Fig. 6: Continuity of the intramolecular tunnel of the R142I ASNS variant as observed by MD simulation. | Nature Communications

Fig. 6: Continuity of the intramolecular tunnel of the R142I ASNS variant as observed by MD simulation.

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

Fig. 6

Snapshots from the MD trajectories computed for (a) the R142I variant and (b) the R142I/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 Ile-142 in the structure. Protein atoms are rendered as surfaces in cyan. Tunnels were identified using the CAVER 3.0 software package89 and visualized in PyMol.

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