70° relative to the X-ray position. We identify this rotary step as the ATP-dependent substep, and find that the associated free energy input supports the mechanism involving concurrent nucleotide binding and release. During the main substep, our simulations show no significant opening of the ATP-bound β subunit; instead, we observe that mechanical energy is transmitted to its nucleotide binding site, thus lowering the affinity for ATP. Simultaneously, the empty subunit assumes a conformation that enables the enzyme to harness the free energy of ADP binding to drive ATP release. Finally, we show that ligand exchange is regulated by a checkpoint mechanism, an apparent prerequisite for high efficiency in protein nanomotors.
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Affiliation(s)
- Jacek Czub
- Department of Physical Chemistry, Gdansk University of Technology , ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Miłosz Wieczór
- Department of Physical Chemistry, Gdansk University of Technology , ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Bartosz Prokopowicz
- Department of Physical Chemistry, Gdansk University of Technology , ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
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14
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Suzuki K, Kimura T, Shinoda H, Bai G, Daniels MJ, Arai Y, Nakano M, Nagai T. Five colour variants of bright luminescent protein for real-time multicolour bioimaging. Nat Commun 2016; 7:13718. [PMID: 27966527 PMCID: PMC5171807 DOI: 10.1038/ncomms13718] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 10/26/2016] [Indexed: 12/20/2022] Open
Abstract
Luminescence imaging has gained attention as a promising bio-imaging modality in situations where fluorescence imaging cannot be applied. However, wider application to multicolour and dynamic imaging is limited by the lack of bright luminescent proteins with emissions across the visible spectrum. Here we report five new spectral variants of the bright luminescent protein, enhanced Nano-lantern (eNL), made by concatenation of the brightest luciferase, NanoLuc, with various colour hues of fluorescent proteins. eNLs allow five-colour live-cell imaging, as well as detection of single protein complexes and even single molecules. We also develop an eNL-based Ca2+ indicator with a 500% signal change, which can image spontaneous Ca2+ dynamics in cardiomyocyte and neural cell models. These eNL probes facilitate not only multicolour imaging in living cells but also sensitive imaging of a wide repertoire of proteins, even at very low expression levels.
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Affiliation(s)
- Kazushi Suzuki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - Taichi Kimura
- Department of Biotechnology, School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - Hajime Shinoda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - Guirong Bai
- Department of Biomolecular Science and Engineering, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Matthew J Daniels
- BHF Centre for Regenerative Medicine, Division of Cardiovascular Medicine, West Wing Level 6, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Yoshiyuki Arai
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan.,Department of Biotechnology, School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan.,Department of Biomolecular Science and Engineering, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Masahiro Nakano
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan.,Department of Biotechnology, School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan.,Department of Biomolecular Science and Engineering, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Takeharu Nagai
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan.,Department of Biotechnology, School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan.,Department of Biomolecular Science and Engineering, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
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15
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Gerle C. On the structural possibility of pore-forming mitochondrial FoF1 ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:1191-1196. [PMID: 26968896 DOI: 10.1016/j.bbabio.2016.03.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 02/23/2016] [Accepted: 03/01/2016] [Indexed: 12/31/2022]
Abstract
The mitochondrial permeability transition is an inner mitochondrial membrane event involving the opening of the permeability transition pore concomitant with a sudden efflux of matrix solutes and breakdown of membrane potential. The mitochondrial F(o)F(1) ATP synthase has been proposed as the molecular identity of the permeability transition pore. The likeliness of potential pore-forming sites in the mitochondrial F(o)F(1) ATP synthase is discussed and a new model, the death finger model, is described. In this model, movement of a p-side density that connects the lipid-plug of the c-ring with the distal membrane bending Fo domain allows reversible opening of the c-ring and structural cross-talk with OSCP and the catalytic (αβ)(3) hexamer. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
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Affiliation(s)
- Christoph Gerle
- Picobiology Institute, Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori, Japan; Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Japan.
