I'd like to label my LDL in a manner that would not affect neither thyrosine or cysteine residues of my ApoB100. What does Dil do to the structure of a protein - I can't find it anywhere.
You can see the structure here: http://en.wikipedia.org/wiki/DiI or here: http://www.lifetechnologies.com/order/catalog/product/D282. DiI has some long hydrophobic chains that interact with lipids. I don't see any evidence that it would affect the tyrosine and cysteine residues of your protein - it really seems to be lipid specific. If you want to be sure, I'd just call up molecular probes and ask.
Dear Hanna,
Amanda is absolutely correct. I could not find any specifics in the literature myself but from my experience with membranes there are two comments going beyond what she stated.
1) Clearly the pseudo indoles groups are much more shielded in a lipid environment that in water so they have a much longer half lifetime so they are not quenched. This fact suggests that the molecule has a realtively well defined conformational state while embedded in a membrane. The only real water propensity it has comes from quaterrnary nitrogens and the rest is lipohilic. This property would suggest that is has very little interaction with proteins and behaves like yet another lipid. It is also not shared by cells what suggests further low level of interactions with proteins.
2) You should seek some structural input to your question. Seek ApoB100 structure and research the distribution of Cys and Tyr. Seek the structural results from long time membrane simulations and see how the acyl chains pack agains each other to understand better the pseudo indole group role. What i can see is that some Tyr residues at the transitionlayer may interact with specific lipids. Besides that I see no problems.
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