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In recent years, there has been a growing interest in engineering dynamic and autonomous systems with robotic functionalities using biomolecules. Specifically, the ability of molecular motors to convert chemical energy to mechanical forces and the programmability of DNA are regarded as promising components for these systems. However, current systems rely on the manual addition of external stimuli, limiting the potential for autonomous molecular systems. Here, we show that DNA-based cascade reactions can act as a molecular controller that drives the autonomous assembly and disassembly of DNA-functionalized microtubules propelled by kinesins. The DNA controller is designed to produce two different DNA strands that program the interaction between the microtubules. The gliding microtubules integrated with the controller autonomously assemble to bundle-like structures and disassemble into discrete filaments without external stimuli, which is observable by fluorescence microscopy. We believe this approach to be a starting point toward more autonomous behavior of motor protein–based multicomponent systems with robotic functionalities.

Biomolecular motor-based micro-sized robots have recently created an innovation in the field of science and technology as molecular transporters. Groups of these tiny robots can work substantially better than individual ones in terms of the transported distance and number or size of cargo. Site-specific molecular delivery, the main feature of these robots, has helped to improve the workability of robots in a more controllable manner.

Microtubules play important roles in biological functions by forming superstructures, such as doublets and branched structures, in vivo. Despite the importance, it is challenging to construct these superstructures in vitro. Here, we designed a tetrameric fluorescent protein Azami-Green (AG) fused with His-tag and Tau-derived peptide (TP), TP-AG, to generate the superstructures. Main binding sites of TP-AG can be controlled to the inside and outside of microtubules by changing the polymerization conditions. The binding of TP-AG to the inside promoted microtubule formation and generated rigid and stable microtubules. The binding of TP-AG to the outside induced various microtubule superstructures, including doublets, multiplets, branched structures, and extremely long microtubules by recruiting tubulins to microtubules. Motile microtubule aster structures were also constructed by TP-AG. The generation of various microtubule superstructures by a single type of exogenous protein is a new concept for understanding the functions of microtubules and constructing microtubule-based nanomaterials.

Microtubules play important roles in biological functions by forming superstructures, such as doublets and branched structures, in vivo. Despite the importance, it is challenging to construct these superstructures in vitro. Here, we designed a tetrameric fluorescent protein Azami-Green (AG) fused with His-tag and Tau-derived peptide (TP), TP-AG, to generate the superstructures. Main binding sites of TP-AG can be controlled to the inside and outside of microtubules by changing the polymerization conditions. The binding of TP-AG to the inside promoted microtubule formation and generated rigid and stable microtubules. The binding of TP-AG to the outside induced various microtubule superstructures, including doublets, multiplets, branched structures, and extremely long microtubules by recruiting tubulins to microtubules. Motile microtubule aster structures were also constructed by TP-AG. The generation of various microtubule superstructures by a single type of exogenous protein is a new concept for understanding the functions of microtubules and constructing microtubule-based nanomaterials., identifier:2375-2548

We constructed GFP-encapsulated microtubules (MTs) using Tauderived peptide which binds to their interior. The encapsulation of GFP dramatically increased the rigidity of MTs, resulting in their enhanced velocity on a kinesin-coated substrate. Moreover, the GFP-encapsulated MTs were significantly more stable compared to normal MTs.

The cyclization of peptides is a valuable strategy for the development of binding motifs to target proteins with improved affinity. Microtubules (MTs) are important targets for therapeutics, and a variety of MT-targeted drugs and peptides have recently been developed. We have previously designed a Tau-derived peptide (TP) that binds to the interior of MTs. In the present study, the development of a cyclic TP (TCP) for enhanced binding to tubulin and the stabilization of MTs is described. The fluorescently labeled cyclic peptide containing three glycine linkers (TCP3-TMR) exhibited a remarkably enhanced binding affinity to tubulin. The cyclic peptide was also demonstrated to stabilize MTs by enhancing polymerization and reducing depolymerization. Moreover, MTs were effectively formed by the treatment of cyclic peptides in the presence of guanosine triphosphate (GTP), while the linear peptide showed no such effect. These findings indicate that TCP is a useful binding motif that can stabilize MTs and is valuable for various therapeutic and material applications.

Dynamic covalent bonds are useful tools in a wide range of applications. Although various reversible chemical reactions have been studied for this purpose, the requirement for harsh conditions, such as high temperature and low or high pH, to activate generally stable covalent bonds limits their potential applications involving biomolecules or household utilization. Here, we report the design, synthesis, characterization, and dynamic covalent bonding properties of 1,2-disubstituted 1,2-dihydro-1,2,4,5-tetrazine-3,6-dione (TETRAD). Hetero-Diels-Alder reactions of TETRAD with furan derivatives and their retro-reactions proceeded rapidly at room temperature under neutral conditions, enabling a chemically induced sol-gel transition system.

The biomolecular motor protein kinesin and its associated filamentous protein microtubule have been finding important nanotechnological applications in the recent years. Rigidity of the microtubules, which are propelled by kinesin motors in an in vitro gliding assay, is an important metric that determines the success of utilization of microtubules and kinesins in various applications, such as transportation, sensing, sorting, molecular robotics, etc. Therefore, regulating the rigidity of kinesin-propelled microtubules has been critical. In this work, we report a simple strategy to regulate the rigidity of kinesin- propelled microtubules in an in vitro gliding assay. We demonstrate that rigidity of the microtubules, propelled by kinesins in an in nitro gliding assay, can be modulated simply by using the natural osmolyte trimethylamine N-oxide (TMAO). By varying the concentration of TMAO in the gliding assay, the rigidity of microtubules can be modulated over a wide range. Based on this strategy, we are able to reduce the persistence length of microtubules, a measure of microtubule rigidity, similar to 8 fold by using TMAO at the concentration of 1.5 M. Furthermore, we found that the decreased rigidity of the kinesin-propelled microtubules can be restored upon elimination of TMAO from the in nitro gliding assay. Alteration in the rigidity of microtubules is accounted for by the non-uniformity of the force applied by kinesins along the microtubules in the presence of TMAO. This work offers a facile strategy to reversibly regulate the rigidity of kinesin-propelled microtubules in situ, which would widen the applications of the biomolecular motor kinesin and its associated protein microtubule in various fields.

