Kinesin is recognized as the workhorse of the cell, hauling chromosomes, neurotransmitters and other vital cargo along microtubules. Understanding kinesin motility will provide new insight into how motor proteins function and possibly open new avenues of investigation for the treatment of cancer and neuro-degenerative diseases. The recent development of optical force clamp and other single-molecule techniques has led to in vitro experimental studies of a single kinesin molecule walking along a microtubule. Through experiments, a great deal has been learned about the motion of kinesin-1 powered by ATP hydrolysis. But we are still not clear about the machinery that drives the transitions between the relevant states. We can see how this little biped's limbs move, but not the operations of its actuators and sensors that produce and control the motion. The experimental results clearly point to the three dimensional (3D) nature of the motor dynamics and the importance of the shape and size of the kinesin heads. However, the current theoretical studies are generally limited to one dimension (1D) models, in which the two heads of kinesin-1 are represented by two shapeless particles moving in 1D. Their conformational and orientational changes are not properly accounted for as essential actions of walking. We propose to advance the theoretical understanding of kinesin-1 by pursuing two specific aims: 1. Study 3D three-body (3D3B) model of kinesin-1. We will model kinesin as a system of 15 degrees of freedom: Two heads as two bodies, free to rotate, six degrees of freedom each;Two neck-linkers as two springs, they join the heads to the hinge (the stalk) that is biased by the cargo load. We will develop techniques of transition-path sampling (TPS) with negative-friction Langevin dynamics (NFLD), hyper molecular dynamics (HMD), and fluctuation dynamics around minimum energy paths (FDMEP). We will employ these highly efficient methods to investigate the 3D dynamics of the 3D3B kinesin model. 2. Establish in silico experiments of kinesin motility. Molecular mechanics force fields will be fed to the PI's TPS with NFLD, HMD, and FDMEP programs to generate transition paths for the chemo-mechanical transitions of the atomistic model of kinesin-1. This enables in silico experiments of kinesin stepping events that are milliseconds apart with atomic, sub-picosecond precision.
Showing the most recent 10 out of 34 publications
