1
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MacTavish B, Zhu D, Shang J, Shao Q, Yang ZJ, Kamenecka TM, Kojetin DJ. Ligand efficacy shifts a nuclear receptor conformational ensemble between transcriptionally active and repressive states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590805. [PMID: 38712087 PMCID: PMC11071369 DOI: 10.1101/2024.04.23.590805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Nuclear receptors (NRs) are thought to dynamically alternate between transcriptionally active and repressive conformations, which are stabilized upon ligand binding. Most NR ligand series exhibit limited bias, primarily consisting of transcriptionally active agonists or neutral antagonists, but not repressive inverse agonists-a limitation that restricts understanding of the functional NR conformational ensemble. Here, we report a NR ligand series for peroxisome proliferator-activated receptor gamma (PPARγ) that spans a pharmacological spectrum from repression (inverse agonism) to activation (agonism) where subtle structural modifications switch compound activity. While crystal structures provide snapshots of the fully repressive state, NMR spectroscopy and conformation-activity relationship analysis reveals that compounds within the series shift the PPARγ conformational ensemble between transcriptionally active and repressive conformations that are populated in the apo/ligand-free ensemble. Our findings reveal a molecular framework for minimal chemical modifications that enhance PPARγ inverse agonism and elucidate their influence on the dynamic PPARγ conformational ensemble.
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Affiliation(s)
- Brian MacTavish
- Department of Integrative Structural and Computational Biology, Scripps Research and The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida 33458, United States
| | - Di Zhu
- Department of Molecular Medicine, Scripps Research and The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida 33458, United States
| | - Jinsai Shang
- Department of Integrative Structural and Computational Biology, Scripps Research and The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida 33458, United States
- School of Basic Medical Sciences, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Qianzhen Shao
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Zhongyue J. Yang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Center for Applied AI in Protein Dynamics, Vanderbilt University, Nashville, Tennessee 37232, United States
- Data Science Institute, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Theodore M. Kamenecka
- Department of Molecular Medicine, Scripps Research and The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida 33458, United States
| | - Douglas J. Kojetin
- Department of Integrative Structural and Computational Biology, Scripps Research and The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida 33458, United States
- Department of Molecular Medicine, Scripps Research and The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida 33458, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Center for Applied AI in Protein Dynamics, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
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2
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Alzahrani AA, Saleh RO, Latypova A, Bokov DO, Kareem AH, Talib HA, Hameed NM, Pramanik A, Alawadi A, Alsalamy A. Therapeutic significance of long noncoding RNAs in estrogen receptor-positive breast cancer. Cell Biochem Funct 2024; 42:e3993. [PMID: 38532685 DOI: 10.1002/cbf.3993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
About 70% of cases of breast cancer are compromised by Estrogen-positive breast cancer. Through its regulation of several processes, including cell proliferation, cell cycle progression, and apoptosis, Estrogen signaling plays a pivotal role in the genesis and progression of this particular kind of breast cancer. One of the best treatment strategies for treating Estrogen-positive breast cancer is blocking Estrogen signaling. However, patients' treatment failure is mainly caused by the emergence of resistance and metastases, necessitating the development of novel therapeutic targets. Numerous studies have shown long noncoding RNAs (lncRNAs) to play a role in Estrogen-mediated carcinogenesis. These lncRNAs interact with co-regulators and the Estrogen signaling cascade components, primarily due to Estrogen activation. Vimentin and E-cadherin are examples of epithelial-to-mesenchymal transition markers, and they regulate genes involved in cell cycle progression, such as Cyclins, to affect the growth, proliferation, and metastasis of Estrogen-positive breast cancer. Furthermore, a few of these lncRNAs contribute to developing resistance to chemotherapy, making them more desirable targets for enhancing results. Thus, to shed light on the creation of fresh approaches for treating this cancer, this review attempts to compile recently conducted studies on the relationship between lncRNAs and the advancement of Estrogen-positive breast cancer.
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Affiliation(s)
| | - Raed Obaid Saleh
- Department of Medical Laboratory Techniques, Al-Maarif University College, Al-Anbar, Iraq
| | - Amaliya Latypova
- Department of Medical and Technical Information Technology, Bauman Moscow State Technical University, Moscow, Russia
- Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Mishref Campus, Kuwait
| | - Dmitry Olegovich Bokov
- Institute of Pharmacy, Sechenov First Moscow State Medical University, Moscow, Russian Federation
- Laboratory of Food Chemistry, Federal Research Center of Nutrition, Biotechnology and Food Safety, Moscow, Russian Federation
| | | | - Hayder Abdullah Talib
- College of Agriculture, National University of Science and Technology, Dhi Qar, Dhi Qar, Iraq
| | - Noora M Hameed
- Anesthesia techniques, Al-Nisour University College, Iraq
| | - Atreyi Pramanik
- Divison of Research and Innovation, School of Applied and Life Sciences, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Ahmed Alawadi
- College of Technical Engineering, the Islamic University, Najaf, Iraq
- College of Technical Engineering, the Islamic University of Al Diwaniyah, Iraq
- College of Technical Engineering, the Islamic University of Babylon, Iraq
| | - Ali Alsalamy
- College of Technical Engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna, Iraq
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3
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Gupta MN, Uversky VN. Protein structure-function continuum model: Emerging nexuses between specificity, evolution, and structure. Protein Sci 2024; 33:e4968. [PMID: 38532700 DOI: 10.1002/pro.4968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/18/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
The rationale for replacing the old binary of structure-function with the trinity of structure, disorder, and function has gained considerable ground in recent years. A continuum model based on the expanded form of the existing paradigm can now subsume importance of both conformational flexibility and intrinsic disorder in protein function. The disorder is actually critical for understanding the protein-protein interactions in many regulatory processes, formation of membrane-less organelles, and our revised notions of specificity as amply illustrated by moonlighting proteins. While its importance in formation of amyloids and function of prions is often discussed, the roles of intrinsic disorder in infectious diseases and protein function under extreme conditions are also becoming clear. This review is an attempt to discuss how our current understanding of protein function, specificity, and evolution fit better with the continuum model. This integration of structure and disorder under a single model may bring greater clarity in our continuing quest for understanding proteins and molecular mechanisms of their functionality.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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4
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McCullagh M, Zeczycki TN, Kariyawasam CS, Durie CL, Halkidis K, Fitzkee NC, Holt JM, Fenton AW. What is allosteric regulation? Exploring the exceptions that prove the rule! J Biol Chem 2024; 300:105672. [PMID: 38272229 PMCID: PMC10897898 DOI: 10.1016/j.jbc.2024.105672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
"Allosteric" was first introduced to mean the other site (i.e., a site distinct from the active or orthosteric site), an adjective for "regulation" to imply a regulatory outcome resulting from ligand binding at another site. That original idea outlines a system with two ligand-binding events at two distinct locations on a macromolecule (originally a protein system), which defines a four-state energy cycle. An allosteric energy cycle provides a quantifiable allosteric coupling constant and focuses our attention on the unique properties of the four equilibrated protein complexes that constitute the energy cycle. Because many observed phenomena have been referenced as "allosteric regulation" in the literature, the goal of this work is to use literature examples to explore which systems are and are not consistent with the two-ligand thermodynamic energy cycle-based definition of allosteric regulation. We emphasize the need for consistent language so comparisons can be made among the ever-increasing number of allosteric systems. Building on the mutually exclusive natures of an energy cycle definition of allosteric regulation versus classic two-state models, we conclude our discussion by outlining how the often-proposed Rube-Goldberg-like mechanisms are likely inconsistent with an energy cycle definition of allosteric regulation.
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Affiliation(s)
- Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Tonya N Zeczycki
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
| | - Chathuri S Kariyawasam
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | - Clarissa L Durie
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Konstantine Halkidis
- Department of Hematologic Malignancies and Cellular Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas, USA; Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | - Jo M Holt
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA.
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5
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Jeanneteau F. Stress and the risk of Alzheimer dementia: Can deconstructed engrams be rebuilt? J Neuroendocrinol 2023; 35:e13235. [PMID: 36775895 DOI: 10.1111/jne.13235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 01/26/2023]
Abstract
The exact neuropathological mechanism by which the dementia process unfolds is under intense scrutiny. The disease affects about 38 million people worldwide, 70% of which are clinically diagnosed with Alzheimer's disease (AD). If the destruction of synapses essential for learning, planning and decision-making is part of the problem, must the restoration of previously lost synapses be part of the solution? It is plausible that neuronal capacity to restitute information corresponds with the adaptive capacity of its connectivity reserve. A challenge will be to promote the functional connectivity that can compensate for the lost one. This will require better clarification of the remodeling of functional connectivity during the progression of AD dementia and its reversal upon experimental treatment. A major difficulty is to promote the neural pathways that are atrophied in AD dementia while suppressing others that are bolstered. Therapeutic strategies should aim at scaling functional connectivity to a just balance between the atrophic and hypertrophic systems. However, the exact factors that can help reach this objective are still unclear. Similarities between the effects of chronic stress and some neuropathological mechanisms underlying AD dementia support the idea that common components deserve prime attention as therapeutic targets.
