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. Author manuscript; available in PMC: 2019 Aug 13.
Published in final edited form as: J Phys Chem Lett. 2018 Mar 2;9(6):1312–1317. doi: 10.1021/acs.jpclett.8b00342

Figure 2.

Figure 2.

(a) A cartoon representation of overlapped structures of isolated Ras, with the PDB IDs: 5P21, 1CTQ, 1QRA, 1P2S, 3L8Y, 3L8Z, 3RRY and 4DLR. The heavy atoms in 3L8Z were taken as the reference for least-square fitting. (b) The measured distances between the O atom of γ-group in GTP and H atom of the hydroxyl group of Tyr32 during a 2 μs MD trajectory. (c) A schematic representation of switching of Tyr32 between “in” and “out” using the snapshots taken from the MD trajectory. (d) Calculated potential of mean force (PMF) for the interconversion of Tyr32out and Tyr32in substates by projecting the REMD trajectory on the reaction coordinate of the dihedral C-CA-CB-CG of Tyr32 residue.