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Kasumov EA, Kasumov RE, Kasumova IV. A mechano-chemiosmotic model for the coupling of electron and proton transfer to ATP synthesis in energy-transforming membranes: a personal perspective. PHOTOSYNTHESIS RESEARCH 2015; 123:1-22. [PMID: 25266924 PMCID: PMC4272416 DOI: 10.1007/s11120-014-0043-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 09/18/2014] [Indexed: 05/03/2023]
Abstract
ATP is synthesized using ATP synthase by utilizing energy either from the oxidation of organic compounds, or from light, via redox reactions (oxidative- or photo phosphorylation), in energy-transforming membranes of mitochondria, chloroplasts, and bacteria. ATP synthase undergoes several changes during its functioning. The generally accepted model for ATP synthesis is the well-known rotatory model (see e.g., Junge et al., Nature 459:364-370, 2009; Junge and Müller, Science 333:704-705, 2011). Here, we present an alternative modified model for the coupling of electron and proton transfer to ATP synthesis, which was initially developed by Albert Lester Lehninger (1917-1986). Details of the molecular mechanism of ATP synthesis are described here that involves cyclic low-amplitude shrinkage and swelling of mitochondria. A comparison of the well-known current model and the mechano-chemiosmotic model is also presented. Based on structural, and other data, we suggest that ATP synthase is a Ca(2+)/H(+)-K(+) Cl(-)-pump-pore-enzyme complex, in which γ-subunit rotates 360° in steps of 30°, and 90° due to the binding of phosphate ions to positively charged amino acid residues in the N-terminal γ-subunit, while in the electric field. The coiled coil b 2-subunits are suggested to act as ropes that are shortened by binding of phosphate ions to positively charged lysines or arginines; this process is suggested to pull the α 3 β 3-hexamer to the membrane during the energization process. ATP is then synthesized during the reverse rotation of the γ-subunit by destabilizing the phosphated N-terminal γ-subunit and b 2-subunits under the influence of Ca(2+) ions, which are pumped over from storage-intermembrane space into the matrix, during swelling of intermembrane space. In the process of ATP synthesis, energy is first, predominantly, used in the delivery of phosphate ions and protons to the α 3 β 3-hexamer against the energy barrier with the help of C-terminal alpha-helix of γ-subunit that acts as a lift; then, in the formation of phosphoryl group; and lastly, in the release of ATP molecules from the active center of the enzyme and the loading of ADP. We are aware that our model is not an accepted model for ATP synthesis, but it is presented here for further examination and test.
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Affiliation(s)
- Eldar A Kasumov
- Research and Production Centre «KORVET», Moscow Region, Domodedovo, Russia,
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2
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Bagkos G, Koufopoulos K, Piperi C. A new model for mitochondrial membrane potential production and storage. Med Hypotheses 2014; 83:175-81. [PMID: 24907229 DOI: 10.1016/j.mehy.2014.05.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 05/10/2014] [Indexed: 02/05/2023]
Abstract
Mitochondrial membrane potential (MMP) is the most reliable indicator of mitochondrial function. The MMP value range of -136 to -140mV has been considered optimal for maximum ATP production for all living organisms. Even small changes from the above range result in a large fall in ATP production and a large increase in ROS production. The resulting bioenergetic deregulation is considered as the causative agent for numerous major human diseases. Normalization of MMP value improves mitochondrial function and gives excellent therapeutic results. In order for a systematic effective treatment of these diseases to be developed, a detailed knowledge of the mechanism of MMP production is absolutely necessary. However, despite the long-standing research efforts, a concrete mechanism for MMP production has not been found yet. The present paper proposes a novel mechanism of MMP production based on new considerations underlying the function of the two basic players of MMP production, the electron transport chain (ETC) and the F1F0 ATP synthase. Under normal conditions, MMP is almost exclusively produced by the electron flow through ETC complexes I-IV, creating a direct electric current that stops in subunit II of complex IV and gradually charges MMP. However, upon ETC dysfunction F1F0 ATP synthase reverses its action and starts to hydrolyze ATP. ATP hydrolysis further produces electric energy which is transferred, in the form of a direct electric current, from F1 to F0 where is used to charge MMP. This new model is expected to redirect current experimental research on mitochondrial bioenergetics and indicate new therapeutic schemes for mitochondrial disorders.
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Affiliation(s)
- Georgios Bagkos
- Department of Biological Chemistry, University of Athens Medical School, Athens, Greece
| | - Kostas Koufopoulos
- Department of Biological Chemistry, University of Athens Medical School, Athens, Greece
| | - Christina Piperi
- Department of Biological Chemistry, University of Athens Medical School, Athens, Greece.
