Browsing by Author "Tsong, Tian Yow"

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A Markovian engine for a biological energy transducer: The catalytic wheel
(2007-04-01)
Tsong, Tian Yow
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Chang, Cheng-Hung
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物理研究所
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Institute of Physics
The molecular machines in biological cells are made of proteins, DNAs and other classes of molecules. The structures of these molecules are characteristically "soft", highly flexible, and yet their interactions with other molecules or ions are specific and selective. This chapter discusses a prevalent form, the catalytic wheel, or the energy transducer of cells, examines its mechanism of action, and extracts from it a set of simple but general rules for understanding the energetics of the biomolecular devices. These rules should also benefit design of manmade nanometer scale machines such as rotary motors or track-guided linear transporters. We will focus on an electric work that, by matching system dynamics and then enhancing the conformational fluctuation of one or several driver proteins, converts stochastic input of energy into rotation or locomotion of a receptor protein. The spatial (or barrier) and temporal symmetry breakings required for selected driver/receptor combinations are examined. This electric ratchet consists of a core engine that follows the Markovian dynamic, alleviates difficulties encountered in rigid mechanical model, and tailors to the soft-matter characteristics of the biomolecules. (c) 2006 Elsevier Ireland Ltd. All rights reserved.
Energy transduction in molecular machines
(2007-10-01)
Chang, Cheng-Hung
;
Tsong, Tian Yow
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交大名義發表
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物理研究所
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National Chiao Tung University
An applied force may cause the conformation and thus, the activity of a biological molecule to change. Here we consider a system in which an oscillating or fluctuating electric field is used to actuate membrane protein activities. Most proteins have electric dipoles and net charges in the structure and their conformations are susceptible to the electric and magnetic perturbation. The shape of a cell may also amplify an electric field across its plasma membrane. Therefore, a membrane integral protein such as an ion channel, an ion pump, or a molecular motor, is especially amenable to electric perturbation. The theory of electroconformational coupling addresses the functional implication of this field effect. When an alternating electric field or a fluctuating electric field is employed to actuate a two-state protein oscillator, the dynamics of the conformational change of the protein can be synchronized with the applied field. Through this two-state protein oscillator, we construct a four-state catalytic wheel by coupling an energy transducer mechanism to the two-state protein oscillator. Analysis shows that the catalytic wheel can extract energy from a disordered external energy source, be it electrical, mechanical, or chemical, and convert this stochastic energy source to a usable energy format. The catalytic wheel is tested with the experimental data on the electric field-stimulated cation pumping of Na, K-ATPase. A dipole ratchet model based on the electroconformational coupling concept will also be discussed and compared with the ATP-dependent rotation of a rotary motor F-1-ATPase. Since the working principle of this model is simpler than that of F-1-ATPase, it provides an easier way to realize a nanoscale rotary motor than artificially reconstructing a F-1-ATPase.