1
|
Frasch WD, Bukhari ZA, Yanagisawa S. F1FO ATP synthase molecular motor mechanisms. Front Microbiol 2022; 13:965620. [PMID: 36081786 PMCID: PMC9447477 DOI: 10.3389/fmicb.2022.965620] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
The F-ATP synthase, consisting of F1 and FO motors connected by a central rotor and the stators, is the enzyme responsible for synthesizing the majority of ATP in all organisms. The F1 (αβ)3 ring stator contains three catalytic sites. Single-molecule F1 rotation studies revealed that ATP hydrolysis at each catalytic site (0°) precedes a power-stroke that rotates subunit-γ 120° with angular velocities that vary with rotational position. Catalytic site conformations vary relative to subunit-γ position (βE, empty; βD, ADP bound; βT, ATP-bound). During a power stroke, βE binds ATP (0°–60°) and βD releases ADP (60°–120°). Årrhenius analysis of the power stroke revealed that elastic energy powers rotation via unwinding the γ-subunit coiled-coil. Energy from ATP binding at 34° closes βE upon subunit-γ to drive rotation to 120° and forcing the subunit-γ to exchange its tether from βE to βD, which changes catalytic site conformations. In F1FO, the membrane-bound FO complex contains a ring of c-subunits that is attached to subunit-γ. This c-ring rotates relative to the subunit-a stator in response to transmembrane proton flow driven by a pH gradient, which drives subunit-γ rotation in the opposite direction to force ATP synthesis in F1. Single-molecule studies of F1FO embedded in lipid bilayer nanodisks showed that the c-ring transiently stopped F1-ATPase-driven rotation every 36° (at each c-subunit in the c10-ring of E. coli F1FO) and was able to rotate 11° in the direction of ATP synthesis. Protonation and deprotonation of the conserved carboxyl group on each c-subunit is facilitated by separate groups of subunit-a residues, which were determined to have different pKa’s. Mutations of any of any residue from either group changed both pKa values, which changed the occurrence of the 11° rotation proportionately. This supports a Grotthuss mechanism for proton translocation and indicates that proton translocation occurs during the 11° steps. This is consistent with a mechanism in which each 36° of rotation the c-ring during ATP synthesis involves a proton translocation-dependent 11° rotation of the c-ring, followed by a 25° rotation driven by electrostatic interaction of the negatively charged unprotonated carboxyl group to the positively charged essential arginine in subunit-a.
Collapse
|
2
|
Vu Huu K, Zangl R, Hoffmann J, Just A, Morgner N. Bacterial F-type ATP synthases follow a well-choreographed assembly pathway. Nat Commun 2022; 13:1218. [PMID: 35260553 PMCID: PMC8904574 DOI: 10.1038/s41467-022-28828-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/04/2022] [Indexed: 12/23/2022] Open
Abstract
F-type ATP synthases are multiprotein complexes composed of two separate coupled motors (F1 and FO) generating adenosine triphosphate (ATP) as the universal major energy source in a variety of relevant biological processes in mitochondria, bacteria and chloroplasts. While the structure of many ATPases is solved today, the precise assembly pathway of F1FO-ATP synthases is still largely unclear. Here, we probe the assembly of the F1 complex from Acetobacterium woodii. Using laser induced liquid bead ion desorption (LILBID) mass spectrometry, we study the self-assembly of purified F1 subunits in different environments under non-denaturing conditions. We report assembly requirements and identify important assembly intermediates in vitro and in cellula. Our data provide evidence that nucleotide binding is crucial for in vitro F1 assembly, whereas ATP hydrolysis appears to be less critical. We correlate our results with activity measurements and propose a model for the assembly pathway of a functional F1 complex. ATPases are the macromolecular machines for cellular energy production. Here the authors investigate factors that govern the assembly of the F1 complex from a bacterial F-type ATPase and relate differences in activity of complexes assembled in cells and in vitro to structural changes.
Collapse
Affiliation(s)
- Khanh Vu Huu
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Rene Zangl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Jan Hoffmann
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Alicia Just
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany.
| |
Collapse
|
3
|
Majewski DD, Worrall LJ, Hong C, Atkinson CE, Vuckovic M, Watanabe N, Yu Z, Strynadka NCJ. Cryo-EM structure of the homohexameric T3SS ATPase-central stalk complex reveals rotary ATPase-like asymmetry. Nat Commun 2019; 10:626. [PMID: 30733444 PMCID: PMC6367419 DOI: 10.1038/s41467-019-08477-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 01/11/2019] [Indexed: 12/31/2022] Open
Abstract
Many Gram-negative bacteria, including causative agents of dysentery, plague, and typhoid fever, rely on a type III secretion system - a multi-membrane spanning syringe-like apparatus - for their pathogenicity. The cytosolic ATPase complex of this injectisome is proposed to play an important role in energizing secretion events and substrate recognition. We present the 3.3 Å resolution cryo-EM structure of the enteropathogenic Escherichia coli ATPase EscN in complex with its central stalk EscO. The structure shows an asymmetric pore with different functional states captured in its six catalytic sites, details directly supporting a rotary catalytic mechanism analogous to that of the heterohexameric F1/V1-ATPases despite its homohexameric nature. Situated at the C-terminal opening of the EscN pore is one molecule of EscO, with primary interaction mediated through an electrostatic interface. The EscN-EscO structure provides significant atomic insights into how the ATPase contributes to type III secretion, including torque generation and binding of chaperone/substrate complexes.