Cooperation is a strategy that has been adopted by groups of organisms to execute complex tasks more efficiently than single entities. Cooperation increases the robustness and flexibility of the working groups and permits sharing of the workload among individuals. However, the utilization of this strategy in artificial systems at the molecular level, which could enable substantial advances in microrobotics and nanotechnology, remains highly challenging. Here, we demonstrate molecular transportation through the cooperative action of a large number of artificial molecular machines, photoresponsive DNA-conjugated microtubules driven by kinesin motor proteins. Mechanical communication via conjugated photoresponsive DNA enables these microtubules to organize into groups upon photoirradiation. The groups of transporters load and transport cargo, and cargo unloading is achieved by dissociating the groups into single microtubules. The group formation permits the loading and transport of cargoes with larger sizes and in larger numbers over long distances compared with single transporters. We also demonstrate that cargo can be collected at user-determined locations defined by ultraviolet light exposure. This work demonstrates cooperative task performance by molecular machines, which will help to construct molecular robots with advanced functionalities in the future.

Nowadays, biomolecular motor-based miniaturized lab-on-a-chip devices have been attracting much attention for their wide range of nanotechnological applications. Most of the applications are dependent on the motor-driven active transportation of their associated filamentous proteins as shuttles. Fluctuation in the movement of the shuttles is a major contributor to the dispersion in motor-driven active transportation, which limits the efficiency of the miniaturized devices. In this work, by employing the biomolecular motor kinesin and its associated protein filament microtubule as a model active transport system, we demonstrate that the deep-sea osmolyte trimethylamine N-oxide (TMAO) is useful in regulating the fluctuation in the motility of microtubule shuttles. We show that the motional diffusion coefficient, a measure of the fluctuation in the movement of the kinesin-propelled microtubules, gradually decreases upon increasing the concentration of TMAO in the transportation system. We have been able to reduce the motional diffusion coefficient of microtubules more than 200 times by employing TMAO at a concentration of 2 M. We also show that upon elimination of TMAO, the motional diffusion coefficient of microtubules can be restored, which confirms that TMAO can be used as a tool to reversibly regulate the fluctuation in the sliding movement of kinesin-propelled microtubule shuttles. Such reversible regulation of the dynamic behavior of the shuttles does not require sacrificing the concentration of fuel used for transportation. Our results confirm the ability to manipulate the nanoscale motion of biomolecular motor-driven active transporters in an artificial environment. This work is expected to further enhance the tunability of biomolecular motor functions, which, in turn, will foster their nanotechnological applications based on active transportation.

Dynamic covalent bonds are useful tools in a wide range of applications. Although various reversible chemical reactions have been studied for this purpose, the requirement for harsh conditions, such as high temperature and low or high pH, to activate generally stable covalent bonds limits their potential applications involving biomolecules or household utilization. Here, we report the design, synthesis, characterization, and dynamic covalent bonding properties of 1,2-disubstituted 1,2-dihydro-1,2,4,5-tetrazine-3,6-dione (TETRAD). Hetero-Diels-Alder reactions of TETRAD with furan derivatives and their retro-reactions proceeded rapidly at room temperature under neutral conditions, enabling a chemically induced sol-gel transition system.

Nowadays, biomolecular motor-based miniaturized lab-on-a-chip devices have been attracting much attention for their wide range of nanotechnological applications. Most of the applications are dependent on the motor-driven active transportation of their associated filamentous proteins as shuttles. Fluctuation in the movement of the shuttles is a major contributor to the dispersion in motor-driven active transportation, which limits the efficiency of the miniaturized devices. In this work, by employing the biomolecular motor kinesin and its associated protein filament microtubule as a model active transport system, we demonstrate that the deep-sea osmolyte trimethylamine N-oxide (TMAO) is useful in regulating the fluctuation in the motility of microtubule shuttles. We show that the motional diffusion coefficient, a measure of the fluctuation in the movement of the kinesin-propelled microtubules, gradually decreases upon increasing the concentration of TMAO in the transportation system. We have been able to reduce the motional diffusion coefficient of microtubules more than 200 times by employing TMAO at a concentration of 2 M. We also show that upon elimination of TMAO, the motional diffusion coefficient of microtubules can be restored, which confirms that TMAO can be used as a tool to reversibly regulate the fluctuation in the sliding movement of kinesin-propelled microtubule shuttles. Such reversible regulation of the dynamic behavior of the shuttles does not require sacrificing the concentration of fuel used for transportation. Our results confirm the ability to manipulate the nanoscale motion of biomolecular motor-driven active transporters in an artificial environment. This work is expected to further enhance the tunability of biomolecular motor functions, which, in turn, will foster their nanotechnological applications based on active transportation.