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3
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Affiliation(s)
- Ross E. Dalbey
- The Ohio State University, Department of Chemistry, Columbus, Ohio 43210;
| | - Peng Wang
- The Ohio State University, Department of Chemistry, Columbus, Ohio 43210;
| | - Andreas Kuhn
- Institute of Microbiology and Molecular Biology, University of Hohenheim, 70599 Stuttgart, Germany;
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4
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Sengupta D, Rampioni A, Marrink SJ. Simulations of thec-subunit of ATP-synthase reveal helix rearrangements. Mol Membr Biol 2009; 26:422-34. [DOI: 10.3109/09687680903321073] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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5
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Muhlia-Almazan A, Martinez-Cruz O, Navarrete del Toro MDLA, Garcia-Carreño F, Arreola R, Sotelo-Mundo R, Yepiz-Plascencia G. Nuclear and mitochondrial subunits from the white shrimp Litopenaeus vannamei F(0)F(1) ATP-synthase complex: cDNA sequence, molecular modeling, and mRNA quantification of atp9 and atp6. J Bioenerg Biomembr 2008; 40:359-69. [PMID: 18770013 DOI: 10.1007/s10863-008-9162-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Accepted: 05/16/2008] [Indexed: 01/29/2023]
Abstract
We studied for the first time the ATP-synthase complex from shrimp as a model to understand the basis of crustacean bioenergetics since they are exposed to endogenous processes as molting that demand high amount of energy. We analyzed the cDNA sequence of two subunits of the Fo sector from mitochondrial ATP-synthase in the white shrimp Litopenaeus vannamei. The nucleus encoded atp9 subunit presents a 773 bp sequence, containing a signal peptide sequence only observed in crustaceans, and the mitochondrial encoded atp6 subunit presents a sequence of 675 bp, and exhibits high identity with homologous sequences from invertebrate species. ATP9 and ATP6 protein structural models interaction suggest specific functional characteristics from both proteins in the mitochondrial enzyme. Differences in the steady-state mRNA levels of atp9 and atp6 from five different tissues correlate with tissue function. Moreover, significant changes in the mRNA levels of both subunits at different molt stages were detected. We discussed some insights about the enzyme structure and the regulation mechanisms from both ATP-synthase subunits related to the energy requirements of shrimp.
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Affiliation(s)
- Adriana Muhlia-Almazan
- Molecular Biology Lab, Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C., Sonora, Mexico.
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6
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Aksimentiev A, Balabin IA, Fillingame RH, Schulten K. Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase. Biophys J 2004; 86:1332-44. [PMID: 14990464 PMCID: PMC1303972 DOI: 10.1016/s0006-3495(04)74205-8] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
F(1)F(o)-ATP synthase is a ubiquitous membrane protein complex that efficiently converts a cell's transmembrane proton gradient into chemical energy stored as ATP. The protein is made of two molecular motors, F(o) and F(1), which are coupled by a central stalk. The membrane unit, F(o), converts the transmembrane electrochemical potential into mechanical rotation of a rotor in F(o) and the physically connected central stalk. Based on available data of individual components, we have built an all-atom model of F(o) and investigated through molecular dynamics simulations and mathematical modeling the mechanism of torque generation in F(o). The mechanism that emerged generates the torque at the interface of the a- and c-subunits of F(o) through side groups aSer-206, aArg-210, and aAsn-214 of the a-subunit and side groups cAsp-61 of the c-subunits. The mechanism couples protonation/deprotonation of two cAsp-61 side groups, juxtaposed to the a-subunit at any moment in time, to rotations of individual c-subunit helices as well as rotation of the entire c-subunit. The aArg-210 side group orients the cAsp-61 side groups and, thereby, establishes proton transfer via aSer-206 and aAsn-214 to proton half-channels, while preventing direct proton transfer between the half-channels. A mathematical model proves the feasibility of torque generation by the stated mechanism against loads typical during ATP synthesis; the essential model characteristics, e.g., helix and subunit rotation and associated friction constants, have been tested and furnished by steered molecular dynamics simulations.
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Affiliation(s)
- Aleksij Aksimentiev
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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7
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Abstract
Three protein motors have been unambiguously identified as rotary engines: the bacterial flagellar motor and the two motors that constitute ATP synthase (F(0)F(1) ATPase). Of these, the bacterial flagellar motor and F(0) motors derive their energy from a transmembrane ion-motive force, whereas the F(1) motor is driven by ATP hydrolysis. Here, we review the current understanding of how these protein motors convert their energy supply into a rotary torque.
