Kinetic modelling of the proton translocating CF<sub>0</sub>CF<sub>1</sub>‐ATP synthase from spinach

Pänke, Oliver; Rumberg, B.

doi:10.1016/0014-5793(96)00246-3

Cited by 35 publications

(36 citation statements)

References 21 publications

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“…Increased friction then is a likely explanation. Under these conditions product dissociation would not be rate-limiting (41,42) but perhaps the nucleotide binding affinity change brought about by extensive conformational changes (4). Without a crystal structure of the truncated enzyme this remains speculation, though.…”

Section: Table I Growth Doubling Times Yields Atpase Activities Amentioning

confidence: 99%

F1-ATPase, the C-terminal End of Subunit γ Is Not Required for ATP Hydrolysis-driven Rotation

Müller

Pänke

Junge

et al. 2002

Journal of Biological Chemistry

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ATP hydrolysis by the isolated F 1 -ATPase drives the rotation of the central shaft, subunit ␥, which is located within a hexagon formed by subunits (␣␤) 3 . The C-terminal end of ␥ forms an ␣-helix which properly fits into the "hydrophobic bearing" provided by loops of subunits ␣ and ␤. This "bearing" is expected to be essential for the rotary function. We checked the importance of this contact region by successive C-terminal deletions of 3, 6, 9, 12, 15, and 18 amino acid residues (Escherichia coli F 1 -ATPase). The ATP hydrolysis activity of a loadfree ensemble of F 1 with 12 residues deleted decreased to 24% of the control. EF 1 with deletions of 15 or 18 residues was inactive, probably because it failed to assemble. The average torque generated by a single molecule of EF 1 when loaded by a fluorescent actin filament was, however, unaffected by deletions of up to 12 residues, as was their rotational behavior (all samples rotated during 60 ؎ 19% of the observation time). Activation energy analysis with the ensemble revealed a moderate decrease from 54 kJ/mol for EF 1 (full-length ␥) to 34 kJ/mol for EF 1 (␥-12). These observations imply that the intactness of the C terminus of subunit ␥ provides structural stability and/or routing during assembly of the enzyme, but that it is not required for the rotary action under load, proper.ATP is the universal free energy currency of prokaryotic and eukaryotic cells. It is synthesized in mitochondria, chloroplasts, and the cytoplasm of prokaryotic cells by F 0 F 1 -ATP synthase (cf. Refs. 1-6 for recent reviews). The enzyme works like a (reversible) rotary molecular machine with two motors/ generators mounted on a common shaft and hold together by an eccentric stator (7-11). In ATP synthesis mode the F 0 part translocates protons, thereby converting protonmotive force into the mechanical energy of rotary motion. Rotation is forwarded through the shaft into the F 1 part where it drives ATP synthesis. In ATP hydrolysis mode the rotation is reversed, and ions are pumped through F 0 in the opposite direction. The Escherichia coli enzyme (EF 1 ), 1 has the simplest subunit composition. It consists of eight different subunits, five in the peripheral F 1 portion and three in the membrane-intrinsic F 0 , with stoichiometries of (␣␤) 3 ␥␦⑀ for F 1 and probably ab 2 c 10 for F 0 (12). In view of the rotary mechanism they also can be organized into "rotor" (␥⑀c) and "stator" (␣␤␦ab). According to the crystal structure of bovine heart mitochondrial F 1 (13) the C-terminal region of subunit ␥ properly fits into a supposed "hydrophobic bearing" formed by loops in the upper portion of the hexagon of subunits (␣␤) 3 . Multiple sequence alignments showed that this region of ␥ is more conserved than the remainder (14, 15). One would expect therefore that truncations, point mutations, and covalent cross-links between the "bearing" and the rotor should inhibit the activity. But this expectation was not always met. 1) EF 1 with truncated ␥ (lacking 10 C-terminal residues) was still active (...