Collapse
Affiliation(s)
- Dorothy D Majewski
- Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - Liam J Worrall
- Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver, BC, Canada
- HRMEM Facility, University of British Columbia, Vancouver, BC, Canada
| | - Chuan Hong
- CryoEM Shared Resources, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA
- Merck & Co., Department of Biochemical Engineering and Structure, 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Claire E Atkinson
- Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver, BC, Canada
- HRMEM Facility, University of British Columbia, Vancouver, BC, Canada
| | - Marija Vuckovic
- Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - Nobuhiko Watanabe
- Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - Zhiheng Yu
- CryoEM Shared Resources, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA.
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
4
|
Mnatsakanyan N, Li Y, Weber J. Identification of two segments of the γ subunit of ATP synthase responsible for the different affinities of the catalytic nucleotide-binding sites. J Biol Chem 2018; 294:1152-1160. [PMID: 30510135 DOI: 10.1074/jbc.ra118.002504] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 11/26/2018] [Indexed: 11/06/2022] Open
Abstract
ATP synthase uses a rotary mechanism to couple transmembrane proton translocation to ATP synthesis and hydrolysis, which occur at the catalytic sites in the β subunits. In the presence of Mg2+, the three catalytic sites of ATP synthase have vastly different affinities for nucleotides, and the position of the central γ subunit determines which site has high, medium, or low affinity. Affinity differences and their changes as rotation progresses underpin the ATP synthase catalytic mechanism. Here, we used a series of variants with up to 45- and 60-residue-long truncations of the N- and C-terminal helices of the γ subunit, respectively, to identify the segment(s) responsible for the affinity differences of the catalytic sites. We found that each helix carries an affinity-determining segment of ∼10 residues. Our findings suggest that the affinity regulation by these segments is transmitted to the catalytic sites by the DELSEED loop in the C-terminal domain of the β subunits. For the N-terminal truncation variants, presence of the affinity-determining segment and therefore emergence of a high-affinity binding site resulted in WT-like catalytic activity. At the C terminus, additional residues outside of the affinity-determining segment were required for optimal enzymatic activity. Alanine substitutions revealed that the affinity changes of the catalytic sites required no specific interactions between amino acid side chains in the γ and α3β3 subunits but were caused by the presence of the helices themselves. Our findings help unravel the molecular basis for the affinity changes of the catalytic sites during ATP synthase rotation.
Collapse
Affiliation(s)
- Nelli Mnatsakanyan
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409 and the Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, Texas 79430
| | - Yunxiang Li
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409 and the Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, Texas 79430
| | - Joachim Weber
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409 and the Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, Texas 79430.
| |
Collapse
|
5
|
Murcia Rios A, Vahidi S, Dunn SD, Konermann L. Evidence for a Partially Stalled γ Rotor in F 1-ATPase from Hydrogen-Deuterium Exchange Experiments and Molecular Dynamics Simulations. J Am Chem Soc 2018; 140:14860-14869. [PMID: 30339028 DOI: 10.1021/jacs.8b08692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
F1-ATPase uses ATP hydrolysis to drive rotation of the γ subunit. The γ C-terminal helix constitutes the rotor tip that is seated in an apical bearing formed by α3β3. It remains uncertain to what extent the γ conformation during rotation differs from that seen in rigid crystal structures. Existing models assume that the entire γ subunit participates in every rotation. Here we interrogated E. coli F1-ATPase by hydrogen-deuterium exchange (HDX) mass spectrometry. Rotation of γ caused greatly enhanced deuteration in the γ C-terminal helix. The HDX kinetics implied that most F1 complexes operate with an intact rotor at any given time, but that the rotor tip is prone to occasional unfolding. A molecular dynamics (MD) strategy was developed to model the off-axis forces acting on γ. MD runs showed stalling of the rotor tip and unfolding of the γ C-terminal helix. MD-predicted H-bond opening events coincided with experimental HDX patterns. Our data suggest that in vitro operation of F1-ATPase is associated with significant rotational resistance in the apical bearing. These conditions cause the γ C-terminal helix to get "stuck" (and unfold) sporadically while the remainder of γ continues to rotate. This scenario contrasts the traditional "greasy bearing" model that envisions smooth rotation of the γ C-terminal helix. The fragility of the apical rotor tip in F1-ATPase is attributed to the absence of a c10 ring that stabilizes the rotation axis in intact FoF1. Overall, the MD/HDX strategy introduced here appears well suited for interrogating the inner workings of molecular motors.
Collapse
Affiliation(s)
- Angela Murcia Rios
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
| | - Siavash Vahidi
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
| | - Stanley D Dunn
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
| | - Lars Konermann
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
| |
Collapse
|
6
|
Elastic coupling power stroke mechanism of the F 1-ATPase molecular motor. Proc Natl Acad Sci U S A 2018; 115:5750-5755. [PMID: 29760063 PMCID: PMC5984535 DOI: 10.1073/pnas.1803147115] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The angular velocity profile of the 120° F1-ATPase power stroke was resolved as a function of temperature from 16.3 to 44.6 °C using a ΔμATP = -31.25 kBT at a time resolution of 10 μs. Angular velocities during the first 60° of the power stroke (phase 1) varied inversely with temperature, resulting in negative activation energies with a parabolic dependence. This is direct evidence that phase 1 rotation derives from elastic energy (spring constant, κ = 50 kBT·rad-2). Phase 2 of the power stroke had an enthalpic component indicating that additional energy input occurred to enable the γ-subunit to overcome energy stored by the spring after rotating beyond its 34° equilibrium position. The correlation between the probability distribution of ATP binding to the empty catalytic site and the negative Ea values of the power stroke during phase 1 suggests that this additional energy is derived from the binding of ATP to the empty catalytic site. A second torsion spring (κ = 150 kBT·rad-2; equilibrium position, 90°) was also evident that mitigated the enthalpic cost of phase 2 rotation. The maximum ΔGǂ was 22.6 kBT, and maximum efficiency was 72%. An elastic coupling mechanism is proposed that uses the coiled-coil domain of the γ-subunit rotor as a torsion spring during phase 1, and then as a crankshaft driven by ATP-binding-dependent conformational changes during phase 2 to drive the power stroke.
