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Kumar R. Structure and functions of the N-terminal domain of steroid hormone receptors. VITAMINS AND HORMONES 2023; 123:399-416. [PMID: 37717992 DOI: 10.1016/bs.vh.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
The steroid hormone receptors (SHRs) belong to the large superfamily of nuclear receptors that selectively modulate gene expression in response to specific hormone ligands. The SHRs are required in a broad range of normal physiological processes as well as associated with numerous pathological conditions. Over years, the understanding of the SHR biology and mechanisms of their actions on target cells have found many clinical applications and management of various endocrine-related disorders. However, the effectiveness of SHR-based therapies in endocrine-related cancers remain a clinical challenge. This, in part, is due to the lack of in-depth understanding of structural dynamics and functions of SHRs' intrinsically disordered N-terminal domain (NTD). Recent progress in delineating SHR structural information and their correlations with receptor action in a highly dynamic environment is ultimately helping to explain how diverse SHR signaling mechanisms can elicit selective biological effects. Recent developments are providing new insights of how NTD's structural flexibility plays an important role in SHRs' allosteric regulation leading to the fine tuning of target gene expression to more precisely control SHRs' cell/tissue-specific functions. In this review article, we are discussing the up-to-date knowledge about the SHR actions with a particular emphasis on the structure and functions of the NTD.
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Affiliation(s)
- Raj Kumar
- Department of Pharmaceutical and Biomedical Sciences, Touro College of Pharmacy, New York, NY, United States.
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2
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Dube N, Khan SH, Sasse R, Okafor CD. Identification of an Evolutionarily Conserved Allosteric Network in Steroid Receptors. J Chem Inf Model 2023; 63:571-582. [PMID: 36594606 PMCID: PMC9875803 DOI: 10.1021/acs.jcim.2c01096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Indexed: 01/04/2023]
Abstract
Allosteric pathways in proteins describe networks comprising amino acid residues which may facilitate the propagation of signals between distant sites. Through inter-residue interactions, dynamic and conformational changes can be transmitted from the site of perturbation to an allosteric site. While sophisticated computational methods have been developed to characterize such allosteric pathways linking specific sites on proteins, few attempts have been made to apply these approaches toward identifying new allosteric sites. Here, we use molecular dynamics simulations and suboptimal path analysis to discover new allosteric networks in steroid receptors with a focus on evolutionarily conserved pathways. Using modern receptors and a reconstructed ancestral receptor, we identify networks connecting several sites to the activation function surface 2 (AF-2), the site of coregulator recruitment. One of these networks is conserved across the entire family, connecting a predicted allosteric site located between helices 9 and 10 of the ligand-binding domain. We investigate the basis of this conserved network as well as the importance of this site, discovering that the site lies in a region of the ligand-binding domain characterized by conserved inter-residue contacts. This study suggests an evolutionarily importance of the helix 9-helix 10 site in steroid receptors and identifies an approach that may be applied to discover previously unknown allosteric sites in proteins.
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Affiliation(s)
- Namita Dube
- Department
of Biochemistry and Molecular Biology, Pennsylvania
State University, University Park, State College, Pennsylvania 16802, United States
| | - Sabab Hasan Khan
- Department
of Biochemistry and Molecular Biology, Pennsylvania
State University, University Park, State College, Pennsylvania 16802, United States
| | - Riley Sasse
- Department
of Chemistry, Pennsylvania State University, University Park, State College, Pennsylvania 16802, United States
| | - C. Denise Okafor
- Department
of Biochemistry and Molecular Biology, Pennsylvania
State University, University Park, State College, Pennsylvania 16802, United States
- Department
of Chemistry, Pennsylvania State University, University Park, State College, Pennsylvania 16802, United States
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3
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Khan SH, Braet SM, Koehler SJ, Elacqua E, Anand GS, Okafor CD. Ligand-induced shifts in conformational ensembles that describe transcriptional activation. eLife 2022; 11:80140. [PMID: 36222302 PMCID: PMC9555869 DOI: 10.7554/elife.80140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/14/2022] [Indexed: 11/15/2022] Open
Abstract
Nuclear receptors function as ligand-regulated transcription factors whose ability to regulate diverse physiological processes is closely linked with conformational changes induced upon ligand binding. Understanding how conformational populations of nuclear receptors are shifted by various ligands could illuminate strategies for the design of synthetic modulators to regulate specific transcriptional programs. Here, we investigate ligand-induced conformational changes using a reconstructed, ancestral nuclear receptor. By making substitutions at a key position, we engineer receptor variants with altered ligand specificities. We combine cellular and biophysical experiments to characterize transcriptional activity, as well as elucidate mechanisms underlying altered transcription in receptor variants. We then use atomistic molecular dynamics (MD) simulations with enhanced sampling to generate ensembles of wildtype and engineered receptors in combination with multiple ligands, followed by conformational analysis and correlation of MD-based predictions with functional ligand profiles. We determine that conformational ensembles accurately describe ligand responses based on observed population shifts. These studies provide a platform which will allow structural characterization of physiologically-relevant conformational ensembles, as well as provide the ability to design and predict transcriptional responses in novel ligands.