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Affiliation(s)
- Freddy Jeanneteau
- Institut de génomique fonctionnelle, Université de Montpellier, INSERM, CNRS, Montpellier, France
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6
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Sołtys K, Ożyhar A. Phase separation propensity of the intrinsically disordered AB region of human RXRβ. Cell Commun Signal 2023; 21:92. [PMID: 37143076 PMCID: PMC10157963 DOI: 10.1186/s12964-023-01113-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/25/2023] [Indexed: 05/06/2023] Open
Abstract
RXRβ is one of three subtypes of human retinoid X receptor (RXR), a transcription factor that belongs to the nuclear receptor superfamily. Its expression can be detected in almost all tissues. In contrast to other subtypes - RXRα and RXRγ - RXRβ has the longest and unique N-terminal sequence called the AB region, which harbors a ligand-independent activation function. In contrast to the functional properties of this sequence, the molecular properties of the AB region of human RXRβ (AB_hRXRB) have not yet been characterized. Here, we present a systematic biochemical and biophysical analysis of recombinant AB_hRXRB, along with in silico examinations, which demonstrate that AB_hRXRB exhibits properties of a coil-like intrinsically disordered region. AB_hRXRB possesses a flexible structure that is able to adopt a more ordered conformation under the influence of different environmental factors. Interestingly, AB_hRXRB promotes the formation of liquid-liquid phase separation (LLPS), a phenomenon previously observed for the AB region of another human subtype of RXR - RXRγ (AB_hRXRG). Although both AB regions seem to be similar in terms of their ability to induce phase separation, they clearly differ in the sensitivity to factors driving and regulating LLPS. This distinct LLPS response to environmental factors driven by the unique amino acid compositions of AB_hRXRB and AB_hRXRG can be significant for the specific modulation of the transcriptional activation of target genes by different subtypes of RXR. Video Abstract.
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Affiliation(s)
- Katarzyna Sołtys
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
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7
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Jeanneteau F, Meijer OC, Moisan MP. Structural basis of glucocorticoid receptor signaling bias. J Neuroendocrinol 2023; 35:e13203. [PMID: 36221223 DOI: 10.1111/jne.13203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 11/30/2022]
Abstract
Dissociation between the healthy and toxic effects of cortisol, a major stress-responding hormone has been a widely used strategy to develop anti-inflammatory glucocorticoids with fewer side effects. Such strategy falls short when treating brain disorders as timing and activity state within large-scale neuronal networks determine the physiological and behavioral specificity of cortisol response. Advances in structural molecular dynamics posit the bases for engineering glucocorticoids with precision bias for select downstream signaling pathways. Design of allosteric and/or cooperative control for the glucocorticoid receptor could help promote the beneficial and reduce the deleterious effects of cortisol on brain and behavior in disease conditions.
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Affiliation(s)
- Freddy Jeanneteau
- Institut de génomique fonctionnelle, Université de Montpellier, INSERM, CNRS, Montpellier, France
| | - Onno C Meijer
- Leiden University Medical Center, Leiden, The Netherlands
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8
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Katsu Y, Oana S, Lin X, Hyodo S, Baker ME. Aldosterone and dexamethasone activate African lungfish mineralocorticoid receptor: Increased activation after removal of the amino-terminal domain. J Steroid Biochem Mol Biol 2022; 215:106024. [PMID: 34774724 DOI: 10.1016/j.jsbmb.2021.106024] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/28/2021] [Accepted: 11/09/2021] [Indexed: 12/18/2022]
Abstract
Aldosterone, the main physiological mineralocorticoid in humans and other terrestrial vertebrates, first appears in lungfish, which are lobe-finned fish that are forerunners of terrestrial vertebrates. Aldosterone activation of the MR regulates internal homeostasis of water, sodium and potassium, which was critical in the conquest of land by vertebrates. We studied transcriptional activation of the slender African lungfish MR by aldosterone, other corticosteroids and progesterone and find that aldosterone, 11-deoxycorticosterone, 11-deoxycortisol and progesterone have half-maximal responses (EC50 s) below 1 nM and are potential physiological mineralocorticoids. In contrast, EC50 s for corticosterone and cortisol were 23 nM and 66 nM, respectively. Unexpectedly, truncated lungfish MR, consisting of the DNA-binding, hinge and steroid-binding domains, had a stronger response to corticosteroids and progesterone than full-length lungfish MR, indicating that the N-terminal domain represses steroid activation of lungfish MR, unlike human MR in which the N-terminal domain contains an activation function. BLAST searches of GenBank did not retrieve a GR ortholog, leading us to test dexamethasone and triamcinolone for activation of lungfish MR. At 10 nM, both synthetic glucocorticoids are about 4-fold stronger than 10 nM aldosterone in activating full-length lungfish MR, leading us to propose that lungfish MR also functions as a GR.
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Affiliation(s)
- Yoshinao Katsu
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan; Faculty of Sciences, Hokkaido University, Sapporo, Japan.
| | - Shin Oana
- Faculty of Sciences, Hokkaido University, Sapporo, Japan
| | - Xiaozhi Lin
- Faculty of Sciences, Hokkaido University, Sapporo, Japan
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, University of Tokyo, Chiba, Japan
| | - Michael E Baker
- Division of Nephrology-Hypertension, Department of Medicine, 0693, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0693, United States; Center for Academic Research and Training in Anthropogeny (CARTA), University of California, San Diego, La Jolla, CA, 92093, United States.
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9
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Sadar MD. Drugging the Undruggable: Targeting the N-Terminal Domain of Nuclear Hormone Receptors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1390:311-326. [PMID: 36107327 DOI: 10.1007/978-3-031-11836-4_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This chapter focuses on the development of drugs targeting the N-terminal domain of nuclear hormone receptors, using progress with the androgen receptor as an example. Historically, development of therapies targeting nuclear hormone receptors has focused on the folded C-terminal ligand-binding domain. Therapies were traditionally not developed to target the intrinsically disordered N-terminal domain as it was considered "undruggable". Recent developments have now shown it is possible to direct therapies to the N-terminal domain. This chapter will provide an introduction of the structure and function of the domains of nuclear hormone receptors, followed by a discussion of the rationale supporting the development of N-terminal domain inhibitors. Chemistry and mechanisms of action of small molecule inhibitors will be described with emphasis on N-terminal domain inhibitors developed to the androgen receptor including those in clinical trials.
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Affiliation(s)
- Marianne D Sadar
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC, Canada.
- Department of Pathology and Laboratory Science, University of British Columbia, Vancouver, BC, Canada.
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10
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Sołtys K, Ożyhar A. Transcription Regulators and Membraneless Organelles Challenges to Investigate Them. Int J Mol Sci 2021; 22:12758. [PMID: 34884563 PMCID: PMC8657783 DOI: 10.3390/ijms222312758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 12/13/2022] Open
Abstract
Eukaryotic cells are composed of different bio-macromolecules that are divided into compartments called organelles providing optimal microenvironments for many cellular processes. A specific type of organelles is membraneless organelles. They are formed via a process called liquid-liquid phase separation that is driven by weak multivalent interactions between particular bio-macromolecules. In this review, we gather crucial information regarding different classes of transcription regulators with the propensity to undergo liquid-liquid phase separation and stress the role of intrinsically disordered regions in this phenomenon. We also discuss recently developed experimental systems for studying formation and properties of membraneless organelles.
