<<< Time Table >>> (最近の更新6/1/2010)
Poster Session 1 / Coffee (10:00~11:30)
Poster Presentations.(追加が有ります。)
Lunch (11:30~12:50)
0:Ryo Akiyama (Kyushu Univ., Japan)
Opening Remarks
(12:50~13:00)
1:Yuichi Harano (原野雄一) (Osaka Univ., Japan)
Title: Development of Predicting the Native Structure of a Protein Focusing on Water Entropy
(水のエントロピーに着目したタンパク質立体構造予測法の開発)
(13:00~13:30)
2:Tadanao Ito (伊藤忠直) (Sizuoka Univ., Japan)
Title: The response of F-actin solution to osmotic stress
(Ｆ−アクチン溶液の浸透圧ストレス応答)
(13:30~14:00)
3:Tomonari Sumi (墨智成) (Toyohashi Univ. of Tech., Japan)
Title: A possible mechanism of high-pressure unfolding of proteins: a formation of high-density hydration shell
(蛋白質の高圧変性メカニズム：界面高密度水和層の形成)
(14:00~14:30)
Poster Preview (14:30~15:00?)
Poster Session 2 / Coffee (15:00~16:30)
Poster Presentations.(追加が有ります。)
4:Daisuke Yokogawa (横川大輔) (Osaka Univ., Japan)
Title: Calculation of thermodynamic quantities based on DFT in the energy
representation
(エネルギー表示の密度汎関数理論に基づく熱力学量の計算法の開発)
(16:30~17:00)
5:Tadashi Kamiyama (神山匡) (Kinki Univ., Japan)
Title: Partial specific volume, compressibility, and coefficient of thermal expansion of protein in solution
(タンパク質の部分比容、圧縮率、熱膨張率)
(17:00~17:30)
6:Shoichi Toyabe (鳥谷部祥一) (Chuo Univ., Japan)
Title: Single-molecule nonequilibrium energetics of a molecular-motor F1-ATPase
(分子モーターF1-ATPaseの一分子非平衡エナジェティクス)
(17:30~18:00)
<<< Abstract >>>
Yuichi Harano (原野雄一) (Osaka Univ., Japan)
Title: Development of Predicting the Native Structure of a Protein Focusing on Water Entropy
(水のエントロピーに着目したタンパク質立体構造予測法の開発)
Abstract:
We have recently shown that the water entropy is the key quantity in elucidating the folding/unfolding mechanisms for proteins.
Based on the water entropy, the free energy function is developed for predicting the native structure of a proteins.
It simply consists of two terms, hydration entropy and dehydration penalty, for calculating the free energy instead of accounting all the atomic interactions within the system.
We show that It performs better than any other physics-based or knowledge-based potential function in terms of the accuracy in discriminating the native fold from misfolded decoys.
Tadanao Ito (伊藤忠直) (Sizuoka Univ., Japan)
Title: The response of actin filament solution to osmotic stress
(アクチンフィラメント溶液の浸透圧応答)
Abstract:
Actin filaments (F-actin) inhibit osmotic stress-driven water flow across a semi-permeable membrane in proportion to the filament concentration . When the filaments are crosslinked by F-actin binding protein, Filamin A, this flow is stopped completely . No conventional theory accurately accounts for these results. Here, we analyze this response by formulating the entropy of the system under osmotic stress. Results demonstrate that the response of the actin filaments to osmotic stress is governed by the Le Chatelier’s principle, which states that an external interaction that disturbs the equilibrium brings about processes in the body that tend to reduce the effects of this interaction. This is the first report demonstrating that the Le Chatelier’s principle applies to the reaction of biopolymers against equilibrium disturbances such as osmotic stress.
Tomonari Sumi (墨智成) (Toyohashi Univ. of Tech., Japan)
Title: A possible mechanism of high-pressure unfolding of proteins: a formation of high-density hydration shell
(蛋白質の高圧変性メカニズム：界面高密度水和層の形成)
Abstract:
A multiscale simulation of hydrophobic polymer chain immersed in water is presented.
In this method, all the hydration effects are taken into account through a hydration
free energy surface provided by a liquid-state density-functional theory.
To the best of our knowledge, high-pressure unfolding of protein has not
been reproduced even if all-atom-type molecular dynamics simulations are performed.
In our approach, a hydrophobic polymer chain is employed as a probe molecule for
investigating qualitative change of a hydration free energy surface acting on proteins.
The multiscale simulation analysis suggests that high-pressure unfolding
of protein is caused by a formation of an interfacial high-density hydration shell
in which a collapse of hydrogen-bond network is induced by the protein surface.
Daisuke Yokogawa (横川大輔) (Osaka Univ., Japan)
Title: Calculation of thermodynamic quantities based on DFT in the energy
representation
(エネルギー表示の密度汎関数理論に基づく熱力学量の計算法の開発)
Abstract:
We have developed a new approach to accurately calculate thermodynamic quantities based on density functional theory in the energy representation. The derived equation is expressed with only energy distribution functions, which can be easily computed by molecular dynamics. This approach was applied to a harmonic oscillator, an alanine dipeptide, and a small protein. We found that the results were accurate compared to conventional approaches, such as the quasiharmonic approximation.
Tadashi Kamiyama (神山匡) (Kinki Univ., Japan)
Title: Partial specific volume, compressibility, and coefficient of thermal expansion of protein in solution
(タンパク質の部分比容、圧縮率、熱膨張率)
Abstract:
Partial specific volume, compressibility, and coefficient of thermal expansion of protein in solution can sensitively reflect the compactness and flexibility of protein. These values are effective thermodynamic parameters to reveal macroscopic changes in the protein conformation and the protein-solvent interactions induced by temperature, pressure, solvent, additives, and so on. In ternary mixtures (water + dimethyl sulfoxide + lysozyme), lysozyme was unfolded with changes in the partial specific volume reflecting changes in the cavity volume and preferential hydration or solvation. The inclusion mechanism of cyclodextrin with butanediol isomers as the model of ligand binding to enzyme were also revealed by the partial specific volume and the volume changes were compared to the calculated values by computer. Some recent works about isothermal compressibility will be introduced together.
Shoichi Toyabe (鳥谷部祥一) (Chuo Univ., Japan)
Title: Single-molecule nonequilibrium energetics of a molecular-motor F1-ATPase
(分子モーターF1-ATPaseの一分子非平衡エナジェティクス)
Abstract:
Molecular motors drive mechanical motions utilizing the free energy
liberated from chemical reactions such as ATP hydrolysis. Using a new
nonequilibrium theory and a new micro-manipulation technique, we
measured the amount of thermodynamic quantities of a molecular motor,
F1-ATPase, at a single molecule level. We measured the violation of
the fluctuation dissipation theorem of rotating F1-ATPase by
electrorotation method to apply controlled external torque. From the
extent of this violation, the amount of thermodynamic quantities such
as work and heat was evaluated using Harada and Sasa's equality. Our
results indicate that F1-ATPase works at an efficiency of nearly 100%
under various conditions.
4th Mini-Symposium on Liquids 準備委員会（甲賀、秋山）