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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.


Comparison between the numbers of stable contacts estimated by the MD simulation with all-atom potentials34 and the water-entropy gain upon the formation of subunit pair i–j, Sij/kB. Each value is shown in the original paper19 and in the supporting information of the paper of Ito and Ikeguchi34.
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f4-7_113: Comparison between the numbers of stable contacts estimated by the MD simulation with all-atom potentials34 and the water-entropy gain upon the formation of subunit pair i–j, Sij/kB. Each value is shown in the original paper19 and in the supporting information of the paper of Ito and Ikeguchi34.

Mentions: As shown in Figure 4, ΔSij/kB is highly correlated with the number of stable contacts obtained in the MD simulation by Ito and Ikeguchi34 (the correlation coefficient is 0.96). Thus, the framework of the results of the MD simulation is successfully reproduced using our hybrid method focused on the water-entropy effect. In the MD simulation, quite a long computation is inevitable. On the other hand, the calculation of the HE for one subunit pair is finished only in a few seconds by our hybrid method. Nevertheless, the packing characteristics estimated by the MD simulation can beautifully be reproduced, which is remarkable.


Importance of water entropy in rotation mechanism of F 1 -ATPase
Comparison between the numbers of stable contacts estimated by the MD simulation with all-atom potentials34 and the water-entropy gain upon the formation of subunit pair i–j, Sij/kB. Each value is shown in the original paper19 and in the supporting information of the paper of Ito and Ikeguchi34.
© Copyright Policy
Related In: Results  -  Collection

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

f4-7_113: Comparison between the numbers of stable contacts estimated by the MD simulation with all-atom potentials34 and the water-entropy gain upon the formation of subunit pair i–j, Sij/kB. Each value is shown in the original paper19 and in the supporting information of the paper of Ito and Ikeguchi34.
Mentions: As shown in Figure 4, ΔSij/kB is highly correlated with the number of stable contacts obtained in the MD simulation by Ito and Ikeguchi34 (the correlation coefficient is 0.96). Thus, the framework of the results of the MD simulation is successfully reproduced using our hybrid method focused on the water-entropy effect. In the MD simulation, quite a long computation is inevitable. On the other hand, the calculation of the HE for one subunit pair is finished only in a few seconds by our hybrid method. Nevertheless, the packing characteristics estimated by the MD simulation can beautifully be reproduced, which is remarkable.

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.