Modelling of internal architecture of kinesin nanomotor as a machine language

Abstract

Kinesin is a protein-based natural nanomotor that transports molecular cargoes within cells by walking along microtubules. Kinesin nanomotor is considered as a bio-nanoagent which is able to sense the cell through its sensors (i.e. its heads and tail), make the decision internally and perform actions on the cell through its actuator (i.e. its motor domain). The study maps the agent-based architectural model of internal decision-making process of kinesin nanomotor to a machine language using an automata algorithm. The applied automata algorithm receives the internal agent-based architectural model of kinesin nanomotor as a deterministic finite automaton (DFA) model and generates a regular machine language. The generated regular machine language was acceptable by the architectural DFA model of the nanomotor and also in good agreement with its natural behaviour. The internal agent-based architectural model of kinesin nanomotor indicates the degree of autonomy and intelligence of the nanomotor interactions with its cell. Thus, our developed regular machine language can model the degree of autonomy and intelligence of kinesin nanomotor interactions with its cell as a language. Modelling of internal architectures of autonomous and intelligent bio-nanosystems as machine languages can lay the foundation towards the concept of bio-nanoswarms and next phases of the bio-nanorobotic systems development.

Construction of Asymmetrical Hexameric Biomimetic Motors with Continuous Single-Directional Motion by Sequential Coordination

“…Biological macromolecules of DNA, RNA, and proteins are essential and powerful chemical building blocks of all organisms based on their intrinsically defined features at the nanometer scale . Construction of self‐propelling nanomotors has been a popular subject in the field of nanotechnology . The emerging field of nanotechnology has led to the advancement of biomaterials engineering and synthetic biology .…”

Computational Modeling of Kinesin Stepping

“…Conventional kinesin is a double-headed and adenosine triphosphate (ATP)-driven motor protein that walks processively in discrete 8.2 nm steps and in an asymmetric hand-over-hand fashion toward the plus end of microtubules (MTs) , in the presence of ATP or in the absence of ATP if external load is applied to the motor . Kinesin stepping exerts localized forces on nanostructures, and thus can be exploited in nanorobotics by designing synthetic nanodevices powered by kinesin − and in the controlled propagation architecture of nanonetworks in which information molecules are carried by kinesin motors between transmitter and receiver nanomachines. , Synthetic nanodevices and nanonetworks are anticipated to contribute in medical diagnostics as well as engineering applications. ,, Despite this progress, artificial nanomotors still lack the functionality and efficiency of their biological counterparts. − One of the issues frequently raised in designing nanodevices with capability of molecular communication and computing is the connectivity of molecules when the output from one molecule is used to control another …”

“…Kinesin is considered to be a basic protein nanomachine capable of sensing, processing information, and actuating. − Meanwhile, the mechanical kinetics driving kinesin motion are fundamentally different from those of macroscopic motors . Representing the mechanical kinetics underlying the stepping cycles of kinesin using computational logic models used to model the control flow of macroscopic systems’ behaviors would allow us to describe how the cellular inputs sensed by kinesin are transferred into mechanical steps.…”