| 1. |
K. Tawada, Yasuhiro Imafuku, Y. Y. Toyoshima, A single-track fluctuation analysis in the sliding movement by protein motors in vitro, Biophysical Journal, 68, 4 SUPPL., 1995. |
| 2. |
Yasuhiro Imafuku, Yoko Y. Toyoshima & Katsuhisa Tawada, Fluctuation in the microtubule sliding movement driven by kinesin in vitro, Biophysical Journal 70 (2): 878-886, 70, 2, 878-886, 1996.02. |
| 3. |
Yasuhiro Imafuku, Yoko Y. Toyoshima, Katsuhisa Tawada, Fluctuation in the microtubule sliding movement driven by kinesin in vitro, Biophysical Journal, 70, 2 I, 878-886, 1996.02, We studied the fluctuation in the translational sliding movement of microtubules driven by kinesin in a motility assay in vitro. By calculating the mean-square displacement deviation from the average as a function of time, we obtained motional diffusion coefficients for microtubules and analyzed the dependence of the coefficients on microtubule length. Our analyses suggest that 1) the motional diffusion coefficient consists of the sum of two terms, one that is proportional to the inverse of the microtubule length (as the longitudinal diffusion coefficient of a filament in Brownian movement is) and another that is independent of the length, and 2) the length-dependent term decreases with increasing kinesin concentration. This latter term almost vanishes within the length range we studied at high kinesin concentrations. From the length-dependence relationship, we evaluated the friction coefficient for sliding microtubules. This value is much larger than the solvent friction and thus consistent with protein friction. The length independence of the motional diffusion coefficient observed at sufficiently high kinesin concentrations indicates the presence of correlation in the sliding movement fluctuation. This places significant constraint on the possible mechanisms of the sliding movement generation by kinesin motors in vitro.. |
| 4. |
Yasuhiro Imafuku, Yoko Y. Toyoshima & Katsuhisa Tawada, Monte Carlo study for fluctuation analysis of the in vitro motility driven by protein motors, Biophysical Chemistry 59 (1-2): 139-153, 10.1016/0301-4622(95)00123-9, 59, 1-2, 139-153, 1996.03. |
| 5. |
Yasuhiro Imafuku, Yoko Y. Toyoshima & Katsuhisa Tawada, Length dependence of displacement fluctuations and velocity in microtubule sliding movement driven by sea urchin sperm outer arm beta dynein in vitro, Biophysical Chemistry 67 (1-3): 117-125, 10.1016/S0301-4622(97)00028-8, 67, 1-3, 117-125, 1997.09. |
| 6. |
K. Tawada, M. Toyoda, Yasuhiro Imafuku, A. Yamada, Fluctuation correlation in the sliding movement generated by protein motors in vitro, Advances in Experimental Medicine and Biology, 453, 47-51, 1998, The fluctuation in the sliding distance of cytoskeletal filaments driven to move by protein motors in vitro does not depend on the filament length. This is in sharp contrast to the case of Brownian movement of filamentous particles in their longitudinal directions, in which the positional fluctuation is proportional to the inverse of the length (L) of filaments. This latter 1/L dependence is a direct consequence of the central limit theorem: the statistical independence and randomness of the solvent molecule collisions with filaments, the collisions of which cause the random Brownian movement. The above length-independence in the sliding distance fluctuation found in the in vitro motility indicates the presence of correlation in the fluctuation. A possible explanation for the correlation is to assume that there is an extended time-correlation in the sliding movement, a correlation which could be produced by the actions on a sliding filament of protein motors with their heads randomly oriented in the in vitro motility assay system. We have checked this possibility by using long myosin thick filaments of molluscan smooth muscles, on which myosin heads are uniformly oriented, and have found that even with such myosin filaments with oriented myosin heads, the positional fluctuation of actin sliding distance does not depend on the actin filament length. This result thus indicates that the actions of protein motors on a sliding filament are not statistically independent or random, so that the positional fluctuation of filaments in the motor- generated sliding movement does not depend on the filament length.. |
| 7. |
Toshio Ichikawa, Yasuhiro Imafuku & Katsuhisa Tawada, Synchronous firing patterns of a set of insect neurosecretory cells, NEUROSCI LETT 264 (1-3): 85-88 APR 2 1999, 10.1016/S0304-3940(99)00164-0, 264, 1-3, 85-88, 1999.04. |
| 8. |
Neil Thomas, Yasuhiro Imafuku & Katsuhisa Tawada, Molecular motors: thermodynamics and the random walk, P ROY SOC LOND B BIO 268 (1481): 2113-2122, 268, 1481, 2113-2122, 2001.10. |
| 9. |
N. Thomas, Yasuhiro Imafuku, K. Tawada, Molecular motors
