Investigating conformational changes of Prefoldin β1 as result of applying external mechanical force without any position constraint

Manipulating molecular scale bio-nanorobots and influencing their behaviour is one of the major challenges of new researches. Many coiled coil type proteins are involved in important biological functions due to physical properties that make them ideal for both nanoscale manipulation and sensing. The Prefoldin beta subunit from Thermococcus strain KS-1(Prefoldin β1) is one of the possible proteins that can serve as a new bio-nano-actuator. Besides having a balanced architecture, Prefoldin β1 can exhibit a wide range of exclusive authorities. In this study, steered molecular dynamics simulation is applied along with the centre of mass pulling and analyses of Prefoldin β1 conformational changes to characterise some of those abilities. Thus, applying external mechanical force without any position constraint shows that it has no movement throughout simulations. This proposes a novel method to capture different sizes and shapes of cargoes. During simulations, each arm was found to be very flexible, allowing it to enlarge its central cavity and capture different cargoes. For a more accurate analysis, the variations in the cavity of nano-actuator are investigated qualitatively and quantitatively with different parameters. Also, the force analysis of the arms can provide us with decent information about the performance of this nano-actuator.

Modelling of internal architecture of kinesin nanomotor as a machine language

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.