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Affiliation(s)
- George Oster
- Depts Molecular and Cellular Biology and ESPM, College of Natural Resources, University of California, Berkeley, CA 94720, USA.
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8
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Abstract
The role of subunit a in proton translocation by the Escherichia coli F(1)F(o) ATP synthase is poorly understood. In the membrane-bound F(o) sector of the enzyme, H(+) binding and release occurs at Asp(61) in the middle of the second transmembrane helix (TMH) of subunit c. Protons are thought to reach Asp(61) via an aqueous access pathway formed at least in part by one or more of the five TMHs of subunit a. In this report, we have substituted Cys into a 19-residue span of the fourth TMH of subunit a and used chemical modification to obtain information about the aqueous accessibility of residues along this helix. Residues 206, 210, and 214 are N-ethylmaleimide-accessible from the cytoplasmic side of the membrane and may lie on the H(+) transport route. Residues 215 and 218 on TMH4, as well as residue 245 on TMH5, are Ag(+)-accessible but N-ethylmaleimide-inaccessible and may form part of an aqueous pocket extending from Asp(61) of subunit c to the periplasmic surface.
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Affiliation(s)
- Christine M Angevine
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison, Wisconsin 53706, USA
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9
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Fillingame RH, Dmitriev OY. Structural model of the transmembrane Fo rotary sector of H+-transporting ATP synthase derived by solution NMR and intersubunit cross-linking in situ. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1565:232-45. [PMID: 12409198 DOI: 10.1016/s0005-2736(02)00572-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
H(+)-transporting, F(1)F(o)-type ATP synthases utilize a transmembrane H(+) potential to drive ATP formation by a rotary catalytic mechanism. ATP is formed in alternating beta subunits of the extramembranous F(1) sector of the enzyme, synthesis being driven by rotation of the gamma subunit in the center of the F(1) molecule between the alternating catalytic sites. The H(+) electrochemical potential is thought to drive gamma subunit rotation by first coupling H(+) transport to rotation of an oligomeric rotor of c subunits within the transmembrane F(o) sector. The gamma subunit is forced to turn with the c-oligomeric rotor due to connections between subunit c and the gamma and epsilon subunits of F(1). In this essay we will review recent studies on the Escherichia coli F(o) sector. The monomeric structure of subunit c, determined by NMR, shows that subunit c folds in a helical hairpin with the proton carrying Asp(61) centered in the second transmembrane helix (TMH). A model for the structural organization of the c(10) oligomer in F(o) was deduced from extensive cross-linking studies and by molecular modeling. The model indicates that the H(+)-carrying carboxyl of subunit c is occluded between neighboring subunits of the c(10) oligomer and that two c subunits pack in a "front-to-back" manner to form the H(+) (cation) binding site. In order for protons to gain access to Asp(61) during the protonation/deprotonation cycle, we propose that the outer, Asp(61)-bearing TMH-2s of the c-ring and TMHs from subunits composing the inlet and outlet channels must turn relative to each other, and that the swiveling motion associated with Asp(61) protonation/deprotonation drives the rotation of the c-ring. The NMR structures of wild-type subunit c differs according to the protonation state of Asp(61). The idea that the conformational state of subunit c changes during the catalytic cycle is supported by the cross-linking evidence in situ, and two recent NMR structures of functional mutant proteins in which critical residues have been switched between TMH-1 and TMH-2. The structural information is considered in the context of the possible mechanism of rotary movement of the c(10) oligomer during coupled synthesis of ATP.
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Affiliation(s)
- Robert H Fillingame
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, 1300 University Avenue, Madison, WI 53706-1532, USA.
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10
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Dmitriev OY, Abildgaard F, Markley JL, Fillingame RH. Structure of Ala24/Asp61 --> Asp24/Asn61 substituted subunit c of Escherichia coli ATP synthase: implications for the mechanism of proton transport and rotary movement in the F0 complex. Biochemistry 2002; 41:5537-47. [PMID: 11969414 DOI: 10.1021/bi012198l] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structure of the A24D/D61N substituted subunit c of Escherichia coli ATP synthase, in which the essential carboxylate has been switched from residue 61 of the second transmembrane helix (TMH) to residue 24 of the first TMH, has been determined by heteronuclear multidimensional NMR in a monophasic chloroform/methanol/water (4:4:1) solvent mixture. As in the case of the wild-type protein, A24D/D61N substituted subunit c forms a hairpin of two extended alpha-helices (residues 5-39 and 46-78), with residues 40-45 forming a connecting loop at the center of the protein. The structure was determined at pH 5, where Asp24 is fully protonated. The relative orientation of the two extended helices in the A24D/D61N structure is different from that in the protonated form of the wild-type protein, also determined at pH 5. The C-terminal helix is rotated by 150 degrees relative to the wild-type structure, and the N-terminal helix is rotated such that the essential Asp24 carboxyl group packs on the same side of the molecule as Asp61 in the wild-type protein. The changes in helix-helix orientation lead to a structure that is quite similar to that of the deprotonated form of wild-type subunit c, determined at pH 8. When a decameric ring of c subunits was modeled from the new structure, the Asp24 carboxyl group was found to pack in a cavity at the interface between two subunits that is similar to the cavity in which Asp61 of the wild-type protein is predicted to pack. The interacting faces of the packed subunits in this model are also similar to those in the wild-type model. The results provide further evidence that subunit c is likely to fold in at least two conformational states differing most notably in the orientation of the C-terminal helix. Based upon the structure, a mechanistic model is discussed that indicates how the wild-type and A24D/D61N subunits could utilize similar helical movements during H(+) transport-coupled rotation of the decameric c ring.
