This is an email i sent out earlier. I thought it was interesting enough to post here. The residues and secondary structure elements are referenced from the protein I study Avena sativa LOV2.
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I think from our study and logically what appears to be a good model of protein function is one in which every residue is important in a context dependent manner. What this means is that one can mutate a residue but the protein can make up for it by certain residues having a new function or a new chi angle or something. If we mutate out one proposed pathway in our protein another can take over. Maybe the protein went through this transformation during evolution in the reverse. Maybe the beta sheets at one time were the only way to signal the Jalpha helix and then the A'a helix evolved to control the Jalpha because it is more energetically favourable than the beta sheets. The beta sheet function is still under slight selective pressure so it sticks around. Now if I disrupted the A'a helix the beta sheet function can take over. Imagine this on a smaller scale with residues. If I make L408A mutation and it removes the interaction between the A'a helix and Jalpha helix that is bad but maybe T407 forms a previously not found interaction due to the new phi/psi/chi angle it adopts and it appears from our mutation that L408A does nothing. The model is that every residue in a protein is context dependent but they all function in a thermodynamic way to give a protein it's structure and function. In one protein we might mutate a residue on the surface and nothing happens because other residues can easily make up for any loss of conformational energy or function. Maybe in another protein the residues can't. However, both residues could effectively have the same role. If I lose my pinky it would suck but my hand could compensate for it. If I lose my thumb it will definitely be a lot more difficult to make up for but both technically play a similar role.
