Molecular dynamics simulations of nuclear receptors: ligand-protein free energy estimates

Abstract

Nuclear receptors are a superfamily of proteins responsible for the transcription of several genes involved in fundamental biological processes, like cellular differentiation, control of metabolic rates, hormone regulation, reproduction, morphogenesis, etc.. Much of the cellular activity of these proteins is mediated by their association with hormones. The biophysical and biochemical studies of this class of proteins are in an advanced stage regarding the biological activity of several families of receptors, the identification of activators hormones and the study of the structure of different structural domains. However, studies on the relationship between structure and activity of these proteins are limited to the crystallographic structures of the main areas of the best-known receptors and to macroscopic properties such as site-directed mutagenesis or selectivity for different ligands. Little is known about the molecular mechanisms of activity, selectivity, specificity and dynamical behavior of this class of proteins. This project aims to apply molecular dynamics (MD) technique to study the interactions between NRs and their natural ligands (hormones) and synthetic analogues, expecting to contribute on the elucidation of the reasons for selectivity and affinity. Also, we intend to estimate the difference on free energy related to ligand-protein association. The initial focus of the research are the thyroid hormone receptors (TR), then proceeding the underway work of this lab group. After that, it may be extended to other members of this protein family. We aim to provide additional information, at a molecular level, to studies that have been developed by the groups of Prof. Dr. Igor Polikarpov (CBME/IFSC-USP / São Carlos) and Dr. Paul Webb and Dr. John Baxter (The Methodist Hospital Research Institute, Houston, Texas), specially concerning on the dynamics of ligand-protein system and on its inherent structural fluctuations. State-of-the-art MD techniques will be employed on the following problems:1.Computing the DeltaG of the binding of thyroid hormone to the new TR LBD site;2. Estimating DeltaG of bonding and elucidating the reasons for selectivity and affinity of the following problems involving TR ligands:a) Importance of the methylene bridge of GC-1 ligand and it analogues to the affinity for TR;b) Reasons for selectivity and affinity of KB-141 ligand;c) Importance of residue N331 for beta-selectivity.3. Computing free energies of binding and elucidation of the reasons for selectivity and high affinity of ligands of ERs and PPARs.