1 / 40

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

valdemar
Download Presentation

Rectified Brownian Motion in Subcellular Biology

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

  2. RF Fox FNAL 2006

  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

  13. RF Fox FNAL 2006

  14. RF Fox FNAL 2006

  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

  21. RF Fox FNAL 2006

  22. RF Fox FNAL 2006

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

  24. RF Fox FNAL 2006

  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

  27. RF Fox FNAL 2006

  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

  29. RF Fox FNAL 2006

  30. RF Fox FNAL 2006

  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

  32. RF Fox FNAL 2006

  33. RF Fox FNAL 2006

  34. RF Fox FNAL 2006

  35. RF Fox FNAL 2006

  36. RF Fox FNAL 2006

  37. RF Fox FNAL 2006

  38. RF Fox FNAL 2006

  39. RF Fox FNAL 2006

  40. RF Fox FNAL 2006

More Related