Computational docking of L-arginine and its structural analogues to C-terminal domain of Escherichia coli arginine repressor protein (ArgRc).
The arginine repressor (ArgR) of Escherichia coli binds to six L-arginine molecules that act as its co-repressor in order to bind to DNA. The binding of L-arginine molecules as well as its structural analogues is compared by means of computational docking. A grid-based energy evaluation method combined with a Monte Carlo simulated annealing process was used in the automated docking. For all ligands, the docking procedure proposed more than one binding site in the C-terminal domain of ArgR (ArgRc). Interaction patterns of ArgRc with L-arginine were also observed for L-canavanine and L-citrulline. L-lysine and L-homoarginine, on the other hand, were shown to bind poorly at the binding site. Figure A general overview of the sites found from docking the various ligands into ArgRc ( grey ribbons). Red coloured sticks: residues in binding site H that was selected for docking
Kueh
Rowyna
R
Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
Rahman
Noorsaadah Abdul
NA
Merican
Amir Feisal
AF
D001120:Arginine / Q000737:chemistry*; D001665:Binding Sites; D002172:Canavanine / Q000737:chemistry; D002956:Citrulline / Q000737:chemistry; D003198:Computer Simulation; D003460:Crystallization; D029968:Escherichia coli Proteins / Q000737:chemistry*; D006709:Homoarginine / Q000737:chemistry; D008239:Lysine / Q000737:chemistry; D008958:Models, Molecular; D015394:Molecular Structure; D011485:Protein Binding; D011487:Protein Conformation; D012097:Repressor Proteins / Q000737:chemistry*
C490177:ArgR protein, E coli; D029968:Escherichia coli Proteins; D012097:Repressor Proteins; D006709:Homoarginine; D002956:Citrulline; D002172:Canavanine; D001120:Arginine; D008239:Lysine