Fig. 2: HDX-MS reveals an extended interface of the ACBI1-induced SMARCA2BD:VHL ternary complex compared to crystallographic data. | Nature Communications

Fig. 2: HDX-MS reveals an extended interface of the ACBI1-induced SMARCA2BD:VHL ternary complex compared to crystallographic data.

From: Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry

Fig. 2

a SMARCA2BD HDX difference plots covering residues 1408–1424. Binary as compared to the APO, and ternary as compared to the binary states reveal increased protection induced by the presence of ACBI1 and VCB complex. b VHL HDX difference plots covering residues 52–76. Binary compared to APO and ternary compared to binary states of the VHL subunit highlighting extended exchange patterns due to the presence of the ternary complex. c Exchange patterns induced by the binary and ternary forms of the complex superimposed on the crystal structure (PDB ID: 7S4E). d Binary-specific induced HD exchange near the E3-ligand and warhead binding sites of VHL and SMARCA2BD. e Ternary-specific induced HD exchange near the E3-ligand and warhead binding sites of VHL and SMARCA2BD. f Proposed solution-state extended protein interface that may take advantage of salt-bridge interactions to increase cooperativity of the protein–protein complex.

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