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Affiliation(s)
- Katarzyna Sołtys
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland;
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11
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Grasso EM, Majumdar A, Wrabl JO, Frueh DP, Hilser VJ. Conserved allosteric ensembles in disordered proteins using TROSY/anti-TROSY R 2-filtered spectroscopy. Biophys J 2021; 120:2498-2510. [PMID: 33901472 PMCID: PMC8390865 DOI: 10.1016/j.bpj.2021.04.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/11/2021] [Accepted: 04/16/2021] [Indexed: 11/22/2022] Open
Abstract
Defining the role of intrinsic disorder in proteins in the myriad of biological processes with which it is involved represents a significant goal in modern biophysics. Toward this end, NMR is uniquely suited for molecular studies of dynamic and disordered regions, but studying these regions in concert with their more structured domains and binding partners presents spectroscopic challenges. Here, we investigate the interactions between the structured and disordered regions of the human glucocorticoid receptor (GR). To do this, we developed an NMR strategy that relies on a novel relaxation filter for the simultaneous study of structured and unstructured regions. Using this approach, we conducted a comparative analysis of three translational isoforms of GR containing a folded DNA-binding domain (DBD) and two disordered regions that flank the DBD, one of which varies in size in the different isoforms. Notably, we were able to assign resonances that had previously been inaccessible because of the spectral complexity of the translational isoforms, which in turn allowed us to 1) identify a region of the structured DBD that undergoes significant changes in the local chemical environment in the presence of the disordered region and 2) determine differences in the conformational ensembles of the disordered regions of the translational isoforms. Furthermore, an ensemble-based thermodynamic analysis of the isoforms reveals conserved patterns of stability within the N-terminal domain of GR that persist despite low sequence conservation. These studies provide an avenue for further investigations of the mechanistic underpinnings of the functional relevance of the translational isoforms of GR while also providing a general NMR strategy for studying systems containing both structured and disordered regions.
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Affiliation(s)
- Emily M Grasso
- Department of Biology, Johns Hopkins University, Baltimore, Maryland; T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Ananya Majumdar
- The Biomolecular NMR Center, Johns Hopkins University, Baltimore, Maryland
| | - James O Wrabl
- Department of Biology, Johns Hopkins University, Baltimore, Maryland
| | - Dominique P Frueh
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, Baltimore, Maryland; T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
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12
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Sołtys K, Wycisk K, Ożyhar A. Liquid-liquid phase separation of the intrinsically disordered AB region of hRXRγ is driven by hydrophobic interactions. Int J Biol Macromol 2021; 183:936-949. [PMID: 33971237 DOI: 10.1016/j.ijbiomac.2021.05.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 12/22/2022]
Abstract
Nuclear receptors (NRs) are a family of transcription factors that are regulated endogenously by small lipophilic ligands. Recently, liquid-liquid phase separation (LLPS) has appeared as a new aspect of NR function. In the human retinoid X receptor γ (hRXRγ), the inherently disordered AB region undergoes LLPS via homotypic multivalent interactions. To better understand the functions of liquid condensates, a clear view of the molecular interactions underlying the LLPS are required. The phase separation propensity of the AB region of hRXRγ (AB_hRXG) at a high NaCl concentration, a lower critical solution temperature behavior, and also sensitivity to kosmotropic salts and 1,6-hexanediol, which all indicate the importance of hydrophobic interactions in the formation of AB_hRXG liquid condensates, is presented in the paper. Additionally, molecular crowding agents and TMAO shift the equilibrium, in turn enabling phase transition at lower AB_hRXG concentrations. Although the LLPS of the proteins can lead to aggregation, AB_hRXG liquid condensates are not aggregation prone. Interestingly, the formation of AB_hRXG liquid condensates has an impact on the rest of the receptor, as AB_hRXG liquid condensates recruit the remaining fragment of hRXRγ into the droplets. The ability of AB_hRXG to undergo LLPS might be important for gene expression regulation.
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Affiliation(s)
- Katarzyna Sołtys
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
| | - Krzysztof Wycisk
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
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13
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Sicoli G, Kress T, Vezin H, Ledolter K, Kurzbach D. A Switch between Two Intrinsically Disordered Conformational Ensembles Modulates the Active Site of a Basic-Helix-Loop-Helix Transcription Factor. J Phys Chem Lett 2020; 11:8944-8951. [PMID: 33030907 PMCID: PMC7649839 DOI: 10.1021/acs.jpclett.0c02242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We report a conformational switch between two distinct intrinsically disordered subensembles within the active site of a transcription factor. This switch highlights an evolutionary benefit conferred by the high plasticity of intrinsically disordered domains, namely, their potential to dynamically sample a heterogeneous conformational space housing multiple states with tailored properties. We focus on proto-oncogenic basic-helix-loop-helix (bHLH)-type transcription factors, as these play key roles in cell regulation and function. Despite intense research efforts, the understanding of structure-function relations of these transcription factors remains incomplete as they feature intrinsically disordered DNA-interaction domains that are difficult to characterize, theoretically as well as experimentally. Here we characterize the structural dynamics of the intrinsically disordered region DNA-binding site of the vital MYC-associated transcription factor X (MAX). Integrating nuclear magnetic resonance (NMR) measurements, molecular dynamics (MD) simulations, and electron paramagnetic resonance (EPR) measurements, we show that, in the absence of DNA, the binding site of the free MAX2 homodimer samples two intrinsically disordered conformational subensembles. These feature distinct structural properties: one subensemble consists of a set of highly flexible and spatially extended conformers, while the second features a set of "hinged" conformations. In this latter ensemble, the disordered N-terminal tails of MAX2 fold back along the dimer, forming transient long-range contacts with the HLH-region and thereby exposing the DNA binding site to the solvent. The features of these divergent substates suggest two mechanisms by which protein conformational dynamics in MAX2 might modulate DNA-complex formation: by enhanced initial recruitment of free DNA ligands, as a result of the wider conformational space sampled by the extended ensemble, and by direct exposure of the binding site and the corresponding strong electrostatic attractions presented while in the hinged conformations.
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Affiliation(s)
- Giuseppe Sicoli
- Laboratoire
Avancé de Spectroscopie pour les Interactions, la Réactivité
et l’Environnement (LASIRE), UMR CNRS 8516, Université de Lille, Avenue Paul Langevin − C4, F-59655 Villeneuve d’Ascq, France
| | - Thomas Kress
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Hervé Vezin
- Laboratoire
Avancé de Spectroscopie pour les Interactions, la Réactivité
et l’Environnement (LASIRE), UMR CNRS 8516, Université de Lille, Avenue Paul Langevin − C4, F-59655 Villeneuve d’Ascq, France
| | - Karin Ledolter
- Department
for Structural and Computational Biology, Max F. Perutz Laboratories, University Vienna, Campus Vienna BioCenter 5, 1030 Vienna, Austria
| | - Dennis Kurzbach
- Faculty
of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
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14
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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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15
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Sołtys K, Ożyhar A. Ordered structure-forming properties of the intrinsically disordered AB region of hRXRγ and its ability to promote liquid-liquid phase separation. J Steroid Biochem Mol Biol 2020; 198:105571. [PMID: 31881311 DOI: 10.1016/j.jsbmb.2019.105571] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 12/31/2022]
Abstract
The retinoid X receptor (RXR) is a member of the nuclear receptor (NR) superfamily that occupies the central position among other NRs by forming both homodimers and heterodimers with other representatives of the family. RXR shares similar structural domains with other members of NRs. The major differences in the subtypes and isoforms of RXR are in the AB region. To date, there have been no data concerning the molecular properties of the AB region of hRXRγ (AB_hRXG). Here, we describe the biochemical and biophysical properties of the recombinant AB_hRXG. The results indicate that AB_hRXG shows the structural and functional characteristics of the pre-molten globule-like (PMG-like) group of intrinsically disordered proteins (IDPs) and also has a significant propensity for folding. We also present the first experimental evidence showing that the AB region of NRs promotes the formation of liquid-liquid phase separation (LLPS).
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Affiliation(s)
- Katarzyna Sołtys
- Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wroclaw, Poland.
| | - Andrzej Ożyhar
- Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wroclaw, Poland
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16
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Millard PS, Bugge K, Marabini R, Boomsma W, Burow M, Kragelund BB. IDDomainSpotter: Compositional bias reveals domains in long disordered protein regions-Insights from transcription factors. Protein Sci 2020; 29:169-183. [PMID: 31642121 PMCID: PMC6933863 DOI: 10.1002/pro.3754] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/16/2019] [Accepted: 10/16/2019] [Indexed: 12/12/2022]
Abstract
Protein domains constitute regions of distinct structural properties and molecular functions that are retained when removed from the rest of the protein. However, due to the lack of tertiary structure, the identification of domains has been largely neglected for long (>50 residues) intrinsically disordered regions. Here we present a sequence-based approach to assess and visualize domain organization in long intrinsically disordered regions based on compositional sequence biases. An online tool to find putative intrinsically disordered domains (IDDomainSpotter) in any protein sequence or sequence alignment using any particular sequence trait is available at http://www.bio.ku.dk/sbinlab/IDDomainSpotter. Using this tool, we have identified a putative domain enriched in hydrophilic and disorder-promoting residues (Pro, Ser, and Thr) and depleted in positive charges (Arg and Lys) bordering the folded DNA-binding domains of several transcription factors (p53, GCR, NAC46, MYB28, and MYB29). This domain, from two different MYB transcription factors, was characterized biophysically to determine its properties. Our analyses show the domain to be extended, dynamic and highly disordered. It connects the DNA-binding domain to other disordered domains and is present and conserved in several transcription factors from different families and domains of life. This example illustrates the potential of IDDomainSpotter to predict, from sequence alone, putative domains of functional interest in otherwise uncharacterized disordered proteins.