Dynamic covalent bonds are useful tools in a wide range of applications. Although various reversible chemical reactions have been studied for this purpose, the requirement for harsh conditions, such as high temperature and low or high pH, to activate generally stable covalent bonds limits their potential applications involving biomolecules or household utilization. Here, we report the design, synthesis, characterization, and dynamic covalent bonding properties of 1,2-disubstituted 1,2-dihydro-1,2,4,5-tetrazine-3,6-dione (TETRAD). Hetero-Diels-Alder reactions of TETRAD with furan derivatives and their retro-reactions proceeded rapidly at room temperature under neutral conditions, enabling a chemically induced sol-gel transition system.

Microtubules play important roles in biological functions by forming superstructures, such as doublets and branched structures, in vivo. Despite the importance, it is challenging to construct these superstructures in vitro. Here, we designed a tetrameric fluorescent protein Azami-Green (AG) fused with His-tag and Tau-derived peptide (TP), TP-AG, to generate the superstructures. Main binding sites of TP-AG can be controlled to the inside and outside of microtubules by changing the polymerization conditions. The binding of TP-AG to the inside promoted microtubule formation and generated rigid and stable microtubules. The binding of TP-AG to the outside induced various microtubule superstructures, including doublets, multiplets, branched structures, and extremely long microtubules by recruiting tubulins to microtubules. Motile microtubule aster structures were also constructed by TP-AG. The generation of various microtubule superstructures by a single type of exogenous protein is a new concept for understanding the functions of microtubules and constructing microtubule-based nanomaterials.

Cooperation is a strategy that has been adopted by groups of organisms to execute complex tasks more efficiently than single entities. Cooperation increases the robustness and flexibility of the working groups and permits sharing of the workload among individuals. However, the utilization of this strategy in artificial systems at the molecular level, which could enable substantial advances in microrobotics and nanotechnology, remains highly challenging. Here, we demonstrate molecular transportation through the cooperative action of a large number of artificial molecular machines, photoresponsive DNA-conjugated microtubules driven by kinesin motor proteins. Mechanical communication via conjugated photoresponsive DNA enables these microtubules to organize into groups upon photoirradiation. The groups of transporters load and transport cargo, and cargo unloading is achieved by dissociating the groups into single microtubules. The group formation permits the loading and transport of cargoes with larger sizes and in larger numbers over long distances compared with single transporters. We also demonstrate that cargo can be collected at user-determined locations defined by ultraviolet light exposure. This work demonstrates cooperative task performance by molecular machines, which will help to construct molecular robots with advanced functionalities in the future.

Microtubules play important roles in biological functions by forming superstructures, such as doublets and branched structures, in vivo. Despite the importance, it is challenging to construct these superstructures in vitro. Here, we designed a tetrameric fluorescent protein Azami-Green (AG) fused with His-tag and Tau-derived peptide (TP), TP-AG, to generate the superstructures. Main binding sites of TP-AG can be controlled to the inside and outside of microtubules by changing the polymerization conditions. The binding of TP-AG to the inside promoted microtubule formation and generated rigid and stable microtubules. The binding of TP-AG to the outside induced various microtubule superstructures, including doublets, multiplets, branched structures, and extremely long microtubules by recruiting tubulins to microtubules. Motile microtubule aster structures were also constructed by TP-AG. The generation of various microtubule superstructures by a single type of exogenous protein is a new concept for understanding the functions of microtubules and constructing microtubule-based nanomaterials., journal article

Dynamic covalent bonds are useful tools in a wide range of applications. Although various reversible chemical reactions have been studied for this purpose, the requirement for harsh conditions, such as high temperature and low or high pH, to activate generally stable covalent bonds limits their potential applications involving biomolecules or household utilization. Here, we report the design, synthesis, characterization, and dynamic covalent bonding properties of 1,2-disubstituted 1,2-dihydro-1,2,4,5-tetrazine-3,6-dione (TETRAD). Hetero-Diels-Alder reactions of TETRAD with furan derivatives and their retro-reactions proceeded rapidly at room temperature under neutral conditions, enabling a chemically induced sol-gel transition system.

Nowadays, biomolecular motor-based miniaturized lab-on-a-chip devices have been attracting much attention for their wide range of nanotechnological applications. Most of the applications are dependent on the motor-driven active transportation of their associated filamentous proteins as shuttles. Fluctuation in the movement of the shuttles is a major contributor to the dispersion in motor-driven active transportation, which limits the efficiency of the miniaturized devices. In this work, by employing the biomolecular motor kinesin and its associated protein filament microtubule as a model active transport system, we demonstrate that the deep-sea osmolyte trimethylamine N-oxide (TMAO) is useful in regulating the fluctuation in the motility of microtubule shuttles. We show that the motional diffusion coefficient, a measure of the fluctuation in the movement of the kinesin-propelled microtubules, gradually decreases upon increasing the concentration of TMAO in the transportation system. We have been able to reduce the motional diffusion coefficient of microtubules more than 200 times by employing TMAO at a concentration of 2 M. We also show that upon elimination of TMAO, the motional diffusion coefficient of microtubules can be restored, which confirms that TMAO can be used as a tool to reversibly regulate the fluctuation in the sliding movement of kinesin-propelled microtubule shuttles. Such reversible regulation of the dynamic behavior of the shuttles does not require sacrificing the concentration of fuel used for transportation. Our results confirm the ability to manipulate the nanoscale motion of biomolecular motor-driven active transporters in an artificial environment. This work is expected to further enhance the tunability of biomolecular motor functions, which, in turn, will foster their nanotechnological applications based on active transportation.