Collapse
|
7
|
Dai L, Flechsig H, Yu J. Deciphering Intrinsic Inter-subunit Couplings that Lead to Sequential Hydrolysis of F 1-ATPase Ring. Biophys J 2017; 113:1440-1453. [PMID: 28978438 PMCID: PMC5627347 DOI: 10.1016/j.bpj.2017.08.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 07/31/2017] [Accepted: 08/04/2017] [Indexed: 11/05/2022] Open
Abstract
Rotary sequential hydrolysis of the metabolic machine F1-ATPase is a prominent manifestation of high coordination among multiple chemical sites in ring-shaped molecular machines, and it is also functionally essential for F1 to tightly couple chemical reactions and central γ-shaft rotation. High-speed AFM experiments have identified that sequential hydrolysis is maintained in the F1 stator ring even in the absence of the γ-rotor. To explore the origins of intrinsic sequential performance, we computationally investigated essential inter-subunit couplings on the hexameric ring of mitochondrial and bacterial F1. We first reproduced in stochastic Monte Carlo simulations the experimentally determined sequential hydrolysis schemes by kinetically imposing inter-subunit couplings and following subsequent tri-site ATP hydrolysis cycles on the F1 ring. We found that the key couplings to support the sequential hydrolysis are those that accelerate neighbor-site ADP and Pi release upon a certain ATP binding or hydrolysis reaction. The kinetically identified couplings were then examined in atomistic molecular dynamics simulations at a coarse-grained level to reveal the underlying structural mechanisms. To do that, we enforced targeted conformational changes of ATP binding or hydrolysis to one chemical site on the F1 ring and monitored the ensuing conformational responses of the neighboring sites using structure-based simulations. Notably, we found asymmetrical neighbor-site opening that facilitates ADP release upon enforced ATP binding. We also captured a complete charge-hopping process of the Pi release subsequent to enforced ATP hydrolysis in the neighbor site, confirming recent single-molecule analyses with regard to the role of ATP hydrolysis in F1. Our studies therefore elucidate both the coordinated chemical kinetics and structural dynamics mechanisms underpinning the sequential operation of the F1 ring.
Collapse
Affiliation(s)
- Liqiang Dai
- Complex System Research Division, Beijing Computational Science Research Center, Beijing, China
| | - Holger Flechsig
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan
| | - Jin Yu
- Complex System Research Division, Beijing Computational Science Research Center, Beijing, China.
| |
Collapse
|
8
|
Hahn-Herrera O, Salcedo G, Barril X, García-Hernández E. Inherent conformational flexibility of F1-ATPase α-subunit. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1392-1402. [PMID: 27137408 DOI: 10.1016/j.bbabio.2016.04.283] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/12/2016] [Accepted: 04/28/2016] [Indexed: 12/30/2022]
Abstract
The core of F1-ATPase consists of three catalytic (β) and three noncatalytic (α) subunits, forming a hexameric ring in alternating positions. A wealth of experimental and theoretical data has provided a detailed picture of the complex role played by catalytic subunits. Although major conformational changes have only been seen in β-subunits, it is clear that α-subunits have to respond to these changes in order to be able to transmit information during the rotary mechanism. However, the conformational behavior of α-subunits has not been explored in detail. Here, we have combined unbiased molecular dynamics (MD) simulations and calorimetrically measured thermodynamic signatures to investigate the conformational flexibility of isolated α-subunits, as a step toward deepening our understanding of its function inside the α3β3 ring. The simulations indicate that the open-to-closed conformational transition of the α-subunit is essentially barrierless, which is ideal to accompany and transmit the movement of the catalytic subunits. Calorimetric measurements of the recombinant α-subunit from Geobacillus kaustophilus indicate that the isolated subunit undergoes no significant conformational changes upon nucleotide binding. Simulations confirm that the nucleotide-free and nucleotide-bound subunits show average conformations similar to that observed in the F1 crystal structure, but they reveal an increased conformational flexibility of the isolated α-subunit upon MgATP binding, which might explain the evolutionary conserved capacity of α-subunits to recognize nucleotides with considerable strength. Furthermore, we elucidate the different dependencies that α- and β-subunits show on Mg(II) for recognizing ATP.
Collapse
Affiliation(s)
- Otto Hahn-Herrera
- Instituto de Química Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México 04630, D.F., Mexico
| | - Guillermo Salcedo
- Instituto de Química Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México 04630, D.F., Mexico
| | - Xavier Barril
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain; Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
| | - Enrique García-Hernández
- Instituto de Química Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México 04630, D.F., Mexico.
| |
Collapse
|
9
|
Chou YC, Hsiao YF, Hwang GJ, To K. Torque generation through the random movement of an asymmetric rotor: A potential rotational mechanism of the γ subunit of F(1)-ATPase. Phys Rev E 2016; 93:022408. [PMID: 26986363 DOI: 10.1103/physreve.93.022408] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Indexed: 11/07/2022]
Abstract
The rotation of the γ subunit of F(1)-ATPase is stochastic, processive, unidirectional, reversible through an external torque, and stepwise with a slow rotation. We propose a mechanism that can explain these properties of the rotary molecular motor, and that can determine the direction of rotation. The asymmetric structures of the γ subunit, both at the tip of the shaft (C and N termini) and at the part (ε subunit) protruding from the α(3)β(3) subunits, are critical. The torque required for stochastic rotation is generated from the impulsive reactive force due to the random collisions between the γ subunit and the quasihexagonal α(3)β(3) subunits. The rotation is the result of the random motion of the confined asymmetric γ subunit. The steps originate from the chemical reactions of the γ subunit and physical interaction between the γ subunit and the flexible protrusions of the α(3)β(3) subunits. An external torque as well as a configurational modification in the γ subunit (the central rotor) can reverse the rotational direction. We demonstrate the applicability of the mechanism to a macroscopic simulation system, which has the essential ingredients of the F(1)-ATPase structure, by reproducing the dynamic properties of the rotation.
