Theoretical perspectives on biological machines

Abstract

Many biological functions are executed by molecular machines, which like man made motors consume energy and convert it into mechanical work. Biological machines have evolved to transport cargo, facilitate folding of proteins and RNA, remodel chromatin and replicate DNA. A common aspect of these machines is that their functions are driven by fuel provided by hydrolysis of ATP or GTP, thus driving them out of equilibrium. It is a challenge to provide a general framework for understanding the functions of biological machines, such as molecular motors (kinesin, dynein, and myosin), molecular chaperones, and helicases. Using these machines, whose structures have little resemblance to one another, as prototypical examples, we describe a few general theoretical methods that have provided insights into their functions. Although the theories rely on coarse-graining of these complex systems they have proven useful in not only accounting for many in vitro experiments but also address questions such as how the trade-off between precision, energetic costs and optimal performances are balanced. However, many complexities associated with biological machines will require one to go beyond current theoretical methods. We point out that simple point mutations in the enzyme could drastically alter functions, making the motors bi-directional or result in unexpected diseases or dramatically restrict the capacity of molecular chaperones to help proteins fold. These examples are reminders that while the search for principles of generality in biology is intellectually stimulating, one also ought to keep in mind that molecular details must be accounted for to develop a deeper understanding of processes driven by biological machines. Going beyond generic descriptions of in vitro behavior to making genuine understanding of in vivo functions will likely remain a major challenge for some time to come. In this context, the combination of careful experiments and the use of physics and physical chemistry principles will be useful in elucidating the rules governing the workings of biological machines.

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Theory and Simulations of condensin mediated loop extrusion in DNA

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Modeling and Performance Optimization of an Irreversible Two-Stage Combined Thermal Brownian Heat Engine

“…It realizes energy conversion through the movement of microscopic particles in viscous medium (VM) with different reservoirs. Many scholars studied the thermodynamic performance of such micro-motors and drew a lot of meaningful conclusions [ 3 ].…”