Hej All,
I started some MD and enhanced sampling simulations starting from a PDB structure where a tyrosine residue made a stable hydrogen bond interaction with a tryptophan residue and led to a conformation which I called 'Normal'. During simulation with different protocols we saw that there is a probability that the same tyrosine will forma hydrogen bond interaction with an catalytic Asp residue which will led to a 'closed' state. We have a solid data from multiple simulations with different protcols blah blah blah to verify this. And previous studies on similar proteins also agrees with this fact. I wonder how can one study this phenomena experimentally? Any ideas will be appreciated. I guess NMR can do that. But can someone elaborate?
P.S: However there is no crystal structure for this closed conformation.
From the RCSB PDB, select two structures of the same proten, but in different. conformational states. Then compare their hydrogen bond contents. Select also two structures of the same protein, one with bound ligand, and the other without bound ligand. Then compare their hydrogen bond contents. In fact you don't have to prove to the community that hydrogen bonds are dynamic in nature - we all know it, because it is a very basic fact in the life sciences. We learned it from high school chemistry and/or biology. Relax.
Maybe with 2D-NMR, especially 1H-13C HMBC. If there is a hydrogen bond you may expect a correlation between the hydrogen and the C of the Asp-carboxyl
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