Simple Physical Models For Complex Protein Machines

Artificial protein like structures with machine properties could be moreover designed by running a computer evolution of elastic networks. The living cell can be viewed as a factory where protein machines are in charge of various processes; such as transport of material inside the cell or operations with other macromolecules like DNA.

The complexity of interactions between atoms in a protein machine is so high; that even world’s best supercomputers cannot reproduce just one of their operation cycles. In this review article; it is however demonstrating that essential aspects of the operation of such natural nano devices can be already revealed by exploring very simple mechanical models of proteins; i.e. by treating such macromolecules as elastic networks obtained by connecting particles by a set of elastic springs.

Complex protein machines

Their operation is typically fueling by ATP molecules; the major energy carrier in biological cells. The chemical energy gaining through ATP hydrolysis is using by a protein machine to cyclically change its shape; and thus to perform a particular function.

But elastic networks corresponding to protein machines with functional dynamics have special properties; emerging in the process of biological evolution. Despite an apparent complexity; internal motions in such systems proceed in an ordereding manner; as if guiding along hidden rail tracks. Thus, a molecular machine behaves similar to macroscopic mechanical devices with highly coordinating movements of their parts.

Macroscopic mechanical devices

Thus, a molecular machine behaves similar to macroscopic mechanical devices with highly coordinating movements of their parts. This ensures that the cellular factory can function robustly despite strong fluctuations present at nanoscales. The elementary units of proteins are residues (amino acids) and therefore it is natural to work with the coarse graining descriptions at the level of such atomic groups.

Protein machines represent a special class of enzymes. An enzyme is a protein that acts as a single molecule catalyst accelerating a chemical reaction. The reaction event itself takes place at an active centre inside the enzyme. Catalytic reactions can involve conversion of one or two substrates into one or two products; and several intermediate products can also be formed. For simplicity, we shall however assume below that one substrate molecule is converted into one product molecule in a turnover cycle.