Collapse
Affiliation(s)
- Y C Chou
- Department of Physics, National Tsing-Hua University, Hsinchu, Taiwan, Republic of China
| | - Yi-Feng Hsiao
- Department of Physics, National Tsing-Hua University, Hsinchu, Taiwan, Republic of China
| | - Gwo-Jen Hwang
- Department of Electronic Engineering, St. John's University, Tamsui District, New Taipei City, Taiwan, Republic of China
| | - Kiwing To
- Institute of Physics, Academia Sinca, Taipei, Taiwan, Republic of China
| |
Collapse
|
10
|
Nakanishi-Matsui M, Sekiya M, Futai M. ATP synthase from Escherichia coli : Mechanism of rotational catalysis, and inhibition with the ε subunit and phytopolyphenols. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:129-140. [DOI: 10.1016/j.bbabio.2015.11.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/19/2015] [Accepted: 11/13/2015] [Indexed: 10/22/2022]
|
11
|
Xu T, Pagadala V, Mueller DM. Understanding structure, function, and mutations in the mitochondrial ATP synthase. MICROBIAL CELL 2015; 2:105-125. [PMID: 25938092 PMCID: PMC4415626 DOI: 10.15698/mic2015.04.197] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The mitochondrial ATP synthase is a multimeric enzyme complex with an overall molecular weight of about 600,000 Da. The ATP synthase is a molecular motor composed of two separable parts: F1 and Fo. The F1 portion contains the catalytic sites for ATP synthesis and protrudes into the mitochondrial matrix. Fo forms a proton turbine that is embedded in the inner membrane and connected to the rotor of F1. The flux of protons flowing down a potential gradient powers the rotation of the rotor driving the synthesis of ATP. Thus, the flow of protons though Fo is coupled to the synthesis of ATP. This review will discuss the structure/function relationship in the ATP synthase as determined by biochemical, crystallographic, and genetic studies. An emphasis will be placed on linking the structure/function relationship with understanding how disease causing mutations or putative single nucleotide polymorphisms (SNPs) in genes encoding the subunits of the ATP synthase, will affect the function of the enzyme and the health of the individual. The review will start by summarizing the current understanding of the subunit composition of the enzyme and the role of the subunits followed by a discussion on known mutations and their effect on the activity of the ATP synthase. The review will conclude with a summary of mutations in genes encoding subunits of the ATP synthase that are known to be responsible for human disease, and a brief discussion on SNPs.
Collapse
Affiliation(s)
- Ting Xu
- Department of Biochemistry and Molecular Biology, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064
| | - Vijayakanth Pagadala
- Department of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC
| | - David M Mueller
- Department of Biochemistry and Molecular Biology, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064
| |
Collapse
|
12
|
Abstract
Oxygenic photosynthesis is the principal converter of sunlight into chemical energy. Cyanobacteria and plants provide aerobic life with oxygen, food, fuel, fibers, and platform chemicals. Four multisubunit membrane proteins are involved: photosystem I (PSI), photosystem II (PSII), cytochrome b6f (cyt b6f), and ATP synthase (FOF1). ATP synthase is likewise a key enzyme of cell respiration. Over three billion years, the basic machinery of oxygenic photosynthesis and respiration has been perfected to minimize wasteful reactions. The proton-driven ATP synthase is embedded in a proton tight-coupling membrane. It is composed of two rotary motors/generators, FO and F1, which do not slip against each other. The proton-driven FO and the ATP-synthesizing F1 are coupled via elastic torque transmission. Elastic transmission decouples the two motors in kinetic detail but keeps them perfectly coupled in thermodynamic equilibrium and (time-averaged) under steady turnover. Elastic transmission enables operation with different gear ratios in different organisms.
Collapse
Affiliation(s)
- Wolfgang Junge
- Department of Biophysics, Universität Osnabrück, DE-49069 Osnabrück, Germany;
| | | |
Collapse
|
13
|
Chiwata R, Kohori A, Kawakami T, Shiroguchi K, Furuike S, Adachi K, Sutoh K, Yoshida M, Kinosita K. None of the rotor residues of F1-ATPase are essential for torque generation. Biophys J 2014; 106:2166-74. [PMID: 24853745 PMCID: PMC4052266 DOI: 10.1016/j.bpj.2014.04.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 04/04/2014] [Accepted: 04/07/2014] [Indexed: 11/28/2022] Open
Abstract
F1-ATPase is a powerful rotary molecular motor that can rotate an object several hundred times as large as the motor itself against the viscous friction of water. Forced reverse rotation has been shown to lead to ATP synthesis, implying that the mechanical work against the motor’s high torque can be converted into the chemical energy of ATP. The minimal composition of the motor protein is α3β3γ subunits, where the central rotor subunit γ turns inside a stator cylinder made of alternately arranged α3β3 subunits using the energy derived from ATP hydrolysis. The rotor consists of an axle, a coiled coil of the amino- and carboxyl-terminal α-helices of γ, which deeply penetrates the stator cylinder, and a globular protrusion that juts out from the stator. Previous work has shown that, for a thermophilic F1, significant portions of the axle can be truncated and the motor still rotates a submicron sized bead duplex, indicating generation of up to half the wild-type (WT) torque. Here, we inquire if any specific interactions between the stator and the rest of the rotor are needed for the generation of a sizable torque. We truncated the protruding portion of the rotor and replaced part of the remaining axle residues such that every residue of the rotor has been deleted or replaced in this or previous truncation mutants. This protrusionless construct showed an unloaded rotary speed about a quarter of the WT, and generated one-third to one-half of the WT torque. No residue-specific interactions are needed for this much performance. F1 is so designed that the basic rotor-stator interactions for torque generation and control of catalysis rely solely upon the shape and size of the rotor at very low resolution. Additional tailored interactions augment the torque to allow ATP synthesis under physiological conditions.