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Affiliation(s)
- Oleg Y Dmitriev
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison, Wisconsin 53706, USA
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11
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Abstract
The F(1)F(0)-type ATP synthase is a key enzyme in cellular energy interconversion. During ATP synthesis, this large protein complex uses a proton gradient and the associated membrane potential to synthesize ATP. It can also reverse and hydrolyze ATP to generate a proton gradient. The structure of this enzyme in different functional forms is now being rapidly elucidated. The emerging consensus is that the enzyme is constructed as two rotary motors, one in the F(1) part that links catalytic site events with movements of an internal rotor, and the other in the F(0) part, linking proton translocation to movements of this F(0) rotor. Although both motors can work separately, they must be connected together to interconvert energy. Evidence for the function of the rotary motor, from structural, genetic and biophysical studies, is reviewed here, and some uncertainties and remaining mysteries of the enzyme mechanism are also discussed.
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Affiliation(s)
- Roderick A Capaldi
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403-1229, USA.
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Valiyaveetil F, Hermolin J, Fillingame RH. pH dependent inactivation of solubilized F1F0 ATP synthase by dicyclohexylcarbodiimide: pK(a) of detergent unmasked aspartyl-61 in Escherichia coli subunit c. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1553:296-301. [PMID: 11997138 DOI: 10.1016/s0005-2728(01)00251-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The pH dependence of the reaction of dicyclohexylcarbodiimide with the essential aspartyl-61 residue in subunit c of Escherichia coli ATP synthase was compared in membranes and in a detergent dispersed preparation of the enzyme. The rate of reaction was estimated by measuring the inactivation of ATPase activity. The reaction with the detergent dispersed form of the enzyme proved to be pH sensitive with the essential aspartyl group titrating with a pK(a)=8. However, when measured with E. coli membranes, the reaction proved to be pH insensitive. The results suggest that the reacting aspartyl-61 residues are shielded from the bulk aqueous solvent when in the membrane, but then become aqueous-accessible following detergent solubilization.
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Affiliation(s)
- Francis Valiyaveetil
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, 1300 University Avenue, Madison, WI 53706, USA
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Jiang W, Hermolin J, Fillingame RH. The preferred stoichiometry of c subunits in the rotary motor sector of Escherichia coli ATP synthase is 10. Proc Natl Acad Sci U S A 2001; 98:4966-71. [PMID: 11320246 PMCID: PMC33147 DOI: 10.1073/pnas.081424898] [Citation(s) in RCA: 213] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The stoichiometry of c subunits in the H(+)-transporting F(o) rotary motor of ATP synthase is uncertain, the most recent suggestions varying from 10 to 14. The stoichiometry will determine the number of H(+) transported per ATP synthesized and will directly relate to the P/O ratio of oxidative phosphorylation. The experiments described here show that the number of c subunits in functional complexes of F(o)F(1) ATP synthase from Escherichia coli can be manipulated, but that the preferred number is 10. Mixtures of genetically fused cysteine-substituted trimers (c(3)) and tetramers (c(4)) of subunit c were coexpressed and the c subunits crosslinked in the plasma membrane. Prominent products corresponding to oligomers of c(7) and c(10) were observed in the membrane and purified F(o)F(1) complex, indicating that the c(10) oligomer formed naturally. Oligomers larger than c(10) were also observed in the membrane fraction of cells expressing c(3) or c(4) individually, or in cells coexpressing c(3) and c(4) together, but these larger oligomers did not copurify with the functional F(o)F(1) complex and were concluded to be aberrant products of assembly in the membrane.
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Affiliation(s)
- W Jiang
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, 1300 University Avenue, Madison, WI 53706, USA
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