ABSTRACT
Minimal Model ............................................................................................. 11 1.3.1 Internal Strain Regulation as an Underlying Mechanism
for a High Processivity ..................................................................... 11 1.3.2 Stepping Dynamics of Kinesins ...................................................... 12 1.3.3 Partial Unfolding of Structure Facilitates
the Binding Process ......................................................................... 17 1.4 Future Work and Concluding Remarks ......................................................... 17 Acknowledgments ....................................................................................................18 References ................................................................................................................ 18
Dynamics of biological systems occur with their characteristic length and energy scales. Although Newtonian mechanics can be used for describing events of any scale, our intuition based on Newtonian mechanics for macroscopic energy and length scales often fails to capture the essence of dynamics in biological systems. The length scale of basic biomaterials such as proteins, RNA, DNA, and cytoskeletal laments ranges from nanometers to micrometers; the energy scale associated with their interaction, leading to the self-assembly and mutual interaction, is on the order of the thermal energy, ∼1-20kBT. Since the energy scale of thermal uctuations (= kBT) of environment is comparable to the interaction energy, the entire molecule as well as the individual noncovalent bond jiggles and wiggles incessantly; hence in biological systems, there is neither smooth trajectory nor rigid body motion as observed in the macroscopic world. In addition to these length and energy scales, the dynamics of bioworld is characterized by a low Reynolds number hydrodynamics (Reynolds number Re = finertial /ffriction ∼10−5 where finertial and ffriction are the inertial
force and the frictional force, respectively), which results from the large viscosity value of water environment (∼1 cP). Consequently, the dynamics of biological systems vastly differ from the typical phenomena observed in human life. For instance, a “molecular ball” of nanometer size readily loses the memory of its original velocity in less than a picosecond; hence playing football is impossible in the bioworld. All these factors (size, energy, viscosity) make the dynamics in biological systems unique in the sense that biological nanomachines employ a different strategy from human-made macroscopic machines to operate in such a severe environment. In this chapter, we discuss one of the extensively studied biological nanomachines, the conventional kinesin, which the evolutionary processes have tailored over billions of years for its current biological functions, such as organelle transports and force generations.
