Location of Repository

Only subtle protein conformational adaptations are required for ligand binding to thyroid hormone receptors: Simulations using a novel multipoint steered molecular dynamics approach

By Leandro MARTINEZ, Igor POLIKARPOV and Munir S. SKAF

Abstract

Thyroid hormone receptors (TR) are hormone-dependent transcription regulators that play a major role in human health, development, and metabolic functions. The thyroid hormone resistance syndrome, diabetes, obesity, and some types of cancer are just a few examples of important diseases that are related to TR malfunctioning, particularly impaired hormone binding. Ligand binding to and dissociation from the receptor ultimately control gene transcription and, thus, detailed knowledge of binding and release mechanisms are fundamental for the comprehension of the receptor`s biological function and development of pharmaceuticals. In this work, we present the first computational study of ligand entry into the ligand binding domain (LBD) of a nuclear receptor. We report molecular dynamics simulations of ligand binding to TRs using a generalization of the steered molecular dynamics technique designed to perform single-molecule pulling simulations along arbitrarily nonlinear driving pathways. We show that only gentle protein movements and conformational adaptations are required for ligand entry into the LBDs and that the magnitude of the forces applied to assist ligand binding are of the order of the forces involved in ligand dissociation. Our simulations suggest an alternative view for the mechanisms ligand binding and dissociation of ligands from nuclear receptors in which ligands can simply diffuse through the protein surface to reach proper positioning within the binding pocket. The proposed picture indicates that the large-amplitude protein motions suggested by the apo- and holo-RXR alpha crystallographic structures are not required, reconciling conformational changes of LBDs required for ligand entry with other nuclear receptors apo-structures that resemble the ligand-bound LBDs

Topics: RETINOIC ACID RECEPTOR, ESTROGEN-RECEPTOR, CRYSTAL-STRUCTURE, STRUCTURAL BASIS, RXR-ALPHA, DOMAIN, SELECTIVITY, GAMMA, DESIGN, BETA, Chemistry, Physical
Publisher: AMER CHEMICAL SOC
Year: 2013
OAI identifier: oai:agregador.ibict.br.RI_UNICAMP:oai:unicamp.sibi.usp.br:SBURI/1042
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • http://www.rcaap.pt/detail.jsp... (external link)
  • Suggested articles


    To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.