The biomolecular motor protein kinesin and its associated filamentous protein microtubule have been finding important nanotechnological applications in the recent years. Rigidity of the microtubules, which are propelled by kinesin motors in an in vitro gliding assay, is an important metric that determines the success of utilization of microtubules and kinesins in various applications, such as transportation, sensing, sorting, molecular robotics, etc. Therefore, regulating the rigidity of kinesin-propelled microtubules has been critical. In this work, we report a simple strategy to regulate the rigidity of kinesin- propelled microtubules in an in vitro gliding assay. We demonstrate that rigidity of the microtubules, propelled by kinesins in an in nitro gliding assay, can be modulated simply by using the natural osmolyte trimethylamine N-oxide (TMAO). By varying the concentration of TMAO in the gliding assay, the rigidity of microtubules can be modulated over a wide range. Based on this strategy, we are able to reduce the persistence length of microtubules, a measure of microtubule rigidity, similar to 8 fold by using TMAO at the concentration of 1.5 M. Furthermore, we found that the decreased rigidity of the kinesin-propelled microtubules can be restored upon elimination of TMAO from the in nitro gliding assay. Alteration in the rigidity of microtubules is accounted for by the non-uniformity of the force applied by kinesins along the microtubules in the presence of TMAO. This work offers a facile strategy to reversibly regulate the rigidity of kinesin-propelled microtubules in situ, which would widen the applications of the biomolecular motor kinesin and its associated protein microtubule in various fields.

In order to construct reliable deposited-aerosol database on the Anthropocene (from 1850 to 2020), we obtained a 250-meter-long ice core from the Southeastern Greenland Dome on May and June 2021, where is one of the highest accumulation domes in Greenland. The age of the ice core at a depth of 250 m was roughly estimated to be AD 1827 based on the timescale from a previously analyzed shallower ice core. The age of the sampled ice core satisfied the prerequisite conditions for constructing aerosol deposition database for Anthropocene. In addition, surface elevation, borehole temperatures, and internal stratigraphy of the ice sheet were performed, and meteorological and snow-pit observations were also conducted. Furthermore, we sampled aerosol and snow from the ice sheet for chemical and physical analyses.

Microtubules, the most rigid components of the cytoskeleton, can be key transduction elements between external forces and the cellular environment. Mechanical forces induce microtubule deformation, which is presumed to be critical for the mechanoregulation of cellular events. However, concrete evidence is lacking. In this work, with high-speed atomic force microscopy, we unravel how microtubule deformation regulates the translocation of the microtubule-associated motor protein kinesin-1, responsible for intracellular transport. Our results show that the microtubule deformation by bending impedes the translocation dynamics of kinesins along them. Molecular dynamics simulation shows that the hindered translocation of kinesins can be attributed to an enhanced affinity of kinesins to the microtubule structural units in microtubules deformed by bending. This study advances our understanding of the role of cytoskeletal components in mechanotransduction.

In order to construct reliable deposited-aerosol database on the Anthropocene (from 1850 to 2020), we obtained a 250-meter-long ice core from the Southeastern Greenland Dome on May and June 2021, where is one of the highest accumulation domes in Greenland. The age of the ice core at a depth of 250 m was roughly estimated to be AD 1827 based on the timescale from a previously analyzed shallower ice core. The age of the sampled ice core satisfied the prerequisite conditions for constructing aerosol deposition database for Anthropocene. In addition, surface elevation, borehole temperatures, and internal stratigraphy of the ice sheet were performed, and meteorological and snow-pit observations were also conducted. Furthermore, we sampled aerosol and snow from the ice sheet for chemical and physical analyses.

Flocking is a fascinating coordinated behavior of living organisms or self-propelled particles (SPPs). Particularly, monopolar flocking has been attractive due to its potential applications in various fields. However, the underlying mechanism behind flocking and emergence of monopolar motion in flocking of SPPs has remained obscured. Here, we demonstrate monopolar flocking of kinesin-driven microtubules, a self-propelled biomolecular motor system. Microtubules with an intrinsic structural chirality preferentially move towards counter-clockwise direction. At high density, the CCW motion of microtubules facilitates monopolar flocking and formation of a spiral pattern. The monopolar flocking of microtubules is accounted for by a torque generated when the motion of microtubules was obstructed due to collisions. Our results shed light on flocking and emergence of monopolar motion in flocking of chiral active matters. This work will help regulate the polarity in collective motion of SPPs which in turn will widen their applications in nanotechnology, materials science and engineering.

Flocking is a fascinating coordinated behavior of living organisms or self-propelled particles (SPPs). Particularly, monopolar flocking has been attractive due to its potential applications in various fields. However, the underlying mechanism behind flocking and emergence of monopolar motion in flocking of SPPs has remained obscured. Here, we demonstrate monopolar flocking of kinesin-driven microtubules, a self-propelled biomolecular motor system. Microtubules with an intrinsic structural chirality preferentially move towards counter-clockwise direction. At high density, the CCW motion of microtubules facilitates monopolar flocking and formation of a spiral pattern. The monopolar flocking of microtubules is accounted for by a torque generated when the motion of microtubules was obstructed due to collisions. Our results shed light on flocking and emergence of monopolar motion in flocking of chiral active matters. This work will help regulate the polarity in collective motion of SPPs which in turn will widen their applications in nanotechnology, materials science and engineering.

In order to construct reliable deposited-aerosol database on the Anthropocene (from 1850 to 2020), we obtained a 250-meter-long ice core from the Southeastern Greenland Dome on May and June 2021, where is one of the highest accumulation domes in Greenland. The age of the ice core at a depth of 250 m was roughly estimated to be AD 1827 based on the timescale from a previously analyzed shallower ice core. The age of the sampled ice core satisfied the prerequisite conditions for constructing aerosol deposition database for Anthropocene. In addition, surface elevation, borehole temperatures, and internal stratigraphy of the ice sheet were performed, and meteorological and snow-pit observations were also conducted. Furthermore, we sampled aerosol and snow from the ice sheet for chemical and physical analyses.

