Active Nuclear Receptors Exhibit Highly Correlated AF-2 Domain Motions: e1000111

• Published in: PLoS computational biology 2008-07, Vol.4 (7)
• Main Authors: Teotico, Denise G, Frazier, Monica L, Ding, Feng, Dokholyan, Nikolay V, Temple, Brenda RS, Redinbo, Matthew R
• Format: Article
• Language: English
• Subjects: Binding sites; Biochemistry; Enzymes; Gene expression; Homeostasis; Ligands; Proteins
• ISSN: 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1000111

Nuclear receptor ligand binding domains (LBDs) convert ligand binding events into changes in gene expression by recruiting transcriptional coregulators to a conserved activation function-2 (AF-2) surface. While most nuclear receptor LBDs form homo- or heterodimers, the human nuclear receptor pregnane X receptor (PXR) forms a unique and essential homodimer and is proposed to assemble into a functional heterotetramer with the retinoid X receptor (RXR). How the homodimer interface, which is located 30 Å from the AF-2, would affect function at this critical surface has remained unclear. By using 20- to 30-ns molecular dynamics simulations on PXR in various oligomerization states, we observed a remarkably high degree of correlated motion in the PXR-RXR heterotetramer, most notably in the four helices that create the AF-2 domain. The function of such correlation may be to create "active-capable" receptor complexes that are ready to bind to transcriptional coactivators. Indeed, we found in additional simulations that active-capable receptor complexes involving other orphan or steroid nuclear receptors also exhibit highly correlated AF-2 domain motions. We further propose a mechanism for the transmission of long-range motions through the nuclear receptor LBD to the AF-2 surface. Taken together, our findings indicate that long-range motions within the LBD scaffold are critical to nuclear receptor function by promoting a mobile AF-2 state ready to bind coactivators.