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Nils Gustafsson

Issue: 1 Date: February 10, 2012

School of Physics and Astronomy University of Birmingham Birmingham, B15 2TT E-Mail: nsg960@bham.ac.uk

. . . . . • Characterise the co-operation of the molecular motors in the various phases and at the phase transitions by studying the auto-correlation of the spring length. . . . . . . . .2 Mean Field Theory . . . • Use the auto-correlation in the spring length to produce a power spectrum of tension ﬂuctuations using Fourier analysis and the Wiener-Khintchine relations. . . . . . . . . . . . via the protein shaft γ. . . . . . . . . . . . . . Molecular motors. .3 Langevin Noise Theory . . . . . . to the F1 motor. . . . . . . . . . . . . the F0 motor is a rotary motor driven by the proton gradient page 1 of 6 . thermodynamically driven in opposing directions but connected by a spring. . . . . . . . . using Langevin noise theory. . . .. . 2008]. . 2000] and kinesin [Howard et al. . . . 3. . In the same sense free energy is made available on the molecular scale through chemical processes allowing biological nanomachines to perform useful work. Many molecular motors including those mentioned obtain free energy from the hydrolysis of Adenosine Triphosphate (ATP) simpliﬁed to AT P → ADP + Pi . . . . . . . . . 1993]. . . . . . . . . the magnitude of which will be informed by the power spectrum. Detailed Objectives: • Describe the function of the coupled molecular motors in the terms of a three phase system. . . .2 Auto-Correlation . . Motivation for the study of the ATPase is driven by the importance of ATP synthesis to life. . . . . myosin V [Rief et al. . . . . . .4 Monte Carlo Simulations . . ATP is so integral to life that in the human body approximately 2 × 1026 molecules or equivalently 160kg of ATP can be synthesised daily [Karp. . . Auto-correlation 1 Aims Overall Objective: Use a Monte Carlo simulation of two linear molecular motors. . . . . . . . . . . . . . . . . ATP Synthase. . .CONTENTS Project Proposal Nils Gustafsson Contents 1 Aims 2 Introduction 3 Planned Approach 3. . . . . . . . Furthermore. to explore the conditions required for compound biological nanomotors such as F0 F1 ATP Synthase to work eﬀectively. . 5 Time Table Keywords: Thermodynamics. . .1 ATPase Synthesis Rate . . . . . . . 1989] which are integral to cellular functions in their roll as molecular tethers and transporters respectively. . .. . . . . . . responsible for muscle contraction. . . . 2000] [Walker et al. the ‘forward’ phase. . . . . . . In the case of ATPase these are the membrane embedded F0 motor connected. Phase Transitions. . . . . . This molecular scale environment is characterized as a thermal bath [Bobylev and Cercignani. . . . . ATPase belongs to a class to molecular motors which consist of two coupled motors working co-operatively to perform useful work. . . . . . . . . . . Consequently ﬂuctuations due to thermal noise become signiﬁcant so the behavior of the molecular motor is stochastic and it will execute a random walk [Berg. . . 3. . . . the ‘locked’ phase and the ‘backward’ phase and characterise the phase transitions. . . .1 Thermodynamics and Kinetics 3. . . . . . . . . . . . . . . . . 1 1 2 2 3 3 3 3 4 4 5 . . . . . . . . . . . . . in humans. . . . . . . 2002] of nonzero temperature particles performing Brownian motion. . is found on the inner membrane of the mitocondria and is the primary focus of this project. . Examples of biological nanomotors include myosin II. . 1997] which. . . . 2 Introduction Macroscopic thermodynamic cycles can make use of free energy from heat to perform work. 4. . . 4 Preliminary Results 4. . . . . . . • Development of the mean ﬁeld theory of coupled molecular motors by adding tension ﬂuctuations. . .. . This vital synthesis is performed by a molecular motor called F0 F1 ATP Synthesis (ATPase) [Boyer. . . . . . . . . .