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Section: Table I Growth Doubling Times Yields Atpase Activities Amentioning

confidence: 99%

F1-ATPase, the C-terminal End of Subunit γ Is Not Required for ATP Hydrolysis-driven Rotation

Müller

Pänke

Junge

et al. 2002

Journal of Biological Chemistry

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“…A role for ion channels in the inner plastid envelope (Pottosin 1992) is unlikely. requirement for CO2 fixation by the photosynthetic carbon reduction cycle at high CO2/O"^ ratios is 3 mol ATP per mol CO2, and 4 mol H"*^ are needed to generate 1 mol ATP in photophosphorylation (Kobayashi, Kaiser & Heber 1995;Berry & Rumberg 1996;Panke & Rumberg 1996;van Walraven et al 1996; cf. the 3HVATP which was the accepted value at the time of writing of Pronina & Semenenko 1992, and hence was the value used in their energetic calculations).…”

Section: Hc03~ Transport Across the Thylakoid Membranementioning

confidence: 99%

“…not involved in the HCO3' to CO2 conversion) thylakoid area of 2-88 x 10"^ mĉ eir'. With 1 |imol H"^ pumped per m^ of thylakoid area per second at light saturation, and 4 mol H"^ needed to phosphorylate 1 mol ADP (Kobayashi et al 1995;Berry & Rumberg 1996;Panke & Rumberg 1996;van Walraven & Bakels 1996;van Walraven et al 1996), photophosphorylation yields 7-2 x 10"'^ mol ATP cell"' s~'. With a total of 6 mol ATP needed per mol inorganic C assimilated during photolithotrophic growth in continuous saturating light (Raven 1984), this means a C assimilation rate of 1-2 x 10"'^ mol C cell"' s"'.…”

Section: Conversion To Co2 In the Thyiakoid Iumenmentioning

confidence: 99%

CO₂‐concentrating mechanisms: a direct role for thylakoid lumen acidification?

Raven

1997

Plant Cell & Environment

179

144

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A testable mechanism of CO2 accumulation in photolithotrophs, originally suggested by Pronina & Semenenko, is quantitatively analysed. Tbe mecbanism involves (as does tbe most widely accepted bypotbesis) tbe delivery of HCO3~ to tbe compartment containing Rubisco. It differs in proposing subsequent HCO3~ entry (by passive uniport) to tbe tbylakoid lumen, followed by carbonic anbydrase activity in tbe lumen; uncatalysed conversion of HCO," to CO2, even at tbe low pH of tbe lumen, is at least 300 times too slow to account for tbe rate of inorganic C acquisition. Carbonic anbydrase converts tbe HCO3~ to CO2 at tbe lower pH maintained in tbe illuminated tbylakoid lumen by tbe ligbt-driven H"^ pump, generating CO2 at 10 times or more tbe tbylakoid HCO3c oncentration. Efflux of tbis CO2 can suppress Rubisco oxygenase activity and stimulate carboxylase activity in tbe stroma. Tbis mecbanism differs from tbe widely accepted bypotbeses in tbe required location of carbonic anbydrase, i.e. in tbe tbylakoid lumen ratber tban tbe stroma or pyrenoid, and in tbe need for HCO," influx to tbylakoids. Tbe capacity for anion (assayed as CP) entry by passive uniport reported for tbylakoid membranes is adequate for tbe proposed mecbanism; if tbe CP cbannel does not transport HCO3~, HCO3~ entry could be by combination of tbe cr cbannel witb a CP HCO," antiporter. Tbis mecbanism is particularly appropriate for organisms wbicb lack overt accumulation of total inorganic C in cells, but wbicb nevertbeless bave tbe gas excbange cbaracteristics of an organism witb a CO2-concentrating mecbanism.

