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Importance of water entropy in rotation mechanism of F 1 -ATPase

View Article: PubMed Central - PubMed

ABSTRACT

We briefly review our theoretical study on the rotation scheme of F1-ATPase. In the scheme, the key factor is the water entropy which has been shown to drive a variety of self-assembly processes in biological systems. We decompose the crystal structure of F1-ATPase into three sub-complexes each of which is composed of the γ subunit, one of the β subunits, and two α subunits adjacent to them. The βE, βTP, and βDP subunits are involved in the sub-complexes I, II, and III, respectively. We calculate the hydration entropy of each sub-complex using a hybrid of the integral equation theory for molecular liquids and the morphometric approach. It is found that the absolute value of the hydration entropy follows the order, sub-complex I > sub-complex II > sub-complex III. Moreover, the differences are quite large, which manifests highly asymmetrical packing of F1-ATPase. In our picture, this asymmetrical packing plays crucially important roles in the rotation of the γ subunit. We discuss how the rotation is induced by the water-entropy effect coupled with such chemical processes as ATP binding, ATP hydrolysis, and release of the products.

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Summary of experimental results using schematic representation of the α3β3γ complex viewed from the Fo side. (a) Schematic representations of the crystal structure shown in Figure 1. The yellow lines represent that the packing in two adjacent subunits is especially tight34. Three circular arcs denote sub-complexes I (green), II (red), and III (blue), respectively. The definition of each sub-complex is described in “Hydration entropies of three sub-complexes”. The other figures represent (b) the overall conformation after the first 40° rotation of the γ subunit and (c) the overall conformation after the second 80° rotation of the γ subunit. Primes are added to the subunits in (b) because their conformations should be different from those in (a). The definition of the arrow at the center of the γ subunit is shown in the original paper19.
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f3-7_113: Summary of experimental results using schematic representation of the α3β3γ complex viewed from the Fo side. (a) Schematic representations of the crystal structure shown in Figure 1. The yellow lines represent that the packing in two adjacent subunits is especially tight34. Three circular arcs denote sub-complexes I (green), II (red), and III (blue), respectively. The definition of each sub-complex is described in “Hydration entropies of three sub-complexes”. The other figures represent (b) the overall conformation after the first 40° rotation of the γ subunit and (c) the overall conformation after the second 80° rotation of the γ subunit. Primes are added to the subunits in (b) because their conformations should be different from those in (a). The definition of the arrow at the center of the γ subunit is shown in the original paper19.

Mentions: It has been pointed out that the packing of the α3β3γ complex in crystal structures is highly asymmetrical. For example, using an all-atom molecular dynamics (MD) simulation, Ito and Ikeguchi34 have analyzed packing at the interfaces between adjacent subunits in terms of the number of stable contacts. The stable contacts are defined as the inter-subunit residue pairs maintaining their inter-atomic distances less than 4.5Å for 98% of snapshots in the MD trajectory. The number of stable contacts can be a measure of tightness of packing at the interfaces between adjacent subunits. Ito and Ikeguchi have found that the packing at the interfaces between βDP, adjacent α subunits, and γ subunit is especially tight, implying that the four subunits are strongly interacted (See Fig. 3(a)). Experimental studies have shown that in the structure illustrated in Figures 1 and 3(a), the rotation of the γ subunit occurs upon a structural change of βDP, the catalytically active subunit7,9. It is likely that perturbation of the tight packing by the structural change of βDP induces the movement of the γ subunit.


Importance of water entropy in rotation mechanism of F 1 -ATPase
Summary of experimental results using schematic representation of the α3β3γ complex viewed from the Fo side. (a) Schematic representations of the crystal structure shown in Figure 1. The yellow lines represent that the packing in two adjacent subunits is especially tight34. Three circular arcs denote sub-complexes I (green), II (red), and III (blue), respectively. The definition of each sub-complex is described in “Hydration entropies of three sub-complexes”. The other figures represent (b) the overall conformation after the first 40° rotation of the γ subunit and (c) the overall conformation after the second 80° rotation of the γ subunit. Primes are added to the subunits in (b) because their conformations should be different from those in (a). The definition of the arrow at the center of the γ subunit is shown in the original paper19.
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Related In: Results  -  Collection

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f3-7_113: Summary of experimental results using schematic representation of the α3β3γ complex viewed from the Fo side. (a) Schematic representations of the crystal structure shown in Figure 1. The yellow lines represent that the packing in two adjacent subunits is especially tight34. Three circular arcs denote sub-complexes I (green), II (red), and III (blue), respectively. The definition of each sub-complex is described in “Hydration entropies of three sub-complexes”. The other figures represent (b) the overall conformation after the first 40° rotation of the γ subunit and (c) the overall conformation after the second 80° rotation of the γ subunit. Primes are added to the subunits in (b) because their conformations should be different from those in (a). The definition of the arrow at the center of the γ subunit is shown in the original paper19.
Mentions: It has been pointed out that the packing of the α3β3γ complex in crystal structures is highly asymmetrical. For example, using an all-atom molecular dynamics (MD) simulation, Ito and Ikeguchi34 have analyzed packing at the interfaces between adjacent subunits in terms of the number of stable contacts. The stable contacts are defined as the inter-subunit residue pairs maintaining their inter-atomic distances less than 4.5Å for 98% of snapshots in the MD trajectory. The number of stable contacts can be a measure of tightness of packing at the interfaces between adjacent subunits. Ito and Ikeguchi have found that the packing at the interfaces between βDP, adjacent α subunits, and γ subunit is especially tight, implying that the four subunits are strongly interacted (See Fig. 3(a)). Experimental studies have shown that in the structure illustrated in Figures 1 and 3(a), the rotation of the γ subunit occurs upon a structural change of βDP, the catalytically active subunit7,9. It is likely that perturbation of the tight packing by the structural change of βDP induces the movement of the γ subunit.

View Article: PubMed Central - PubMed

ABSTRACT

We briefly review our theoretical study on the rotation scheme of F1-ATPase. In the scheme, the key factor is the water entropy which has been shown to drive a variety of self-assembly processes in biological systems. We decompose the crystal structure of F1-ATPase into three sub-complexes each of which is composed of the γ subunit, one of the β subunits, and two α subunits adjacent to them. The βE, βTP, and βDP subunits are involved in the sub-complexes I, II, and III, respectively. We calculate the hydration entropy of each sub-complex using a hybrid of the integral equation theory for molecular liquids and the morphometric approach. It is found that the absolute value of the hydration entropy follows the order, sub-complex I > sub-complex II > sub-complex III. Moreover, the differences are quite large, which manifests highly asymmetrical packing of F1-ATPase. In our picture, this asymmetrical packing plays crucially important roles in the rotation of the γ subunit. We discuss how the rotation is induced by the water-entropy effect coupled with such chemical processes as ATP binding, ATP hydrolysis, and release of the products.

No MeSH data available.


Related in: MedlinePlus