Collapse
Affiliation(s)
- Ryohei Chiwata
- Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Ayako Kohori
- Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Tomonari Kawakami
- Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Katsuyuki Shiroguchi
- Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Shou Furuike
- Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Kengo Adachi
- Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Kazuo Sutoh
- Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Masasuke Yoshida
- ATP Synthesis Regulation Project, ICORP, Japan Science and Technology Agency (JST), Aomi 2-41, Koto-ku, Tokyo, Japan; Department of Molecular Bioscience, Kyoto Sangyo University, Motoyama, Kamigamo, Kyoto, Japan
| | - Kazuhiko Kinosita
- Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan.
| |
Collapse
|
14
|
Liu S, Chistol G, Bustamante C. Mechanical operation and intersubunit coordination of ring-shaped molecular motors: insights from single-molecule studies. Biophys J 2014; 106:1844-58. [PMID: 24806916 DOI: 10.1016/j.bpj.2014.03.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/19/2014] [Indexed: 01/27/2023] Open
Abstract
Ring NTPases represent a large and diverse group of proteins that couple their nucleotide hydrolysis activity to a mechanical task involving force generation and some type of transport process in the cell. Because of their shape, these enzymes often operate as gates that separate distinct cellular compartments to control and regulate the passage of chemical species across them. In this manner, ions and small molecules are moved across membranes, biopolymer substrates are segregated between cells or moved into confined spaces, double-stranded nucleic acids are separated into single strands to provide access to the genetic information, and polypeptides are unfolded and processed for recycling. Here we review the recent advances in the characterization of these motors using single-molecule manipulation and detection approaches. We describe the various mechanisms by which ring motors convert chemical energy to mechanical force or torque and coordinate the activities of individual subunits that constitute the ring. We also examine how single-molecule studies have contributed to a better understanding of the structural elements involved in motor-substrate interaction, mechanochemical coupling, and intersubunit coordination. Finally, we discuss how these molecular motors tailor their operation-often through regulation by other cofactors-to suit their unique biological functions.
Collapse
Affiliation(s)
- Shixin Liu
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California; California Institute for Quantitative Biosciences, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California
| | - Gheorghe Chistol
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California; Department of Physics, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California
| | - Carlos Bustamante
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California; California Institute for Quantitative Biosciences, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California; Department of Physics, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California; Department of Molecular and Cell Biology, Department of Chemistry, Howard Hughes Medical Institute, and Kavli Energy NanoSciences Institute, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California.
| |
Collapse
|
15
|
Ando T, Uchihashi T, Scheuring S. Filming biomolecular processes by high-speed atomic force microscopy. Chem Rev 2014; 114:3120-88. [PMID: 24476364 PMCID: PMC4076042 DOI: 10.1021/cr4003837] [Citation(s) in RCA: 234] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Toshio Ando
- Department of Physics, and Bio-AFM Frontier
Research Center, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- CREST,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi 332-0012, Japan
| | - Takayuki Uchihashi
- Department of Physics, and Bio-AFM Frontier
Research Center, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- CREST,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi 332-0012, Japan
| | - Simon Scheuring
- U1006
INSERM/Aix-Marseille Université, Parc Scientifique et Technologique
de Luminy Bâtiment Inserm TPR2 bloc 5, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
| |
Collapse
|
16
|
Ito Y, Yoshidome T, Matubayasi N, Kinoshita M, Ikeguchi M. Molecular dynamics simulations of yeast F1-ATPase before and after 16° rotation of the γ subunit. J Phys Chem B 2013; 117:3298-307. [PMID: 23452086 DOI: 10.1021/jp312499u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have recently proposed the "packing exchange mechanism" for F1-ATPase, wherein the perturbation by a substrate binding/release or an ATP hydrolysis is followed by the reorganization of the asymmetric packing structure of the α3β3 complex, accompanying the γ subunit rotation. As part of a further investigation of this rotational mechanism, we performed all-atom molecular dynamics simulations for yeast F1-ATPase both before and after a 16° rotation of the γ subunit triggered by a Pi release. We analyzed the structural fluctuations, the subunit interface interactions, and the dynamics of the relative subunit arrangements before and after the rotation. We found that with the Pi release the αEβE subunit interface becomes looser, which also allosterically makes the αDPβDP subunit interface looser. This structural communication between these interfaces takes place through a tightening of the αTPβTP subunit interface. The γ subunit interacts less strongly with αDP and βDP and more strongly with αTP and βTP. After the Pi release, the tightly packed interfaces are reorganized from the interfaces around βDP to those around βTP, inducing the 16° rotation. These results, which are consistent with the packing exchange mechanism, allow us to deduce a view of the structural change during the 40° rotation.
