Annual Report DiCK / SLaBS RCAS, Academia Sinica

1. Annual ReportDiCK/ SLaBSRCAS, Academia Sinica PI: Kuo Kan Liang 梁國淦 RCAS, AS and BST, NTU

2. Theme of Researches • Chemical reactions and transport processes in biological systems • Special emphases: Membrane protein ion channels • Methodology: • Spectroscopic methods • Electrochemistry methods • Both include theory and experiments RCAS, AS and BST, NTU

3. Methodology:Spectroscopic Methods • Eternal goal: Spectroscopic observation of the kinetics with as little labeling as possible • IR spectroscopy; • Mid-IR range observation of amide-I peaks • Ultrafast multiphoton coherent spectroscopy such as 2D-IR • Time-resolved FT-IR • Fluorescence spectroscopy: • Natural amino acids: Tryptophan, tyrosine RCAS, AS and BST, NTU

4. Methodology:Spectroscopic Methods • Protein backbone modes couplings can be observed as vibration coherence as well as mode anharmonicity • Past achievements • Theory of anharmonic effect on absorption lineshape • Theory of effect of near-by vibronic level on the 3-pulse photon echo signal of a vibration mode • Theory of anharmonic and mode-mode coupling effect on the 3-pulse photon echo signal of a vibration mode. RCAS, AS and BST, NTU

5. Publications:Spectroscopic Methods • Chu, Z.*; Liang, K. K.*; Hayashi, M.; Lin, S. H., “Theoretical treatment of anharmonic effect on molecular absorption, fluorescence spectra, and electron transfer”, Chem. Phys. 2009, 358, 137. RCAS, AS and BST, NTU

6. Publications:Spectroscopic Methods Villaeys, A. A.*; Dappe, Y.; Liang, K. K.; Lin, S. H., “Influence of neighboring levels in three-pulse photon-echo processes”, Phys. Rev. A2009, 79, 053418. (Virtual Journal of Ultrafast Science 2009, Vol. 8, Issue 6) RCAS, AS and BST, NTU

7. Publications:Spectroscopic Methods Liang, K. K.*; Villaeys, A. A., “Anharmonicity and mode-mode coupling effects analyzed by 4WM photon-echo spectroscopy”, Phys. Rev. A 2010 (Accepted with minor corrections). RCAS, AS and BST, NTU

8. Methodology:Electrochemistry Methods • Impedance spectroscopy (transfer function) of ion channels • Modified electrophysiology (patch-clamp) experiments • Patch-clamp impedance spectroscopy • Patch-Clamp fluorometry (Electrophysiology + Spectroscopy) • Time-resolved experiments: synchronization method

9. Publication:Electrophysiology Methods Hill plot: Hill coefficient ~ 2.5 Indicating that cooperative binding is not the sole story Chang, H.-K.; Martin, L. J.; Liang, K. K.; Shieh, R.-C.*, “K+ binding in G-loop and water cavity facilitates Ba2+ movement in the Kir2.1 Channel”, Biochim. Biophys. Acta 2009, 1788, 500. RCAS, AS and BST, NTU

10. Further Developments:Short term • Theory of kinetics of cooperative systems * • Stochastic model of ion transport in channels * • Molecular dynamics simulations and analysis of hydrated cationstransport in bulk and in artificial channels • Patch-clamp fluorometry of unlabeled Kir 2.1/ 2.2 channels RCAS, AS and BST, NTU

11. Further Developments:Mid-term • Impedance of ion channels • Theoretical method: Chemical kinetics simulation of the ion transport process in ion channels • Experimental method: AC patch-clamp • Advanced materials for CO2separation • Theory of CO2 or CO32– transport in pores such as in polymer-metal framework (PMF) • Model system construction for cell-free CO2 reduction using enzymes RCAS, AS and BST, NTU

12. Further Developments:Long-term • Thermodynamics and kinetics of single- / few- biological-macromolecule events • Theory of reactive transport in pores / channels • Thermodynamics and kinetics of binding in channels • Thermodynamics systems with electrostatic works • Electrochemical and structural kinetics of cells • Synchronous observations of reactions, transport processes, and structural changes on membrane • Engineering of cellular or cell-free molecular factories RCAS, AS and BST, NTU