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16
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Kemmer GC, Bogh SA, Urban M, Palmgren MG, Vosch T, Schiller J, Günther Pomorski T. Lipid-conjugated fluorescent pH sensors for monitoring pH changes in reconstituted membrane systems. Analyst 2016; 140:6313-20. [PMID: 26280031 DOI: 10.1039/c5an01180a] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Accurate real-time measurements of the dynamics of proton concentration gradients are crucial for detailed molecular studies of proton translocation by membrane-bound enzymes. To reduce complexity, these measurements are often carried out with purified, reconstituted enzyme systems. Yet the most paramount problem to detect pH changes in reconstituted systems is that soluble pH reporters leak out of the vesicle system during the reconstitution procedure. This requires loading of substantial amounts of pH-sensors into the lumen of unilamellar liposomes during reconstitution. Here, we report the synthesis and detailed characterisation of two lipid-linked pH sensors employing amine-reactive forms of seminaphthorhodafluors (SNARF®-1 dye) and rhodamine probes (pHrodo™ Red dye). Lipid-conjugation of both dyes allowed for efficient detergent-based reconstitution of these pH indicators into liposomes. Vesicle-embedded pHrodo™ displayed excellent photostability and an optimal pH-response between 4 and 7. The suitability of the lipid-linked pHrodo™ probe as a pH reporter was demonstrated by assaying the activity of a plant plasma membrane H(+)-ATPase (proton pump) reconstituted in proteoliposomes.
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Affiliation(s)
- Gerdi Christine Kemmer
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Department of Plant Biology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.
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17
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Biological Nanomotors with a Revolution, Linear, or Rotation Motion Mechanism. Microbiol Mol Biol Rev 2016; 80:161-86. [PMID: 26819321 DOI: 10.1128/mmbr.00056-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ubiquitous biological nanomotors were classified into two categories in the past: linear and rotation motors. In 2013, a third type of biomotor, revolution without rotation (http://rnanano.osu.edu/movie.html), was discovered and found to be widespread among bacteria, eukaryotic viruses, and double-stranded DNA (dsDNA) bacteriophages. This review focuses on recent findings about various aspects of motors, including chirality, stoichiometry, channel size, entropy, conformational change, and energy usage rate, in a variety of well-studied motors, including FoF1 ATPase, helicases, viral dsDNA-packaging motors, bacterial chromosome translocases, myosin, kinesin, and dynein. In particular, dsDNA translocases are used to illustrate how these features relate to the motion mechanism and how nature elegantly evolved a revolution mechanism to avoid coiling and tangling during lengthy dsDNA genome transportation in cell division. Motor chirality and channel size are two factors that distinguish rotation motors from revolution motors. Rotation motors use right-handed channels to drive the right-handed dsDNA, similar to the way a nut drives the bolt with threads in same orientation; revolution motors use left-handed motor channels to revolve the right-handed dsDNA. Rotation motors use small channels (<2 nm in diameter) for the close contact of the channel wall with single-stranded DNA (ssDNA) or the 2-nm dsDNA bolt; revolution motors use larger channels (>3 nm) with room for the bolt to revolve. Binding and hydrolysis of ATP are linked to different conformational entropy changes in the motor that lead to altered affinity for the substrate and allow work to be done, for example, helicase unwinding of DNA or translocase directional movement of DNA.
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18
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Watanabe R, Koyasu K, You H, Tanigawara M, Noji H. Torque transmission mechanism via DELSEED loop of F1-ATPase. Biophys J 2016; 108:1144-52. [PMID: 25762326 DOI: 10.1016/j.bpj.2015.01.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/16/2015] [Accepted: 01/21/2015] [Indexed: 12/01/2022] Open
Abstract
F1-ATPase (F1) is an ATP-driven rotary motor in which the three catalytic β subunits in the stator ring sequentially induce the unidirectional rotation of the rotary γ subunit. Many lines of evidence have revealed open-to-closed conformational transitions in the β subunit that swing the C-terminal domain inward. This conformational transition causes a C-terminal protruding loop with conserved sequence DELSEED to push the γ subunit. Previous work, where all residues of DELSEED were substituted with glycine to disrupt the specific interaction with γ and introduce conformational flexibility, showed that F1 still rotated, but that the torque was halved, indicating a remarkable impact on torque transmission. In this study, we conducted a stall-and-release experiment on F1 with a glycine-substituted DELSEED loop to investigate the impact of the glycine substitution on torque transmission upon ATP binding and ATP hydrolysis. The mutant F1 showed a significantly reduced angle-dependent change in ATP affinity, whereas there was no change in the equilibrium for ATP hydrolysis. These findings indicate that the DELSEED loop is predominantly responsible for torque transmission upon ATP binding but not for that upon ATP hydrolysis.