Figure 1: Linear analogue of F0 F1 ATP Synthase The law of mass action is applied to the rate constants from which it follows that k1+ /k1− = exp[−(∆G1 + ∆W1 )/kT ]. when F1 is driven in reverse by the rotation of the F0 motor it synthesizes ATP. 1999] and current computational simulations [Czub and a Grubm¨ller.. Thomas et al. 2011]. When this is not the case ATPase will act as a proton pump [Czub and Grubm¨ller. 1998] on the F1 motor in isolation guides the choice of ‘Case B’ over others discussed in Thomas et al.1 Planned Approach Thermodynamics and Kinetics For the purposes of this project a linear analogue of ATPase. The shaft. One of these. The Monte Carlo methods outlined in this proposal present a further computational method for analysing the torsional rigidity of γ and the results will aim to add to this growing body of literature.Project Proposal Nils Gustafsson across the membrane and the F1 motor is a rotary motor which in isolation would normally be driven by the hydrolysis of ATP. ‘Case B’. Also. biased in opposing directions and coupled by a spring of stiﬀness λ (Figure 1) will be employed. consisting of two linear motors executing random walks. However. A value of approximately 100 pNnm is quoted as an upper bound to λ with 65% of this stiﬀness being a consequence of the coupling to the α − β structure. 3 3. consequently γ can only transfer energy eﬀectively if suﬃcient torsional ﬂexibility in the shaft exists [Czub and Grubm¨ller. In addition no previous studies have been found to date which consider changing the value of λ and observing the simulated eﬀects on the functionality of ATPase. [2001]. This equation provides the link between the thermodynamics. The rate constants for forward and backward transitions are denoted by k1+ and k1− respectively. 2000] [Kato-Yamada et al. plays a vital role in the transferal of energy from F0 to F1 . 2011]. [2001] discuss three idealised cases for the one state motor. Comparing the force-velocity relation to previous work [Masaike et al. which determines the amount of work which can be done. which describes the stochastic nature of the system. The linear motors will be assumed to move processively along the tracks n and m (Figure 1) performing a ﬁxed amount of work ∆Wi (T ) with a ﬁxed increase ∆Gi per step of ﬁxed length ui where i denotes either the l0 or l1 motor. Working in this limit allows exact calculation of the backwards rate constant and consequently the instantaneous velocity. takes the forward rate constant k1+ to be a constant thereby treating the motor as a chemically driven ratchet. (1) using the free energy of reaction and Einstein’s principal of detailed balance as discussed in Thomas et al. However. ATPase and speciﬁcally the torsional rigidity of γ is the subject of previous experimental research and computational simulations [P¨nke and Rumberg.. for synthesis to be possible the free energy available from the proton gradient must exceed the free energy provided by ATP hydrolysis. 2011]. page 2 of 6 . while the F0 motor completes 10 discreet steps per 360 degree rotation. Czub and Grubm¨ller u [2011] used atomistic simulations to study the spatial and structural properties of ATPase determining λ from the intrinsic elasticity of γ and the eﬀective potential from the binding to the catalytic α − β protein structure that forms the main body of F1 . P¨nke and Rumberg [1999] varied the proton gradient across the membrane experimentally u a and measured the changes in synthesis rate. the F1 motor only completes 3. The transition between u these two phases of operation and the ‘locked’ phase observed at large values of λ will also be studied in detail. γ. and the kinetics. [2001]. The experimental results were used to determine input parameters to ﬁt a computational simulation onto the results and a value of 30 pNnm is quoted for λ. Fixing the position of the l0 motor such that only the l1 motor is allowed to make transitions between states allows us to consider the biochemical cycle of this individual molecular motor. u Varying the torsional rigidity (λ) of γ and studying the eﬀects on ATP synthesis rate and the correlation in the motion of the two motors will form the main focus for this project.

