Cross-talk between the ligand- and DNA-binding domains of estrogen receptor

Abstract

Estrogen receptor alpha (ERα) is a hormone-responsive transcription factor that contains several discrete functional domains, including a ligand-binding domain (LBD) and a DNA-binding domain (DBD). Despite a wealth of knowledge about the behaviors of individual domains, the molecular mechanisms of cross-talk between LBD and DBD during signal transduction from hormone to DNA-binding of ERα remain elusive. Here, we apply a multiscale approach combining coarse-grained (CG) and atomistically detailed simulations to characterize this cross-talk mechanism via an investigation of the ERα conformational landscape. First, a CG model of ERα is built based on crystal structures of individual LBDs and DBDs, with more emphasis on their interdomain interactions. Second, molecular dynamics simulations are implemented and enhanced sampling is achieved via the "push-pull-release" strategy in the search for different LBD-DBD orientations. Third, multiple energetically stable ERα conformations are identified on the landscape. A key finding is that estradiol-bound LBDs utilize the well-described activation helix H12 to pack and stabilize LBD-DBD interactions. Our results suggest that the estradiol-bound LBDs can serve as a scaffold to position and stabilize the DBD-DNA complex, consistent with experimental observations of enhanced DNA binding with the LBD. Final assessment using atomic-level simulations shows that these CG-predicted models are significantly stable within a 15-ns simulation window and that specific pairs of lysine residues in close proximity at the domain interfaces could serve as candidate sites for chemical cross-linking studies. Together, these simulation results provide a molecular view of the role of ERα domain interactions in response to hormone binding.

Methods for SAXS‐Based Structure Determination of Biomolecular Complexes

“…Recently, a specific push‐pull‐release (PPR) method was designed to facilitate the complex formation by enhancing the sampling of inter‐protein translations . Figure A illustrates a recent example of using the mostly translation‐driven PPR simulations to identify the top conformations of an estrogen‐receptor/DNA complex . To achieve an exhaustive search, we have further extended this PPR sampling with a rotation‐based pose generation that uniformly covers the conformational space of five rotational degrees of freedom.…”

Identification of candidate drugs using tensor-decomposition-based unsupervised feature extraction in integrated analysis of gene expression between diseases and DrugMatrix datasets

“…7B ). Given that the structure of the ligand-binding domain is supposed to affect that of the DNA-binding domain 35 (even can enhance the binding), and HNF4A is a transcription factor that can affect cirrhosis 36 , bezafibrate may also be a drug for cirrhosis from this point of view.…”

Theoretical modeling of multiprotein complexes by iSPOT: Integration of small-angle X-ray scattering, hydroxyl radical footprinting, and computational docking

“…This docking was achieved via coarse-grained molecular dynamics (MD) simulations (Elcock et al, 2001; Zacharias, 2003) and by imposing a varying harmonic restraint between the centers-of-mass of two proteins along the center-of-mass distance R 6 (Fig. 2 and SI Fig.1B), thus coaxing the two proteins to dock together, specifically along inter-protein translational directions (Huang et al, 2013; Ravikumar et al, 2012) (see Methods). The PPR works by repeating multiple pull-push-release cycles to facilitate the docking of interacting proteins while allowing for protein flexibility.…”

“…The all-atom reconstruction was based on iSPOT-predicted structures and crystal structures of individual proteins. This is followed by targeted or restrained MD simulations to achieve a realistic structure of the complex, free from steric clashes particularly at the docking interface (Huang et al, 2013). Final all-atom, explicit-solvent NPT simulations, free of any bias, were used for model assessment.…”