kcal bonus for aptamers

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I'm working on a prototype web-based switch design tool. I need to program in the aptamer bonus in kcal. The current lab tool suggests it is 4.0 kcal independent of the aptamer. Some interactions with Nando years ago suggested it might be 4.86 kcal for FMN at least. The fact that expected maximal fold changes can vary by aptamer suggest to me that the actual bonus might vary for different aptamers. What is the real case? Is it 4.0kcal, 4.86, or does it really vary by aptamer, and if so, what values should I use?
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Posted 2 years ago

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Photo of Brourd


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The binding energy is dependent on the concentration of the substrate, and those binding affinities are all reported in the literature somewhere. I imagine if they use the same free energies for each aptamer, then they may be using concentrations that result in similar theoretical binding energies.
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Omei Turnbull, Player Developer

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Jeff, I had been hoping Nando or one of the lab scientists would give you a definitive answer.  That hasn't happened, so I'll tell you what I think is true.

As Brourd said, the binding energy will differ with the choice of ligands and their concentrations.  Therefore, the small molecule puzzles always use a fixed energy bonus of 4.0 kcal/mole and the experimenters try to adjust the concentration of each ligand independently, to make the binding energy as close to that as possible.
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LFP6, Player Developer

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To piggyback on what Omei has said, within the puzzle definition for “aptamer” puzzles, all that’s defined (from what I was able to tell) is a concentration (plus the binding site). There happens to be a default concentration used in the puzzle maker, but I imagine that for labs it is chosen as Omei and Brourd have described.