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Affiliation(s)
- Peter S. Millard
- DynaMo Center, Department of Plant and Environmental SciencesUniversity of CopenhagenCopenhagenDenmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Katrine Bugge
- Structural Biology and NMR Laboratory, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Riccardo Marabini
- Structural Biology and NMR Laboratory, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Wouter Boomsma
- Department of Computer ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Meike Burow
- DynaMo Center, Department of Plant and Environmental SciencesUniversity of CopenhagenCopenhagenDenmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Birthe B. Kragelund
- Structural Biology and NMR Laboratory, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
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17
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Guillien M, le Maire A, Mouhand A, Bernadó P, Bourguet W, Banères JL, Sibille N. IDPs and their complexes in GPCR and nuclear receptor signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:105-155. [DOI: 10.1016/bs.pmbts.2020.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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18
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Sicoli G, Vezin H, Ledolter K, Kress T, Kurzbach D. Conformational tuning of a DNA-bound transcription factor. Nucleic Acids Res 2019; 47:5429-5435. [PMID: 31020309 PMCID: PMC6547406 DOI: 10.1093/nar/gkz291] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 04/05/2019] [Accepted: 04/10/2019] [Indexed: 11/14/2022] Open
Abstract
Transcription factors are involved in many cellular processes that take place remote from their cognate DNA sequences. The efficiencies of these activities are thus in principle counteracted by high binding affinities of the factors to their cognate DNAs. Models such as facilitated diffusion or dissociation address this apparent contradiction. We show that the MYC associated transcription factor X (MAX) undergoes nanoscale conformational fluctuations in the DNA-bound state, which is consistent with facilitated dissociation from or diffusion along DNA strands by transiently reducing binding energies. An integrative approach involving EPR, NMR, crystallographic and molecular dynamics analyses demonstrates that the N-terminal domain of MAX constantly opens and closes around a bound DNA ligand thereby dynamically tuning the binding epitope and the mode of interaction.
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Affiliation(s)
- Giuseppe Sicoli
- Univ. Lille, CNRS, UMR 8516 - LASIR - Laboratoire de Spectrochimie Infrarouge et Raman, F-59000 Lille, France
| | - Hervé Vezin
- Univ. Lille, CNRS, UMR 8516 - LASIR - Laboratoire de Spectrochimie Infrarouge et Raman, F-59000 Lille, France
| | - Karin Ledolter
- University Vienna, Department for Structural and Computational Biology, Max F. Perutz Laboratories, Campus Vienna BioCenter 5, 1030 Vienna, Austria
| | - Thomas Kress
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.,University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090 Vienna, Austria
| | - Dennis Kurzbach
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090 Vienna, Austria
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19
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Drake JA, Pettitt BM. Thermodynamics of Conformational Transitions in a Disordered Protein Backbone Model. Biophys J 2019; 114:2799-2810. [PMID: 29925017 DOI: 10.1016/j.bpj.2018.04.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/28/2018] [Accepted: 04/16/2018] [Indexed: 12/11/2022] Open
Abstract
Conformational entropy is expected to contribute significantly to the thermodynamics of structural transitions in intrinsically disordered proteins or regions in response to protein/ligand binding, posttranslational modifications, and environmental changes. We calculated the backbone (dihedral) conformational entropy of oligoglycine (GlyN), a protein backbone mimic and model intrinsically disordered region, as a function of chain length (N=3, 4, 5, 10, and 15) from simulations using three different approaches. The backbone conformational entropy scales linearly with chain length with a slope consistent with the entropy of folding of well-structured proteins. The entropic contributions of second-order dihedral correlations are predominantly through intraresidue ϕ-ψ pairs, suggesting that oligoglycine may be thermodynamically modeled as a system of independent glycine residues. We find the backbone conformational entropy to be largely independent of global structural parameters, like the end-to-end distance and radius of gyration. We introduce a framework referred to herein as "ensemble confinement" to estimate the loss (gain) of conformational free energy and its entropic component when individual residues are constrained to (released from) particular regions of the ϕ-ψ map. Quantitatively, we show that our protein backbone model resists ordering/folding with a significant, unfavorable ensemble confinement free energy because of the loss of a substantial portion of the absolute backbone entropy. Proteins can couple this free-energy reservoir to distal binding events as a regulatory mechanism to promote or suppress binding.
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Affiliation(s)
- Justin A Drake
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, Texas
| | - B Montgomery Pettitt
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, Texas.
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20
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Krężel W, Rühl R, de Lera AR. Alternative retinoid X receptor (RXR) ligands. Mol Cell Endocrinol 2019; 491:110436. [PMID: 31026478 DOI: 10.1016/j.mce.2019.04.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/06/2019] [Accepted: 04/22/2019] [Indexed: 12/15/2022]
Abstract
Retinoid X receptors (RXRs) control a wide variety of functions by virtue of their dimerization with other nuclear hormone receptors (NRs), contributing thereby to activities of different signaling pathways. We review known RXR ligands as transcriptional modulators of specific RXR-dimers and the associated biological processes. We also discuss the physiological relevance of such ligands, which remains frequently a matter of debate and which at present is best met by member(s) of a novel family of retinoids, postulated as Vitamin A5. Through comparison with other natural, but also with synthetic ligands, we discuss high diversity in the modes of ligand binding to RXRs resulting in agonistic or antagonistic profiles and selectivity towards specific subtypes of permissive heterodimers. Despite such diversity, direct ligand binding to the ligand binding pocket resulting in agonistic activity was preferentially preserved in the course of animal evolution pointing to its functional relevance, and potential for existence of other, species-specific endogenous RXR ligands sharing the same mode of function.
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Affiliation(s)
- Wojciech Krężel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U 1258, Illkirch, France; Université de Strasbourg, Illkirch, France.
| | - Ralph Rühl
- Paprika Bioanalytics BT, Debrecen, Hungary
| | - Angel R de Lera
- Departamento de Química Orgánica, Facultade de Química, Lagoas-Marcosende, 36310, Vigo, Spain
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21
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Liu X, Sakai H, Nishigori M, Suyama K, Nawaji T, Ikeda S, Nishigouchi M, Okada H, Matsushima A, Nose T, Shimohigashi M, Shimohigashi Y. Receptor-binding affinities of bisphenol A and its next-generation analogs for human nuclear receptors. Toxicol Appl Pharmacol 2019; 377:114610. [PMID: 31195007 DOI: 10.1016/j.taap.2019.114610] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/26/2019] [Accepted: 06/03/2019] [Indexed: 12/12/2022]
Abstract
An endocrine-disrupting chemical Bisphenol A (BPA) binds specifically to a nuclear receptor (NR) named ERRγ. Although the importance of receptor-binding evaluation for human NRs is often stressed, the binding characteristics of so-called next-generation (NextGen) bisphenol compounds are still poorly understood. The ultimate objective of this investigation was to evaluate BPA and its NextGen analogs for their abilities to bind to 21 human NRs, the greatest members of NRs for which tritium-labeled specific ligands were available. After establishing the detailed assay conditions for each NR, the receptor binding affinities of total 11 bisphenols were evaluated in competitive binding assays. The results clearly revealed that BPA and the NextGen bisphenols of BPAF, BPAP, BPB, BPC, BPE, and BPZ were highly potent against one or more of NRs such as CAR, ERα, ERβ, ERRγ, and GR, with IC50 values of 3.3-73 nM. These bisphenols were suggested strongly to be disruptive to these NRs. BPM and BPP also appeared to be disruptive, but less potently. BPF exhibited only weak effects and only against estrogen-related NRs. Surprisingly, most doubtful bisphenol BPS was supposed not to be disruptive. The NRs to which BPA and NextGen bisphenols did not bind were RARα, RARβ, RARγ, and VDR. PPARγ, RORα, RORβ, RORγ, RXRα, RXRβ, and RXRγ, exhibited very weak interaction with these bisphenols. The ten remaining NRs, namely, ERRγ, ERβ, ERα, CAR, GR, PXR, PR, AR, LXRβ, and LXRα, showed distinctly strong binding to some bisphenols in this order, being likely to have consequential endocrine-disruption effects.
