My protein has two tryptophans. The indole resonance of one disappears while unfolding and then reappears when the protein completely unfolds. What could be the possible reasons?
My guess would decrease in T2 (signal relaxes too fast) or some kind of exchange. This is just a guess, as I am not a protein person.
Exchange with the solvent is certainly one option. But I would also check if it is not just shifting somewhere else. What pulse sequence are you using. If the sequence includes a 3919 part make the interpulse delay quite a bit shorter to make sure the resonance did not fall into the next null.
Dear Rudraksha, Clemens and Takuya,
Thank you for your answers. I too agree with fast exchange concept but what I am worried with is - the fact that I know my tryptophan is present at the protein's core when its NMR resonance is lost. Thus, fast exchange with solvent seems not possible. Also during fully unfolded state when I can expect fastest exchange I could capture the resonance. I am not sure regarding any other exchange that can occur at protein's interior, that may cause disappearance of resonance.
I am not an NMR person but your suggestions regarding playing with the parameters should be advantageous.
What happens in absence of exchange? Say if the tryptophan has no solvent around, it shall undergo no exchange, how does the resonance looks in such a scenario?
Dear Manika, if trp does not show exchange or shows slow exchange you shoule be able to observe the resonance. Instead of exchange of the hydrogen with the solvent there is also the possibility of a conformational exchange. This can also lead to the disappearance of a signal.
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