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Abstract Targeted protein degradation (TPD) is a promising approach in drug discovery for degrading proteins implicated in diseases. A key step in this process is the formation of a ternary complex where a heterobifunctional molecule induces proximity of an E3 ligase to a protein of interest (POI), thus facilitating ubiquitin transfer to the POI. In this work, we characterize 3 steps in the TPD process. (1) We simulate the ternary complex formation of SMARCA2 bromodomain and VHL E3 ligase by combining hydrogen-deuterium exchange mass spectrometry with weighted ensemble molecular dynamics (MD). (2) We characterize the conformational heterogeneity of the ternary complex using Hamiltonian replica exchange simulations and small-angle X-ray scattering. (3) We assess the ubiquitination of the POI in the context of the full Cullin-RING Ligase, confirming experimental ubiquitinomics results. Differences in degradation efficiency can be explained by the proximity of lysine residues on the POI relative to ubiquitin.more » « less
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Shrestha, Utsab R. ; Bhowmik, Debsindhu ; Van Delinder, Kurt W. ; Mamontov, Eugene ; O’Neill, Hugh ; Zhang, Qiu ; Alatas, Ahmet ; Chu, Xiang-Qiang ( , The Journal of Physical Chemistry B)
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Shrestha, Utsab R. ; Perera, Suchithranga M. ; Bhowmik, Debsindhu ; Chawla, Udeep ; Mamontov, Eugene ; Brown, Michael F. ; Chu, Xiang-Qiang ( , The Journal of Physical Chemistry Letters)
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Shrestha, Utsab R. ; Bhowmik, Debsindhu ; Copley, John R. ; Tyagi, Madhusudan ; Leão, Juscelino B. ; Chu, Xiang-qiang ( , Proceedings of the National Academy of Sciences)