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Affiliation(s)
- Xiaohui Liu
- Laboratory of Structure-Function Biochemistry, Department of Chemistry, Faculty of Science, Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan; Risk Science Research Center, Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Hiroki Sakai
- Laboratory of Structure-Function Biochemistry, Department of Chemistry, Faculty of Science, Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Mitsuhiro Nishigori
- Laboratory of Structure-Function Biochemistry, Department of Chemistry, Faculty of Science, Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Keitaro Suyama
- Laboratory of Structure-Function Biochemistry, Department of Chemistry, Faculty of Science, Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Tasuku Nawaji
- Laboratory of Structure-Function Biochemistry, Department of Chemistry, Faculty of Science, Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Shin Ikeda
- Laboratory of Structure-Function Biochemistry, Department of Chemistry, Faculty of Science, Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Makoto Nishigouchi
- Laboratory of Structure-Function Biochemistry, Department of Chemistry, Faculty of Science, Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Hiroyuki Okada
- Laboratory of Structure-Function Biochemistry, Department of Chemistry, Faculty of Science, Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ayami Matsushima
- Laboratory of Structure-Function Biochemistry, Department of Chemistry, Faculty of Science, Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan; Risk Science Research Center, Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takeru Nose
- Laboratory of Structure-Function Biochemistry, Department of Chemistry, Faculty of Science, Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan; Risk Science Research Center, Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Miki Shimohigashi
- Division of Biology, Department of Earth System of Science, Faculty of Science, Fukuoka University, Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan; Risk Science Research Institute, Ikimatsudai 3-7-5, Nishi-ku, Fukuoka 819-0044, Japan
| | - Yasuyuki Shimohigashi
- Laboratory of Structure-Function Biochemistry, Department of Chemistry, Faculty of Science, Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan; Risk Science Research Center, Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan; Risk Science Research Institute, Ikimatsudai 3-7-5, Nishi-ku, Fukuoka 819-0044, Japan.
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22
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Meijer FA, Leijten-van de Gevel IA, de Vries RMJM, Brunsveld L. Allosteric small molecule modulators of nuclear receptors. Mol Cell Endocrinol 2019; 485:20-34. [PMID: 30703487 DOI: 10.1016/j.mce.2019.01.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/23/2019] [Accepted: 01/25/2019] [Indexed: 02/08/2023]
Abstract
Nuclear Receptors (NRs) are multi-domain proteins, whose natural regulation occurs via ligands for a classical, orthosteric, binding pocket and via intra- and inter-domain allosteric mechanisms. Allosteric modulation of NRs via synthetic small molecules has recently emerged as an interesting entry to address the need for small molecules targeting NRs in pathology, via novel modes of action and with beneficial profiles. In this review the general concept of allosteric modulation in drug discovery is first discussed, serving as a background and inspiration for NRs. Subsequently, the review focuses on examples of small molecules that allosterically modulate NRs, with a strong focus on structural information and the ligand binding domain. Recently discovered nanomolar potent allosteric site NR modulators are catapulting allosteric targeting of NRs to the center of attention. The obtained insights serve as a basis for recommendations for the next steps to take in allosteric small molecular targeting of NRs.
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Affiliation(s)
- Femke A Meijer
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Iris A Leijten-van de Gevel
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Rens M J M de Vries
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands.
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23
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Okafor CD, Colucci JK, Ortlund EA. Ligand-Induced Allosteric Effects Governing SR Signaling. NUCLEAR RECEPTOR RESEARCH 2019. [DOI: 10.32527/2019/101382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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24
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Li J, Hilser VJ. Assessing Allostery in Intrinsically Disordered Proteins With Ensemble Allosteric Model. Methods Enzymol 2018; 611:531-557. [PMID: 30471699 DOI: 10.1016/bs.mie.2018.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Intrinsically disordered (ID) proteins have been shown to play a major role in signaling in a broad range of proteins, using a process known as allostery, wherein the protein can integrate one or a number of inputs to regulate its function. The disorder-mediated allostery can be understood energetically with ensemble allosteric model (EAM). In this model, the molecule without effectors is considered as an ensemble of preexisting conformations, and effector binding is treated as an energetic perturbation of the ensemble to redistribute the microstates that are favorable or unfavorable to the second binding partner. As it only considers the intrinsic energetics of the system and does not depend on a crystallographic structure, it can be applied to both structured proteins, ID proteins, and mixed proteins with both structured and ID domains. Simulation with EAM on the basis of experimental data can help quantitatively explain experimental observations, as well as to make predictions to direct future research. This has recently been illustrated with the case of human glucocorticoid receptor, a multidomain transcription factor that contains both structured and disordered regions. In this chapter, we describe the assays for measuring the transcriptional activity, binding affinity to cognate DNA, conformational stability, either on single domain or tandem coupled domains in the GR two-domain isoforms. We then explain how these data are utilized as input parameters or constraints in the EAM for quantitative estimates of stabilities and coupling energies for each domain through global minimization method.
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Affiliation(s)
- Jing Li
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States
| | - Vincent J Hilser
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States; Department of Biology, Johns Hopkins University, Baltimore, MD, United States.
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25
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Hewitt SC, Korach KS. Estrogen Receptors: New Directions in the New Millennium. Endocr Rev 2018; 39:664-675. [PMID: 29901737 PMCID: PMC6173474 DOI: 10.1210/er.2018-00087] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/07/2018] [Indexed: 12/19/2022]
Abstract
Nineteen years have passed since our previous review in this journal in 1999 regarding estrogen receptors. At that time, we described the current assessments of the physiological activities of estrogen and estrogen receptors. Since that time there has been an explosion of progress in our understanding of details of estrogen receptor-mediated processes from the molecular and cellular level to the whole organism. In this review we discuss the basic understanding of estrogen signaling and then elaborate on the progress and current understanding of estrogen receptor actions that have developed using new models and continuing clinical studies.
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Affiliation(s)
- Sylvia C Hewitt
- Receptor Biology Section, Reproductive and Developmental Endocrinology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Kenneth S Korach
- Receptor Biology Section, Reproductive and Developmental Endocrinology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
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26
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White JT, Li J, Grasso E, Wrabl JO, Hilser VJ. Ensemble allosteric model: energetic frustration within the intrinsically disordered glucocorticoid receptor. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170175. [PMID: 29735729 PMCID: PMC5941170 DOI: 10.1098/rstb.2017.0175] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2018] [Indexed: 01/21/2023] Open
Abstract
Allostery is an important regulatory phenomenon enabling precise control of biological function. Initial understanding of allostery was gained from seminal work on conformational changes exhibited by structured proteins. Within the last decade, protein allostery has also been demonstrated to occur within intrinsically disordered proteins. This emerging concept of disorder-mediated allostery can be usefully understood in the context of a thermodynamic ensemble. The advantage of this ensemble allosteric model is that it unifies the explanations of allostery occurring within both structured and disordered proteins. One central finding from this model is that energetic coupling, the transmission of a signal between separate regions (or domains) of a protein, is maximized when one or more domains are disordered. This is due to a disorder-order transition that contributes additional coupling energy to the allosteric system through formation of a molecular interaction surface or interface. A second key finding is that multiple interfaces may constructively or destructively interfere with each other, resulting in a new form of allosteric regulation called 'energetic frustration'. Articulating protein allostery in terms of the thermodynamic ensemble permits formulation of experimentally testable hypotheses which can increase fundamental understanding and direct drug-design efforts. These ideas are illustrated here with the specific case of human glucocorticoid receptor, a medically important multi-domain allosteric protein that contains both structured and disordered regions and exemplifies 'energetic frustration'.This article is part of a discussion meeting issue 'Allostery and molecular machines'.
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Affiliation(s)
- Jordan T White
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Jing Li
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Emily Grasso
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - James O Wrabl
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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27
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Berlow RB, Dyson HJ, Wright PE. Expanding the Paradigm: Intrinsically Disordered Proteins and Allosteric Regulation. J Mol Biol 2018; 430:2309-2320. [PMID: 29634920 DOI: 10.1016/j.jmb.2018.04.003] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/23/2018] [Accepted: 04/03/2018] [Indexed: 11/30/2022]
Abstract
Allosteric regulatory processes are implicated at all levels of biological function. Recent advances in our understanding of the diverse and functionally significant class of intrinsically disordered proteins have identified a multitude of ways in which disordered proteins function within the confines of the allosteric paradigm. Allostery within or mediated by intrinsically disordered proteins ensures robust and efficient signal integration through mechanisms that would be extremely unfavorable or even impossible for globular protein interaction partners. Here, we highlight recent examples that indicate the breadth of biological outcomes that can be achieved through allosteric regulation by intrinsically disordered proteins. Ongoing and future work in this rapidly evolving area of research will expand our appreciation of the central role of intrinsically disordered proteins in ensuring the fidelity and efficiency of cellular regulation.
