How subunit coupling produces the γ-subunit rotary motion in F
            <sub>1</sub>
            -ATPase

Pu, Jingzhi; Karplus, Martin

doi:10.1073/pnas.0708746105

Cited by 112 publications

(154 citation statements)

References 44 publications

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“…Because the sequence of the four active site conformations considered here is most likely β TP → β DP → β HC → β E toward direction of hydrolysis (12,25), we conclude that III TS and II TS are most likely somewhat separated in time by the conformational changes of the active site. We notice that hydrolysis of ATP takes place after an approximately 90°substep of the γ-subunit (10) and P i release also takes place following an approximately 90°γ-subunit substep (10,20).…”

Section: Resultsmentioning

confidence: 99%

“…Considering the function of the ATP synthase, structure determinations (12)(13)(14)(15)(16), mutation studies on the α-, β-, and γ-subunits (1,(17)(18)(19)(20), single-molecule studies (6,7,10), and simulations (11,(21)(22)(23)(24)(25)(26)(27)) have contributed to a rather detailed understanding of its mode of mechanical action. However, one of several issues that need to be better characterized (1) is the mechanistic resolution of the chemical reaction steps on the way from ADP to ATP at an atomic level.…”

mentioning

confidence: 99%

“…Single-molecule studies showed that the 120°rotational steps can be further divided into approximately 90°and 30°substeps during hydrolysis (7, 10). A roughly 2-ms waiting time is observed between these substeps, most likely due to two separate 1-ms steps, one corresponding to the hydrolysis or synthesis step, the other to P i release or binding (10).Considering the function of the ATP synthase, structure determinations (12-16), mutation studies on the α-, β-, and γ-subunits (1, 17-20), single-molecule studies (6, 7, 10), and simulations (11,(21)(22)(23)(24)(25)(26)(27)) have contributed to a rather detailed understanding of its mode of mechanical action. However, one of several issues that need to be better characterized (1) is the mechanistic resolution of the chemical reaction steps on the way from ADP to ATP at an atomic level.…”

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confidence: 99%

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Double-lock ratchet mechanism revealing the role of αSER-344 in F _o F ₁ ATP synthase

Beke‐Somfai

Lincoln²,

Nordén³

2011

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

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In a majority of living organisms, F o F 1 ATP synthase performs the fundamental process of ATP synthesis. Despite the simple net reaction formula, ADP þ P i → ATP þ H 2 O, the detailed step-by-step mechanism of the reaction yet remains to be resolved owing to the complexity of this multisubunit enzyme. Based on quantum mechanical computations using recent high resolution X-ray structures, we propose that during ATP synthesis the enzyme first prepares the inorganic phosphate for the γP-O ADP bond-forming step via a double-proton transfer. At this step, the highly conserved αS344 side chain plays a catalytic role. The reaction thereafter progresses through another transition state (TS) having a planar PO 3 − ion configuration to finally form ATP. These two TSs are concluded crucial for ATP synthesis. Using stepwise scans and several models of the nucleotide-bound active site, some of the most important conformational changes were traced toward direction of synthesis. Interestingly, as the active site geometry progresses toward the ATP-favoring tight binding site, at both of these TSs, a dramatic increase in barrier heights is observed for the reverse direction, i.e., hydrolysis of ATP. This change could indicate a "ratchet" mechanism for the enzyme to ensure efficacy of ATP synthesis by shifting residue conformation and thus locking access to the crucial TSs.quantum mechanics | reaction mechanism | molecular motor T he F o F 1 -ATP synthase is vital for cell energy production, being responsible for most of the ATP synthesis in membranes of bacteria, chloroplasts, and mitochondria. This multisubunit enzyme complex has high structural similarity among different species. It produces ATP as a biological nanomotor driven by an electrochemical potential difference across membranes as part of respiration or photosynthesis (1). The active sites are located in the F 1 domain, which in Escherichia coli consists of α 3 β 3 γδϵ subunits, three αβ-pairs surrounding a central α-helical coiled coil γ-subunit. The ATP synthesiswith P i ¼ H 2 PO 4 − , occurs at catalytic sites formed in the three β-subunits at the α/β-interfaces (2). The most prominent model assumes that the ATP-producing reaction occurs due to a rotation of the γ-shaft, inducing conformational changes in the surrounding αβ-subunit pairs according to the unbinding and rotational coupling mechanism (3-7). It was also demonstrated that excess ATP may be hydrolyzed by isolated F 1 resulting in reverse rotation of the γ-subunit (7). In the first crystal structure of F 1 -ATPase (3), the three catalytic sites contained a nonhydrolyzable ATP analogue in one site, an ADP in the other, the third site being empty. Because of this observation, also supported by ATP binding affinity measurements (8, 9), the sites were named "tight binding site" (β TP ), "loose binding site" (β DP ), and "empty site" (β E ). According to the trisite mechanism model, during ATP synthesis each of the three αβ-subunit pairs changes conformation along the repeating cycle, β E → β DP → β TP → β E...