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Affiliation(s)
- Rikiya Watanabe
- Department of Applied Chemistry, Graduate School of Engineering, University of Tokyo, Tokyo, Japan; PRESTO, Japan Science and Technology Agency, Tokyo, Japan; CREST, Japan Science and Technology Agency, Tokyo, Japan
| | - Kazuma Koyasu
- Department of Applied Chemistry, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Huijuan You
- Department of Applied Chemistry, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Mizue Tanigawara
- Department of Applied Chemistry, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Hiroyuki Noji
- Department of Applied Chemistry, Graduate School of Engineering, University of Tokyo, Tokyo, Japan; CREST, Japan Science and Technology Agency, Tokyo, Japan.
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19
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Liu J, Fu X, Chang Z. A reciprocating motion-driven rotation mechanism for the ATP synthase. SCIENCE CHINA-LIFE SCIENCES 2015; 59:44-8. [DOI: 10.1007/s11427-015-4995-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/27/2015] [Indexed: 10/22/2022]
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20
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Watson MA, Cockroft SL. An Autonomously Reciprocating Transmembrane Nanoactuator. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508845] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Matthew A. Watson
- EaStCHEM School of Chemistry; University of Edinburgh; Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry; University of Edinburgh; Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
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21
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Watson MA, Cockroft SL. An Autonomously Reciprocating Transmembrane Nanoactuator. Angew Chem Int Ed Engl 2015; 55:1345-9. [DOI: 10.1002/anie.201508845] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/09/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Matthew A. Watson
- EaStCHEM School of Chemistry; University of Edinburgh; Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry; University of Edinburgh; Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
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22
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Elasticity, friction, and pathway of γ-subunit rotation in FoF1-ATP synthase. Proc Natl Acad Sci U S A 2015; 112:10720-5. [PMID: 26261344 DOI: 10.1073/pnas.1500691112] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We combine molecular simulations and mechanical modeling to explore the mechanism of energy conversion in the coupled rotary motors of FoF1-ATP synthase. A torsional viscoelastic model with frictional dissipation quantitatively reproduces the dynamics and energetics seen in atomistic molecular dynamics simulations of torque-driven γ-subunit rotation in the F1-ATPase rotary motor. The torsional elastic coefficients determined from the simulations agree with results from independent single-molecule experiments probing different segments of the γ-subunit, which resolves a long-lasting controversy. At steady rotational speeds of ∼ 1 kHz corresponding to experimental turnover, the calculated frictional dissipation of less than k(B)T per rotation is consistent with the high thermodynamic efficiency of the fully reversible motor. Without load, the maximum rotational speed during transitions between dwells is reached at ∼ 1 MHz. Energetic constraints dictate a unique pathway for the coupled rotations of the Fo and F1 rotary motors in ATP synthase, and explain the need for the finer stepping of the F1 motor in the mammalian system, as seen in recent experiments. Compensating for incommensurate eightfold and threefold rotational symmetries in Fo and F1, respectively, a significant fraction of the external mechanical work is transiently stored as elastic energy in the γ-subunit. The general framework developed here should be applicable to other molecular machines.
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23
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Martin J, Hudson J, Hornung T, Frasch WD. Fo-driven Rotation in the ATP Synthase Direction against the Force of F1 ATPase in the FoF1 ATP Synthase. J Biol Chem 2015; 290:10717-28. [PMID: 25713065 DOI: 10.1074/jbc.m115.646430] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Indexed: 11/06/2022] Open
Abstract
Living organisms rely on the FoF1 ATP synthase to maintain the non-equilibrium chemical gradient of ATP to ADP and phosphate that provides the primary energy source for cellular processes. How the Fo motor uses a transmembrane electrochemical ion gradient to create clockwise torque that overcomes F1 ATPase-driven counterclockwise torque at high ATP is a major unresolved question. Using single FoF1 molecules embedded in lipid bilayer nanodiscs, we now report the observation of Fo-dependent rotation of the c10 ring in the ATP synthase (clockwise) direction against the counterclockwise force of ATPase-driven rotation that occurs upon formation of a leash with Fo stator subunit a. Mutational studies indicate that the leash is important for ATP synthase activity and support a mechanism in which residues aGlu-196 and cArg-50 participate in the cytoplasmic proton half-channel to promote leash formation.