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Affiliation(s)
- Rebecca B Berlow
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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28
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Abstract
The nuclear receptor family of transcription factor proteins mediates endocrine function and plays critical roles in the development, physiology and pharmacology. Malfunctioning nuclear receptors are associated with several disease states. The functional activity of nuclear receptors is regulated by small molecular hormonal and synthetic molecules. Multiple sources of evidence have identified and distinguished between the different allosteric pathways initiated by ligands, DNA and cofactors such as co-activators and co-repressors. Also, these biophysical studies are attempting to determine how these pathways that regulate co-activator and DNA recognition can control gene transcription. Thus, there is a growing interest in determining the genome-scale impact of allostery in nuclear receptors. Today, it is accepted that a detailed understanding of the allosteric regulatory pathways within the nuclear receptor molecular complex will enable the development of efficient drug therapies in the long term.
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Affiliation(s)
- Elias J Fernandez
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, USA.
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29
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Regulation of Androgen Receptor Activity by Transient Interactions of Its Transactivation Domain with General Transcription Regulators. Structure 2017; 26:145-152.e3. [PMID: 29225078 DOI: 10.1016/j.str.2017.11.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/12/2017] [Accepted: 11/10/2017] [Indexed: 11/23/2022]
Abstract
The androgen receptor is a transcription factor that plays a key role in the development of prostate cancer, and its interactions with general transcription regulators are therefore of potential therapeutic interest. The mechanistic basis of these interactions is poorly understood due to the intrinsically disordered nature of the transactivation domain of the androgen receptor and the generally transient nature of the protein-protein interactions that trigger transcription. Here, we identify a motif of the transactivation domain that contributes to transcriptional activity by recruiting the C-terminal domain of subunit 1 of the general transcription regulator TFIIF. These findings provide molecular insights into the regulation of androgen receptor function and suggest strategies for treating castration-resistant prostate cancer.
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30
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Li J, White JT, Saavedra H, Wrabl JO, Motlagh HN, Liu K, Sowers J, Schroer TA, Thompson EB, Hilser VJ. Genetically tunable frustration controls allostery in an intrinsically disordered transcription factor. eLife 2017; 6:30688. [PMID: 29022880 PMCID: PMC5697930 DOI: 10.7554/elife.30688] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/11/2017] [Indexed: 01/08/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) present a functional paradox because they lack stable tertiary structure, but nonetheless play a central role in signaling, utilizing a process known as allostery. Historically, allostery in structured proteins has been interpreted in terms of propagated structural changes that are induced by effector binding. Thus, it is not clear how IDPs, lacking such well-defined structures, can allosterically affect function. Here, we show a mechanism by which an IDP can allosterically control function by simultaneously tuning transcriptional activation and repression, using a novel strategy that relies on the principle of ‘energetic frustration’. We demonstrate that human glucocorticoid receptor tunes this signaling in vivo by producing translational isoforms differing only in the length of the disordered region, which modulates the degree of frustration. We expect this frustration-based model of allostery will prove to be generally important in explaining signaling in other IDPs. Proteins carry out most of the key tasks inside cells. To perform these roles, proteins must fold up to form complex three-dimensional structures. Researchers used to think that the useful parts of proteins all had set structures. However, we now know that ‘disordered’ proteins with variable structures are common and disordered parts of proteins can have vital roles. In a process called allosteric regulation, regulator molecules can increase or decrease the activity of a protein by binding to it. This binding was thought to work by changing the structure of the protein, but it was not clear how this works in disordered proteins. To investigate, Li et al. studied a disordered protein called glucocorticoid receptor, and found that disordered regions can have opposing effects on other regions of the protein. This creates a ‘tug-of-war’ that Li et al. term “energetic frustration”, whereby the activity of the protein results from the combination of the opposing interactions. Further investigation revealed that the glucorticoid receptor produces different versions of itself that have different degrees of energetic frustration, which alters how effectively the proteins perform their tasks. This means that the protein can regulate its own activity even in the absence of binding to regulator molecules. The concept of energetic frustration could enhance our understanding of the many different proteins that contain disordered regions. Eventually, this knowledge could be used to develop drugs that alter the activity of these proteins and so could form part of treatments for a wide range of conditions including autoimmune diseases (such as rheumatoid arthritis and lupus), cancers, and organ rejection for transplant patients. The results presented by Li et al. suggest where more research is needed to achieve this goal. For example, we need to understand more about the stability of disordered protein regions, and to identify which surfaces of the proteins interact with each other.
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Affiliation(s)
- Jing Li
- Department of Biology, Johns Hopkins University, Baltimore, United States.,TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Jordan T White
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - Harry Saavedra
- Department of Biology, Johns Hopkins University, Baltimore, United States.,TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - James O Wrabl
- Department of Biology, Johns Hopkins University, Baltimore, United States.,TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Hesam N Motlagh
- Department of Biology, Johns Hopkins University, Baltimore, United States.,TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Kaixian Liu
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - James Sowers
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - Trina A Schroer
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - E Brad Thompson
- Department of Biology, Johns Hopkins University, Baltimore, United States.,Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, United States
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, Baltimore, United States.,TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
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31
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Fernandez EJ, Gahlot V, Rodriguez C, Amburn J. DNA-induced unfolding of the thyroid hormone receptor α A/B domain through allostery. FEBS Open Bio 2017; 7:854-864. [PMID: 28593140 PMCID: PMC5458466 DOI: 10.1002/2211-5463.12229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 01/22/2023] Open
Affiliation(s)
- Elias J. Fernandez
- Biochemistry & Cellular and Molecular Biology; University of Tennessee; Knoxville TN USA
| | - Vandna Gahlot
- Biochemistry & Cellular and Molecular Biology; University of Tennessee; Knoxville TN USA
| | - Celeste Rodriguez
- Biochemistry & Cellular and Molecular Biology; University of Tennessee; Knoxville TN USA
| | - Jacob Amburn
- Biochemistry & Cellular and Molecular Biology; University of Tennessee; Knoxville TN USA
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32
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Russo A, Manna SL, Novellino E, Malfitano AM, Marasco D. Molecular signaling involving intrinsically disordered proteins in prostate cancer. Asian J Androl 2017; 18:673-81. [PMID: 27212129 PMCID: PMC5000787 DOI: 10.4103/1008-682x.181817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Investigations on cellular protein interaction networks (PINs) reveal that proteins that constitute hubs in a PIN are notably enriched in Intrinsically Disordered Proteins (IDPs) compared to proteins that constitute edges, highlighting the role of IDPs in signaling pathways. Most IDPs rapidly undergo disorder-to-order transitions upon binding to their biological targets to perform their function. Conformational dynamics enables IDPs to be versatile and to interact with a broad range of interactors under normal physiological conditions where their expression is tightly modulated. IDPs are involved in many cellular processes such as cellular signaling, transcriptional regulation, and splicing; thus, their high-specificity/low-affinity interactions play crucial roles in many human diseases including cancer. Prostate cancer (PCa) is one of the leading causes of cancer-related mortality in men worldwide. Therefore, identifying molecular mechanisms of the oncogenic signaling pathways that are involved in prostate carcinogenesis is crucial. In this review, we focus on the aspects of cellular pathways leading to PCa in which IDPs exert a primary role.
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Affiliation(s)
- Anna Russo
- Department of Pharmacy, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134 Naples, Italy
| | - Sara La Manna
- Department of Pharmacy, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134 Naples, Italy
| | - Ettore Novellino
- Department of Pharmacy, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134 Naples, Italy
| | - Anna Maria Malfitano
- Department of Pharmacy, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134 Naples, Italy
| | - Daniela Marasco
- Department of Pharmacy, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134 Naples, Italy
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33
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Shammas SL. Mechanistic roles of protein disorder within transcription. Curr Opin Struct Biol 2017; 42:155-161. [PMID: 28262589 DOI: 10.1016/j.sbi.2017.02.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/26/2017] [Accepted: 02/13/2017] [Indexed: 12/28/2022]
Abstract
Understanding the interactions of proteins involved in transcriptional regulation is critical to describing biological systems because they control the expression profile of the cell. Yet sadly they belong to a less well biophysically characterized subset of proteins; they frequently contain long disordered regions that are highly dynamic. A key question therefore is, why? What functional roles does protein disorder play in transcriptional regulation? Experimental data exemplifying these roles are starting to emerge, with common themes being enabling complexity within networks and quick responses. Most recently a role for disorder in mediating phase transitions of membrane-less organelles has been proposed.
