During a molecular dynamics simulation i have found salt bridges being format being N(eta) atoms of Arg and OXT atom of Asp. What is the role of OXT atom and is such a salt bridge formation possible?
You may need to pay attention to this when going from simulation to actual wet-lab experiments: Normally in experiments, N-or C-terminal tags are added to the protein to aid expression, purification and detection of the protein. If your simulations indicate that N- or C-terminal charges are important for function, make sure to communicate this to the experimentalists. On the other hand, if you are simulating a single domain out of a multi-domain protein, you might want to suppress terminal charges, e.g. work with N-and C-terminal amides to better simulate a continuing protein backbone.
OXT is the standard name for a C-terminal oxygen atom in its deprotonated (conjugate base) form. It's just like any other carboxylate in a protein.
You may need to pay attention to this when going from simulation to actual wet-lab experiments: Normally in experiments, N-or C-terminal tags are added to the protein to aid expression, purification and detection of the protein. If your simulations indicate that N- or C-terminal charges are important for function, make sure to communicate this to the experimentalists. On the other hand, if you are simulating a single domain out of a multi-domain protein, you might want to suppress terminal charges, e.g. work with N-and C-terminal amides to better simulate a continuing protein backbone.
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