Collapse
Affiliation(s)
- Yuko Ito
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29, Yokohama, 230-0045 Japan
| | | | | | | | | |
Collapse
|
17
|
Tanigawara M, Tabata KV, Ito Y, Ito J, Watanabe R, Ueno H, Ikeguchi M, Noji H. Role of the DELSEED loop in torque transmission of F1-ATPase. Biophys J 2013; 103:970-8. [PMID: 23009846 DOI: 10.1016/j.bpj.2012.06.054] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 05/23/2012] [Accepted: 06/25/2012] [Indexed: 11/18/2022] Open
Abstract
F(1)-ATPase is an ATP-driven rotary motor that generates torque at the interface between the catalytic β-subunits and the rotor γ-subunit. The β-subunit inwardly rotates the C-terminal domain upon nucleotide binding/dissociation; hence, the region of the C-terminal domain that is in direct contact with γ-termed the DELSEED loop-is thought to play a critical role in torque transmission. We substituted all the DELSEED loop residues with alanine to diminish specific DELSEED loop-γ interactions and with glycine to disrupt the loop structure. All the mutants rotated unidirectionally with kinetic parameters comparable to those of the wild-type F(1), suggesting that the specific interactions between DELSEED loop and γ is not involved in cooperative interplays between the catalytic β-subunits. Glycine substitution mutants generated half the torque of the wild-type F(1), whereas the alanine mutant generated comparable torque. Fluctuation analyses of the glycine/alanine mutants revealed that the γ-subunit was less tightly held in the α(3)β(3)-stator ring of the glycine mutant than in the wild-type F(1) and the alanine mutant. Molecular dynamics simulation showed that the DELSEED loop was disordered by the glycine substitution, whereas it formed an α-helix in the alanine mutant. Our results emphasize the importance of loop rigidity for efficient torque transmissions.
Collapse
Affiliation(s)
- Mizue Tanigawara
- Graduate School of Frontier Bioscience, Osaka University, Osaka, Japan
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Iino R, Noji H. Intersubunit coordination and cooperativity in ring-shaped NTPases. Curr Opin Struct Biol 2013; 23:229-34. [PMID: 23395511 DOI: 10.1016/j.sbi.2013.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 12/27/2012] [Accepted: 01/17/2013] [Indexed: 01/28/2023]
Abstract
Ring-shaped nucleoside triphosphatases (ring NTPases) are biological molecular machines powered by energy from NTP hydrolysis and are responsible for various cellular activities. These ring NTPases translocate their substrates or rotate their own subunits to/in the hole of the ring. Coordination and cooperativity among subunits in the oligomer ring is a topic of debate focused on understanding the operation mechanism of these protein machines. With the help of X-ray crystallographic structural analysis and optical microscopic single-molecules studies, distinct models, including stochastic, concerted, and rotary catalysis have been proposed. Here, we discuss these models and introduce high-speed atomic force microscopy as a new potent tool for verification of the model, with our recent example of the rotary catalysis of the stator ring of F1-adenosine triphosphatase.
Collapse
Affiliation(s)
- Ryota Iino
- Department of Applied Chemistry, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | | |
Collapse
|
19
|
Hilbers F, Junge W, Sielaff H. The torque of rotary F-ATPase can unfold subunit gamma if rotor and stator are cross-linked. PLoS One 2013; 8:e53754. [PMID: 23301103 PMCID: PMC3536650 DOI: 10.1371/journal.pone.0053754] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 12/04/2012] [Indexed: 12/02/2022] Open
Abstract
During ATP hydrolysis by F1-ATPase subunit γ rotates in a hydrophobic bearing, formed by the N-terminal ends of the stator subunits (αβ)3. If the penultimate residue at the α-helical C-terminal end of subunit γ is artificially cross-linked (via an engineered disulfide bridge) with the bearing, the rotary function of F1 persists. This observation has been tentatively interpreted by the unfolding of the α-helix and swiveling rotation in some dihedral angles between lower residues. Here, we screened the domain between rotor and bearing where an artificial disulfide bridge did not impair the rotary ATPase activity. We newly engineered three mutants with double cysteines farther away from the C-terminus of subunit γ, while the results of three further mutants were published before. We found ATPase and rotary activity for mutants with cross-links in the single α-helical, C-terminal portion of subunit γ (from γ285 to γ276 in E. coli), and virtually no activity when the cross-link was placed farther down, where the C-terminal α-helix meets its N-terminal counterpart to form a supposedly stable coiled coil. In conclusion, only the C-terminal singular α-helix is prone to unwinding and can form a swivel joint, whereas the coiled coil portion seems to resist the enzyme's torque.
Collapse
Affiliation(s)
- Florian Hilbers
- Department of Molecular Membrane Biology, MPI of Biophysics, Frankfurt, Germany
| | - Wolfgang Junge
- Division of Biophysics, University of Osnabrück, Osnabrück, Germany
| | - Hendrik Sielaff
- Single-Molecule Microscopy Group, Jena University Hospital, Jena, Germany
- * E-mail:
| |
Collapse
|
20
|
Iino R, Noji H. Rotary catalysis of the stator ring of F(1)-ATPase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1732-9. [PMID: 22465022 DOI: 10.1016/j.bbabio.2012.03.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 03/06/2012] [Accepted: 03/08/2012] [Indexed: 11/28/2022]
Abstract
F(1)-ATPase is a rotary motor protein in which 3 catalytic β-subunits in a stator α(3)β(3) ring undergo unidirectional and cooperative conformational changes to rotate the rotor γ-subunit upon adenosine triphosphate hydrolysis. The prevailing view of the mechanism behind this rotary catalysis elevated the γ-subunit as a "dictator" completely controlling the chemical and conformational states of the 3 catalytic β-subunits. However, our recent observations using high-speed atomic force microscopy clearly revealed that the 3 β-subunits undergo cyclic conformational changes even in the absence of the rotor γ-subunit, thus dethroning it from its dictatorial position. Here, we introduce our results in detail and discuss the possible operating principle behind the F(1)-ATPase, along with structurally related hexameric ATPases, also mentioning the possibility of generating hybrid nanomotors. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
Collapse
Affiliation(s)
- Ryota Iino
- Department of Applied Chemistry, the University of Tokyo, Tokyo, Japan.
