Molecular Dynamics Simulations of a Chimeric Androgen Receptor Protein (SPARKI) Confirm the Importance of the Dimerization Domain on DNA Binding Specificity.

Mahdi Bagherpoor Helabad,Petra Imhof,Senta Volkenandt

doi:10.3389/fmolb.2020.00004

Mahdi Bagherpoor Helabad, Petra Imhof + Show 1 more

Open Access

https://doi.org/10.3389/fmolb.2020.00004

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Journal: Frontiers in Molecular Biosciences	Publication Date: Jan 31, 2020
Citations: 7	License type: CC BY 4.0

Affiliation: Freie Universität Berlin

Abstract

The DNA binding domains of Androgen/Glucocorticoid receptors (AR/GR), members of class I steroid receptors, bind as a homo-dimer to a cis-regulatory element. These response elements are arranged as inverted repeat (IR) of hexamer “AGAACA”, separated with a 3 base pairs spacer. DNA binding domains of the Androgen receptor, AR-DBDs, in addition, selectively recognize a direct-like repeat (DR) arrangement of this hexamer. A chimeric AR protein, termed SPARKI, in which the second zinc-binding motif of AR is swapped with that of GR, however, fails to recognize DR-like elements. By molecular dynamic simulations, we identify how the DNA binding domains of the wild type AR/GR, and also the chimeric SPARKI model, distinctly interact with both IR and DR response elements. AR binds more strongly to DR than GR binds to IR elements. A SPARKI model built from the structure of the AR (SPARKI-AR) shows significantly fewer hydrogen bond interactions in complex with a DR sequence than with an IR sequence. Moreover, a SPARKI model based on the structure of the GR (SPARKI-GR) shows a considerable distortion in its dimerization domain when complexed to a DR-DNA whereas it remains in a stable conformation in a complex with an IR-DNA. The diminished interaction of SPARKI-AR with and the instability of SPARKI-GR on DR response elements agree with SPARKI's lack of affinity for these sequences. The more GR-like binding specificity of the chimeric SPARKI protein is further emphasized by both SPARKI models binding even more strongly to IR elements than observed for the DNA binding domain of the GR.

Highlights

Steroid receptors (SRs), a subfamily of nuclear receptors, are ligand-activated transcription factors that bind to a specific DNA target sequence in order to enhance or repress gene transcription (Evans, 1988; Corson, 2005; Bunce and Campbell, 2010).Members of SRs, i.e., Androgen receptor (AR), Glucocorticoid receptor (GR), Mineralocorticoid receptor (MR), and Progesterone receptor (PR), bind as a homo-dimer to consensus 15 base pairDNA Binding Specificity of SPARKI Receptor palindromic DNA sequences, termed classical response elements (CREs) (Ham et al, 1988)
The results are organized to first present a comparison of the overall structure of the complexes
Our results indicate that the dimer interface of the AR-direct-like repeat (DR) system forms more strong hydrogenbond interactions than those seen in the SPARKI systems and in the GR-inverted repeat (IR)

Summary

Introduction

DNA Binding Specificity of SPARKI Receptor (bp) palindromic DNA sequences, termed classical response elements (CREs) (Ham et al, 1988). The DNA of CREs is organized as an inverted repeat (IR) of hexamer “AGAACA”, separated with a 3 bp DNA sequence, called spacer (Beato et al, 1995) (Figures 1B,D). Among the CREs, the first hexamer (HS1) elements are almost invariant and suggested as high affinity DNA sequences for receptor binding (La Baer and Yamamoto, 1994). The DNA binding domain (DBD) of the proteins, which includes about 70 amino acid residues, contains two vital subdomains, each identified with a zinc ion that is coordinated by four Cysteine residues. The second subdomain holds a loop domain, termed Dim, which is responsible for proteinprotein dimerization (Luisi et al, 1991; Kumar and Thompson, 1999) (see Figures 1A,D). A flexible loop, named lever arm connects these subdomains to each other (Figure 1D)

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