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Affiliation(s)
- James Martin
- From the School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501
| | - Jennifer Hudson
- From the School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501
| | - Tassilo Hornung
- From the School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501
| | - Wayne D Frasch
- From the School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501
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24
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Arrayed lipid bilayer chambers allow single-molecule analysis of membrane transporter activity. Nat Commun 2014; 5:4519. [PMID: 25058452 PMCID: PMC4124872 DOI: 10.1038/ncomms5519] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/25/2014] [Indexed: 11/09/2022] Open
Abstract
Nano- to micron-size reaction chamber arrays (femtolitre chamber arrays) have facilitated the development of sensitive and quantitative biological assays, such as single-molecule enzymatic assays, digital PCR and digital ELISA. However, the versatility of femtolitre chamber arrays is limited to reactions that occur in aqueous solutions. Here we report an arrayed lipid bilayer chamber system (ALBiC) that contains sub-million femtolitre chambers, each sealed with a stable 4-μm-diameter lipid bilayer membrane. When reconstituted with a limiting amount of the membrane transporter proteins α-hemolysin or F0F1-ATP synthase, the chambers within the ALBiC exhibit stochastic and quantized transporting activities. This demonstrates that the single-molecule analysis of passive and active membrane transport is achievable with the ALBiC system. This new platform broadens the versatility of femtolitre chamber arrays and paves the way for novel applications aimed at furthering our mechanistic understanding of membrane proteins' function.
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25
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Murai M, Miyoshi H. Chemical modifications of respiratory complex I for structural and functional studies. J Bioenerg Biomembr 2014; 46:313-21. [DOI: 10.1007/s10863-014-9562-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 06/26/2014] [Indexed: 01/07/2023]
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26
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Masuya T, Murai M, Ifuku K, Morisaka H, Miyoshi H. Site-Specific Chemical Labeling of Mitochondrial Respiratory Complex I through Ligand-Directed Tosylate Chemistry. Biochemistry 2014; 53:2307-17. [DOI: 10.1021/bi500205x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Takahiro Masuya
- Division of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masatoshi Murai
- Division of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kentaro Ifuku
- Division of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hironobu Morisaka
- Division of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hideto Miyoshi
- Division of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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27
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Bockenhauer SD, Duncan TM, Moerner WE, Börsch M. The regulatory switch of F 1-ATPase studied by single-molecule FRET in the ABEL Trap. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2014; 8950:89500H. [PMID: 25309100 DOI: 10.1117/12.2042688] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
F1-ATPase is the soluble portion of the membrane-embedded enzyme FoF1-ATP synthase that catalyzes the production of adenosine triphosphate in eukaryotic and eubacterial cells. In reverse, the F1 part can also hydrolyze ATP quickly at three catalytic binding sites. Therefore, catalysis of 'non-productive' ATP hydrolysis by F1 (or FoF1) must be minimized in the cell. In bacteria, the ε subunit is thought to control and block ATP hydrolysis by mechanically inserting its C-terminus into the rotary motor region of F1. We investigate this proposed mechanism by labeling F1 specifically with two fluorophores to monitor the C-terminus of the ε subunit by Förster resonance energy transfer. Single F1 molecules are trapped in solution by an Anti-Brownian electrokinetic trap which keeps the FRET-labeled F1 in place for extended observation times of several hundreds of milliseconds, limited by photobleaching. FRET changes in single F1 and FRET histograms for different biochemical conditions are compared to evaluate the proposed regulatory mechanism.
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Affiliation(s)
- Samuel D Bockenhauer
- Department of Chemistry, Stanford University, Stanford, CA, USA ; Department of Physics, Stanford University, Stanford, CA, USA
| | - Thomas M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
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28
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Watanabe R, Noji H. Timing of inorganic phosphate release modulates the catalytic activity of ATP-driven rotary motor protein. Nat Commun 2014; 5:3486. [PMID: 24686317 PMCID: PMC3988807 DOI: 10.1038/ncomms4486] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 02/21/2014] [Indexed: 12/04/2022] Open
Abstract
F1-ATPase is a rotary motor protein driven by ATP hydrolysis. The rotary motion of F1-ATPase is tightly coupled to catalysis, in which the catalytic sites strictly obey the reaction sequences at the resolution of elementary reaction steps. This fine coordination of the reaction scheme is thought to be important to achieve extremely high chemomechanical coupling efficiency and reversibility, which is the prominent feature of F1-ATPase among molecular motor proteins. In this study, we intentionally change the reaction scheme by using single-molecule manipulation, and we examine the resulting effect on the rotary motion of F1-ATPase. When the sequence of the products released, that is, ADP and inorganic phosphate, is switched, we find that F1 frequently stops rotating for a long time, which corresponds to inactivation of catalysis. This inactive state presents MgADP inhibition, and thus, we find that an improper reaction sequence of F1-ATPase catalysis induces MgADP inhibition. The F1-ATPase is a motor protein which exhibits rotary motion as a result of catalytic hydrolysis of ATP. Here, the authors investigate how the sequence of this reaction influences molecular rotation, showing that premature product release can result in protein inactivation.