Thermodynamics and the random walk, Proceedings of the Royal Society B: Biological Sciences, 10.1098/rspb.2001.1764, 268, 1481, 2113-2122, 2001.10, The biochemical cycle of a molecular motor provides the essential link between its thermodynamics and kinetics. The thermodynamics of the cycle determine the motor's ability to perform mechanical work, whilst the kinetics of the cycle govern its stochastic behaviour. We concentrate here on tightly coupled, processive molecular motors, such as kinesin and myosin V, which hydrolyse one molecule of ATP per forward step. Thermodynamics require that, when such a motor pulls against a constant load f, the ratio of the forward and backward products of the rate constants for its cycle is exp[-(ΔG + u0f)/kT], where - ΔG is the free energy available from ATP hydrolysis and u0 is the motor's step size. A hypothetical one-state motor can therefore act as a chemically driven ratchet executing a biased random walk. Treating this random walk as a diffusion problem, we calculate the forward velocity v and the diffusion coefficient D and we find that its randomness parameter r is determined solely by thermodynamics. However, real molecular motors pass through several states at each attachment site. They satisfy a modified diffusion equation that follows directly from the rate equations for the biochemical cycle and their effective diffusion coefficient is reduced to D - v2τ, where τ is the time-constant for the motor to reach the steady state. Hence, the randomness of multistate motors is reduced compared with the one-state case and can be used for determining τ. Our analysis therefore demonstrates the intimate relationship between the biochemical cycle, the force - velocity relation and the random motion of molecular motors.. |
| 10. |
Neil Thomas, Yasuhiro Imafuku & Katsuhisa Tawada, Kinesin: a molecular motor with a spring in its step, P ROY SOC LOND B BIO 269 (1507): 2363-2371, 10.1098/rspb.2002.2117, 269, 1507, 2363-2371, 2002.11. |
| 11. |
Katsuhisa Tawada, Yasuhiro Imafuku, Neil Thomas, Themodynamic mechano-chemistry of single motor enzymes, Advances in Experimental Medicine and Biology, 538, 361-367, 2004. |
| 12. |
Naoki Noda, Yasuhiro Imafuku, Akira Yamada and Katsuhisa Tawada, Fluctuation of actin sliding over myosin thick filaments in vitro, Biophysics Vol.1, pp45-53 (2005)., 2005.01. |
| 13. |
Naoki Noda, Yasuhiro Imafuku, Akira Yamada, Katsuhisa Tawada, Fluctuation of actin sliding over myosin thick filaments in vitro, 2006 IEEE International Symposium on Micro-Nano Mechanical and Human Science, MHS
2006 IEEE International Symposium on Micro-Nano Mechanical and Human Science, MHS, 10.1109/MHS.2006.320292, 2006, It is customarily assumed that myosin motors act as independent force generators. Here, we tested this assumption by analyzing the fluctuation of the actin sliding movement in vitro over long native thick filaments from shell fish smooth muscle. This analysis is based on the prediction that the effective diffusion coefficient of actin, a measure of the fluctuation, is proportional to the inverse of the number of myosin motors generating the sliding movement of an actin filament, hence proportional to the inverse of the actin length, if the actions of the motors are independent. Contrary to this prediction, we found the effective diffusion coefficient to be independent of the actin length. This result shows that the myosin motors are not independent force generators when generating the continuous sliding movement of actin in vitro.. |
| 14. |
N. Noda, Y. Imafuku, A. Yamada & K. Tawada, Fluctuation of actin sliding over myosin thick filaments in vitro, IEEE MHS2006 & Micro-Nano COE Vol.1, pp460-465 (2006). , 2006.11. |
| 15. |
Yasuhiro Imafuku, Namiko Mitarai, Katsuhisa Tawada, Hiizu Nakanishi, Fluctuations in sliding motion of cytoskeltal filament driven by molecular motors, 2007 International Symposium on Micro-NanoMechatronics and Human Science, MHS
2007 International Symposium on Micro-NanoMechatronics and Human Science, MHS, 10.1109/MHS.2007.4420851, 193-198, 2007, It has been found in several in vitro experiments that cytoskeletal filaments driven by molecular motors show finite diffusion in sliding movement even in the long filament limit (Imafuku et al., 1996a, 1997; Noda et al., 2005). This anomalous fluctuation can be evidence that there exists some cooperativity among the motors in action because fluctuation should be averaged out if the action of each motor is independent. In order to understand the nature of the cooperativity in existing models of molecular motors, we perform numerical simulations and analyze velocity correlation on three models that are known to show some kind of cooperativity and/or large diffusion coefficient in the long filament limit. It is shown that Prost model (1994) and Duke model (1999) do not give a finite diffusion in the long filament limit in spite of collective action of motors. Quenched randomness in Sekimoto-Tawada model (1995) has been shown to give constant diffusion coefficient independent of filament length because of long time correlation proportional to filament length, but such a long correlation time is found to conflict with the experimental time scales. We conclude that none of the three models represent experimental findings, and a mechanism to be understood should allow both the amplitude and the time scale of the velocity correlation to be independent of the filament length.. |
