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. 2023 Apr 18;12(4):613. doi: 10.3390/biology12040613

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© 2023 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

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Thermodynamic stability of the simulated small molecules bound to RhoGEFs. (A) Alpha-carbon atom RMSDs for RhoGEF proteins. (B) Sole ligand RMSDs in relation to simulation time frames in nanoseconds (ns). (C) Overlaid ligand/RhoGEF trajectories at initial and final time frames. Ligands (sticks) and bound RhoGEF proteins (cartoon) are colored green and red with respect to 0 ns and 100 ns extracted frames. For ECT2 proteins, Pro703 β4-sheet tip and C-terminal Cys765 at the PH domain are annotated. (D) Difference RMSF (ΔRMSF) trajectories for ECT2 target proteins along the whole molecular dynamic simulations in relation to apo/unliganded state.

Thermodynamic stability of the simulated small molecules bound to RhoGEFs. (A) Alpha-carbon atom RMSDs for RhoGEF proteins. (B) Sole ligand RMSDs in relation to simulation time frames in nanoseconds (ns). (C) Overlaid ligand/RhoGEF trajectories at initial and final time frames. Ligands (sticks) and bound RhoGEF proteins (cartoon) are colored green and red with respect to 0 ns and 100 ns extracted frames. For ECT2 proteins, Pro703 β4-sheet tip and C-terminal Cys765 at the PH domain are annotated. (D) Difference RMSF (ΔRMSF) trajectories for ECT2 target proteins along the whole molecular dynamic simulations in relation to apo/unliganded state.