This analysis requires a thermodynamic constraint which sets all negative results for the velocity to zero. against time • The velocity of a chemically driven ratchet in one dimension against the load applied [Thomas et al. for example evaluation of the kth moment and the central limit theorem. 1998]. Before any conclusions are drawn from the Monte Carlo simulations statistical tests.2 Mean Field Theory Project Proposal Nils Gustafsson 3.1] can be used to determine the type of transition. 3.4 Monte Carlo Simulations The stochastic nature of biological nanomachines lends itself to simulation by Monte Carlo methods. The strength of these ﬂuctuations is then tuned to produce an eﬀect of the correct magnitude. This is done in order that the net free energy used by the system does not exceed the net free energy available. pulling on a constant load. 2001] page 3 of 6 .3 Langevin Noise Theory Langevin noise theory [Reif. • The number of un-decayed radioactive nuclei against time • The position of a particle executing a biased random walk in a one dimension against time [Berg. The dwell time at any one site must be exponentially distributed with a mean related to the rate constants for the possible transitions. the Monte Carlo methods to be used in the linear ATPase simulation were veriﬁed by simulating ﬁve stochastic processes which have analytical solutions to the rate equations. This is done using the transition probabilities δpi = ki δt and choosing δt such that the total sum of the transition probabilities is of the order of 0. Two methods are used for the simulations in this study. 1993] • The position of a chemically driven ratchet in one dimension. It is anticipated that this pseudo mean ﬁeld theory will agree with simulated rates far from the transition between the ‘forward’ and ‘locked’ states but as with other mean ﬁeld theories will deviate close to the phase transition [Lerner. 3. This can be done using Fourier analysis of the auto-correlation function (as per the Wiener-Khintchine relations. The transition probability must be small to reduce the probability of two transitions occurring in time δt to a statistically insigniﬁcant value. Reif [1965]) and it is anticipated this will inform the analytical Langevin approach. over a very large period (of the order of 109 ).01. 1965] introduces randomly ﬂuctuating forces into an equation of motion. Noise terms were introduced into the steady state rate equations and treated in the frequency domain. It is hoped an improved theory can be achieved using Langevin noise theory. The strength of the noise terms was normalised to the mean square ﬂuctuation in transition probability calculated from binomial statistics.2 Mean Field Theory Similar treatment of the l0 motor will produce a force-velocity relation that intersects the force-velocity relation for l1 indicating the operating point of the two coupled motors. Previous work by Thomas and Thornhill [1995] has shown that it is possible to use Langevin noise terms in the rate equations of muscle cross bridges to model tension ﬂuctuations. Solving for the velocity and tension co-ordinates of this intersection (using MatLab) will allow calculation of the overall rate of the coupled motor system at a mean tension of the spring. The ﬁrst method requires an average of 100 random numbers to be sampled for every transition but this can be reduced to just two per transition using the dwell time distribution.. will be used to conﬁrm the statistical randomness of the generator used.1] to determine if a transition occurs in a time step δt and if so what that transition will be. 4 Preliminary Results As proof of principal. Monte Carlo methods are computational algorithms which repeatedly sample randomly from a probability distribution to produce inputs for a deterministic computation. Auto-correlation data from the Monte Carlo simulation (Section 3. Sampling randomly from this distribution allows us to determine when a transition has occurred and a second random number sampled from a uniform distribution [0. 2011].3. The Mersenne Twister random number generator has the required properties [Matsumoto and Nishimura. The ﬁrst uses random numbers sampled from a uniform distribution over [0. The result of the simulation is vastly improved by aggregating the results of a large number of truly random samples.4) can be used to produce a power spectrum of tension ﬂuctuations in the coupling spring. This requires a pseudo random number generator with a very high statistical randomness.

1965]. ∆G1 = −10 kJM −1 . At critical values of λ close to the phase transition (B) this exponential decay is seen as an envelope to an emergent oscillatory behavior in the auto-correlation function. While it is expected that there will be discrepancies between these models near the transition it is not anticipated that the discrepancy will be of the order of a factor of two in the λ direction.1 ATPase Synthesis Rate Project Proposal Nils Gustafsson • The probability of site occupation of a chemically driven ratchet tethered to a ﬁxed point by a spring There are no discrepancies to report.5. There is agreement at small values of λ and as λ is increased there is a transition from the ‘forward’ to the ‘locked’ phase. u0 = 1 nm and thesis) to ‘Backward’ (proton pumping). Varying the net free energy availFigure 2: Comparison of the mean ﬁeld velocity to the able from negative to positive is also possible.2 Auto-Correlation While the Monte Carlo simulation may not be quantitatively correct it appears to behave well qualitatively and interesting results have been obtained for the auto-correlation of the spring length. Figure 3: Auto-correlation functions of the spring length for (A) λ = 0. 4. ∆G0 = direction of the ATPase from ‘Forward’ (ATP syn−20 kJM −1 . When informed by the time series data for the positions of the two motors and the length of the spring it is apparent that co-operation between the motors in the form of a ‘ﬂip-ﬂop’ type behavior is responsible for this. The mean ﬁeld theory however shows a discontinuity at the zero net free energy point transitioning immediately from the ‘locked’ phase to the maximum allowed backward velocity.2) is shown in Figure 2.1 ATPase Synthesis Rate A comparison of the results for the velocity of the ATPase from the preliminary version of the Monte Carlo simulation of the model outlined in Figure 1. (B) λ = 25 and (C) λ = 50 using k0+ = k1+ = 1 s−1 . It is believed that this behavior may be the cause of the increase in velocity of the ATPase in comparison to the mean ﬁeld theory. This Monte Carlo velocity of the ATPase coupled motor syssimulates a change in the thermodynamically allowed tem for various λ using k0+ = k1+ = 1 s−1 . u0 = 1 nm and u1 = 10/3 nm page 4 of 6 . Consequently any quantitative results from the current version of the simulation will be treated with caution until extensive revision of both the mean ﬁeld theory and the Monte Carlo simulation conﬁrms this discrepancy. ∆G1 = −10 kJM −1 . The discrepancies between these models must be resolved and doing so may inform the discrepancy in ﬁgure 2. Figure 3 shows that in the ‘forward’ phase (A) at small values of λ the auto correlation function decays exponentially as expected for a system governed by Brownian motion [Reif. Preliminary u1 = 10/3 nm results from the Monte Carlo simulation mirror the behavior of the transition from the ‘locked’ phase to the ‘backward’ phase seen in the ‘forward’ regime. When in the ‘locked’ phase (C) this oscillatory behavior dominates but is now not suﬃcient to overcome the constraints imposed by the large elastic energies associated with the multiple l0 steps required to drive the l1 motor. to the mean ﬁeld theory (section 3. 4. ∆G0 = −20 kJM −1 .4.

