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

Takada S (2013) Structure-based Molecular Simulations Reveal the Enhancement of Biased Brownian Motions in Single- headed Kinesin. PLoS Comput Biol 9(2): e1002907. doi:10.1371/journal.pcbi.1002907 Structure-based Molecular Simulations Reveal the Enhancement of Biased Brownian Motions in Single- headed Kinesin Ryo Kanada 0 1 Takeshi Kuwata 0 1 Hiroo Kenzaki 0 1 Shoji Takada 0 1 Devarajan Thirumalai, University of Maryland, United States of America 0 1 Department of Biophysics Graduate School of Science, Kyoto University , Kyoto , Japan , 2 Graduate School of Science and Technology, Kobe University , Kobe , Japan , 3 CREST Japan Science and Technology Agency , Kawaguchi, Saitama , Japan 1 PLOS Computational Biology 2 www.ploscompbiol.org 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.'' PLOS Computational Biology | www.ploscompbiol.org - Funding: This work was supported partly by Research and Development of the Next-Generation Integrated Simulation of Living Matter and partly by Grand-inAid for Scientific Research of the Ministry of Education, Culture, Sports, Science and Technology. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Time dependent structural information is of central importance to understand detailed mechanisms of biomolecular systems. In particular, biomolecular machines dynamically transit many structurally and chemically distinct states making cycles in state space, by which they fulfill their functions. Unfortunately, no single experimental technique provides sufficient spatio-temporal resolution for them. X-ray crystallography and others provide structural information at high resolution, but this is primarily static. Biochemical and single molecular experiments tell us kinetic and dynamic behaviors, but their spatial resolution is limited. To fill the gap among them, molecular dynamics (MD) simulations have been playing important roles. Yet, due to their size and long time scale involved, atomistic MD cannot cover an entire cycle of molecular machines at the moment [1]. To overcome this limitation, recently, we initiated to use structure-based coarse grained MD (CGMD) methods [2,3] to mimic the cycle of machines for the case of F1-ATPase and others [4,5]. Notably, most of these machines contain more than one ATPase domains and their coordinated dynamics are crucial to understand the mechanisms [6,7,8,9]. This is an interesting issue, but at the same time, makes the cycle unavoidably complicated. Thus, for the simplicity and clarity, it is good to study those that contain only one ATPase domain and that have much of crystallographic information. In this sense, a single-headed kinesin, KIF1A, is an ideal target system, for which here we performed CGMD simulations mimicking an entire ATP hydrolysis cycle. Kinesin is a family of molecular motors that move unidirectionally along microtubule (MT) using ATP hydrolysis free energy [10]. In the family, the conventional kinesin, kinesin-1, was experimentally characterized to move toward the plus ends of MT processively with discrete 8-nm steps per one ATP hydrolysis reaction, where the coupling between ATP hydrolysis reactions and 8-nm steps is rather tight [11,12,13,14,15,16]. The conventional kinesin is a two-headed motor and has been shown to walk in a hand-over-hand fashion by coordinated motions of the two heads [6,9,17,18]. In this sense, it is a surprise that even though KIF1A, a member of kinesin family, is a single-head motor, it still can move processively and directionally along MT, as observed by single molecule experiments [19,20,21]. In particular, the mechano-chemical coupling of KIF1A is loose: KIF1A can move back and forth stochastically with an average biased towards the forward direction, with step sizes in multiples of 8-nm. This is in contrast to conventional kinesin that seldom shows backward steps without a large load and that shows a uniform step size of 8-nm per one ATP hydrolysis [19,20,21]. Thus, KIF1A must use a different mechanism from the conventional kinesin to 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 coarsegrained 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. achieve the overall unidirectional motions. How KIF1A, with only one head, can generate the unidirectional movements driven by ATP-hydrolysis reaction is unclear in terms of structural dynamics, which we address in this paper by structure-based CG (...truncated)