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Rectified Brownian Motion in Subcellular Biology

Rectified Brownian Motion in Subcellular Biology. Ronald F. Fox Mee Choi William Mather School of Physics Georgia Institute of Technology. Nanobiology Biochemistry Molecular biology. Can we learn mechanisms from nanobiology that are applicable to nanotechnology?. One such lesson is

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Rectified Brownian Motion in Subcellular Biology

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  1. Rectified Brownian Motion in Subcellular Biology Ronald F. Fox Mee Choi William Mather School of Physics Georgia Institute of Technology RF Fox FNAL 2006

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  3. Nanobiology Biochemistry Molecular biology Can we learn mechanisms from nanobiology that are applicable to nanotechnology? RF Fox FNAL 2006

  4. One such lesson is the constructive use of thermal energy. Such a mechanism is called Rectified Brownian Motion. RF Fox FNAL 2006

  5. A Few Antecedents A. F.HuxleyProg. Biophys. Chem. 7, 255 (1957)M.Meister, S. R.Caplan and H. C.BergBiophys. J. 55, 905 (1989)R. D.Vale and F.OosawaAdv. Biophys. 26, 97 (1990) RF Fox FNAL 2006

  6. Rectified Brownian Movement in Molecular and Cell Biology Phys. Rev. E 57, 2177 (1998) Rectified Brownian Motion and Kinesin Motion Along Microtubules Phys. Rev. E 63, 051901 (2001) (with Mee Choi) Kinesin’s Biased Stepping Mechanism: Amplification of Neck Linker Zippering Biophysical Journal, 91 2416-2426 (2006) (with William Mather) RF Fox FNAL 2006

  7. A Minnow RF Fox FNAL 2006

  8. A Minnow and an E. Coli RF Fox FNAL 2006

  9. A Minnow, an E. Coli and Ubiquinone RF Fox FNAL 2006

  10. Reynolds Number RF Fox FNAL 2006

  11. Biological Energy Couplings Photon energy (electron excitation) Electron energy (redox reaction) Proton energy (pH gradient) Phosphate energy (monomer activation) RF Fox FNAL 2006

  12. Redox reaction variety Pure, 1 electron transfer Iron, copper, zinc… 1 electron and 1 proton transfer FADH2, UQH2,.. 2 electrons and 1 proton transfer NAD+, NADH,.. RF Fox FNAL 2006

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  15. diffusion for reduced ubiquinone boundary layer equation RF Fox FNAL 2006

  16. diffusive rate parameter reaction rate parameter RF Fox FNAL 2006

  17. implications Weak linear steady state gradients Negligible energy dissipation associated with the gradients according to non-equilibrium steady state thermodynamics RF Fox FNAL 2006

  18. Langevin equation Einstein’s Relation 1905 RF Fox FNAL 2006

  19. Brownian Work Theorem Secular power from secular force Stochastic power from Brownian force Power expended by drag force RF Fox FNAL 2006

  20. Rotary Enzymes Lipoamide 1.4 nm long acetyl or succinyl carrier pyruvate and a-ketoglutarate dehydrogenases Biocytin 1.4 nm long CO2 carrier pyruvate carboxylase and fatty acid synthetase Phosphopantetheine 2.0 nm long thioester carrier gramicidin and tyrocidine synthetases fatty acid synthetase, polyketide synthetase RF Fox FNAL 2006

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  23. Kinesin A two “headed” motor protein that “walks” on microtubules Processivity Bias Coordination RF Fox FNAL 2006

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  25. Mechanisms Direct Chemo-Mechanical Energy Conversion “Power Stroke” ATP Powered Conformation Change Rectified Brownian Motion ATPase Switch Heat Powered Conformation Change RF Fox FNAL 2006

  26. POWER STROKE The trailing head is “thrown forward” in a way that is “akin to a judo expert throwing an opponent with a rearward-to-forward swing of the arm.” b-sheet boundary hydrogen bonds ATP powered b-sheet closure [Vale and Milligan, Science 288, 88 (2000)] RF Fox FNAL 2006

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  28. Forces Covalent C-C, C-N and C-O bonds 4.0 - 4.3 nano-Newtons Hydrogen bonds ~0.1 - ~50(?) pico-Newtons Unbound kinesin head neck linker tensions 100 - 200 pico-Newtons RF Fox FNAL 2006

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  31. Measured neck linker free energy of binding to the edge of the b-sheet is only a few kT. This is enough energy to cause a significant bias for attachment in the forward direction, or plus end of the microtubule. Rectified Brownian Motion RF Fox FNAL 2006

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