Post on 27-Dec-2015
Anatoly B. Kolomeisky
UNDERSTANDING MECHANOCHEMICAL COUPLING IN KINESINS USING FIRST-
PASSAGE PROCESSES
Collaboration:
Alex Popov, Evgeny Stukalin – Rice University
Prof. Michael E. Fisher -University of Maryland
Prof. Ben Widom – Cornell University
Financial Support:
National Science Foundation
Dreyfus Foundation
Welch Foundation
Rice University
PUBLICATIONS:1) J. Stat. Phys., 93, 633 (1998).
2) PNAS USA, 96, 6597 (1999).
3) Physica A, 274, 241 (1999).
3) Physica A, 279, 1 (2000).
4) J. Chem. Phys., 113, 10867 (2000).
5) PNAS USA, 98, 7748 (2001).
6) J. Chem. Phys., 115, 7253 (2001).
7) PNAS USA, 98, 7748 (2001).
8) Biophys. J., 84, 1642 (2003).
Motor ProteinsEnzymes that convert the chemical energy into
mechanical work
Functions: cell motility, cellular transport, cell division and growth, muscles, …
Courtesy of Marie Curie Research Institute, Molecular Motor Group
Motor Proteins:
kinesin myosin-II
RNA-polymerazeF0F1-ATPase
There are many types: linear, rotational, processive, non-processive
Motor Proteins
Properties:
Non-equilibrium systems
Velocities: 0.01-100 m/s
Step Sizes: 0.3-40 nm
Forces: 1-60 pN
Fuel: hydrolysis of ATP, or related compound, polymerization
Efficiency: 50-100% (!!!)
Motor ProteinsMain Problems: What mechanism of motility? How many mechanisms?
THEORETICAL MODELING1) Thermal Ratchet Models
periodic spatially asymmetric potentials
2) Multi-State Chemical Kinetic (Stochastic) Models
sequence of discrete biochemical states
Ratchet ModelsIdea: motor proteins are particles that move in periodic but asymmetric potentials, stochastically switching between them
Advantages:
1) continuum description, well developed formalism;
2) convenient for numerical calculations and simulations;
3) small number of parameters;Disadvantages:
1) mainly numerical or simulations results;
2) results depend on potentials used in calculations;
3) hard to make quantitative comparisons with experiments;
4) not flexible in description of complex biochemical networks;
Multi-State Chemical Kinetic (Stochastic) Models
Assumption: the motor protein molecule steps through a sequence of discrete biochemical states
Multi-State Chemical Kinetic (Stochastic) Models
Advantages:
1) Exact results
2) Agreement with biochemical observations
3) Flexibility in description of complex biochemical systems
4) Agreement with experiments
Disadvantages:
1) Discreteness
2) Mathematical complexity
3) Large number of parameters
Single-Molecules Experiments
microtubule
bead
kinesin
Optical Trap Experiment:
laser
Optical trap works like an electronic spring
EXPERIMENTS ON KINESINoptical force clamp with a feedback-driven optical trap
Visscher,Schnitzer,Block (1999) Nature 400, 184-189
precise observations:
mean velocity V(F,[ATP])
SFstall force
dispersion D(F,[ATP])
mean run length L(F,[ATP])
step-size d=8.2 nm
Theoretical Problems:
• Description of biophysical properties of motor proteins (velocities, dispersions, stall forces, …) as the functions of concentrations and external loads
• Detailed mechanism of motor proteins motility
a) coupling between ATP hydrolysis and the protein motion
b) stepping mechanism – hand-over-hand versus inchworm
c) conformational changes during the motion
d) …
OUR THEORETICAL APPROACH
j=0,1,2,…,N-1 – intermediate biochemical states
kinesin/
microtubule
kinesin/
microtubule/ATP
kinesin/
microtubule/ADP/Pi
kinesin/
microtubule/ADP
N=4 model
OUR THEORETICAL APPROACH
our model periodic hopping model on 1D lattice
exact and explicit expressions for asymptotic (long-time) for any N!
Derrida, J. Stat. Phys. 31 (1983) 433-450
22 )()(2
1}),({
,)(}),({
lim
lim
txtxdt
dwuDD
txdt
dwuVV
tjj
tjj
dispersion
x(t) – spatial displacement along the motor track
dV
Dr
2
drift velocity
randomness bound! r >1/N
stall force
1
0
B
)0(
)0(ln
N
j j
jS w
u
d
TkF 0)( SFFV
OUR THEORETICAL APPROACHEffect of an external load F:
TkFdjjj
TkFdjjj
jj ewFwweuFuu BB // )0()(,)0()(
jj and load distribution factors 1)(
1
0
N
jjj
activation barrier aE
Fdj
Fdj1
F=0F >0
j
j+1j
j+1
TkEj
aeu B/
RESULTS FOR KINESINSstall force depends on [ATP]
Michaelis-Menten plots
F=1.05 pNF=3.59 pN
N=2 model
)(
)(
1010
1010
wwuu
wwuudV
1
0
B
)0(
)0(ln
N
j j
jS w
u
d
TkF
RESULTS FOR KINESINS
force-velocity curves randomness
Mechanochemical Coupling in Kinesins
• How many molecules of ATP are consumed per kinesin step?
• Is ATP hydrolysis coupled to forward and/or backward steps?
