I work on the interaction of CNT and proteins. The results show that the tertiary and secondary structure of proteins are changed (effected by CNT). VMD sequence viewer shows that the primary structure of the protein (that absorbed on the surface of CNT) has not any changes. My question is: Can MD simulation show the changes of protein's primary structure, or is MD not able to investigate the changes of primary structure, generally?
MD simulation is not able to investigate the changes of primary structure. You can mutate the residues with chimera or MOE, then run the MD simulation to see the changes of protein structure. The changes of tertiary and secondary structure of proteins are not only due to the change of protein primary structure. In your case, it is rather the allosteric change induced by CNT.
HI Hamid,
The Pymol package is also capable to mutate protein residue. It is possible to see changes running MD simulation after the mutation of residue.
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