Flocking is a fascinating coordinated behavior of living organisms or self-propelled particles (SPPs). Particularly, monopolar flocking has been attractive due to its potential applications in various fields. However, the underlying mechanism behind flocking and emergence of monopolar motion in flocking of SPPs has remained obscured. Here, we demonstrate monopolar flocking of kinesin-driven microtubules, a self-propelled biomolecular motor system. Microtubules with an intrinsic structural chirality preferentially move towards counter-clockwise direction. At high density, the CCW motion of microtubules facilitates monopolar flocking and formation of a spiral pattern. The monopolar flocking of microtubules is accounted for by a torque generated when the motion of microtubules was obstructed due to collisions. Our results shed light on flocking and emergence of monopolar motion in flocking of chiral active matters. This work will help regulate the polarity in collective motion of SPPs which in turn will widen their applications in nanotechnology, materials science and engineering.

Microtubules, the most rigid components of the cytoskeleton, can be key transduction elements between external forces and the cellular environment. Mechanical forces induce microtubule deformation, which is presumed to be critical for the mechanoregulation of cellular events. However, concrete evidence is lacking. In this work, with high-speed atomic force microscopy, we unravel how microtubule deformation regulates the translocation of the microtubule-associated motor protein kinesin-1, responsible for intracellular transport. Our results show that the microtubule deformation by bending impedes the translocation dynamics of kinesins along them. Molecular dynamics simulation shows that the hindered translocation of kinesins can be attributed to an enhanced affinity of kinesins to the microtubule structural units in microtubules deformed by bending. This study advances our understanding of the role of cytoskeletal components in mechanotransduction.

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Keya, J. J., Kudoh, H., Kabir, A. M. R., Inoue, D., Miyamoto, N., Tani, T., Kakugo, A., & Shikinaka, K. Radial alignment of microtubules through tubulin polymerization in an evaporating droplet. Plos One, 15(4), (2020): e0231352, doi:10.1371/journal.pone.0231352., We report the formation of spherulites from droplets of highly concentrated tubulin solution via nucleation and subsequent polymerization to microtubules (MTs) under water evaporation by heating. Radial alignment of MTs in the spherulites was confirmed by the optical properties of the spherulites observed using polarized optical microscopy and fluorescence microscopy. Temperature and concentration of tubulins were found as important parameters to control the spherulite pattern formation of MTs where evaporation plays a significant role. The alignment of MTs was regulated reversibly by temperature induced polymerization and depolymerization of tubulins. The formation of the MTs patterns was also confirmed at the molecular level from the small angle X-ray measurements. This work provides a simple method for obtaining radially aligned arrays of MTs., Fund receiver: Akira Kakugo Grant-in-Aid for Scientific Research on Innovative Areas (Grant Nos. JP24104004 and 18H05423) and a Grant-in-Aid for Scientific Research (A) (Grant No. 18H03673) from kaken. NO - The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Keya, J. J., Kudoh, H., Kabir, A. M. R., Inoue, D., Miyamoto, N., Tani, T., Kakugo, A., & Shikinaka, K. Radial alignment of microtubules through tubulin polymerization in an evaporating droplet. Plos One, 15(4), (2020): e0231352, doi:10.1371/journal.pone.0231352., We report the formation of spherulites from droplets of highly concentrated tubulin solution via nucleation and subsequent polymerization to microtubules (MTs) under water evaporation by heating. Radial alignment of MTs in the spherulites was confirmed by the optical properties of the spherulites observed using polarized optical microscopy and fluorescence microscopy. Temperature and concentration of tubulins were found as important parameters to control the spherulite pattern formation of MTs where evaporation plays a significant role. The alignment of MTs was regulated reversibly by temperature induced polymerization and depolymerization of tubulins. The formation of the MTs patterns was also confirmed at the molecular level from the small angle X-ray measurements. This work provides a simple method for obtaining radially aligned arrays of MTs., Fund receiver: Akira Kakugo Grant-in-Aid for Scientific Research on Innovative Areas (Grant Nos. JP24104004 and 18H05423) and a Grant-in-Aid for Scientific Research (A) (Grant No. 18H03673) from kaken. NO - The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Keya, J. J., Kudoh, H., Kabir, A. M. R., Inoue, D., Miyamoto, N., Tani, T., Kakugo, A., & Shikinaka, K. Radial alignment of microtubules through tubulin polymerization in an evaporating droplet. Plos One, 15(4), (2020): e0231352, doi:10.1371/journal.pone.0231352., We report the formation of spherulites from droplets of highly concentrated tubulin solution via nucleation and subsequent polymerization to microtubules (MTs) under water evaporation by heating. Radial alignment of MTs in the spherulites was confirmed by the optical properties of the spherulites observed using polarized optical microscopy and fluorescence microscopy. Temperature and concentration of tubulins were found as important parameters to control the spherulite pattern formation of MTs where evaporation plays a significant role. The alignment of MTs was regulated reversibly by temperature induced polymerization and depolymerization of tubulins. The formation of the MTs patterns was also confirmed at the molecular level from the small angle X-ray measurements. This work provides a simple method for obtaining radially aligned arrays of MTs., Fund receiver: Akira Kakugo Grant-in-Aid for Scientific Research on Innovative Areas (Grant Nos. JP24104004 and 18H05423) and a Grant-in-Aid for Scientific Research (A) (Grant No. 18H03673) from kaken. NO - The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Trimethylamine N-oxide is found to be effective in regulating the interaction between microtubules and kinesins over a wide temperature range. The lifetime of the motility of microtubules on kinesins at high temperatures is prolonged using trimethylamine N-oxide. The activation energy of microtubule motility is increased by trimethylamine N-oxide. Prolonged operation at high temperatures decreased the activation energy of MT motility despite the increase in concentration of trimethylamine N-oxide.