| | | |
Collapse
|
21
|
Usukura E, Suzuki T, Furuike S, Soga N, Saita EI, Hisabori T, Kinosita K, Yoshida M. Torque generation and utilization in motor enzyme F0F1-ATP synthase: half-torque F1 with short-sized pushrod helix and reduced ATP Synthesis by half-torque F0F1. J Biol Chem 2011; 287:1884-91. [PMID: 22128167 DOI: 10.1074/jbc.m111.305938] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ATP synthase (F(0)F(1)) is made of two motors, a proton-driven motor (F(0)) and an ATP-driven motor (F(1)), connected by a common rotary shaft, and catalyzes proton flow-driven ATP synthesis and ATP-driven proton pumping. In F(1), the central γ subunit rotates inside the α(3)β(3) ring. Here we report structural features of F(1) responsible for torque generation and the catalytic ability of the low-torque F(0)F(1). (i) Deletion of one or two turns in the α-helix in the C-terminal domain of catalytic β subunit at the rotor/stator contact region generates mutant F(1)s, termed F(1)(1/2)s, that rotate with about half of the normal torque. This helix would support the helix-loop-helix structure acting as a solid "pushrod" to push the rotor γ subunit, but the short helix in F(1)(1/2)s would fail to accomplish this task. (ii) Three different half-torque F(0)F(1)(1/2)s were purified and reconstituted into proteoliposomes. They carry out ATP-driven proton pumping and build up the same small transmembrane ΔpH, indicating that the final ΔpH is directly related to the amount of torque. (iii) The half-torque F(0)F(1)(1/2)s can catalyze ATP synthesis, although slowly. The rate of synthesis varies widely among the three F(0)F(1)(1/2)s, which suggests that the rate reflects subtle conformational variations of individual mutants.
Collapse
Affiliation(s)
- Eiji Usukura
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226-8503
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Kohori A, Chiwata R, Hossain MD, Furuike S, Shiroguchi K, Adachi K, Yoshida M, Kinosita K. Torque generation in F1-ATPase devoid of the entire amino-terminal helix of the rotor that fills half of the stator orifice. Biophys J 2011; 101:188-95. [PMID: 21723829 DOI: 10.1016/j.bpj.2011.05.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 04/28/2011] [Accepted: 05/03/2011] [Indexed: 11/28/2022] Open
Abstract
F(1)-ATPase is an ATP-driven rotary molecular motor in which the central γ-subunit rotates inside a cylinder made of α(3)β(3) subunits. The amino and carboxyl termini of the γ rotor form a coiled coil of α-helices that penetrates the stator cylinder to serve as an axle. Crystal structures indicate that the axle is supported by the stator at two positions, at the orifice and by the hydrophobic sleeve surrounding the axle tip. The sleeve contacts are almost exclusively to the longer carboxyl-terminal helix, whereas nearly half the orifice contacts are to the amino-terminal helix. Here, we truncated the amino-terminal helix stepwise up to 50 residues, removing one half of the axle all the way up and far beyond the orifice. The half-sliced axle still rotated with an unloaded speed a quarter of the wild-type speed, with torque nearly half the wild-type torque. The truncations were made in a construct where the rotor tip was connected to a β-subunit via a short peptide linker. Linking alone did not change the rotational characteristics significantly. These and previous results show that nearly half the normal torque is generated if rotor-stator interactions either at the orifice or at the sleeve are preserved, suggesting that the make of the motor is quite robust.
Collapse
Affiliation(s)
- Ayako Kohori
- Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku,Tokyo, Japan
| | | | | | | | | | | | | | | |
Collapse
|
23
|
Abstract
F(1)-ATPase is a nanosized biological energy transducer working as part of F(o)F(1)-ATP synthase. Its rotary machinery transduces energy between chemical free energy and mechanical work and plays a central role in the cellular energy transduction by synthesizing most ATP in virtually all organisms. However, information about its energetics is limited compared to that of the reaction scheme. Actually, fundamental questions such as how efficiently F(1)-ATPase transduces free energy remain unanswered. Here, we demonstrated reversible rotations of isolated F(1)-ATPase in discrete 120° steps by precisely controlling both the external torque and the chemical potential of ATP hydrolysis as a model system of F(o)F(1)-ATP synthase. We found that the maximum work performed by F(1)-ATPase per 120° step is nearly equal to the thermodynamical maximum work that can be extracted from a single ATP hydrolysis under a broad range of conditions. Our results suggested a 100% free-energy transduction efficiency and a tight mechanochemical coupling of F(1)-ATPase.
Collapse
|
24
|
Torres-Bacete J, Sinha PK, Matsuno-Yagi A, Yagi T. Structural contribution of C-terminal segments of NuoL (ND5) and NuoM (ND4) subunits of complex I from Escherichia coli. J Biol Chem 2011; 286:34007-14. [PMID: 21835926 DOI: 10.1074/jbc.m111.260968] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The proton-translocating NADH-quinone oxidoreductase (complex I/NDH-1) is a multisubunit enzymatic complex. It has a characteristic L-shaped form with two domains, a hydrophilic peripheral domain and a hydrophobic membrane domain. The membrane domain contains three antiporter-like subunits (NuoL, NuoM, and NuoN, Escherichia coli naming) that are considered to be involved in the proton translocation. Deletion of either NuoL or NuoM resulted in an incomplete assembly of NDH-1 and a total loss of the NADH-quinone oxidoreductase activity. We have truncated the C terminus segments of NuoM and NuoL by introducing STOP codons at different locations using site-directed mutagenesis of chromosomal DNA. Our results suggest an important structural role for the C-terminal segments of both subunits. The data further advocate that the elimination of the last transmembrane helix (TM14) of NuoM and the TM16 (at least C-terminal seven residues) or together with the HL helix and the TM15 of the NuoL subunit lead to reduced stability of the membrane arm and therefore of the whole NDH-1 complex. A region of NuoL critical for stability of NDH-1 architecture has been discussed.