| 16. |
Y. Imafuku, N. Mitarai, K. Tawada, and H. Nakanishi
, Fluctuations in sliding motion of cytoskeltal filament driven by molecular motors
, IEEE MHS2007 & Micro-Nano COE Vol.1, pp193-198 (2006)., 2007.11. |
| 17. |
Yasuhiro Imafuku, Namiko Mitarai, Katsuhisa Tawada, Hiizu Nakanishi, Anomalous fluctuations in sliding motion of cytoskeletal filaments driven by molecular motors
Model simulations, Journal of Physical Chemistry B Materials, 10.1021/jp074838l, 112, 5, 1487-1493, 2008.02, It has been found in in vitro experiments that cytoskeletal filaments driven by molecular motors show finite diffusion in sliding motion even in the long filament limit [Imafuku, Y. et al. Biophys. J. 1996, 70, 878-886. Noda, N. et al. Biophysics 2005, 1, 45-53]. This anomalous fluctuation can be evidence for cooperativity among the motors in action because fluctuation should be averaged out for a long filament if the action of each motor is independent. In order to understand the nature of the fluctuation in molecular motors, we perform numerical simulations and analyze velocity correlation in three existing models that are known to show some kind of cooperativity and/or large diffusion coefficient, i.e., the Sekimoto-Tawada model [Sekimoto, K.; Tawada, K. Phys. Rev. Lett. 1995, 75, 180], the Prost model [Prost, J. et al. Phys. Rev. Lett. 1994, 72, 2652], and the Duke model [Duke, T. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 2770]. It is shown that the Prost model and the Duke model do not give a finite diffusion in the long filament limit, in spite of the collective action of motors. On the other hand, the Sekimoto-Tawada model has been shown to give a diffusion coefficient that is independent of filament length, but it comes from the long time correlation whose time scale is proportional to filament length, and our simulations show that such a long correlation time conflicts with the experimental time scales. We conclude that none of the three models represent experimental findings. In order to explain the observed anomalous diffusion, we have to search for a mechanism that will allow both the amplitude and the time scale of the velocity correlation to be independent of the filament length.. |
| 18. |
Toshiki Taba, Masaki Edamatsu, Shiori Toba, Keitaro Shibata, Yasuhiro Imafuku, Yoko Yano Toyoshima, Katsuhisa Tawada, Akira Yamada, Direction and speed of microtubule movements driven by kinesin motors arranged on catchin thick filaments, Cytoskeleton, 10.1002/cm.20303, 65, 10, 816-826, 2008.10, Conventional kinesin (Kinesin-1) is a microtubule-based molecular motor that supports intracellular vesicle/organelle transport in various eukaryotic cells. To arrange kinesin motors similarly to myosin motors on thick filaments in muscles, the motor domain of rat conventional kinesin (amino acid residues 1-430) fused to the C-terminal 829 amino acid residues of catchin (KHC430Cat) was bacterially expressed and attached to catchin filaments that can attach to and arrange myosin molecules in a bipolar manner on their surface. Unlike the case of myosin where actin filaments move toward the center much faster than in the opposite direction along the catchin filaments, microtubules moved at the same speed in both directions. In addition, many microtubules moved across the filaments at the same speed with various angles between the axes of the microtubule and catchin filament. Kinesin/catchin chimera proteins with a shorter kinesin neck domain were also prepared. Those without the whole hinge 1 domain and the C-terminal part of the neck helix moved microtubules toward the center of the catchin filaments significantly, but only slightly, faster than in the opposite direction, although the movements in both directions were slower than those of the KHC430Cat construct. The results suggest that kinesin has substantial mechanical flexibility within the motor domain, possibly within the neck linker, enabling its interaction with microtubules having any orientation.. |
| 19. |