Nature Cell Biology, 4, 790-797 (2002)
Mechanochemical Coupling• Kinesin molecules hydrolyze a single ATP molecule
per 8-nm advance
• The hydrolysis of ATP molecule is coupled to either the forward or the backward movement (!!!!!!!!!!)
Schnitzer and Block, Nature, 388, 386-390 (1997)
Hua et al., Nature, 388, 390-394 (1997)
Coy et al., J. Biol. Chem., 274, 3667-3671 (1999)
Problem: back steps ignored in the analysis
Nishiyama et al., Nature Cell Biology, 4, 790-797 (2002)
Backward steps are taken into account
Mechanochemical Coupling
Nishiyama et al., Nature Cell Biology, 4, 790-797 (2002)
Investigation of kinesin motor proteins motion using optical trapping nanometry system
Mechanochemical Coupling
Fraction of 8-nm forward and backward steps, and detachments as a function of the force at different ATP concentrations
circles - forward steps;
triangles - backward steps;
squares – detachments
Stall force – when the ratio of forward to backward steps =1
Nishiyama et al., Nature Cell Biology, 4, 790-797 (2002)
Mechanochemical Coupling
Dwell times between the adjacent stepwise movements
Dwell times of the backward steps+detachments are the same as for the forward 8-nm steps
Both forward and backward movements of kinesin molecules are coupled to ATP hydrolysis
Nishiyama et al., Nature Cell Biology, 4, 790-797 (2002)
Mechanochemical Coupling
Branched kinetic pathway model with asymmetric potential of the activation energy
Idea: barrier to the forward motion is lower than for the backward motion
)()(
111
3321 FkFkkk fb
Nishiyama et al., Nature Cell Biology, 4, 790-797 (2002)
Conclusion: kinesin hydrolyses ATP at any forward or backward step
Mechanochemical Coupling PROBLEMS:
1) Backward biochemical reactions are not taken into account
2) Asymmetric potential violates the periodic symmetry of the system and the principle of microscopic reversibility
3) Detachments are not explained
Nishiyama et al., Nature Cell Biology, 4, 790-797 (2002)
Our Approach
The protein molecule moves from one binding site to another one through the sequence of discrete biochemical states, i.e., only forward motions are coupled with ATP hydrolysis
Random walker hopping on a periodic random infinite 1D lattice
Dwell times – mean first-passage times;Fractions – splitting probabilities
Our Approach
N,j – the probability that N is reached before –N, starting from the site j
1,1,,
jN
jj
jjN
jj
jjN wu
w
wu
u
0 ,1 ,, NNNN Boundary conditions:
N.G. van Kampen, Stochastic Processes in Physics and Chemistry, Elseiver, 1992
Our Approach
0,N -splitting probability to go to site N, starting from the site 0,
fraction of forward steps
0,0, 1 NN fraction of backward steps
1
0
0,
1
1N
j j
jN
u
w
Our Approach
TN,j – mean first-passage time to reach N, starting from j
TN,0 – dwell time for the forward motion;
T-N,0 – dwell time for the backward motion
eff
NN
eff
NN w
Tu
T 0,0,
0,0, ,
)1(
1 ,
1 1
1 11
0
N
k
kj
ji i
i
jjN
jj
eff u
w
ur
ru
with
1
00,
0,N
j j
j
N
N
eff
eff
w
u
w
u
Our Approach
0,0,0,0, but , NNNN TT
eff
NN
eff
NN w
Tu
T 0,0,
0,0, ,
Important observation:
Dwell times for the forward and backward steps are the same, probabilities are different
)( effeff wudV Drift velocity
Our Approach
jWith irreversible detachments
j, -probability to dissociate before reaching N or -N, starting from j
1,,, jjNjN - fractions of steps forward, backward and detachments
1,1,,
jN
jjj
jjN
jjj
jjN wu
w
wu
u
Our ApproachjWith irreversible detachments
1*
1*
,*,
,*,
,
, ,
jjjjjj
j
jNjN
j
jNjN
uwuu
TT
Define new parameters:
j – the solution of matrix equation 0M* 1,,...,,...,,1 11 NjN -vector
;1for ,
;1for ,
;for ),(
1
1
iju
ijw
jiwu
M
i
i
jjj
ij
matrix elements
Our ApproachjWith irreversible detachments
Model with detachments jNjNjj Twu ,, ,,,
Model without detachments *
,*
,** ,,, jNjNjj Twu
N=1 case:
wuTTT
wuwu
w
wu
u
1
, , ,
0,0,10,1
0,0,10,1
Our ApproachjWith irreversible detachments
Description of experimental data using N=2 model; reasonable for kinesins
Fisher and Kolomeisky, PNAS USA, 98, 7748 (2001).
)exp()0()(
)exp()0()(
Tk
FduFw
Tk
FduFu
B
jjj
B
jjj
Load dependence of rates
Comparison with Experiments
Fractions of forward and backward steps, and detachments
[ATP]=10M [ATP]=1mM
Comparison with Experiments
Dwell times before forward and backward steps, and before the detachments at different ATP concentrations
APPLICATION FOR MYOSIN-V
N=2 model
mean forward-step first-passage time )(
)(
1010
1010
wwuu
wwuu
Kolomeisky and Fisher, Biophys. J., 84, 1642 (2003)
CONCLUSIONS
• Analysis of motor protein motility using first-passage processes is presented
• Effect of irreversible detachments is taken into account
• Our analysis of experimental data suggests that 1 ATP molecule is hydrolyzed when the kinesin moves forward 1 step