Arif Md. Rashedul Kabir

Prolongation of the Active Lifetime of a Biomolecular Motor for in Vitro Motility Assay by Using an Inert Atmosphere

Over the last few decades, the in vitro motility assay has been performed to probe the biophysical and chemo-mechanical properties as well as the self-organization process of biomolecular motor systems such as actin-myosin and microtubule-kinesin. However, aggression of the reactive oxygen species (ROS) and concomitant termination of the activity of biomolecular motors during investigation remains a drawback of this assay. Despite enzymatic protection that makes use of a combination of glucose, glucose oxidase, and catalase, the active lifetime of biomolecular motors is found to be only a few hours and this short lifetime restricts further study on those systems. We have solved this problem by using a newly developed system of the in vitro motility assay that is conducted in an inert nitrogen gas atmosphere free of ROS. Using microtubule-kinesin as a model system we have shown that our system has prolonged the active lifetime of the biomolecular motor until several days and even a week by protecting it from oxidative damage.

Formation of ring-shaped assembly of microtubules with a narrow size distribution at an air–buffer interface

Biopolymers such as actin, microtubules and DNA are well known for their fascinating in vivo self-organization phenomena. Considerable efforts have been devoted to mimicking their organization process in vitro that produced ring-shaped or toroid structures in an irreversible manner. However, understanding the factors that lead to formation of such assembled structures deserves more investigation to achieve a unified insight into the assembly process, particularly of the microtubules. Here, we report an active assembly process of microtubules (MTs) at an air–buffer interface that resulted in ring-shaped microtubule structures with a narrow size distribution and a high yield. Using an “air–buffer interface control system” combined with the newly developed “inert chamber system (ICS)” we have also successfully observed the reversible conformational transition between ring- and linear-shaped microtubules at the air–buffer interface. This is the first ever direct in situ observation of a reversible assembly process of MTs and probably provides us with valuable discernment to understand the in vivo organizational behavior of biopolymers.

Growth of ring-shaped microtubule assemblies through stepwise active self-organisation

The microtubule (MT)–kinesin system is a promising candidate for constructing artificial biomachines. The active self-organisation (AcSO) method has been developed to integrate MT filaments into highly organised assembled structures. The creation of ring-shaped MT assemblies is one of the outcomes of the organisation process and holds prospects for use in future nano-technological applications. However, making use of ring-shaped MT assemblies in practical applications requires further control of the size of these assemblies, which has not yet been addressed. In this work, we demonstrated AcSO of MTs in a stepwise manner inside an inert atmosphere. We show that in an inert atmosphere, AcSO could be performed several times (at least nine times), and as a result, this method successfully increased the thickness of ring-shaped MT assemblies.

Controlled Clockwise–Counterclockwise Motion of the Ring-Shaped Microtubules Assembly

The microtubule (MT)-kinesin system has been proposed as the building block of biomolecular motor based artificial biomachines. Considerable efforts have been devoted to integrate this system that produced a variety of ordered structures including the ring-shaped MT assembly which is being considered as a promising candidate for the further development of the biomachines. However, lack of proper knowledge that might help tune the direction of motion of ring-shaped microtubule assembly from counterclockwise to clockwise direction, and vice versa, significantly restricted their potential applications. We report our success in controlling the direction of rotational motion of ring-shaped MT assembly by altering the preparation conditions of microtubules. The change in the direction of rotation of MT rings could be interpreted in terms of the accompanied structural rearrangement of the MT lattice. For achieving handedness-regulated efficient biomachines having tunable asymmetric property, our study will be significantly directive.

Depletion force induced collective motion of microtubules driven by kinesin

Collective motion is a fascinating example of coordinated behavior of self-propelled objects, which is often associated with the formation of large scale patterns. Nowadays, the in vitro gliding assay is being considered a model system to experimentally investigate various aspects of group behavior and pattern formation by self-propelled objects. In the in vitro gliding assay, cytoskeletal filaments F-actin or microtubules are driven by the surface immobilized associated biomolecular motors myosin or dynein respectively. Although the F-actin/myosin or microtubule/dynein system was found to be promising in understanding the collective motion and pattern formation by self-propelled objects, the most widely used biomolecular motor system microtubule/kinesin could not be successfully employed so far in this regard. Failure in exhibiting collective motion by kinesin driven microtubules is attributed to the intrinsic properties of kinesin, which was speculated to affect the behavior of individual gliding microtubules and mutual interactions among them. In this work, for the first time, we have demonstrated the collective motion of kinesin driven microtubules by regulating the mutual interaction among the gliding microtubules, by employing a depletion force among them. Proper regulation of the mutual interaction among the gliding microtubules through the employment of the depletion force was found to allow the exhibition of collective motion and stream pattern formation by the microtubules. This work offers a universal means for demonstrating the collective motion using the in vitro gliding assay of biomolecular motor systems and will help obtain a meticulous understanding of the fascinating coordinated behavior and pattern formation by self-propelled objects.

Buckling of Microtubules on a 2D Elastic Medium.

