Computer simulations of helix 12 conformational free energy profiles of Peroxisome Proliferator Actived Receptors

Abstract

Nuclear Hormone Receptors comprise a protein superfamily responsible for regulation of the expression of genes associated with various fundamental biological processes such as cell differentiation, metabolic rate control, hormonal regulation, reproduction, morphogenesis, etc. These proteins are regulated by well known ligands, as molecules of estrogen, progesterone and thyroid hormone. They are composed by three domains: a variable N-terminal domain, a central DNA-binding domain and a C-terminal ligand-binding domain (LBD), which selectively recognizes hormones. The ligand-binding domain is the largest of the three domains, being formed of about 260 residues, 12 alpha helices and two beta sheets, arranged in a globular structure. Due to the functional importance of nuclear receptors, many biophysical and biochemical studies concerning the biological activity of several nuclear receptor's families seeking the identification of ligands with specific pharmacological activity are being developed and are quite advanced. Studies about the relationship between structure and activity of these proteins show the importance of helix 12 (H12 - LBD's C-terminal helix) in the mechanism of transcription activation, revealing conformational differences associated with the presence of different ligands. These studies also show the importance of dynamic properties of helix 12 in receptor activation. Together, structural studies and biochemical and biophysical analyzes show that the interaction with ligands affects the structure and most importantly, the mobility of H12, which is the main mechanism of transcription activation and repression. Although structural and dynamic characteristics of the LBDs are the focus of many studies, there are still limitations in understanding the conformational changes undergone by H12 and the functional importance of each conformation. In this project, we intend to apply molecular dynamics (MD) simulations using mainly ABF (Adaptive Biasing Force), to determine the free energy changes associated with transitions between conformations adopted by H12 of PPAR. The determination of ”\DeltaG provides the relative stability of conformations, which will be used to understand the functional relevance of each structure.