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

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confidence: 99%

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Double-lock ratchet mechanism revealing the role of αSER-344 in F _o F ₁ ATP synthase

Beke‐Somfai

Lincoln²,

Nordén³

2011

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

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“…This figure was originally presented in (Mukherjee & Warshel, 2011). problem far beyond anything that has been obtained so far from other studies of the system, and can provide consistent insight into the events occurring in the F 1 -ATPase system. Now several works have proposed a steric mechanism (Koga & Takada, 2006 ;Pu & Karplus, 2008), or a somewhat related elastic spring model (Czub & Grubmueller, 2011), and asserted that such a mechanism emerged from their calculations. However, these works forced the system to move in the desired direction (by applying very large forces) rather than allowing the system to be driven by the chemical potential or by the proper external torque.…”

Section: The Coupling Between the Subunitsmentioning

confidence: 99%

Why nature really chose phosphate

Kamerlin

Sharma

Prasad

et al. 2013

Quart. Rev. Biophys.

332

448

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Phosphoryl transfer plays key roles in signaling, energy transduction, protein synthesis, and maintaining the integrity of the genetic material. On the surface, it would appear to be a simple nucleophile displacement reaction. However, this simplicity is deceptive, as, even in aqueous solution, the low-lying d-orbitals on the phosphorus atom allow for eight distinct mechanistic possibilities, before even introducing the complexities of the enzyme catalyzed reactions. To further complicate matters, while powerful, traditional experimental techniques such as the use of linear free-energy relationships (LFER) or measuring isotope effects cannot make unique distinctions between different potential mechanisms. A quarter of a century has passed since Westheimer wrote his seminal review, ‘Why Nature Chose Phosphate’ (Science 235 (1987), 1173), and a lot has changed in the field since then. The present review revisits this biologically crucial issue, exploring both relevant enzymatic systems as well as the corresponding chemistry in aqueous solution, and demonstrating that the only way key questions in this field are likely to be resolved is through careful theoretical studies (which of course should be able to reproduce all relevant experimental data). Finally, we demonstrate that the reason that naturereallychose phosphate is due to interplay between two counteracting effects: on the one hand, phosphates are negatively charged and the resulting charge-charge repulsion with the attacking nucleophile contributes to the very high barrier for hydrolysis, making phosphate esters among the most inert compounds known. However, biology is not only about reducing the barrier to unfavorable chemical reactions. That is, the same charge-charge repulsion that makes phosphate ester hydrolysis so unfavorable also makes it possible to regulate, by exploiting the electrostatics. This means that phosphate ester hydrolysis can not only be turned on, but also be turned off, by fine tuning the electrostatic environment and the present review demonstrates numerous examples where this is the case. Without this capacity for regulation, it would be impossible to have for instance a signaling or metabolic cascade, where the action of each participant is determined by the fine-tuned activity of the previous piece in the production line. This makes phosphate esters the ideal compounds to facilitate life as we know it.