Collapse
Affiliation(s)
- Jesus Torres-Bacete
- Department of Molecular and Experimental Medicine, MEM-256, The Scripps Research Institute, La Jolla, California 92037, USA
| | | | | | | |
Collapse
|
25
|
Ito Y, Oroguchi T, Ikeguchi M. Mechanism of the conformational change of the F1-ATPase β subunit revealed by free energy simulations. J Am Chem Soc 2011; 133:3372-80. [PMID: 21341660 DOI: 10.1021/ja1070152] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
F(1)-ATPase is an ATP-driven rotary motor enzyme. The β subunit changes its conformation from an open to a closed form upon ATP binding. The motion in the β subunit is regarded as a major driving force for rotation of the central stalk. In this Article, we explore the conformational change of the β subunit using all-atom free energy simulations with explicit solvent and propose a detailed mechanism for the conformational change. The β subunit conformational change is accomplished roughly in two characteristic steps: changing of the hydrogen-bond network around ATP and the dynamic movement of the C-terminal domain via sliding of the B-helix. The details of the former step agree well with experimental data. In the latter step, sliding of the B-helix enhances the hydrophobic stabilization due to the exclusion of water molecules from the interface and improved packing in the hydrophobic core. This step contributes to a decrease in free energy, leading to the generation of torque in the F(1)-ATPase upon ATP binding.
Collapse
Affiliation(s)
- Yuko Ito
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | | | | |
Collapse
|
26
|
Ito Y, Ikeguchi M. Structural fluctuation and concerted motions in F(1)-ATPase: A molecular dynamics study. J Comput Chem 2010; 31:2175-85. [PMID: 20336770 DOI: 10.1002/jcc.21508] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
F(1)-ATPase is an adenosine tri-phosphate (ATP)-driven rotary motor enzyme. We investigated the structural fluctuations and concerted motions of subunits in F(1)-ATPase using molecular dynamics (MD) simulations. An MD simulation for the alpha(3)beta(3)gamma complex was carried out for 30 ns. Although large fluctuations of the N-terminal domain observed in simulations of the isolated beta(E) subunit were suppressed in the complex simulation, the magnitude of fluctuations in the C-terminal domain was clearly different among the three beta subunits (beta(E), beta(TP), and beta(DP)). Despite fairly similar conformations of the beta(TP) and beta(DP) subunits, the beta(DP) subunit exhibits smaller fluctuations in the C-terminal domain than the beta(TP) subunit due to their dissimilar interface configurations. Compared with the beta(TP) subunit, the beta(DP) subunit stably interacts with both the adjacent alpha(DP) and alpha(E) subunits. This sandwiched configuration in the beta(DP) subunit leads to strongly correlated motions between the beta(DP) and adjacent alpha subunits. The beta(DP) subunit exhibits an extensive network of highly correlated motions with bound ATP and the gamma subunit, as well as with the adjacent alpha subunits, suggesting that the structural changes occurring in the catalytically active beta(DP) subunit can effectively induce movements of the gamma subunit.
Collapse
Affiliation(s)
- Yuko Ito
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | | |
Collapse
|
27
|
Adachi K, Furuike S, Hossain MD, Itoh H, Kinosita K, Onoue Y, Shimo-Kon R. Chemo-Mechanical Coupling in the Rotary Molecular Motor F1-ATPase. SINGLE MOLECULE SPECTROSCOPY IN CHEMISTRY, PHYSICS AND BIOLOGY 2010. [DOI: 10.1007/978-3-642-02597-6_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
28
|
Romanovsky Y, Tikhonov AN. Molecular energy transducers of the living cell. Proton ATP synthase: a rotating molecular motor. ACTA ACUST UNITED AC 2010. [DOI: 10.3367/ufnr.0180.201009b.0931] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
|
29
|
|
30
|
Mnatsakanyan N, Hook JA, Quisenberry L, Weber J. ATP synthase with its gamma subunit reduced to the N-terminal helix can still catalyze ATP synthesis. J Biol Chem 2009; 284:26519-25. [PMID: 19636076 DOI: 10.1074/jbc.m109.030528] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ATP synthase uses a unique rotary mechanism to couple ATP synthesis and hydrolysis to transmembrane proton translocation. As part of the synthesis mechanism, the torque of the rotor has to be converted into conformational rearrangements of the catalytic binding sites on the stator to allow synthesis and release of ATP. The gamma subunit of the rotor, which plays a central role in the energy conversion, consists of two long helices inside the central cavity of the stator cylinder plus a globular portion outside the cylinder. Here, we show that the N-terminal helix alone is able to fulfill the function of full-length gamma in ATP synthesis as long as it connects to the rest of the rotor. This connection can occur via the epsilon subunit. No direct contact between gamma and the c ring seems to be required. In addition, the results indicate that the epsilon subunit of the rotor exists in two different conformations during ATP synthesis and ATP hydrolysis.
Collapse
Affiliation(s)
- Nelli Mnatsakanyan
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
| | | | | | | |
Collapse
|