Activation mechanism of the human Smoothened receptor

Prateek Bansal
Soumajit Dutta
Diwakar Shukla author has email address

Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, 61801

https://doi.org/10.63204/4757.1

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Figures and data

Major structural changes during SMO Activation. (A) Comparison of the broken D-R-E network and the W-R ionic lock, and the expanded tunnel, in inactive (green) vs active (red) SMO (B)-(D) Comparison of inactive and active SMO, indicating the outward movement of the TM6 and TM3 and inward movement of TM5 in active SMO.

Molecular metrics integral to SMO Activation. (A) Rearrangement of the WGM motif, a conserved molecular switch across class F GPCRs, undergoes rearrangement on SMO activation. (B) Relative free energies from MSM-weighted simulation data plotted on the TM3-TM6 distance vs TM3-TM5 distance measured at residues W339^3.50, M449^6.30 and G422^5.61. (C) Breaking of the D-R-E network on the extracellular end of the TMD. (D) SImilar to (B), but for TM3-TM6 distance vs the D-E distance. (E) The ionic lock breaks by the sidechain rotation of W535^7.55. (F) Same as (B) but for TM3-TM6 distance vs χ₂ dihedral measured at W535^7.55.

Overall activation of SMO involves residues at CRD-TMD junction. (A)-(F) Snapshots and probability density plots outlining the salt-bridge rearrangements at the CRD-TMD interface during SMO activation.

(A)Relative free energies from MSM-weighted simulation data of Apo-SMO plotted along tIC1 and tIC2, the 2 slowest components, with the intermediate states I₁₋₃ as shown. (B) Overall transition pathway of SMO activation process.

Tunnel radius plots for SMO. (A) Free energy plot of the tunnel diameter along the z-coordinate for SANT1-bound SMO. (C) same as (A), but for Apo-SMO. (E) same as (A), but for SAG-bound SMO. SAG-bound SMO clearly shows the expansion of the tunnel as compared to Apo-SMO and SANT1-SMO. (B), (D), (F) - representative fi for SANT-1 SMO, Apo-SMO and SAG-SMO. Tunnel radii were calculated using the HOLE program⁶⁶ transduction. Allosteric pathways contain a series of conformationally-coupled residues that link dynamically active and spatially distant residues. In Class A GPCRs, allosteric pathways are responsible for communicating conformational changes from the extracellular end to the intracellular end, completing the process of signal transduction.^68–70 Since SMO’s activation process involves allosteric communication between the extracellular ligand binding site (D-R-E network) and the G-protein coupling site (WGM motif), we sought to analyze the allosteric pathways that connect the two sites. We computed the dynamic pairwise mutual information of Inactive-Apo-SMO, Active-Apo-SMO, SANT1-SMO and SAG-SMO on a residue-level basis, and construct a graphical network of residues that are allosterically linked. Based on this network, we present the allosteric pathway between the intra- and extracellular ends of TMD.

Allosteric pathways between E518^7.38 and W339^3.50. (A) - Pathway in Apo-Inactive-SMO. Since the tunnel radius is decreased, TM6 outward movement is restricted, and therefore the entire allosteric communications occurs via TM6. (B) In SANT1-SMO, due to slight outward movement of TM6, the pathways switches from TM7 to TM6 to TM3. (C,D) SAG-SMO and Apo-Active SMO show the same allosteric pathway, which spans TM7-TM6-TM5-TM3.