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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. 

Abstract Protein docking is essential for structural characterization of protein interactions. Besides providing the structure of protein complexes, modeling of proteins and their complexes is important for understanding the fundamental principles and specific aspects of protein interactions. The accuracy of protein modeling, in general, is still less than that of the experimental approaches. Thus, it is important to investigate the applicability of docking techniques to modeled proteins. We present new comprehensive benchmark sets of protein models for the development and validation of protein docking, as well as a systematic assessment of free and template‐based docking techniques on these sets. As opposed to previous studies, the benchmark sets reflect the real case modeling/docking scenario where the accuracy of the models is assessed by the modeling procedure, without reference to the native structure (which would be unknown in practical applications). We also expanded the analysis to include docking of protein pairs where proteins have different structural accuracy. The results show that, in general, the template‐based docking is less sensitive to the structural inaccuracies of the models than the free docking. The near‐native docking poses generated by the template‐based approach, typically, also have higher ranks than those produces by the free docking (although the free docking is indispensable in modeling the multiplicity of protein interactions in a crowded cellular environment). The results show that docking techniques are applicable to protein models in a broad range of modeling accuracy. The study provides clear guidelines for practical applications of docking to protein models.