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Several problems in free energy calculation

Several problems in free energy calculation. JI Qing. 河北工业大学 生物物理研究所. Institute of Biophysics Hebei University of Technology. July 2013, Beijing. 1. Free energy change for kinesin’s neck linker docking. Force generation vs neck linker docking.

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Several problems in free energy calculation

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  1. Several problems in free energy calculation JI Qing 河北工业大学 生物物理研究所 Institute of Biophysics Hebei University of Technology July 2013, Beijing

  2. 1. Free energy change for kinesin’s neck linker docking Force generation vs neck linker docking Rice et al., Biophysical Journal, 2003 Method: EPR, spin marker mobile + intermediate probes K = immobilized probes Free energy change for NL docking Too small ! Hackney, PNAS, 2005 ATP hydrolysis: Work: R.Vale & R.Milligan, Science, 2000.

  3. What’s the problem? The problem arises from the understanding of the neck linker docking mechanism. Neck linker (~ 14 AA) consists of three parts: extra turn, b9 and b10. Neck linker docking consists of three steps: (1) Extra turn formation, (2) b9 docking, (3) b10 docking. b10 b0 CNB Cover-neck-bundle (CNB) = b0+ neck linker (b9) b9 Hwang et al., Structure, 2008 extra turn Rice et al., Nature, 1999

  4. 2. System-environment interaction vs free energy calculation Jarzynski’s equality (JE)： Jarzynski, PRL, 1997 (2) Steered molecular dynamics simulation (1) Single-molecule measurement Liphardt et al., Science, 2002 Park et al., JCP, 2003 in solution in vacuum

  5. Weak coupling assumption ? Jarzynski, PRL, 1997 JE is valid for sufficiently weak coupling between the system and reservoir. Neglecting Hint The fluctuations in the work W must not be much greater than kBT. This condition pretty much rules out macroscopic systemsof interest. ATP hydrolysis: Work by kinesin : H-bond energy: The free energy change for the hydrophobic binding of two methane molecules (CH4) in water : Je-Luen Li, Roberto Car, Chao Tang, and Ned S. Wingreen, PNAS, 2007

  6. 3. Water system: hydrogen bond identification Electronic orbitals of water dimer hydrogen bonds Geometric criterion for H bond: “r-q” criterion : 1.59 Å < rO…H < 2.27 Å,q> 140° Kuo et al., Science, 2007 Energy criterion for H bond: H-H radial distribution function for bulk water Pan et al., JCP, 2012 CPMD method, 64 water molecules 1000 water pairs Number of H bond “r-q” criterion 701 Energy criterion 528 Soper, Chem. Phys., 2000 repulsion

  7. Summary 1. The understanding of the system operating mechanism might affect the experiment design and calculation of free energy. 2. When Hint is comparable with Hsystem, can I directly use Jarzynski’s equality? 3. Water is the most important environment in our world. Water molecule is one of the most important biomolecules. The statistical description of the macroscopic behavior of water must be based on the quantitative knowledge of the microscopic structure and interaction of water molecules. The quantitative calculation of the free energy of water system is still a difficult task.

  8. Acknowledgement My students： My friends and collaborators： 卓益忠（Yin-Zhong Zhuo) 吕 刚（Gang Lv) 张 辉（Hui Zhang） 张 博（Bo Zhang） 张秀欣（Xiu-Xin Zhang） 潘 章（Zhang Pan） 耿轶钊（Yi-Zhao Geng） 李 铁（Tie Li） 覃静宇（Jing-Yu Qin） 刘书霞（Shu-Xia Liu） 柳睿殊（Rui-Shu Liu） 包景东（Jing-Dong Bao) 张红雨（Hong-Yu Zhang) 晏世伟（Shi-Wei Yan) The National Natural Science Foundation of China，No. 90403007 The National Natural Science Foundation of China，No. 10975044

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