Yasuhiro Imafuku, Neil Thomas, Katsuhisa Tawada, Hopping and stalling of processive molecular motors, Journal of Theoretical Biology, 10.1016/j.jtbi.2009.07.011, 261, 1, 43-49, 2009.11, When a two-headed molecular motor such as kinesin is attached to its track by just a single head in the presence of an applied load, thermally activated head detachment followed by rapid re-attachment at another binding site can cause the motor to 'hop' backwards. Such hopping, on its own, would produce a linear force-velocity relation. However, for kinesin, we must incorporate hopping into the motor's alternating-head scheme, where we expect it to be most important for the state prior to neck-linker docking. We show that hopping can account for the backward steps, run length and stalling of conventional kinesin. In particular, although hopping does not hydrolyse ATP, we find that the hopping rate obeys the same Michaelis-Menten relation as the ATP hydrolysis rate. Hopping can also account for the reduced processivity observed in kinesins with mutations in their tubulin-binding loop. Indeed, it may provide a general mechanism for the breakdown of perfect processivity in two-headed molecular motors.. |
| 20. |
Neil Thomas, Yasuhiro Imafuku, Effect of elastic energy on the folding of an RNA hairpin, Journal of Theoretical Biology, 10.1016/j.jtbi.2012.07.021, 312, 96-104, 2012.11, We analyse the folding and unfolding of an RNA hairpin using a conventional zipping model that includes both the free energy for RNA binding and the elastic free energy of the system. Unfolding under isotonic conditions (where we control the applied load) is known to occur at a well-defined critical load. In marked contrast, we find that unfolding under isometric conditions (where we control the extension of the hairpin) produces a series of sharp peaks in the average load as the stem of the hairpin starts to unzip base by base. A peak occurs when the elastic energy stored in the unzipped arms of the hairpin becomes so large that it is energetically favourable for the next base pair to unzip: the consequent increase in the contour length of the unzipped arms reduces their elastic energy and causes the average load to fall abruptly. However, as the contour length of the unzipped arms increases, the peaks become less distinct. Moreover, when we include the long DNA/RNA handles that have been used in single-molecule experiments, the unzipping of individual base pairs cannot be resolved at all. Instead, with the hairpin in the folded state, the average load increases with extension until the elastic energy stored in the handles makes it energetically favourable for the hairpin to unzip over a narrow range of extensions. The resultant yield point produces a mechanical hysteresis loop with a negative slope, as observed experimentally. Unfolding of the hairpin is also affected by the elastic energy stored in a compliant force transducer. We find that short, stiff handles and a stiff force transducer could improve the resolution of mechanical experiments on single molecules.. |
| 21. |
Yasuhiro Imafuku, Koh ichi Enomoto, Hiroko Kataoka, Isao Ito, Takashi Maeno, Novel Distinctive Roles of Docking Proteins in Short-term Synaptic Plasticity of Frog Neuromuscular Transmission Revealed by Botulinum Neurotoxins, Neuroscience, 10.1016/j.neuroscience.2017.11.022, 369, 374-385, 2018.01, Short-term synaptic plasticity (SSP) is a basic mechanism for temporal processing of neural information in synaptic transmission. Facilitation, the fastest component of SSP, has been extensively investigated with regard to Ca2+ signaling and other relevant substances. However, systematic analyses on the slower components of SSP, originated by Magleby and Zengel, have remained stagnant for decades, as few chemicals directly modifying these slower components have been identified. In combination with refined experimental protocols designed to study the stimulation frequency-dependence of SSP and botulinum neurotoxins A and C (BoNT-A and BoNT-C), we investigated SSP of frog neuromuscular transmission to clarify the roles of synaptosomal-associated protein of 25 kDa (SNAP-25) and syntaxin, SNARE proteins exclusively participating in vesicular events including docking, priming and exocytosis. We found that BoNT-A treatment eliminated slow potentiation, and BoNT-C poisoning abolished intermediate augmentation, two components of SSP. Fast facilitation was maintained after double poisoning with BoNT-A and -C, but the postsynaptic response became biphasic. A novel depression, termed repression, emerged by double poisoning. Repression was different from depletion because it developed even at a low-frequency stimulation of 1 Hz. We conclude that SNAP-25 and syntaxin not only play roles as cooperative exocytotic machinery, but also have roles in SSP.. |