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“…Recent molecular dynamics simulation aimed at understanding the effect of the γ-subunit rotation (18, 19) was instructive but could not capture the relevant energy of the actual millisecond process of the complete F1-ATPase motor. Attempts to understand the rotary mechanism, using coarse-grained models (18,20), forced the rotation rather than reproduce it from structurally based energetics (see Background). Other computational studies are also discussed in the SI Text.…”

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confidence: 99%

Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase

Mukherjee

Warshel

2011

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

101

152

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Understanding the nature of energy transduction in life processes requires a quantitative description of the energetics of the conversion of ATP to ADP by ATPases. Previous attempts to do so have provided an interesting insight but could not account for the rotary mechanism by a nonphenomenological structure/energy description. In particular it has been very challenging to account for the observations of the 80°and 40°rotational substates, without any prior information about such states in the simulation procedure. Here we use a coarse-grained model of F1-ATPase and generate, without the adjustment of phenomenological parameters, a structure-based free energy landscape that reproduces the energetics of the mechanochemical process. It is found that the landscape along the relevant rotary path is determined by the electrostatic free energy and not by steric effects. Furthermore, the generated surface and the corresponding Langevin dynamics simulations identify a hidden conformational barrier that provides a new fundamental interpretation of the catalytic dwell and illuminate the nature of the energy conversion process.bioenergetics | chemical-conformational coupling | molecular motors | coarse grain model U nderstanding the energetics of the biological conversion of ATP to ADP is crucial for elucidating the nature of energy transduction in life processes and also for practical understanding of the action of molecular motors (1, 2). At present it seems that the detailed nature of this biological energy conversion process has remained a major puzzle (1-7). For example, despite the fact that the structures of several ATPases have been elucidated (e.g., refs. 4 and 8) and recent advances in detailed elucidation of some key steps have been made (9-11), it is not completely clear at what stage in the reaction energy is actually released and, in turn, what is the nature of the energy conversion process. Some workers have suggested that the major source of the energy release is the conversion of the free energy of ATP binding into elastic strain, which is subsequently released by a coordinated and tightly coupled conformational mechanism (6). It was also postulated that the energy conversion involves an inertial energy release (12), whereas our works (13, 14) have suggested that the energetics is associated with the electrostatic work, and the origin of the free energy change involves a significant contribution from the charge separation in solution outside the ATPase active sites. Furthermore, biochemical and structural studies have provided a molecular model for the action of ATPases (1-4), and remarkable phenomenological analyses (6, 7) indicated what are the conditions for effective action. However, we still do not have a clear structure function correlation that involves both the chemistry and the conformational coupling. The challenge became even more exciting in view of the remarkable progress in single-molecule studies that directly visualized the γ-subunit rotation in a unidirectional way, while revealing several...

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How subunit coupling produces the γ-subunit rotary motion in F ₁ -ATPase

Cited by 112 publications

References 44 publications

Double-lock ratchet mechanism revealing the role of αSER-344 in F _o F ₁ ATP synthase

Double-lock ratchet mechanism revealing the role of αSER-344 in F _o F ₁ ATP synthase

Why nature really chose phosphate

Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase

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How subunit coupling produces the γ-subunit rotary motion in F 1 -ATPase

Cited by 112 publications

References 44 publications

Double-lock ratchet mechanism revealing the role of αSER-344 in F o F 1 ATP synthase

Double-lock ratchet mechanism revealing the role of αSER-344 in F o F 1 ATP synthase

Why nature really chose phosphate

Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase

Contact Info

Product

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How subunit coupling produces the γ-subunit rotary motion in F ₁ -ATPase

Double-lock ratchet mechanism revealing the role of αSER-344 in F _o F ₁ ATP synthase

Double-lock ratchet mechanism revealing the role of αSER-344 in F _o F ₁ ATP synthase