We have demonstrated compression stress induced mechanical deformation of microtubules (MTs) on a two-dimensional elastic medium and investigated the role of compression strain, strain rate, and a MT-associated protein in the deformation of MTs. We show that MTs, supported on a two-dimensional substrate by a MT-associated protein kinesin, undergo buckling when they are subjected to compression stress. Compression strain strongly affects the extent of buckling, although compression rate has no substantial effect on the buckling of MTs. Most importantly, the density of kinesin is found to play the key role in determining the buckling mode of MTs. We have made a comparison between our experimental results and the ‘elastic foundation model’ that theoretically predicts the buckling behavior of MTs and its connection to MT-associated proteins. Taking into consideration the role of kinesin in altering the mechanical property of MTs, we are able to explain the buckling behavior of MTs by the elastic foundation model. This work will help understand the buckling mechanism of MTs and its connection to MT-associated proteins or surrounding medium, and consequently will aid in obtaining a meticulous scenario of the compression stress induced deformation of MTs in cells.

Biomolecular motor modulates mechanical property of microtubule.

The microtubule (MT) is the stiffest cytoskeletal filamentous protein that takes part in a wide range of cellular activities where its mechanical property plays a crucially significant role. How a single biological entity plays multiple roles in cell has been a mystery for long time. Over the recent years, it has been known that modulation of the mechanical property of MT by different cellular agents is the key to performing manifold in vivo activities by MT. Studying the mechanical property of MT thus has been a prerequisite in understanding how MT plays such diversified in vivo roles. However, the anisotropic structure of MT has been an impediment in obtaining a precise description of the mechanical property of MT along its longitudinal and lateral directions that requires employment of distinct experimental approach and has not been demonstrated yet. In this work, we have developed an experimental system that enabled us to investigate the effect of tensile stress on MT. By using our newly developed system, (1) we have determined the Youngs modulus of MT considering its deformation under applied tensile stress and (2) a new role of MT associated motor protein kinesin in modulating the mechanical property of MT was revealed for the first time. Decrease in Youngs modulus of MT with the increase in interaction with kinesin suggests that kinesin has a softening effect on MT and thereby can modulate the rigidity of MT. This work will be an aid in understanding the modulation of mechanical property of MTs by MT associated proteins and might also help obtain a clear insight of the endurance and mechanical instability of MTs under applied stress.

DNA-assisted swarm control in a biomolecular motor system

In nature, swarming behavior has evolved repeatedly among motile organisms because it confers a variety of beneficial emergent properties. These include improved information gathering, protection from predators, and resource utilization. Some organisms, e.g., locusts, switch between solitary and swarm behavior in response to external stimuli. Aspects of swarming behavior have been demonstrated for motile supramolecular systems composed of biomolecular motors and cytoskeletal filaments, where cross-linkers induce large scale organization. The capabilities of such supramolecular systems may be further extended if the swarming behavior can be programmed and controlled. Here, we demonstrate that the swarming of DNA-functionalized microtubules (MTs) propelled by surface-adhered kinesin motors can be programmed and reversibly regulated by DNA signals. Emergent swarm behavior, such as translational and circular motion, can be selected by tuning the MT stiffness. Photoresponsive DNA containing azobenzene groups enables switching between solitary and swarm behavior in response to stimulation with visible or ultraviolet light.Self-propelled molecular entities enable studying swarm behavior on a macroscopic scale but programmability of interactions has yet not been achieved. Here the authors show reversible regulation of DNA-functionalized microtubules by DNA signals and switching between solitary and swarm behaviour by employing photoresponsive DNA strands.

Sensing surface mechanical deformation using active probes driven by motor proteins

Studying mechanical deformation at the surface of soft materials has been challenging due to the difficulty in separating surface deformation from the bulk elasticity of the materials. Here, we introduce a new approach for studying the surface mechanical deformation of a soft material by utilizing a large number of self-propelled microprobes driven by motor proteins on the surface of the material. Information about the surface mechanical deformation of the soft material is obtained through changes in mobility of the microprobes wandering across the surface of the soft material. The active microprobes respond to mechanical deformation of the surface and readily change their velocity and direction depending on the extent and mode of surface deformation. This highly parallel and reliable method of sensing mechanical deformation at the surface of soft materials is expected to find applications that explore surface mechanics of soft materials and consequently would greatly benefit the surface science.

Controlling the bias of rotational motion of ring-shaped microtubule assembly.

Biomolecular motor system microtubule (MT)-kinesin is considered a building block for developing artificial microdevices. Recently, an active self-organization method has been established to integrate MT filaments into ring-shaped assembly that can produce rotational motion both in the clockwise and in the counterclockwise directions. In this work, we have investigated the effect of parameters such as MT and kinesin concentration, length, and rigidity of MT and type of kinesin (structure of tail region) on the preferential rotation of the ring-shaped MT assembly produced in an active self-organization. We elucidated that these factors can significantly affect the bias of rotation of the ring-shaped MT assembly, which seems to be related to the fluctuation of leading tip of moving MT filaments. This new finding might be important for designing handedness regulated artificial biomachine using the ring-shaped MT assembly in future.