Microtubules, one of the major components of the cytoskeleton, play important roles as pathways for neuronal transport of cellular traffic. The loss of structural stability of microtubules causes detrimental effects on neurons and may contribute to several neurodegenerative diseases, such as Alzheimer's disease, amyotrophic lateral sclerosis, Huntington's disease, etc. The triazolopyrimidine class compound cevipabulin is a synthetic microtubule-stabilizing agent that has recently emerged as a drug for the treatment of Alzheimer's disease. However, the mechanism of microtubule stabilization by cevipabulin has not yet been revealed. Here, we explored the effect of cevipabulin on stabilizing microtubules polymerized from purified tubulins in vitro. We observed the effects of the concentration of microtubule-stabilizing drugs, incubation time, and modification of the cevipabulin structure on the stabilization of microtubules in comparison to those of the most commonly used anticancer drug, paclitaxel. This study will provide insight into the action of cevipabulin in the treatment of neurodegenerative diseases. Stabilization of microtubules occurs by paclitaxel bound to the taxoid site and cevipabulin (and its derivative) bound to the taxoid site and/or vinca alkaloid domain of the beta-tubulin in tubulin heterodimer.

We report the formation of spherulites from droplets of highly concentrated tubulin solution via nucleation and subsequent polymerization to microtubules (MTs) under water evaporation by heating. Radial alignment of MTs in the spherulites was confirmed by the optical properties of the spherulites observed using polarized optical microscopy and fluorescence microscopy. Temperature and concentration of tubulins were found as important parameters to control the spherulite pattern formation of MTs where evaporation plays a significant role. The alignment of MTs was regulated reversibly by temperature induced polymerization and depolymerization of tubulins. The formation of the MTs patterns was also confirmed at the molecular level from the small angle X-ray measurements. This work provides a simple method for obtaining radially aligned arrays of MTs.

The glutaraldehyde fixation method for fixing tissues is attractive for its ease of use and straightforward surface chemistry. We investigated the effect of glutaraldehyde-induced microtubule immobilization on kinesin-driven cargo transport along microtubules and found that at low glutaraldehyde concentrations, the microtubule-kinesin interaction remains unperturbed. Such findings may facilitate the application of the glutaraldehyde fixation method for many in vitro studies aiming to build nanodevices powered by the microtubule-motor protein interaction.

Recent advancements in molecular robotics have been greatly contributed by the progress in various fields of science and technology, particularly in supramolecular chemistry, bio- and nanotechnology, and informatics. Yet one of the biggest challenges in molecular robotics has been controlling a large number of robots at a time and employing the robots for any specific task as flocks in order to harness emergent functions. Swarming of molecular robots has emerged as a new paradigm with potentials to overcome this hurdle in molecular robotics. In this review article, we comprehensively discuss the latest developments in swarm molecular robotics, particularly emphasizing the effective utilization of bio- and nanotechnology in swarming of molecular robots. Importance of tuning the mutual interaction among the molecular robots in regulation of their swarming is introduced. Successful utilization of DNA, photoresponsive molecules, and natural molecular machines in swarming of molecular robots to provide them with processing, sensing, and actuating ability is highlighted. The potentials of molecular swarm robots for practical applications by means of their ability to participate in logical operations and molecular computations are also discussed. Prospects of the molecular swarm robots in utilizing the emergent functions through swarming are also emphasized together with their future perspectives.

Nanoscale transportation in engineered environments is critical towards designing efficient and smart hybrid bio-nanodevices. Biomolecular motors, the smallest natural machines, are promising as actuators as well as sensors in hybrid nanodevices and hold enormous potentials in nanoscale transportation. Highly specific regulation of the activity of biomolecular motors is the key to control such integrated nanodevices. We present a simple method to regulate the activity of a biomolecular motor system, microtubule (MT)-kinesin by using a natural osmolyte trimethylamine-N-oxide (TMAO). Motility of kinesin-driven MTs in an in vitro gliding assay is regulated over a broad spectrum by using TMAO in a concentration dependent manner. The regulation of MT motility is rapid, reversible and repeatable over multiple cycles. Interestingly, the motility of MTs can be completely turned off using TMAO of a relatively high concentration. The halted motility of MTs is fully restored upon elimination of TMAO. Repeated cycles of TMAO addition and removal enable cyclical inhibition and restoration of the motility of MTs. These results demonstrate an ability to control nanoscale motion of a biomolecular motor in an artificial environment. This work facilitates further tunability over functions of biomolecular motors, which in turn will foster their nanotechnological applications, such as in nano-transportation.

