https://phys.org/news/2018-05-code-functional-molecular-machine.html

According to a recent hypothesis, protein function relies on "flexible joints." This study, published in Proceedings of the National Academy of Sciences (PNAS), examines the link between function and flexibility by modelling proteins like elastic networks. In this model, proteins are made of flexible (polar) and rigid (hydrophobic) amino acids connected by molecular "springs". If some regions of the protein are flexible enough, they form a "floppy" channel, and the entire molecular machine can bend like a hinge. This motion allows them to bind effectively to other molecules. The binding between a ligand and a stiff or flexible protein can be thought as a ball landing on a rock or a soft pillow. The ball is likely to bounce away after hitting the rock, but the pillow is more likely to accept it. Therefore, the flexible protein is a better binder.

In this model, genes store the details of the protein design in a binary fashion: flexible amino acids are stored as zeros and rigid amino acids as ones. As a result, the entire protein structure can be simplified as a code, like 11110001...111, similar to the digital memory of a computer. However, not all codes give rise to functional proteins, for example a code with only ones: 111111…1111, would give rise to an entirely stiff protein, unable to move, and nonfunctional. Among all possible codes, only some produce a functional protein with a "floppy" region in the center that can welcome the ligand.