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

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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.


Close packing of three side chains. The excluded volume generated by a side chain is the volume occupied by the side chain itself plus the volume shown in gray. When side chains are closely packed, the excluded volumes overlap. The total volume available to the translational displacement of water molecules increases by the overlapped volume shown in black, leading to a water-entropy gain.
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f2-7_113: Close packing of three side chains. The excluded volume generated by a side chain is the volume occupied by the side chain itself plus the volume shown in gray. When side chains are closely packed, the excluded volumes overlap. The total volume available to the translational displacement of water molecules increases by the overlapped volume shown in black, leading to a water-entropy gain.

Mentions: Our recent theoretical analyses based on statistical thermodynamics of fluids have shown that the water entropy is the key quantity in elucidating the mechanism of such processes as protein folding/unfolding, molecular recognition between guest ligands and host enzymes, and aggregation of protein molecules like the amyloid-fibril formation20,21. As an illustration of the water-entropy effect, we consider a tight packing of the three side chains shown in Figure 2. The tight packing is induced by the excluded volume (EV) effect. Here the EV is defined as the volume which the centers of water molecules cannot enter22. In the left-hand side of Figure 2, for example, the EV corresponds to the molecular volume of the side chains plus the volume shown in gray. When a tight packing is formed, the EVs overlap, leading to a reduction of the EV. This decrease provides a corresponding increase in the total volume available to the translational displacement of the coexisting water molecules and in the number of accessible configurations of the water. Thus, tight packing leads to a gain in the water entropy. The native structure is the structure with almost the maximum water entropy20,21. Note that the interaction between protein atoms arising from the water-entropy effect is an indirect interaction via water molecules. According to the usual view23, the water adjacent to a nonpolar group is entropically unstable, and protein folding is driven by the release of such unfavorable water to the bulk through the burial of nonpolar groups. However, we have shown that the entropic gain originating from this view is too small to reproduce the experimental result of apoplastocyanin (apoPC) folding24. Our recent studies on solvation thermodynamics have shown that “hydrophobic interaction” is driven primarily by the water entropy gain originating from the EV effect20.


Importance of water entropy in rotation mechanism of F 1 -ATPase
Close packing of three side chains. The excluded volume generated by a side chain is the volume occupied by the side chain itself plus the volume shown in gray. When side chains are closely packed, the excluded volumes overlap. The total volume available to the translational displacement of water molecules increases by the overlapped volume shown in black, leading to a water-entropy gain.
© Copyright Policy
Related In: Results  -  Collection

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

f2-7_113: Close packing of three side chains. The excluded volume generated by a side chain is the volume occupied by the side chain itself plus the volume shown in gray. When side chains are closely packed, the excluded volumes overlap. The total volume available to the translational displacement of water molecules increases by the overlapped volume shown in black, leading to a water-entropy gain.
Mentions: Our recent theoretical analyses based on statistical thermodynamics of fluids have shown that the water entropy is the key quantity in elucidating the mechanism of such processes as protein folding/unfolding, molecular recognition between guest ligands and host enzymes, and aggregation of protein molecules like the amyloid-fibril formation20,21. As an illustration of the water-entropy effect, we consider a tight packing of the three side chains shown in Figure 2. The tight packing is induced by the excluded volume (EV) effect. Here the EV is defined as the volume which the centers of water molecules cannot enter22. In the left-hand side of Figure 2, for example, the EV corresponds to the molecular volume of the side chains plus the volume shown in gray. When a tight packing is formed, the EVs overlap, leading to a reduction of the EV. This decrease provides a corresponding increase in the total volume available to the translational displacement of the coexisting water molecules and in the number of accessible configurations of the water. Thus, tight packing leads to a gain in the water entropy. The native structure is the structure with almost the maximum water entropy20,21. Note that the interaction between protein atoms arising from the water-entropy effect is an indirect interaction via water molecules. According to the usual view23, the water adjacent to a nonpolar group is entropically unstable, and protein folding is driven by the release of such unfavorable water to the bulk through the burial of nonpolar groups. However, we have shown that the entropic gain originating from this view is too small to reproduce the experimental result of apoplastocyanin (apoPC) folding24. Our recent studies on solvation thermodynamics have shown that “hydrophobic interaction” is driven primarily by the water entropy gain originating from the EV effect20.

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.