Fig 1.
Sequence alignment between human and E. coli.
(A) Showing that all the active site residues marked yellow of N-terminal are conserved. (B) Showing that all the active site residues marked yellow of C-terminal are conserved except Val of E. coli replaced with Ile of human: semi conserved marked gray.
Fig 2.
Preparation of monomer and gaps filling of missing residues in the PDB structure of target protein.
(A) Dimer structure of the human ASNS protein with chain A (in blue) and B (in red). (B) Monomer structure of the ASNS protein with both domains (N-terminal in purple and C-terminal in green).
Fig 3.
Water and ligand free PDB file of target protein: Showing both domains.
(N-terminal in purple: C-terminal in green). yellow and red parts show the filled gaps in C-terminal.
Fig 4.
(a-d). 3D (Three dimensional) models of all four ligand molecules.
Table 1.
Binding energy and RMSD of selected docking complexes.
Fig 5.
Ligplot showing hydrogen bonding and hydrophobic interaction between the Gln ligand and ASNS.
Gln binds via hydrogen bonds with ASNSat Arg48 with 2.86Å, Asn74 with 2.92Å, Gly75 with 2.88Å and Glu414 with 2.99Å, and via hydrophobic interactions with Val52, Ala50, Val95, Cys1, Glu76 and Tyr73.
Fig 6.
Ligplot showing hydrogen bonding and hydrophobic interaction between the ATP and ASNS protein.
ATP binds with ASNS at Ser257 with 2.83Å, Glu364 with 2.89Å, Ser262 with 2.83Å, Asp261 with 2.86Å, Asp367 with 2.70Å and Asp400 with 2.97Å and via hydrophobic interactions with Glu 368, Phe314, Trp480, Gly343, Ala340 and Met344.
Fig 7.
Ligplot showing hydrogen bonding and hydrophobic interaction between the Asp ligand and ASNS protein.
Asp binds with ASNS at His445 with 2.84Å, and Glu219 with 2.80Å and via hydrophobic interactions with Leu446, Ile227, His212, Asp216, Lys439 and Met435.
Fig 8.
Ligplot showing hydrogen bonding and hydrophobic interaction between the β-Aspartyl AMP ligand and ASNS protein.
β-Aspartyl AMP binds with ASNS via hydrogen bond at Gly363 with 2.94Å and Ser257 with 2.89Å and via hydrophobic interactions with Ile347, Ile287, Met344, Ser262 and Ser362.
Fig 9.
RMSD evaluations of docked complexes between the C-alpha atoms of proteins and ligands in 100ns simulation.
The pink shows the RMSD of the ligands compound and blue color shows the RMSD of the protein (a) shows RMSD plot between protein and ATP, (b) shows the RMSD plot of beta aspartyl AMP (c) shows the plot between Asp and protein and the (d) shows the RMSD evaluation between protein and Gln ligand.
Fig 10.
Residue wise Root Mean Square Fluctuations (RMSF) graphs of the docked complexes.
(a) RMSF plot of docked complex of ATP with protein. (b) RMSF plot of docked complex of beta aspartyl amp with protein. (c) RMSF plot of docked complex of Asp with protein. (d) RMSF plot of docked complex of Glu with protein.
Fig 11.
Distribution of SSE of the protein over the time of the simulation.
(a) Shows the overall distribution of SSEs. (b) Shows each residue with SSE assignment. The alpha helices are represented by the red columns and the beta strand are colored blue.
Fig 12.
Protein-ligand contact and heat map timeline throughout simulation.
(a) Shows protein ligand contacts between the ATP and target protein. (b) Showing the interactions of beta aspartyl amp with target protein. (c) Shows the contacts between Asp and protein. (d) Depicts the protein ligand contacts of Glu with target protein.
Fig 13.
3D model development of human ASNS with N- and C-terminal active sites with their respective ligands.