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Affiliation(s)
- Rikiya Watanabe
- 1] Department of Applied Chemistry, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan [2] PRESTO, JST, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroyuki Noji
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
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29
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Duncan TM, Düser MG, Heitkamp T, McMillan DGG, Börsch M. Regulatory conformational changes of the ε subunit in single FRET-labeled F oF 1-ATP synthase. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2014; 8948:89481J. [PMID: 25076824 DOI: 10.1117/12.2040463] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Subunit ε is an intrinsic regulator of the bacterial FoF1-ATP synthase, the ubiquitous membrane-embedded enzyme that utilizes a proton motive force in most organisms to synthesize adenosine triphosphate (ATP). The C-terminal domain of ε can extend into the central cavity formed by the α and β subunits, as revealed by the recent X-ray structure of the F1 portion of the Escherichia coli enzyme. This insertion blocks the rotation of the central γ subunit and, thereby, prevents wasteful ATP hydrolysis. Here we aim to develop an experimental system that can reveal conditions under which ε inhibits the holoenzyme FoF1-ATP synthase in vitro. Labeling the C-terminal domain of ε and the γ subunit specifically with two different fluorophores for single-molecule Förster resonance energy transfer (smFRET) allowed monitoring of the conformation of ε in the reconstituted enzyme in real time. New mutants were made for future three-color smFRET experiments to unravel the details of regulatory conformational changes in ε.
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Affiliation(s)
- Thomas M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Monika G Düser
- 3 Institute of Physics, Stuttgart University, Stuttgart, Germany
| | - Thomas Heitkamp
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Duncan G G McMillan
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
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30
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Stewart AG, Laming EM, Sobti M, Stock D. Rotary ATPases--dynamic molecular machines. Curr Opin Struct Biol 2013; 25:40-8. [PMID: 24878343 DOI: 10.1016/j.sbi.2013.11.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 11/20/2013] [Accepted: 11/26/2013] [Indexed: 01/14/2023]
Abstract
Recent work has provided the detailed overall architecture and subunit composition of three subtypes of rotary ATPases. Composite models of F-type, V-type and A-type ATPases have been constructed by fitting high-resolution X-ray structures of individual components into electron microscopy derived envelopes of the intact enzymes. Electron cryo-tomography has provided new insights into the supra-molecular arrangement of eukaryotic ATP synthases within mitochondria. An inherent flexibility in rotary ATPases observed by different techniques suggests greater dynamics during operation than previously envisioned. The concerted movement of subunits within the complex might provide means of regulation and information transfer between distant parts of rotary ATPases thereby fine tuning these molecular machines to their cellular environment, while optimizing their efficiency.
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Affiliation(s)
- Alastair G Stewart
- The Victor Chang Cardiac Research Institute, Sydney, NSW, Australia; The University of New South Wales, Sydney, NSW, Australia.
| | - Elise M Laming
- The Victor Chang Cardiac Research Institute, Sydney, NSW, Australia; The University of New South Wales, Sydney, NSW, Australia
| | - Meghna Sobti
- The Victor Chang Cardiac Research Institute, Sydney, NSW, Australia; The University of New South Wales, Sydney, NSW, Australia
| | - Daniela Stock
- The Victor Chang Cardiac Research Institute, Sydney, NSW, Australia; The University of New South Wales, Sydney, NSW, Australia
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31
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Abstract
Molecular bioenergetics deals with the construction, function and regulation of the powerhouses of life. The present overview sketches scenes and actors, farsighted goals and daring hypotheses, meticulous tool-making, painstaking benchwork, lucky discovery, serious scepticism, emphatic believing and strong characters with weak and others with hard arguments, told from a personal, admittedly limited, perspective. Bioenergetics will blossom further with the search focused on both where there is bright light for ever-finer detail and the obvious dark spots for surprise and discovery.
