The Experts below are selected from a list of 3810 Experts worldwide ranked by ideXlab platform
Masahiro Kinoshita - One of the best experts on this subject based on the ideXlab platform.
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Molecular Dynamics Simulations of Yeast F1-ATPase Before and after 16-Degree Rotation of the Gamma Subunit
Biophysical Journal, 2013Co-Authors: Yuko Ito, Takashi Yoshidome, Nobuyuki Matubayasi, Masahiro Kinoshita, Mitsunori IkeguchiAbstract:We performed molecular dynamics simulations for crystal structures of yeast F1-ATPase whose crystallographic unit contains two different states. One complex binds Pi in the βE subunit, and the other liberated it. In the latter structure, the position of central stalk is rotated +16° in the hydrolysis direction. Because single molecule experiments have proven that Pi release occurs at the βE subunit, and the γ subunit is rotated after ATP hydrolysis and Pi release, these structures are supposed to represent snapshots before and after Pi releases for the 40° substep, respectively.We describe how the F1-ATPase complex changes the structure after Pi release, based on the results of the MD simulations for yF1II and yF1I. Then, we propose a possible mechanism of the 40° Rotation of the γ subunit.
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structural characteristics of yeast f1 atpase before and after 16 Degree Rotation of the γ subunit theoretical analysis focused on the water entropy effect
Journal of Chemical Physics, 2012Co-Authors: Takashi Yoshidome, Yuko Ito, Nobuyuki Matubayasi, Mitunori Ikeguchi, Masahiro KinoshitaAbstract:We have recently proposed a novel picture of the Rotation mechanism for F1-ATPase [T. Yoshidome, Y. Ito, M. Ikeguchi, and M. Kinoshita, J. Am. Chem. Soc. 133, 4030 (2011)]10.1021/ja109594y. In the picture, the asymmetric packing in F1-ATPase, originating from the water-entropy effect, plays the key role in the Rotation. Here, we analyze the differences between the experimentally determined structures of yeast F1-ATPase before and after 16° Rotation of the γ subunit with the emphasis on the water-entropy effect. For each of these structures, we calculate the hydration entropies of three sub-complexes comprising the γ subunit, one of the β subunits, and two α subunits adjacent to them. The βE, βTP, and βDP subunits are involved in sub-complexes I, II, and III, respectively. The calculation is performed using a hybrid of the angle-dependent integral equation theory combined with the molecular model for water and the morphometric approach. The absolute value of the hydration entropy is in the following order:...
Takashi Yoshidome - One of the best experts on this subject based on the ideXlab platform.
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Molecular Dynamics Simulations of Yeast F1-ATPase Before and after 16-Degree Rotation of the Gamma Subunit
Biophysical Journal, 2013Co-Authors: Yuko Ito, Takashi Yoshidome, Nobuyuki Matubayasi, Masahiro Kinoshita, Mitsunori IkeguchiAbstract:We performed molecular dynamics simulations for crystal structures of yeast F1-ATPase whose crystallographic unit contains two different states. One complex binds Pi in the βE subunit, and the other liberated it. In the latter structure, the position of central stalk is rotated +16° in the hydrolysis direction. Because single molecule experiments have proven that Pi release occurs at the βE subunit, and the γ subunit is rotated after ATP hydrolysis and Pi release, these structures are supposed to represent snapshots before and after Pi releases for the 40° substep, respectively.We describe how the F1-ATPase complex changes the structure after Pi release, based on the results of the MD simulations for yF1II and yF1I. Then, we propose a possible mechanism of the 40° Rotation of the γ subunit.
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structural characteristics of yeast f1 atpase before and after 16 Degree Rotation of the γ subunit theoretical analysis focused on the water entropy effect
Journal of Chemical Physics, 2012Co-Authors: Takashi Yoshidome, Yuko Ito, Nobuyuki Matubayasi, Mitunori Ikeguchi, Masahiro KinoshitaAbstract:We have recently proposed a novel picture of the Rotation mechanism for F1-ATPase [T. Yoshidome, Y. Ito, M. Ikeguchi, and M. Kinoshita, J. Am. Chem. Soc. 133, 4030 (2011)]10.1021/ja109594y. In the picture, the asymmetric packing in F1-ATPase, originating from the water-entropy effect, plays the key role in the Rotation. Here, we analyze the differences between the experimentally determined structures of yeast F1-ATPase before and after 16° Rotation of the γ subunit with the emphasis on the water-entropy effect. For each of these structures, we calculate the hydration entropies of three sub-complexes comprising the γ subunit, one of the β subunits, and two α subunits adjacent to them. The βE, βTP, and βDP subunits are involved in sub-complexes I, II, and III, respectively. The calculation is performed using a hybrid of the angle-dependent integral equation theory combined with the molecular model for water and the morphometric approach. The absolute value of the hydration entropy is in the following order:...
Yuko Ito - One of the best experts on this subject based on the ideXlab platform.
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Molecular Dynamics Simulations of Yeast F1-ATPase Before and after 16-Degree Rotation of the Gamma Subunit
Biophysical Journal, 2013Co-Authors: Yuko Ito, Takashi Yoshidome, Nobuyuki Matubayasi, Masahiro Kinoshita, Mitsunori IkeguchiAbstract:We performed molecular dynamics simulations for crystal structures of yeast F1-ATPase whose crystallographic unit contains two different states. One complex binds Pi in the βE subunit, and the other liberated it. In the latter structure, the position of central stalk is rotated +16° in the hydrolysis direction. Because single molecule experiments have proven that Pi release occurs at the βE subunit, and the γ subunit is rotated after ATP hydrolysis and Pi release, these structures are supposed to represent snapshots before and after Pi releases for the 40° substep, respectively.We describe how the F1-ATPase complex changes the structure after Pi release, based on the results of the MD simulations for yF1II and yF1I. Then, we propose a possible mechanism of the 40° Rotation of the γ subunit.