The cyclization of peptides is a valuable strategy for the development of binding motifs to target proteins with improved affinity. Microtubules (MTs) are important targets for therapeutics, and a variety of MT-targeted drugs and peptides have recently been developed. We have previously designed a Tau-derived peptide (TP) that binds to the interior of MTs. In the present study, the development of a cyclic TP (TCP) for enhanced binding to tubulin and the stabilization of MTs is described. The fluorescently labeled cyclic peptide containing three glycine linkers (TCP3-TMR) exhibited a remarkably enhanced binding affinity to tubulin. The cyclic peptide was also demonstrated to stabilize MTs by enhancing polymerization and reducing depolymerization. Moreover, MTs were effectively formed by the treatment of cyclic peptides in the presence of guanosine triphosphate (GTP), while the linear peptide showed no such effect. These findings indicate that TCP is a useful binding motif that can stabilize MTs and is valuable for various therapeutic and material applications., identifier:https://doi.org/10.1038/s41428-020-0356-3

Nanoscale transportation in engineered environments is critical towards designing efficient and smart hybrid bio-nanodevices. Biomolecular motors, the smallest natural machines, are promising as actuators as well as sensors in hybrid nanodevices and hold enormous potentials in nanoscale transportation. Highly specific regulation of the activity of biomolecular motors is the key to control such integrated nanodevices. We present a simple method to regulate the activity of a biomolecular motor system, microtubule (MT)-kinesin by using a natural osmolyte trimethylamine-N-oxide (TMAO). Motility of kinesin-driven MTs in an in vitro gliding assay is regulated over a broad spectrum by using TMAO in a concentration dependent manner. The regulation of MT motility is rapid, reversible and repeatable over multiple cycles. Interestingly, the motility of MTs can be completely turned off using TMAO of a relatively high concentration. The halted motility of MTs is fully restored upon elimination of TMAO. Repeated cycles of TMAO addition and removal enable cyclical inhibition and restoration of the motility of MTs. These results demonstrate an ability to control nanoscale motion of a biomolecular motor in an artificial environment. This work facilitates further tunability over functions of biomolecular motors, which in turn will foster their nanotechnological applications, such as in nano-transportation.

Recent advancements in molecular robotics have been greatly contributed by the progress in various fields of science and technology, particularly in supramolecular chemistry, bio- and nanotechnology, and informatics. Yet one of the biggest challenges in molecular robotics has been controlling a large number of robots at a time and employing the robots for any specific task as flocks in order to harness emergent functions. Swarming of molecular robots has emerged as a new paradigm with potentials to overcome this hurdle in molecular robotics. In this review article, we comprehensively discuss the latest developments in swarm molecular robotics, particularly emphasizing the effective utilization of bio- and nanotechnology in swarming of molecular robots. Importance of tuning the mutual interaction among the molecular robots in regulation of their swarming is introduced. Successful utilization of DNA, photoresponsive molecules, and natural molecular machines in swarming of molecular robots to provide them with processing, sensing, and actuating ability is highlighted. The potentials of molecular swarm robots for practical applications by means of their ability to participate in logical operations and molecular computations are also discussed. Prospects of the molecular swarm robots in utilizing the emergent functions through swarming are also emphasized together with their future perspectives.

Trimethylamine N-oxide is found to be effective in regulating the interaction between microtubules and kinesins over a wide temperature range. The lifetime of the motility of microtubules on kinesins at high temperatures is prolonged using trimethylamine N-oxide. The activation energy of microtubule motility is increased by trimethylamine N-oxide. Prolonged operation at high temperatures decreased the activation energy of MT motility despite the increase in concentration of trimethylamine N-oxide.

The glutaraldehyde fixation method for fixing tissues is attractive for its ease of use and straightforward surface chemistry. We investigated the effect of glutaraldehyde-induced microtubule immobilization on kinesin-driven cargo transport along microtubules and found that at low glutaraldehyde concentrations, the microtubule-kinesin interaction remains unperturbed. Such findings may facilitate the application of the glutaraldehyde fixation method for many in vitro studies aiming to build nanodevices powered by the microtubule-motor protein interaction.

Microtubules, one of the major components of the cytoskeleton, play important roles as pathways for neuronal transport of cellular traffic. The loss of structural stability of microtubules causes detrimental effects on neurons and may contribute to several neurodegenerative diseases, such as Alzheimer's disease, amyotrophic lateral sclerosis, Huntington's disease, etc. The triazolopyrimidine class compound cevipabulin is a synthetic microtubule-stabilizing agent that has recently emerged as a drug for the treatment of Alzheimer's disease. However, the mechanism of microtubule stabilization by cevipabulin has not yet been revealed. Here, we explored the effect of cevipabulin on stabilizing microtubules polymerized from purified tubulins in vitro. We observed the effects of the concentration of microtubule-stabilizing drugs, incubation time, and modification of the cevipabulin structure on the stabilization of microtubules in comparison to those of the most commonly used anticancer drug, paclitaxel. This study will provide insight into the action of cevipabulin in the treatment of neurodegenerative diseases. Stabilization of microtubules occurs by paclitaxel bound to the taxoid site and cevipabulin (and its derivative) bound to the taxoid site and/or vinca alkaloid domain of the beta-tubulin in tubulin heterodimer.

We report the formation of spherulites from droplets of highly concentrated tubulin solution via nucleation and subsequent polymerization to microtubules (MTs) under water evaporation by heating. Radial alignment of MTs in the spherulites was confirmed by the optical properties of the spherulites observed using polarized optical microscopy and fluorescence microscopy. Temperature and concentration of tubulins were found as important parameters to control the spherulite pattern formation of MTs where evaporation plays a significant role. The alignment of MTs was regulated reversibly by temperature induced polymerization and depolymerization of tubulins. The formation of the MTs patterns was also confirmed at the molecular level from the small angle X-ray measurements. This work provides a simple method for obtaining radially aligned arrays of MTs.