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Affiliation(s)
- Sabab Hasan Khan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University
| | - Sean M Braet
- Department of Chemistry, Pennsylvania State University
| | | | | | | | - C Denise Okafor
- Department of Biochemistry and Molecular Biology, Pennsylvania State University
- Department of Chemistry, Pennsylvania State University
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4
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La Sala G, Gunnarsson A, Edman K, Tyrchan C, Hogner A, Frolov AI. Unraveling the Allosteric Cross-Talk between the Coactivator Peptide and the Ligand-Binding Site in the Glucocorticoid Receptor. J Chem Inf Model 2021; 61:3667-3680. [PMID: 34156843 DOI: 10.1021/acs.jcim.1c00323] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The glucocorticoid receptor (GR) is a nuclear receptor that controls critical biological processes by regulating the transcription of specific genes. There is a known allosteric cross-talk between the ligand and coregulator binding sites within the GR ligand-binding domain that is crucial for the control of the functional response. However, the molecular mechanisms underlying such an allosteric control remain elusive. Here, molecular dynamics (MD) simulations, bioinformatic analysis, and biophysical measurements are integrated to capture the structural and dynamic features of the allosteric cross-talk within the GR. We identified a network of evolutionarily conserved residues that enables the allosteric signal transduction, in agreement with experimental data. MD simulations clarify how such a network is dynamically interconnected and offer a mechanistic explanation of how different peptides affect the intensity of the allosteric signal. This study provides useful insights to elucidate the GR allosteric regulation, ultimately providing a foundation for designing novel drugs.
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Affiliation(s)
- Giuseppina La Sala
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anders Gunnarsson
- Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Karl Edman
- Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Christian Tyrchan
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anders Hogner
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Andrey I Frolov
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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5
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Shang J, Kojetin DJ. Structural mechanism underlying ligand binding and activation of PPARγ. Structure 2021; 29:940-950.e4. [PMID: 33713599 DOI: 10.1016/j.str.2021.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/27/2021] [Accepted: 02/19/2021] [Indexed: 12/16/2022]
Abstract
Ligands bind to an occluded orthosteric ligand-binding pocket within the nuclear receptor ligand-binding domain. Molecular simulations have revealed theoretical ligand entry/exit pathways to the orthosteric pocket; however, it remains unclear whether ligand binding proceeds through induced fit or conformational selection mechanisms. Here, using nuclear magnetic resonance spectroscopy, isothermal titration calorimetry, and surface plasmon resonance analysis, we provide evidence that structurally distinct agonists bind peroxisome proliferator-activated receptor γ (PPARγ) via a two-step induced fit mechanism involving an initial fast kinetic step followed by a slow conformational change. The agonist encounter complex binding pose is suggested in crystal structures where ligands bind to a surface pore suggested as a ligand entry site in molecular simulations. Our findings suggest an activation mechanism for PPARγ whereby agonist binding occurs through an initial encounter complex followed by a transition of the ligand into the final binding pose within the orthosteric pocket, inducing a transcriptionally active conformation.
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Affiliation(s)
- Jinsai Shang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Douglas J Kojetin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA.
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6
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Köhler C, Carlström G, Gunnarsson A, Weininger U, Tångefjord S, Ullah V, Lepistö M, Karlsson U, Papavoine T, Edman K, Akke M. Dynamic allosteric communication pathway directing differential activation of the glucocorticoid receptor. SCIENCE ADVANCES 2020; 6:eabb5277. [PMID: 32832645 PMCID: PMC7439413 DOI: 10.1126/sciadv.abb5277] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 06/05/2020] [Indexed: 05/07/2023]
Abstract
Allosteric communication within proteins is a hallmark of biochemical signaling, but the dynamic transmission pathways remain poorly characterized. We combined NMR spectroscopy and surface plasmon resonance to reveal these pathways and quantify their energetics in the glucocorticoid receptor, a transcriptional regulator controlling development, metabolism, and immune response. Our results delineate a dynamic communication network of residues linking the ligand-binding pocket to the activation function-2 interface, where helix 12, a switch for transcriptional activation, exhibits ligand- and coregulator-dependent dynamics coupled to graded activation. The allosteric free energy responds to variations in ligand structure: subtle changes gradually tune allostery while preserving the transmission pathway, whereas substitution of the entire pharmacophore leads to divergent allosteric control by apparently rewiring the communication network. Our results provide key insights that should aid in the design of mechanistically differentiated ligands.
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Affiliation(s)
- C. Köhler
- Respiratory, Inflammation and Autoimmunity, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - G. Carlström
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - A. Gunnarsson
- Discovery Sciences, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - U. Weininger
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P. O. Box 124, 221 00 Lund, Sweden
| | - S. Tångefjord
- Respiratory, Inflammation and Autoimmunity, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
- Discovery Sciences, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - V. Ullah
- Respiratory, Inflammation and Autoimmunity, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - M. Lepistö
- Respiratory, Inflammation and Autoimmunity, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - U. Karlsson
- Discovery Sciences, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - T. Papavoine
- Respiratory, Inflammation and Autoimmunity, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - K. Edman
- Discovery Sciences, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - M. Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P. O. Box 124, 221 00 Lund, Sweden
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Rewiring Ancient Residue Interaction Networks Drove the Evolution of Specificity in Steroid Receptors. Structure 2020; 28:196-205.e3. [DOI: 10.1016/j.str.2019.11.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/10/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022]
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