Fig. 5: Continuity of the intramolecular tunnel of WT human ASNS as observed by MD simulation. | Nature Communications

Fig. 5: Continuity of the intramolecular tunnel of WT human ASNS as observed by MD simulation.

From: 3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase

Fig. 5

Snapshots from the MD trajectories computed for (a) the WT apo-ASNS and (b) the WT ASNS/β-aspartyl-AMP/MgPPi ternary complex. The surface of the tunnel is indicated by spheres (t = 20 ns, light purple; t = 80 ns, forest green; t = 140 ns, violet purple; t = 200 ns, lime). Red circles indicate the position of the side chain of Arg-142 in the structures. Protein atoms are rendered as surfaces in cyan. Tunnels were identified using the CAVER 3.0 software package89 and visualized in PyMol. c Superimposed snapshots from the MD trajectory of the WT ASNS/β-aspartyl-AMP/MgPPi ternary complex showing the reorientation of the Arg-142 side chain (carbons are colored in slate (t = 0 ns) or green (t = 200 ns), and oxygen and nitrogen atoms are colored red and blue, respectively). Distances between the Arg-142 side chain and adjacent residues in these trajectories are provided elsewhere (Supplementary Tables S2 and S3).

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