Computational characterization of the binding mode between oncoprotein Ets‐1 and DNA‐repair enzymes

Abstract

The Ets‐1 oncoprotein is a transcription factor that promotes target gene expression in specific biological processes. Typically, Ets‐1 activity is low in healthy cells, but elevated levels of expression have been found in cancerous cells, specifically related to tumor progression. Like the vast majority of the cellular effectors, Ets‐1 does not act alone but in association with partners. Given the important role that is attributed to Ets‐1 in major human diseases, it is crucial to identify its partners and characterize their interactions. In this context, two DNA‐repair enzymes, PARP‐1 and DNA‐PK, have been identified recently as interaction partners of Ets‐1. We here identify their binding mode by means of protein docking. The results identify the interacting surface between Ets‐1 and the two DNA‐repair enzymes centered on the α‐helix H1 of the ETS domain, leaving α‐helix H3 available to bind DNA. The models highlight a hydrophobic patch on Ets‐1 at the center of the interaction interface that includes three tryptophans (Trp338, Trp356, and Trp361). We rationalize the binding mode using a series of computational analyses, including alanine scanning, molecular dynamics simulation, and residue centrality analysis. Our study constitutes a first but important step in the characterization, at the molecular level, of the interaction between an oncoprotein and DNA‐repair enzymes.

Identification of Novel Interaction Partners of Ets-1: Focus on DNA Repair

“…Finally, we performed protein-protein docking between ETS(Ets-1) and identified BRCT and SAP homologs. These were followed by Residue Interaction Networks analyses to compare the predicted binding modes to the established ones for ETS(Ets-1)/BRCT(PARP-1) and ETS(Ets-1)/SAP(Ku70) [3].…”

“…The representative structures of the BRCT or SAP clusters were used and docking only performed for those clusters for which a structure was available (24 for BRCT homologs, 10 for SAP homologs). Subsequently, we ran Residue Centrality Analyses on the best model of each run to identify central residues at the interface and to compare them to the residues identified in [3] for the binding of ETS(Ets-1)/BRCT(PARP-1) and ETS(Ets-1)/SAP(Ku70) (see Appendix A). We calculated these for four sets of structures: all the structures available for the BRCT homologs and the SAP homologs, and the two subsets of those that are associated to DNA repair mechanisms.…”

“…The ETS (Erythroblast Transformation Specific) domain of Ets-1 can interact with the BRCT (BRCA1 C-terminal) domain of PARP-1 or the SAP (SAF-A/B, Acinus and PIAS) domain of Ku70 (70 kDa unit), a subunit of the DNA-PK DNA repair complex. Moreover, we characterized the binding modes of these interactions considering the domains of the Homo sapiens Ets-1, PARP-1 and Ku70 proteins [3]. We found that the binding should occur on the α-helix H1 of the ETS domain, leaving helix H3 available for DNA-binding, and identified a hydrophobic patch in H1 as a central patch of the interaction, which includes three tryptophans (Trp338, Trp356 and Trp361) of Ets-1.…”

Identification of Key Residues in Proteins Through Centrality Analysis and Flexibility Prediction with RINspector

“…In combination with other approaches, centrality analyses can help in the selection of residues that constitute targets for mutagenesis experiments or inhibitor design. The work of de Ruyck, Brysbaert, Villeret, Aumercier, & Lensink () is an example of integration of different methods for the identification of residues essential for the binding of two protein domains. The goal of RINspector was to design a tool that can quickly identify central residues.…”

“…The combination of the three functionalities allows the experimenter to predict the influence of mutation of central residues on local protein flexibility. RINspector has been used in different research projects to help in the identification of important residues in proteins that may be located at their core or surface, alone or in a complex (Brysbaert et al., ; de Ruyck et al., ; Laulumaa et al., ).…”