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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.

No MeSH data available.


Solvent-surface representation of the native structure of yeast frataxin (PDBID: 2ga5)36 drawn by the DS visualizer 2.5. This structure has the large valley marked by the blue ellipse and the tail pointed by the red arrow.
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f6-7_113: Solvent-surface representation of the native structure of yeast frataxin (PDBID: 2ga5)36 drawn by the DS visualizer 2.5. This structure has the large valley marked by the blue ellipse and the tail pointed by the red arrow.

Mentions: Figure 3(a): Two of the β subunits are in closed conformation and the other one takes an open conformation. In this situation, the α3β3γ complex is packed with high asymmetry so that the water entropy in the presence of the α3β3γ complex can be made as high as possible. The tightest packing is formed in sub-complex III. The reasons why such an asymmetric packing is formed are due to an asymmetric nature of the γ subunit and to nonuniform binding of nucleotides to the three β subunits. Here we discuss why such asymmetric packing is formed by the water-entropy effect. As explained in Figure 2, it is desired for a protein or a complex of proteins that the backbones and side chains be tightly packed as a three-dimensional jigsaw puzzle. However, this is not always possible. When the overall, impartial tight packing is not achievable in a protein, the portions which can tightly be packed are chosen for the preferential tight packing. This action is taken by the water-entropy effect. For example, the native structure of yeast frataxin36 has a large valley and a tail as shown in Figure 6. Nevertheless, /S/ of the native structure is almost minimized37 because the other portions are tightly packed. If an impartial packing was undertaken, the valley and/or the tail could be removed but the resultant packing would become rather loose, causing a larger value of /S/.


Importance of water entropy in rotation mechanism of F 1 -ATPase
Solvent-surface representation of the native structure of yeast frataxin (PDBID: 2ga5)36 drawn by the DS visualizer 2.5. This structure has the large valley marked by the blue ellipse and the tail pointed by the red arrow.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC5036781&req=5

f6-7_113: Solvent-surface representation of the native structure of yeast frataxin (PDBID: 2ga5)36 drawn by the DS visualizer 2.5. This structure has the large valley marked by the blue ellipse and the tail pointed by the red arrow.
Mentions: Figure 3(a): Two of the β subunits are in closed conformation and the other one takes an open conformation. In this situation, the α3β3γ complex is packed with high asymmetry so that the water entropy in the presence of the α3β3γ complex can be made as high as possible. The tightest packing is formed in sub-complex III. The reasons why such an asymmetric packing is formed are due to an asymmetric nature of the γ subunit and to nonuniform binding of nucleotides to the three β subunits. Here we discuss why such asymmetric packing is formed by the water-entropy effect. As explained in Figure 2, it is desired for a protein or a complex of proteins that the backbones and side chains be tightly packed as a three-dimensional jigsaw puzzle. However, this is not always possible. When the overall, impartial tight packing is not achievable in a protein, the portions which can tightly be packed are chosen for the preferential tight packing. This action is taken by the water-entropy effect. For example, the native structure of yeast frataxin36 has a large valley and a tail as shown in Figure 6. Nevertheless, /S/ of the native structure is almost minimized37 because the other portions are tightly packed. If an impartial packing was undertaken, the valley and/or the tail could be removed but the resultant packing would become rather loose, causing a larger value of /S/.

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.