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32
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Toei M, Noji H. Single-molecule analysis of F0F1-ATP synthase inhibited by N,N-dicyclohexylcarbodiimide. J Biol Chem 2013; 288:25717-25726. [PMID: 23893417 DOI: 10.1074/jbc.m113.482455] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
N,N-Dicyclohexylcarbodiimide (DCCD) is a classical inhibitor of the F0F1-ATP synthase (F0F1), which covalently binds to the highly conserved carboxylic acid of the proteolipid subunit (c subunit) in F0. Although it is well known that DCCD modification of the c subunit blocks proton translocation in F0 and the coupled ATP hydrolysis activity of F1, how DCCD inhibits the rotary dynamics of F0F1 remains elusive. Here, we carried out single-molecule rotation assays to characterize the DCCD inhibition of Escherichia coli F0F1. Upon the injection of DCCD, rotations irreversibly terminated with first order reaction kinetics, suggesting that the incorporation of a single DCCD moiety is sufficient to block the rotary catalysis of the F0F1. Individual molecules terminated at different angles relative to the three catalytic angles of F1, suggesting that DCCD randomly reacts with one of the 10 c subunits. DCCD-inhibited F0F1 sometimes showed transient activation; molecules abruptly rotated and stopped after one revolution at the original termination angle, suggesting that hindrance by the DCCD moiety is released due to thermal fluctuation. To explore the mechanical activation of DCCD-inhibited molecules, we perturbed inhibited molecules using magnetic tweezers. The probability of transient activation increased upon a forward forcible rotation. Interestingly, during the termination F0F1, showed multiple positional shifts, which implies that F1 stochastically changes the angular position of its rotor upon a catalytic reaction. This effect could be caused by balancing the angular positions of the F1 and the F0 rotors, which are connected via elastic elements.
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Affiliation(s)
- Masashi Toei
- From the Department of Applied Chemistry, School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Hiroyuki Noji
- From the Department of Applied Chemistry, School of Engineering, University of Tokyo, Tokyo 113-8656, Japan.
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33
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Toyabe S, Muneyuki E. Experimental thermodynamics of single molecular motor. Biophysics (Nagoya-shi) 2013; 9:91-8. [PMID: 27493546 PMCID: PMC4629675 DOI: 10.2142/biophysics.9.91] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 06/12/2013] [Indexed: 12/01/2022] Open
Abstract
Molecular motor is a nano-sized chemical engine that converts chemical free energy to mechanical motions. Hence, the energetics is as important as kinetics in order to understand its operation principle. We review experiments to evaluate the thermodynamic properties of a rotational F1-ATPase motor (F1-motor) at a single-molecule level. We show that the F1-motor achieves 100% thermo dynamic efficiency at the stalled state. Furthermore, the motor reduces the internal irreversible heat inside the motor to almost zero and achieves a highly-efficient free energy transduction close to 100% during rotations far from quasistatic process. We discuss the mechanism of how the F1-motor achieves such a high efficiency, which highlights the remarkable property of the nano-sized engine F1-motor.
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Affiliation(s)
- Shoichi Toyabe
- Systems Biophysics, Faculty of Physics, Ludwig-Maximilians-University Munich, Munich 80799, Germany
| | - Eiro Muneyuki
- Department of Physics, Faculty of Science and Engineering, Chuo University, Kasuga, Tokyo 112-8551, Japan
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Watanabe R. Rotary catalysis of FoF1-ATP synthase. Biophysics (Nagoya-shi) 2013; 9:51-6. [PMID: 27493540 PMCID: PMC4629669 DOI: 10.2142/biophysics.9.51] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 04/22/2013] [Indexed: 12/01/2022] Open
Abstract
The synthesis of ATP, the key reaction of biological energy metabolism, is accomplished by the rotary motor protein; FoF1-ATP synthase (FoF1). In vivo, FoF1, located on the cell membrane, carries out ATP synthesis by using the proton motive force. This heterologous energy conversion is supposed to be mediated by the mechanical rotation of FoF1; however, it still remained unclear. Recently, we developed the novel experimental setup to reproduce the proton motive force in vitro and succeeded in directly observing the proton-driven rotation of FoF1. In this review, we describe the interesting working principles determined so far for FoF1 and then introduce results from our recent study.
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Affiliation(s)
- Rikiya Watanabe
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
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Conformational dynamics in phosphoglycerate kinase, an open and shut case? FEBS Lett 2013; 587:1878-83. [DOI: 10.1016/j.febslet.2013.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 05/06/2013] [Indexed: 01/24/2023]
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