1. Chemical-Mechano Free-Energy Transduction: From Muscles to Kinesin Motors and Brownian Ratchets IPAM workshop IV: Molecular Machines. May 23-28, 2004 Yi-der Chen, Laboratory of Biological Modeling, NIDDK, NIH

2. Processive motor: portor Non-processive motor: rower

3. X-ray structure Biochemistry Cryo-electron microscopy Molecular dynamics simulation CMC of single motors System mechanical properties Formalism Chemical-Mechano Cycle (CMC): It describes how the biochemical and mechanical cycles of the motor are coupled at the molecular level

4. M MT T DPDP M + T MT MTM + D + P k1k1 k2k2 k3k3 k4k4 Biochemical Cycle and Chemical-Mechano Cycle AM AMT T DPDP M

6. f g g 0 x F U A fg A. F. Huxley 1957 Basic elements of a Chemical-Mechano Cycle: 1.Contains both attached and detached states; 2.Contains at least one asymmetric rate constants; 3.Contains at least one force-generating step.

7. Thermodynamic Consistency: Each chemical-mechano state is an equilibrium state and therefore has a unique Gibbs free energy. Thus the following two equations must be obeyed when assigning the rate constants to the cycle:

8. http://www.mpimf- heidelberg.mpg.de/~holmes/muscle/muscle1.html AM MT AMDP AMD AM

9. Kinesin has been found: Cell dividing Heavy chain, 124KD Light chain, 64KD Structure and function of kinesin motor Microtubule gliding Kinesin pulls a cargo MT binding site In all types of cells At all stages of cell development 3kin

10. Vale and Milligan, Sci. 288, 88 (2000)

11. F D F D T F D D + PiPi F D F T D a 1-a F D F D F F D T D F T D D D+P i a 1-a Linker-zipping ModelLever-swinging Model *Nucleotide-free: Head attached; linker un- zipped *D state: Head detached; Linker un- zipped. *T and D+P states: Head attached; Linker zipped *Power stroke: 2 to 3 and 4 to 1’. 1 2 3 4 1’1’ *Nucleotide-free: Head attached in 90 o *D state: Detached *T and D+P states: Head attached in 45 o *Power stroke: 2 to 3 and 4 to 1’ Tight coupled model: One step forward for each ATP hydrolyzed

12. Single Kinesin Motility Assay Visscher et al., Nature 400:184-9 (1999)

13. 0123 m = -1 Microtubule lattice F OT

14. 1.Free kinesin in the absence of the bead: The velocity of the motor is directly proportional to the flux of the cycle. Kolomeisky, Fisher

15. a F F r 12 r 21, )1(0 21 Fa e rr   Chemical Kinetic Formalism 2.Kinesin moving against a constant force: when the feedback of the optical trap in the motility assay of Visscher et al is infinitely fast. Equations derived for the free-motor case are still applicable to this case except that the rate constants have to include the effect of force. Kolomeisky, Fisher, Qian

16. 3.Kinesin moving against a randomly fluctuating force: Assay of Visscher et al Question: How does the Brownian motion of the bead affect the velocity of the motor? Slow it down or speed it up?

17. (A). Focus on the movement of the bead: A Brownian motion problem with stochastic pulling of the motor. Fokker-Planck equation (B). Monte Carlo simulation on the movement of the motor and the Brownian motion of the bead simultaneously

19. Strain energy and rate constants The strain energy obeys Hooke’s law: Where x is the position of bead, and x i (m) is the position of the bead when the motor is attached to the lattice site m in state i and the spring is relaxed. Note: x 1 (m) = m and x 2 (m) = m - a. x-dependent rate constants:

20. (3) (4) Sum Eqs. (3) and (4), we have (6) Diffusion-reaction equations of the bead movement (5) At steady-state,.. Thus, u = constant = mean velocity

21. etc. into Eqs. (3)-(5), we get the final ODE at m=0: Substitute

22. L=8 nm   =0.5   =0.5 a=0.5 K=16 (1.03 pN/nm) Chemical Kinetic formalism (CK): Our formalism CK

23. KmKm KeKe KtKt (K t  0.037 pN/nm)

24. 1.Chemical-Kinetic formalism (in the absence of the bead Brownian motion) always gives larger velocities: bead Brownian motion always reduces the velocity of the motor. 2.However, this effect becomes smaller as the elastic coefficient is reduced.

25. state 1state 2state 1 a (  step )(  step ) (A) (B) MT x K Strain energy of spring at z: z-dependent rate constants: (1) To evaluate the dwell time T: state 1 state 2 (2) To determine the move direction: state 1 state 2 Forward if Backward otherwise. Model and Monte Carlo strategy

29. 0123 A single one-headed kinesin can also execute directed movements on a microtubule, if it carries a cargo

30. Flashing Ratchets Astumian and Bier. PRL 72, 1766 (1994) +

31. Flashing Brownian Particle It will not work, because it is against Thermodynamics. +

32. A+B-A+B- A + + B - A+B-A+B- A+A+ A+B-A+B- B-B- A+A+

34. Zhou and Chen Phys. Rev. Lett. 77, 194 (1996).

35. SUMMARY 1.Chemical-Mechano Cycle is important in studying molecular motors. Future biochemical and structural experiments should focus on elucidating the “strain-dependent” rate constants of the cycle (by applying some sorts of force to the motor). 2.When studying the processive movement of a motor carrying a cargo (in vivo or in vitro), it is important to consider the effect of Brownian motion of the cargo. 3.An enzyme catalyzing a non-equilibrium chemical reaction can execute directed movement on an asymmetric static potential. The direction of enzyme movement depends not only on the asymmetry of the potential, but also on the direction of the catalytic cycle. The catalytic cycle of the enzyme can be identified as a working Chemical-Mechano Cycle.

36. Bo Yan, University of Georgia Hwan-Xiang Zhou, University Florida Robert Rubin, LBM, NIH Terrell L. Hill