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structural characteristics of yeast f1 atpase before and after 16 Degree Rotation of the γ subunit theoretical analysis focused on the water entropy effect
Journal of Chemical Physics, 2012Co-Authors: Takashi Yoshidome, Yuko Ito, Nobuyuki Matubayasi, Mitunori Ikeguchi, Masahiro KinoshitaAbstract:We have recently proposed a novel picture of the Rotation mechanism for F1-ATPase [T. Yoshidome, Y. Ito, M. Ikeguchi, and M. Kinoshita, J. Am. Chem. Soc. 133, 4030 (2011)]10.1021/ja109594y. In the picture, the asymmetric packing in F1-ATPase, originating from the water-entropy effect, plays the key role in the Rotation. Here, we analyze the differences between the experimentally determined structures of yeast F1-ATPase before and after 16° Rotation of the γ subunit with the emphasis on the water-entropy effect. For each of these structures, we calculate the hydration entropies of three sub-complexes comprising the γ subunit, one of the β subunits, and two α subunits adjacent to them. The βE, βTP, and βDP subunits are involved in sub-complexes I, II, and III, respectively. The calculation is performed using a hybrid of the angle-dependent integral equation theory combined with the molecular model for water and the morphometric approach. The absolute value of the hydration entropy is in the following order:...
Sang-jin Sin - One of the best experts on this subject based on the ideXlab platform.
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The super-potential and holomorphic properties of the MQCD
Nuclear Physics, 1998Co-Authors: Sang-jin SinAbstract:Abstract We study the holomorphic properties of the MQCD by comparing the super-potentials in MQCD and the gauge theory. First we show that the super-potential defined as an integral of three form is not appropriate for generic situation with quarks. We report a resolution of the problem which works for the brane configurations of 90 Degree Rotation, including the true SQCD. The new definition does not need an auxiliary surface and can be reduced to a contour integral for some cases. We find a relation between the new and old definitions, which is verified by explicit calculation for SU( N ), SO( N ), Sp( N ) simple groups with F of massive quarks,
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The super-potential and holomorphic properties of the MQCD
Nuclear Physics B, 1998Co-Authors: Sang-jin SinAbstract:We study the holomorphic properties of the MQCD by comparing the super-potentials in MQCD and the gauge theory. First we show that the super-potential defined as an integral of three form is NOT appropriate for generic situation with quarks. We report a resolution of the problem which works for the brane configurations of 90 Degree Rotation, including the true SQCD. The new definition does not need auxiliary surface and can be reduced to a contour integral for some cases. We find relation beetween the new and old definitions, which is verified by explicit calculation for SU(N), SO(N), Sp(N) simple groups with $F$ of massive quarks.Comment: 14pages, latex, typos correcte
Nobuyuki Matubayasi - One of the best experts on this subject based on the ideXlab platform.
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Molecular Dynamics Simulations of Yeast F1-ATPase Before and after 16-Degree Rotation of the Gamma Subunit
Biophysical Journal, 2013Co-Authors: Yuko Ito, Takashi Yoshidome, Nobuyuki Matubayasi, Masahiro Kinoshita, Mitsunori IkeguchiAbstract:We performed molecular dynamics simulations for crystal structures of yeast F1-ATPase whose crystallographic unit contains two different states. One complex binds Pi in the βE subunit, and the other liberated it. In the latter structure, the position of central stalk is rotated +16° in the hydrolysis direction. Because single molecule experiments have proven that Pi release occurs at the βE subunit, and the γ subunit is rotated after ATP hydrolysis and Pi release, these structures are supposed to represent snapshots before and after Pi releases for the 40° substep, respectively.We describe how the F1-ATPase complex changes the structure after Pi release, based on the results of the MD simulations for yF1II and yF1I. Then, we propose a possible mechanism of the 40° Rotation of the γ subunit.
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structural characteristics of yeast f1 atpase before and after 16 Degree Rotation of the γ subunit theoretical analysis focused on the water entropy effect
Journal of Chemical Physics, 2012Co-Authors: Takashi Yoshidome, Yuko Ito, Nobuyuki Matubayasi, Mitunori Ikeguchi, Masahiro KinoshitaAbstract:We have recently proposed a novel picture of the Rotation mechanism for F1-ATPase [T. Yoshidome, Y. Ito, M. Ikeguchi, and M. Kinoshita, J. Am. Chem. Soc. 133, 4030 (2011)]10.1021/ja109594y. In the picture, the asymmetric packing in F1-ATPase, originating from the water-entropy effect, plays the key role in the Rotation. Here, we analyze the differences between the experimentally determined structures of yeast F1-ATPase before and after 16° Rotation of the γ subunit with the emphasis on the water-entropy effect. For each of these structures, we calculate the hydration entropies of three sub-complexes comprising the γ subunit, one of the β subunits, and two α subunits adjacent to them. The βE, βTP, and βDP subunits are involved in sub-complexes I, II, and III, respectively. The calculation is performed using a hybrid of the angle-dependent integral equation theory combined with the molecular model for water and the morphometric approach. The absolute value of the hydration entropy is in the following order:...