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Affiliation(s)
- Sarah L Shammas
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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34
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Kim HJ, Nam HG, Lim PO. Regulatory network of NAC transcription factors in leaf senescence. CURRENT OPINION IN PLANT BIOLOGY 2016; 33:48-56. [PMID: 27314623 DOI: 10.1016/j.pbi.2016.06.002] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/30/2016] [Accepted: 06/01/2016] [Indexed: 05/18/2023]
Abstract
Leaf senescence is finely tuned by many regulatory factors such as NAC (NAM/ATAF/CUC) transcription factors (TFs). NACs comprise one of the largest families of TFs in plants, many of which are differentially regulated during leaf senescence and play a major role in leaf senescence. Recent studies advanced our understanding on the structural and functional features of NAC TFs including target binding specificities of the N-terminal DNA binding domain and dynamic interaction of the C-terminal intrinsically disordered domain with other proteins. NAC TFs control other NACs and also interact with NACs or other TFs to fine-tune the expression of target genes. These studies clearly demonstrated the highly complex characteristics of NAC regulatory networks, which are dynamically regulated temporally and spatially and effectively integrate multiple developmental and environmental signals.
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Affiliation(s)
- Hyo Jung Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu 711-873, Republic of Korea
| | - Hong Gil Nam
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu 711-873, Republic of Korea; Department of New Biology, DGIST, Daegu 711-873, Republic of Korea.
| | - Pyung Ok Lim
- Department of New Biology, DGIST, Daegu 711-873, Republic of Korea.
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35
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Belorusova A, Osz J, Petoukhov MV, Peluso-Iltis C, Kieffer B, Svergun DI, Rochel N. Solution Behavior of the Intrinsically Disordered N-Terminal Domain of Retinoid X Receptor α in the Context of the Full-Length Protein. Biochemistry 2016; 55:1741-1748. [PMID: 26937780 DOI: 10.1021/acs.biochem.5b01122] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Retinoid X receptors (RXRs) are transcription factors with important functions in embryonic development, metabolic processes, differentiation, and apoptosis. A particular feature of RXRs is their ability to act as obligatory heterodimerization partners of class II nuclear receptors. At the same time, these receptors are also able to form homodimers that bind to direct repeat separated by one nucleotide hormone response elements. Since the discovery of RXRs, most of the studies focused on its ligand binding and DNA binding domains, while its N-terminal domain (NTD) harboring a ligand-independent activation function remained poorly characterized. Here, we investigated the solution properties of the NTD of RXRα alone and in the context of the full-length receptor using small-angle X-ray scattering and nuclear magnetic resonance spectroscopy. We report the solution structure of the full-length homodimeric RXRα on DNA and show that the NTD remains highly flexible within this complex.
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Affiliation(s)
- Anna Belorusova
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964 / Centre National de la Recherche Scientifique (CNRS) UMR 7104 / Université de Strasbourg, 67404 Illkirch, France
| | - Judit Osz
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964 / Centre National de la Recherche Scientifique (CNRS) UMR 7104 / Université de Strasbourg, 67404 Illkirch, France
| | - Maxim V Petoukhov
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany
| | - Carole Peluso-Iltis
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964 / Centre National de la Recherche Scientifique (CNRS) UMR 7104 / Université de Strasbourg, 67404 Illkirch, France
| | - Bruno Kieffer
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964 / Centre National de la Recherche Scientifique (CNRS) UMR 7104 / Université de Strasbourg, 67404 Illkirch, France
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany
| | - Natacha Rochel
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964 / Centre National de la Recherche Scientifique (CNRS) UMR 7104 / Université de Strasbourg, 67404 Illkirch, France
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36
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Abstract
Estrogen receptor alpha (ERα) is a critical player in development and function of the female reproductive system. Perturbations in ERα response can affect wide-ranging aspects of health in humans as well as in livestock and wildlife. Because of its long-known and broad impact, ERα mechanisms of action continue to be the focus on cutting-edge research efforts. Consequently, novel insights have greatly advanced understanding of every aspect of estrogen signaling. In this review, we attempt to briefly outline the current understanding of ERα mediated mechanisms in the context of the female reproductive system.
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Affiliation(s)
- Sylvia C Hewitt
- Receptor Biology GroupReproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USASchool of Molecular BiosciencesCollege of Veterinary Medicine, Washington State University, Pullman, Washington 99164, USA
| | - Wipawee Winuthayanon
- Receptor Biology GroupReproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USASchool of Molecular BiosciencesCollege of Veterinary Medicine, Washington State University, Pullman, Washington 99164, USA
| | - Kenneth S Korach
- Receptor Biology GroupReproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USASchool of Molecular BiosciencesCollege of Veterinary Medicine, Washington State University, Pullman, Washington 99164, USA
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37
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Yesudhas D, Anwar MA, Panneerselvam S, Durai P, Shah M, Choi S. Structural Mechanism behind Distinct Efficiency of Oct4/Sox2 Proteins in Differentially Spaced DNA Complexes. PLoS One 2016; 11:e0147240. [PMID: 26790000 PMCID: PMC4720428 DOI: 10.1371/journal.pone.0147240] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/30/2015] [Indexed: 01/17/2023] Open
Abstract
The octamer-binding transcription factor 4 (Oct4) and sex-determining region Y (SRY)-box 2 (Sox2) proteins induce various transcriptional regulators to maintain cellular pluripotency. Most Oct4/Sox2 complexes have either 0 base pairs (Oct4/Sox20bp) or 3 base pairs (Oct4/Sox23bp) separation between their DNA-binding sites. Results from previous biochemical studies have shown that the complexes separated by 0 base pairs are associated with a higher pluripotency rate than those separated by 3 base pairs. Here, we performed molecular dynamics (MD) simulations and calculations to determine the binding free energy and per-residue free energy for the Oct4/Sox20bp and Oct4/Sox23bp complexes to identify structural differences that contribute to differences in induction rate. Our MD simulation results showed substantial differences in Oct4/Sox2 domain movements, as well as secondary-structure changes in the Oct4 linker region, suggesting a potential reason underlying the distinct efficiencies of these complexes during reprogramming. Moreover, we identified key residues and hydrogen bonds that potentially facilitate protein-protein and protein-DNA interactions, in agreement with previous experimental findings. Consequently, our results confess that differential spacing of the Oct4/Sox2 DNA binding sites can determine the magnitude of transcription of the targeted genes during reprogramming.
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Affiliation(s)
- Dhanusha Yesudhas
- Department of Molecular Science and Technology, Ajou University, Suwon, 443–749, Korea
| | - Muhammad Ayaz Anwar
- Department of Molecular Science and Technology, Ajou University, Suwon, 443–749, Korea
| | - Suresh Panneerselvam
- Department of Molecular Science and Technology, Ajou University, Suwon, 443–749, Korea
| | | | - Masaud Shah
- Department of Molecular Science and Technology, Ajou University, Suwon, 443–749, Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, 443–749, Korea
- * E-mail:
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38
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Narayan V, Landré V, Ning J, Hernychova L, Muller P, Verma C, Walkinshaw MD, Blackburn EA, Ball KL. Protein-Protein Interactions Modulate the Docking-Dependent E3-Ubiquitin Ligase Activity of Carboxy-Terminus of Hsc70-Interacting Protein (CHIP). Mol Cell Proteomics 2015; 14:2973-87. [PMID: 26330542 PMCID: PMC4638040 DOI: 10.1074/mcp.m115.051169] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Indexed: 11/07/2022] Open
Abstract
CHIP is a tetratricopeptide repeat (TPR) domain protein that functions as an E3-ubiquitin ligase. As well as linking the molecular chaperones to the ubiquitin proteasome system, CHIP also has a docking-dependent mode where it ubiquitinates native substrates, thereby regulating their steady state levels and/or function. Here we explore the effect of Hsp70 on the docking-dependent E3-ligase activity of CHIP. The TPR-domain is revealed as a binding site for allosteric modulators involved in determining CHIP's dynamic conformation and activity. Biochemical, biophysical and modeling evidence demonstrate that Hsp70-binding to the TPR, or Hsp70-mimetic mutations, regulate CHIP-mediated ubiquitination of p53 and IRF-1 through effects on U-box activity and substrate binding. HDX-MS was used to establish that conformational-inhibition-signals extended from the TPR-domain to the U-box. This underscores inter-domain allosteric regulation of CHIP by the core molecular chaperones. Defining the chaperone-associated TPR-domain of CHIP as a manager of inter-domain communication highlights the potential for scaffolding modules to regulate, as well as assemble, complexes that are fundamental to protein homeostatic control.