Boundary conditions are important for pattern formation in active matter. However, it is still not well-understood how alterations in the boundary conditions (dynamic boundary conditions) impact pattern formation. To elucidate the effect of dynamic boundary conditions on the pattern formation by active matter, we investigate an in vitro gliding assay of microtubules on a deformable soft substrate. The dynamic boundary conditions were realized by applying mechanical stress through stretching and compression of the substrate during the gliding assay. A single cycle of stretch-and-compression (relaxation) of the substrate induces perpendicular alignment of microtubules relative to the stretch axis, whereas repeated cycles resulted in zigzag patterns of microtubules. Our model shows that the orientation angles of microtubules correspond to the direction to attain smooth movement without buckling, which is further amplified by the collective migration of the microtubules. Our results provide an insight into understanding the rich dynamics in self-organization arising in active matter subjected to time-dependent boundary conditions.

We constructed GFP-encapsulated microtubules (MTs) using Tauderived peptide which binds to their interior. The encapsulation of GFP dramatically increased the rigidity of MTs, resulting in their enhanced velocity on a kinesin-coated substrate. Moreover, the GFP-encapsulated MTs were significantly more stable compared to normal MTs., identifier:https://doi.org/10.1039/C9CC04345D

Boundary conditions are important for pattern formation in active matter. However, it is still not well-understood how alterations in the boundary conditions (dynamic boundary conditions) impact pattern formation. To elucidate the effect of dynamic boundary conditions on the pattern formation by active matter, we investigate an in vitro gliding assay of microtubules on a deformable soft substrate. The dynamic boundary conditions were realized by applying mechanical stress through stretching and compression of the substrate during the gliding assay. A single cycle of stretch-and-compression (relaxation) of the substrate induces perpendicular alignment of microtubules relative to the stretch axis, whereas repeated cycles resulted in zigzag patterns of microtubules. Our model shows that the orientation angles of microtubules correspond to the direction to attain smooth movement without buckling, which is further amplified by the collective migration of the microtubules. Our results provide an insight into understanding the rich dynamics in self-organization arising in active matter subjected to time-dependent boundary conditions.

Pancreatic ductal adenocarcinoma (PDAC) reportedly progresses very rapidly through the initial carcinogenesis stages including DNA damage and disordered cell death. However, such oncogenic mechanisms are largely studied through observational diagnostic methods, partly because of a lack of live in vitro tumour imaging techniques. Here we demonstrate a simple live-tumour in vitro imaging technique using micro-patterned plates (micro/nanoplates) that allows dynamic visualisation of PDAC microtumours. When PDAC cells were cultured on a micro/nanoplate overnight, the cells self-organised into non-spheroidal microtumours that were anchored to the micro/nanoplate through cell-in-cell invasion. This self-organisation was only efficiently induced in small-diameter rough microislands. Using a time-lapse imaging system, we found that PDAC microtumours actively stretched to catch dead cell debris via filo/lamellipoedia and suction, suggesting that they have a sophisticated survival strategy (analogous to that of starving animals), which implies a context for the development of possible therapies for PDACs. The simple tumour imaging system visualises a potential of PDAC cells, in which the aggressive tumour dynamics reminds us of the need to review traditional PDAC pathogenesis.

Pancreatic ductal adenocarcinoma (PDAC) reportedly progresses very rapidly through the initial carcinogenesis stages including DNA damage and disordered cell death. However, such oncogenic mechanisms are largely studied through observational diagnostic methods, partly because of a lack of live in vitro tumour imaging techniques. Here we demonstrate a simple live-tumour in vitro imaging technique using micro-patterned plates (micro/nanoplates) that allows dynamic visualisation of PDAC microtumours. When PDAC cells were cultured on a micro/nanoplate overnight, the cells self-organised into non-spheroidal microtumours that were anchored to the micro/nanoplate through cell-in-cell invasion. This self-organisation was only efficiently induced in small-diameter rough microislands. Using a time-lapse imaging system, we found that PDAC microtumours actively stretched to catch dead cell debris via filo/lamellipoedia and suction, suggesting that they have a sophisticated survival strategy (analogous to that of starving animals), which implies a context for the development of possible therapies for PDACs. The simple tumour imaging system visualises a potential of PDAC cells, in which the aggressive tumour dynamics reminds us of the need to review traditional PDAC pathogenesis.

In vitro gliding assay of microtubules (MTs) on kinesins has provided us with valuable biophysical and chemo-mechanical insights of this biomolecular motor system. Visualization of MTs in an in vitro gliding assay has been mainly dependent on optical microscopes, limited resolution of which often render them insufficient sources of desired information. In this work, using high speed atomic force microscopy (HS-AFM), which allows imaging with higher resolution, we monitored MTs and protofilaments (PFs) of tubulins while gliding on kinesins. Moreover, under the HS-AFM, we also observed splitting of gliding MTs into single PFs at their leading ends. The split single PFs interacted with kinesins and exhibited translational motion, but with a slower velocity than the MTs. Our investigation at the molecular level, using the HS-AFM, would provide new insights to the mechanics of MTs in dynamic systems and their interaction with motor proteins.

We investigated the role of the concentration of microtubules and depletion force in the emergence of collective motion of microtubules driven by kinesins. Critical concentrations were found for both microtubules and the depletant to demonstrate the collective motion of microtubules. More importantly, the kinetics of the collective motion were found to be significantly dependent on the concentration of microtubules and the depletant. Substantial variations in the time course of emergence of the collective motion of microtubules were observed in response to the changes in concentration of the microtubules and the depletant. This study provides new insights into the kinetics of the collective motion of microtubules driven by kinesins, which might also be useful in understanding the coordinated behavior of other self-propelled systems.