Elastic Model of a Protein Binding to a Ligand (IMAGE)
Caption
(A) When a protein binds to a ligand, it undergoes large scale motion (arrows) which are the signatures of bending functional proteins. This is possible only thanks to the presence of certain "floppy" regions (pink "shear band") across the protein that separate the stiff (blue) regions of the protein into two domains. (B)-(D) The team modelled a 200 amino acid protein during different stages of evolution: passing from a non-functional (B) to a functional (D) state. The protein is modeled as an elastic spring network with two kinds of amino acids, modeled as beads: pink amino acids are flexible and blue amino acids are rigid. The researchers mimic evolution by changing one random amino acid at the time (mutation) from pink to blue. Initially, the protein is mostly rigid and non-functional. During evolution, flexible amino acids are added, some useful, some not. Over time, a "floppy" region forms at the center of the molecule making the protein more flexible to bend and bind to the ligand. The model estimated that an efficient solution is reached after a thousand mutations.
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