Dear Peter

Thanks for adding your answer.

Actually, I am working on lysm domain protein so we are doing an experiment like FRET(fluorescence resonance  energy transfer) in this experiment we calculate the are of overlapping protein with legends hence we calculate the distance of protein and drugs like R and r respectively.

R_0^6=8.79×〖10〗^(-25) K^2 n^(-4)∅J

Where K2 is the factor related to the geometry of the donor and acceptor dipoles, n is the refractive index of the medium, Φ is the fluorescence quantum yield of the donor in the absence of acceptor, and J is the overlap integral of donor fluorescence emission and the acceptor absorption spectra, which can be calculated as

Dear Peter

Thanks a lot for your effort and given valuable time.

I have searched many articles but can not find the refractive index and the κ factor for the Lyme domain protein. if you have any known reference then please send me a link.

Thanks again 

I am very appreciated your time.

Abid Ali

Dear Abid Ali,

Note that the sentence "the κ factor for the Lyme domain protein" does not make much sense. It really depends on where and how you label your protein and with what dyes. Different dye labeling positions will lead to different steric restrictions and specific interactions with the dye. In addition, the protein in different states yield different structural organizations that yield changes in the dye microenvironment. To make it even more complicated, you cannot rely on a simulative calculation of kappa^, since conjugating the dye to a given amino acid may perturb the protein overall structure. Therefore, better measure all variables in your empirical formula and never trust "literature values" because these report on the systems they were conjugated to. You can measure the decay of the fluorescence anisotropy of the dye attached to your protein and fit it with a two component function (local rotational movement of the dye - fast-  and global tumbling of the protein - slow), then see if the rotational correlation time of the local rotation is fast in comparison to the fluorescence lifetime of the dye on top of the protein. If it is, you have an experimental evidence that strengthens the use of the isotropic rotational averaging assumption (=2/3). If, however, the rotation times of the dye about its bond are of the order of the fluorescence lifetime, using this assumption may be faulty. Dale & Eisinger 1978 provide you a method for calculation of the minimal and maximal boundaries for the value of .

The refractive index is indeed a very interesting issue. The refractive index in FRET is usually taken as the value of the bulk solution, but according to FRET theory, it is the refractive index in between the donor and acceptor dipoles,which may be different if the path between the dipoles goes through the protein.