H. Mooseker. Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random number generator. Random walks in biology. The Journal of Experimental Biology. Spudich. V. These programs will then be used to produce results which will inform the characterisation of the phase transitions and analysis of the auto-correlation function. The largest task in the project is anticipated to be the development of the mean ﬁeld theory using Langevin noise theory. Torsional elasticity and energetics of F1 -ATPase. Muneyuki. 1965. E. and M. Yasuda. Mitome. Noji. S. Journal of Statistical Physics. R. 342. January 1998.edu/cu/biology/courses/c2005/ images/.uk/. The ﬁnal report will be submitted before the 23/3/2012. Biochem. Vale. J. Boyer. E. R. A. Yasuda. Yoshida. Proceedings: Biological Sciences. Hudspeth. MatLab. 1997. A. Noji. and M. Yoshida. Wiley. July 1998. Rev. Cheney. Thornhill. Movement of microtubules by single kinesin molecules. D. Reif. G. M. Bobylev and C. MathWorks MatLab version R2010a. Accessed December 2011. P. Berg. Tension ﬂuctuations due to muscle cross-bridges.columbia. A. T. 8. 1993. Cercignani. The ATP Synthase . Rotation of F1 -atpase and the hinge residues of the β subunit. N. Journal of Biological Chemistry. K. The ﬁnalisation of the Monte Carlo simulations and the Mean Field theory into complete programs with simple user interfaces and eﬃcient code having resolved the discrepancies discussed in Section 4. Matsumoto and T Nishimura. Karp. Y.1 is the ﬁrst priority. Rief. D. 259. index. 106. Rock. 1412. Mehtta.Project Proposal Nils Gustafsson 5 Time Table A timetable for the completion of the stated aims (Section 1) is provided in Figure 4. February 2002. march 1995. 2011. a 3D graphical simulation of the Monte Carlo model will be developed to inform discussion and the seminar. McGraw-Hill.co. http://www. Proc. 15.a splendid molecular machine. Lecture Course. N.mathworks. Annu. Myosin-V stepping kinetics: a model for processivity. TOMACS. Princeton University Press. Nature. H. Kinosita Jr. http://www. Lerner. K. 2000. M. 1999. Rumberg. H. P¨nke and B. A. Natl Acad. Masaike. Phase transitions.. C. F. 108. page 5 of 6 . 278. S. Moment equations for a granular material in a thermal bath. Time permitting. and R. 203. 1989. Cell and Molecular Biology. Direct observation of the rotation of subunit in F1 -ATPase. Howard. PNAS. J. A. chap. R. Kinosita JR. Fundamentals of statistical and thermal physics. Sci. M. R. Kinetic modeling of rotary CF0 F1 -ATP synthase: storage of elastic energy during a energy transduction. Grubm¨ller. O. D. Thomas and R. Biochimica et Biophysica Acta. May 2011. and J. I. 2008.. Czub and H. 2000.. Kato-Yamada. u J. Figure 4: Gantt Chart of of proposed project tasks References Biological sciences at columbia university.

Tawada.REFERENCES Project Proposal Nils Gustafsson N. S. Soc. J. Thomas. page 6 of 6 . M. L. Knight. Wang. Nature. J. Molecular motors: thermodynamics and random walk. 2000. and K. Burgess. Lond. J. Sellers. June 2001. A. Trinick. 268. J. Imafuku. B. R. A. Proc. F. Walker. R. Hammer. Y. Two-headed binding of a processive myosin to f-actin. and P. 405.

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