I would like to know the distance between the rings in a ring stacking interaction in proteins.
Do you have a particular protein in mind or just a general stacking motif? Stacking interactions in proteins are influenced by their surroundings. If you ha ve crystal structure (either PDB file or XYZ coordinates) you can use software to calculate the centroid to centroid distance. For a liquid solutions, look for NMR data with NOE data. This will give you a good estimate, but again it could be sequence specific.
Do you have a particular protein in mind or just a general stacking motif? Stacking interactions in proteins are influenced by their surroundings. If you ha ve crystal structure (either PDB file or XYZ coordinates) you can use software to calculate the centroid to centroid distance. For a liquid solutions, look for NMR data with NOE data. This will give you a good estimate, but again it could be sequence specific.
Charles Thanks for ur comment.. In general for a protein what is the minimum distance required so it can be considered a pi stacking interaction? I dont have the crystal structure, but i have a homology model structure of my protein. I was analyzing on rasmol looking for important interactions between the junction of the two domains in my prot. I visualized a tryptophan being very close to a tyrosine and the distance between the two rings was 2.98A. Is this possible?
Ahhh, the plot thickens. I do think you are in the range for pi-stacking, but there are other factors to consider, like pi-plane orientation. A good manuscript would be McGaughey, G.B., Gagnes, M., and Rappe, A.K., J. Biol. Chem 1998, 273(25), 15458-15463. There are good arguments in there for what constitute a pi-pi stack in proteins with aromatic rings.
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