Extended Data Fig. 3: Metadynamics (MetaD) and steered molecular dynamics (SMD) simulations of the TRPV1-capsaicin complex.
From: Mechanism of capsaicin entry into buried vanilloid sites in TRPV1
(a) Definition of the collective variables (CVs) employed in MetaD simulations to explore capsaicin binding and unbinding. (b) Root-mean-square deviation (RMSD) values of the protein Cα atoms (rat TRPV1, rTRPV1, green) and capsaicin atoms (purple) over time in MetaD simulations. (c) Free energy landscapes describing capsaicin’s binding and unbinding pathways within rTRPV1, derived from MetaD simulations. (d) Torsion plots of capsaicin illustrating conformational changes in its rotatable bonds throughout the simulation, with a 2D schematic showing color-coded rotatable bonds (upper right). Radial plots depict torsional conformations over time, while bar plots show probability density, elucidating the ligand’s conformational dynamics stabilizing the rTRPV1-bound state. (e) Statistical analysis of contacts between capsaicin and amino acids along the binding pathway, highlighting key interacting residues at different stages of binding. Orange lines indicate the extent of interaction compactness. (f) Comparative analysis of binding pathway reproducibility using well-tempered MetaD simulations with varied CVs and parameters. Top panels illustrate reconstructed 3D free energy surfaces (FES), highlighting low-energy pathways. Bottom panels show representative snapshots of capsaicin traversing entry points near the TRPV1–lipid hydrophobic interface, engaging residues A539, V658, and F655. (g, h) Side-view (g) and top-view (h) snapshots of the rTRPV1/capsaicin complex during SMD simulations. The green arrow indicates the direction of applied force. Zoomed-in views depict capsaicin’s movement pathways during SMD simulations, with residue A539 highlighted as spheres. (i) Force profile as a function of the center-of-mass (COM) distance between capsaicin and residues at the base of the vanilloid pocket, such as R557. Zoomed-in views detail force fluctuations relative to capsaicin’s progression along the entry route.
