Dear,
In my system ,the loop is part of the active pocket of the protein. when
the ligand is absent, the loop is disordered and if the ligand is present , the
loop can transform into helix.
In order to simulate the disordered loop transform into helix , i should
build a model thant the ligand is in the disoreded loop site. In my system,
there is a NAD+ cofactor in the active site and interact with the ligand.when
the ligand and cofactor NAD+ coexist, the disordered loop can transform into
helix.
In the PDB(protein date base) i find the complex with the liand,NAD+ and the
state of the loop is helix. i also find a protein structure without the
liand, NAD+ and the state of the loop is disordered. The sequences similarity
of the two structure is 100% and sturctue the the RMSD bettwen the two protein
is 0.275 .
i don't know how to build a model that the protein, NAD+ and ligand
coexsit,but the loop of protein is disordered. can i use the Homology modeling
,docking or just use pymol extract the NAD+ and ligand from the complex and the
put them into the protein with the disoreded loop ? And then to make a MD.
In order to make the disordered into the helix using gromacs, how long
should i run the MD and what is the value of dt , 0.001 or 0.002?
thank you very much!
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