2.2. Characterizing the biding mode of TPEARG to arginase
Encouraged by the superior properties of TPEARG, molecular dynamics (MD)
simulations were implemented to confirm the recognition mechanism.
Arginase (PDB: 2CEV) was favourably docked into TPEARG
(Figure 2A). Then a 10 ns MD
simulation was performed based on Amber99SB force field using Gromacs
2018.4 software. Results exhibited that TPEARG molecules mainly bound in
the cavity consisting of Asp126, Asn128, Ser133, Pro134, His139, Gly140,
Ser176, Leu177, Asp178, Glu181, Thr240, and Glu271. The N atoms on the
TPEARG form six hydrogen bonding interactions with Asp126, His139,
Asp178, Thr240 and Glu271 in the protein, respectively (Figure 2B). And
the benzene ring in the TPEARG molecule formed strong hydrophobic
interactions with the hydrophobic amino acids (Asn128, Ser133, Pro134,
Gly140, Ser176, Leu177, Glu181) around the pocket, which further
enhanced the affinity between the TPEARG and arginase (Figure 2C and D).
Root mean square deviation (RMSD) revealed that the average number of
hydrogen bonds formed between arginase and TPEARG was 4.960±0.732
(Figure S4). Accordingly, the interaction between arginase and TPEARG is
stable, leading to an obverse fluorescence emission of TPEARG towards
arginase.