Physical characteristics, molecular dynamics, and cell activities that sustain life are thoroughly shaped as the fundamental aspects that shape the mechanics of cellular operations like protein folding and render energy to molecular engines. Protein folding is spurred by the mix of intramolecular forces, for instance, the attraction of charges and the hydrophobic conversation, the van der Waals forces, and the hydrogen chain linkage, driving the polypeptide order through the tangled energy landscape to its natural structure that is useful. Molecular machines, in contrary, turn the ATP hydrolysis chemical energy into a mechanical order through cyclical dialogues with the cytoskeletal fibers and the ordered shape alterations, which are different from balanced condition. These molecular motors are based on the principles of macromolecular coupling and stochastic thermodynamics to generate force and directional movement despite thermal changes. All in all, these processes demonstrate how the cells manipulate physical ramification to sustain order, perform tasks, and purvey life at the nanoscale.

Protein folding is mainly a problem of thermodynamics and kinetics. The polypeptide chain folds because interactions such as hydrogen bonds, hydrophobic interactions, van der Waals contacts, and electrostatics reduce the free energy of the system. Folding is not a deterministic pathway but stochastic, with barriers and intermediates that can slow or misdirect the process. In the cell, folding is influenced by the crowded environment and assisted by chaperone proteins. Misfolding and aggregation occur when proteins become trapped in local minima, which has biological consequences.

Molecular motors convert the chemical free energy from ATP hydrolysis into mechanical work which happens through cycles of binding, hydrolysis, conformational change, and product release. Two useful models are the power-stroke idea, where conformational changes directly produce motion, and the Brownian ratchet idea, where thermal fluctuations are biased into directional steps by ATP turnover. Motor activity is stochastic, but it can be described using chemomechanical coupling and stochastic thermodynamics, which allow calculation of step sizes, velocities, run lengths, and efficiencies.

References

1) Article Protein Folding and Misfolding

2)Mechanics of motor proteins and the cytoskeleton ; Jonathon Howard.

3) Article The Protein-Folding Problem, 50 Years On