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      Multidomain architecture of estrogen receptor reveals interfacial cross-talk between its DNA-binding and ligand-binding domains

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          Abstract

          Human estrogen receptor alpha (hERα) is a hormone-responsive nuclear receptor (NR) involved in cell growth and survival that contains both a DNA-binding domain (DBD) and a ligand-binding domain (LBD). Functionally relevant inter-domain interactions between the DBD and LBD have been observed in several other NRs, but for hERα, the detailed structural architecture of the complex is unknown. By utilizing integrated complementary techniques of small-angle X-ray scattering, hydroxyl radical protein footprinting and computational modeling, here we report an asymmetric L-shaped “boot” structure of the multidomain hERα and identify the specific sites on each domain at the domain interface involved in DBD–LBD interactions. We demonstrate the functional role of the proposed DBD–LBD domain interface through site-specific mutagenesis altering the hERα interfacial structure and allosteric signaling. The L-shaped structure of hERα is a distinctive DBD–LBD organization of NR complexes and more importantly, reveals a signaling mechanism mediated by inter-domain crosstalk that regulates this receptor’s allosteric function.

          Abstract

          The human estrogen receptor alpha (hERα) is a hormone-responsive transcription factor. Here the authors combine small-angle X-ray scattering, hydroxyl radical protein footprinting and computational modeling and show that multidomain hERα adopts an L-shaped boot-like architecture revealing a cross-talk between its DNA-binding domain and Ligand-binding domain.

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          Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.

          The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer tissues and cell lines into readily understandable genetic, epigenetic, gene expression, and proteomic events. The query interface combined with customized data storage enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes. The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and software programmatic access. The intuitive Web interface of the portal makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries. Here, we provide a practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics.
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            Estrogen receptors and human disease.

            Estrogens influence many physiological processes in mammals, including but not limited to reproduction, cardiovascular health, bone integrity, cognition, and behavior. Given this widespread role for estrogen in human physiology, it is not surprising that estrogen is also implicated in the development or progression of numerous diseases, which include but are not limited to various types of cancer (breast, ovarian, colorectal, prostate, endometrial), osteoporosis, neurodegenerative diseases, cardiovascular disease, insulin resistance, lupus erythematosus, endometriosis, and obesity. In many of these diseases, estrogen mediates its effects through the estrogen receptor (ER), which serves as the basis for many therapeutic interventions. This Review will describe diseases in which estrogen, through the ER, plays a role in the development or severity of disease.
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              A modified TIP3P water potential for simulation with Ewald summation.

              The charges and Lennard-Jones parameters of the TIP3P water potential have been modified to improve its performance under the common condition for molecular dynamics simulations of using Ewald summation in lieu of relatively short nonbonded truncation schemes. These parameters were optimized under the condition that the hydrogen atoms do not have Lennard-Jones parameters, thus making the model independent of the combining rules used for the calculation of nonbonded, heteroatomic interaction energies, and limiting the number of Lennard-Jones calculations required. Under these conditions, this model provides accurate density (rho = 0.997 g/ml) and heat of vaporization (DeltaH(vap) = 10.53 kcal/mol) at 25 degrees C and 1 atm, but also provides improved structure in the second peak of the O-O radial distribution function and improved values for the dielectric constant (epsilon(0) = 89) and the diffusion coefficient (D = 4.0 x 10(-5) cm(2)/s) relative to the original parametrization. Like the original parameterization, however, this model does not show a temperature density maximum. Several similar models are considered with the additional constraint of trying to match the performance of the optimized potentials for liquid simulation atom force field to that obtained when using the simulation conditions under which it was originally designed, but no model was entirely satisfactory in reproducing the relative difference in free energies of hydration between the model compounds, phenol and benzene. Finally, a model that incorporates a long-range correction for truncated Lennard-Jones interactions is presented, which provides a very accurate dielectric constant (epsilon(0) = 76), however, the improvement in this estimate is on the same order as the uncertainty in the calculation. Copyright 2004 American Institute of Physics.
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                Author and article information

                Contributors
                sichun.yang@case.edu
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                30 August 2018
                30 August 2018
                2018
                : 9
                : 3520
                Affiliations
                [1 ]ISNI 0000 0001 2164 3847, GRID grid.67105.35, Center for Proteomics and Department of Nutrition, , Case Western Reserve University, ; 2109 Adelbert Rd, Cleveland, OH 44106-4988 USA
                [2 ]ISNI 0000 0001 2164 3847, GRID grid.67105.35, Department of Biochemistry, , Case Western Reserve University, ; 10900 Euclid Ave, Cleveland, OH 44106 USA
                [3 ]ISNI 0000 0001 2164 3847, GRID grid.67105.35, PEPCC Facility, , Case Western Reserve University, ; 10900 Euclid Ave, Cleveland, OH 44106 USA
                [4 ]ISNI 0000 0001 1939 4845, GRID grid.187073.a, BioCAT-18ID, Advanced Photon Source, , Argonne National Laboratory, ; 9700 S. Cass Avenue, Argonne, IL 60439 USA
                [5 ]ISNI 0000 0001 2231 4551, GRID grid.184769.5, Molecular Biophysics and Integrated Bioimaging, , Lawrence Berkeley National Laboratory, ; Berkeley, CA 94720 USA
                Author information
                http://orcid.org/0000-0002-1726-0576
                Article
                6034
                10.1038/s41467-018-06034-2
                6117352
                30166540
                6ebd0e1b-2fd6-4826-9469-4e73c71416c2
                © The Author(s) 2018

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 22 February 2018
                : 8 August 2018
                Funding
                Funded by: FundRef https://doi.org/10.13039/100000057, U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS);
                Award ID: GM103622
                Award ID: GM114056
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100000015, U.S. Department of Energy (DOE);
                Award ID: AC02-06CH11357
                Award ID: DE-AC02-98CH10886
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100000070, U.S. Department of Health & Human Services | NIH | National Institute of Biomedical Imaging and Bioengineering (NIBIB);
                Award ID: EB009998
                Award Recipient :
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