Exploring Binding Mechanisms in Nuclear Hormone Receptors by Monte Carlo and X-ray-derived Motions
In the present study, we performed an extensive exploration of the ligand entry mechanism for members of the steroid nuclear hormone receptor family (androgen receptor (AR), estrogen receptor α (ERα), glucocorticoid receptor (GR), mineralocorticoid receptor (MR), and progesterone receptor (PR)) and their endogenous ligands. The exploration revealed a shared entry path through the helix 3, 7, and 11 region. Examination of the X-ray structures of the receptor-ligand complexes further showed two
... stinct folds of the helix 6-7 region, classified as "open" and "closed", which could potentially affect ligand binding. To improve sampling of the helix 6-7 loop, we incorporated motion modes based on principal component analysis (PCA) of existing crystal structures of the receptors and applied them to the proteinligand sampling. A detailed comparison with the anisotropic network model (ANM, an elastic network model) highlights the importance of flexibility in the entrance region. While the binding (interaction) energy of individual simulations can be used to score different ligands, extensive sampling further allows to predict absolute binding free energies and analyze reaction kinetics using Markov state models (MSM) and Perron-cluster cluster analysis (PCCA+), respectively. The predicted relative binding free energies for three ligands binding to PR are in very good agreement with experimental results and the PCCA+ analysis revealed the importance of a peripheral binding site. Our analysis revealed that the flexibility of the helix 3, 7, and 11 region represents the most important factor for ligand binding. Furthermore, the hydrophobicity of the ligand influences the transition between peripheral and active binding site. 2 Keywords Nuclear hormone receptors, principal component analysis, Protein Energy Landscape Exploration (PELE), entry pathways, binding free energies, Markov state model (MSM) the binding site cavity; and 2) the hydrophobic nature of the ligand, increasing the transitions between the peripheral and the active binding sites.