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“…2), building on the demonstrated capacity for ATP-hydrolyzing transporters to be driven in reverse to synthesize ATP (34, 35). The discrete-state models do not include structural details, but implicitly incorporate conformational transitions; the models embody the basic mechanisms that have been appreciated over decades of biochemical and structural studies (25)(26)(27)(28)(29)(30)36), as well as thermodynamic constraints (36). In our approach, there is no parameter fitting.…”

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confidence: 99%

Biophysical comparison of ATP synthesis mechanisms shows a kinetic advantage for the rotary process

Anandakrishnan

Zhang

Donovan-Maiye

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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The ATP synthase (F-ATPase) is a highly complex rotary machine that synthesizes ATP, powered by a proton electrochemical gradient. Why did evolution select such an elaborate mechanism over arguably simpler alternating-access processes that can be reversed to perform ATP synthesis? We studied a systematic enumeration of alternative mechanisms, using numerical and theoretical means. When the alternative models are optimized subject to fundamental thermodynamic constraints, they fail to match the kinetic ability of the rotary mechanism over a wide range of conditions, particularly under low-energy conditions. We used a physically interpretable, closed-form solution for the steady-state rate for an arbitrary chemical cycle, which clarifies kinetic effects of complex free-energy landscapes. Our analysis also yields insights into the debated "kinetic equivalence" of ATP synthesis driven by transmembrane pH and potential difference. Overall, our study suggests that the complexity of the F-ATPase may have resulted from positive selection for its kinetic advantage.ATP synthase | kinetic mechanism | free-energy landscape | nonequilibrium steady state | evolution T he F-ATPase performs molecular-level free-energy (FE) transduction to phosphorylate ADP and yield ATP, the primary energy carrier that drives a vast range of cellular processes. It spurred Mitchell's chemiosmotic hypothesis (1) and Boyer's now-validated proposal for the binding-change mechanism (2) in which a proton electrochemical gradient is transduced to rotationbased mechanical energy and then back to chemical FE as ADP is phosphorylated. The F-ATPase's two-domain uniaxial rotary structure is conserved across all three domains of life (3-6), and details of its function have been the subject of a multitude of studies (e.g., refs. 7-30).Here, we address a relatively narrow question with potentially significant evolutionary implications: Why is ATP synthesized by a rotary mechanism instead of a potentially much simpler alternating-access mechanism (Fig. 1)? Using thermodynamic and kinetic constraints, we address the question of whether evolution tends to arrive at optimal molecular processes (31), building on established concepts of optimality-derived evolutionary convergence (32, 33). Presumably, performance advantages in the central task of ATP synthesis would be under significant evolutionary pressure. Previous modeling studies of the F-ATPase have addressed structural and mechanistic questions about the rotary mechanism (e.g., refs. 11-20), but not the metaissue of the mechanism itself compared with alternatives.To assess whether the rotary mechanism possesses any intrinsic performance advantage, we constructed a series of kinetic models abstracted from known mechanisms (Fig. 1). Beyond the rotarybased model, we considered a series of alternating-access analogs (Fig. 2), building on the demonstrated capacity for ATP-hydrolyzing transporters to be driven in reverse to synthesize ATP (34, 35). The discrete-state models do not include structural details, bu...

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Kinetic modelling of the proton translocating CF₀CF₁‐ATP synthase from spinach

Cited by 35 publications

References 21 publications

F1-ATPase, the C-terminal End of Subunit γ Is Not Required for ATP Hydrolysis-driven Rotation

F1-ATPase, the C-terminal End of Subunit γ Is Not Required for ATP Hydrolysis-driven Rotation

CO₂‐concentrating mechanisms: a direct role for thylakoid lumen acidification?

Biophysical comparison of ATP synthesis mechanisms shows a kinetic advantage for the rotary process

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Kinetic modelling of the proton translocating CF0CF1‐ATP synthase from spinach

Cited by 35 publications

References 21 publications

F1-ATPase, the C-terminal End of Subunit γ Is Not Required for ATP Hydrolysis-driven Rotation

F1-ATPase, the C-terminal End of Subunit γ Is Not Required for ATP Hydrolysis-driven Rotation

CO2‐concentrating mechanisms: a direct role for thylakoid lumen acidification?

Biophysical comparison of ATP synthesis mechanisms shows a kinetic advantage for the rotary process

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Kinetic modelling of the proton translocating CF₀CF₁‐ATP synthase from spinach

CO₂‐concentrating mechanisms: a direct role for thylakoid lumen acidification?