Structure-based Molecular Simulations Reveal the Enhancement of Biased Brownian Motions in Single-headed Kinesin

Kinesin is a family of molecular motors that move unidirectionally along microtubules (MT) using ATP hydrolysis free energy. In the family, the conventional two-headed kinesin was experimentally characterized to move unidirectionally through “walking” in a hand-over-hand fashion by coordinated motions of the two heads. Interestingly a single-headed kinesin, a truncated KIF1A, still can generate a biased Brownian movement along MT, as observed by in vitro single molecule experiments. Thus, KIF1A must use a different mechanism from the conventional kinesin to achieve the unidirectional motions. Based on the energy landscape view of proteins, for the first time, we conducted a set of molecular simulations of the truncated KIF1A movements over an ATP hydrolysis cycle and found a mechanism exhibiting and enhancing stochastic forward-biased movements in a similar way to those in experiments. First, simulating stand-alone KIF1A, we did not find any biased movements, while we found that KIF1A with a large friction cargo-analog attached to the C-terminus can generate clearly biased Brownian movements upon an ATP hydrolysis cycle. The linked cargo-analog enhanced the detachment of the KIF1A from MT. Once detached, diffusion of the KIF1A head was restricted around the large cargo which was located in front of the head at the time of detachment, thus generating a forward bias of the diffusion. The cargo plays the role of a diffusional anchor, or cane, in KIF1A “walking.” It is one of the major issues in biophysics how molecular motors such as conventional two-headed kinesin convert the chemical energy released at ATP hydrolysis into mechanical work. While most molecular motors move with more than one catalytic domain working in coordinated fashions, there are some motors that can move with only a single catalytic domain, which provides us a possibly simpler case to understand. A single-headed kinesin, KIF1A, with only one catalytic domain, has been characterized by in vitro single-molecule assay to generate a biased Brownian movement along the microtubule. Here, we conducted a set of structure-based coarse-grained molecular simulations for KIF1A system over an ATP hydrolysis cycle for the first time to our knowledge. Without cargo the simulated stand-alone KIF1A could not generate any directional movement, while a large-friction cargo-analog linked to the C-terminus of KIF1A clearly enhanced the forward-biased Brownian movement of KIF1A significantly. Interestingly, the cargo-analog here is not merely load but an important promoter to enable efficient movements of KIF1A.