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Affiliation(s)
- Vikram Narayan
- From the ‡IGMM, University of Edinburgh Cancer Research Centre, Cell Signalling Unit, Crewe Road South, Edinburgh EH4 2XR, UK
| | - Vivien Landré
- From the ‡IGMM, University of Edinburgh Cancer Research Centre, Cell Signalling Unit, Crewe Road South, Edinburgh EH4 2XR, UK
| | - Jia Ning
- From the ‡IGMM, University of Edinburgh Cancer Research Centre, Cell Signalling Unit, Crewe Road South, Edinburgh EH4 2XR, UK; §CTCB, Institute of Structural and Molecular Biology, University of Edinburgh, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Lenka Hernychova
- ¶Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Petr Muller
- ¶Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Chandra Verma
- ‖Bioinformatics Institute (A*STAR), 30 Biopolis Street, 07-01 Matrix, Singapore 138671; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543; School of Biological Sciences, Nanyang Technological University, 60 Nayang Drive, Singapore 637551
| | - Malcolm D Walkinshaw
- §CTCB, Institute of Structural and Molecular Biology, University of Edinburgh, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Elizabeth A Blackburn
- §CTCB, Institute of Structural and Molecular Biology, University of Edinburgh, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Kathryn L Ball
- From the ‡IGMM, University of Edinburgh Cancer Research Centre, Cell Signalling Unit, Crewe Road South, Edinburgh EH4 2XR, UK;
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39
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Townsend PD, Rodgers TL, Glover LC, Korhonen HJ, Richards SA, Colwell LJ, Pohl E, Wilson MR, Hodgson DRW, McLeish TCB, Cann MJ. The Role of Protein-Ligand Contacts in Allosteric Regulation of the Escherichia coli Catabolite Activator Protein. J Biol Chem 2015; 290:22225-35. [PMID: 26187469 PMCID: PMC4571973 DOI: 10.1074/jbc.m115.669267] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Indexed: 12/20/2022] Open
Abstract
Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distant site. Both experimental and theoretical evidence demonstrate that allostery can be communicated through altered slow relaxation protein dynamics without conformational change. The catabolite activator protein (CAP) of Escherichia coli is an exemplar for the analysis of such entropically driven allostery. Negative allostery in CAP occurs between identical cAMP binding sites. Changes to the cAMP-binding pocket can therefore impact the allosteric properties of CAP. Here we demonstrate, through a combination of coarse-grained modeling, isothermal calorimetry, and structural analysis, that decreasing the affinity of CAP for cAMP enhances negative cooperativity through an entropic penalty for ligand binding. The use of variant cAMP ligands indicates the data are not explained by structural heterogeneity between protein mutants. We observe computationally that altered interaction strength between CAP and cAMP variously modifies the change in allosteric cooperativity due to second site CAP mutations. As the degree of correlated motion between the cAMP-contacting site and a second site on CAP increases, there is a tendency for computed double mutations at these sites to drive CAP toward noncooperativity. Naturally occurring pairs of covarying residues in CAP do not display this tendency, suggesting a selection pressure to fine tune allostery on changes to the CAP ligand-binding pocket without a drive to a noncooperative state. In general, we hypothesize an evolutionary selection pressure to retain slow relaxation dynamics-induced allostery in proteins in which evolution of the ligand-binding site is occurring.
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Affiliation(s)
- Philip D Townsend
- From the School of Biological and Biomedical Sciences, the Biophysical Sciences Institute, and
| | - Thomas L Rodgers
- the School of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Laura C Glover
- From the School of Biological and Biomedical Sciences, the Biophysical Sciences Institute, and the Departments of Chemistry and
| | - Heidi J Korhonen
- the Biophysical Sciences Institute, and the Departments of Chemistry and the Department of Chemistry, University of Turku, 20014 Turku, Finland, and
| | | | - Lucy J Colwell
- the Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Ehmke Pohl
- From the School of Biological and Biomedical Sciences, the Biophysical Sciences Institute, and the Departments of Chemistry and
| | - Mark R Wilson
- the Biophysical Sciences Institute, and the Departments of Chemistry and
| | - David R W Hodgson
- the Biophysical Sciences Institute, and the Departments of Chemistry and
| | - Tom C B McLeish
- the Biophysical Sciences Institute, and the Departments of Chemistry and Physics, Durham University, Durham DH1 3LE, United Kingdom
| | - Martin J Cann
- From the School of Biological and Biomedical Sciences, the Biophysical Sciences Institute, and
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40
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Berlow RB, Dyson HJ, Wright PE. Functional advantages of dynamic protein disorder. FEBS Lett 2015; 589:2433-40. [PMID: 26073260 DOI: 10.1016/j.febslet.2015.06.003] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 05/29/2015] [Accepted: 06/01/2015] [Indexed: 11/19/2022]
Abstract
Intrinsically disordered proteins participate in many important cellular regulatory processes. The absence of a well-defined structure in the free state of a disordered domain, and even on occasion when it is bound to physiological partners, is fundamental to its function. Disordered domains are frequently the location of multiple sites for post-translational modification, the key element of metabolic control in the cell. When a disordered domain folds upon binding to a partner, the resulting complex buries a far greater surface area than in an interaction of comparably-sized folded proteins, thus maximizing specificity at modest protein size. Disorder also maintains accessibility of sites for post-translational modification. Because of their inherent plasticity, disordered domains frequently adopt entirely different structures when bound to different partners, increasing the repertoire of available interactions without the necessity for expression of many different proteins. This feature also adds to the faithfulness of cellular regulation, as the availability of a given disordered domain depends on competition between various partners relevant to different cellular processes.
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Affiliation(s)
- Rebecca B Berlow
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Latysheva NS, Flock T, Weatheritt RJ, Chavali S, Babu MM. How do disordered regions achieve comparable functions to structured domains? Protein Sci 2015; 24:909-22. [PMID: 25752799 PMCID: PMC4456105 DOI: 10.1002/pro.2674] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 02/25/2015] [Accepted: 03/03/2015] [Indexed: 12/19/2022]
Abstract
The traditional structure to function paradigm conceives of a protein's function as emerging from its structure. In recent years, it has been established that unstructured, intrinsically disordered regions (IDRs) in proteins are equally crucial elements for protein function, regulation and homeostasis. In this review, we provide a brief overview of how IDRs can perform similar functions to structured proteins, focusing especially on the formation of protein complexes and assemblies and the mediation of regulated conformational changes. In addition to highlighting instances of such functional equivalence, we explain how differences in the biological and physicochemical properties of IDRs allow them to expand the functional and regulatory repertoire of proteins. We also discuss studies that provide insights into how mutations within functional regions of IDRs can lead to human diseases.
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Affiliation(s)
| | - Tilman Flock
- MRC Laboratory of Molecular BiologyCambridge, CB2 0QH, United Kingdom
| | | | - Sreenivas Chavali
- MRC Laboratory of Molecular BiologyCambridge, CB2 0QH, United Kingdom
| | - M Madan Babu
- MRC Laboratory of Molecular BiologyCambridge, CB2 0QH, United Kingdom
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Rajbhandari P, Ozers MS, Solodin NM, Warren CL, Alarid ET. Peptidylprolyl Isomerase Pin1 Directly Enhances the DNA Binding Functions of Estrogen Receptor α. J Biol Chem 2015; 290:13749-62. [PMID: 25866209 DOI: 10.1074/jbc.m114.621698] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Indexed: 12/26/2022] Open
Abstract
The transcriptional activity of estrogen receptor α (ERα), the key driver of breast cancer proliferation, is enhanced by multiple cellular interactions, including phosphorylation-dependent interaction with Pin1, a proline isomerase, which mediates cis-trans isomerization of the N-terminal Ser(P)(118)-Pro(119) in the intrinsically disordered AF1 (activation function 1) domain of ERα. Because both ERα and Pin1 have multiple cellular partners, it is unclear how Pin1 assists in the regulation of ERα transactivation mechanisms and whether the functional effects of Pin1 on ERα signaling are direct or indirect. Here, we tested the specific action of Pin1 on an essential step in ERα transactivation, binding to specific DNA sites. DNA binding analysis demonstrates that stable overexpression of Pin1 increases endogenous ERα DNA binding activity when activated by estrogen but not by tamoxifen or EGF. Increased DNA binding affinity is a direct effect of Pin1 on ERα because it is observed in solution-based assays with purified components. Further, our data indicate that isomerization is required for Pin1-modulation of ERα-DNA interactions. In an unbiased in vitro DNA binding microarray with hundreds of thousands of permutations of ERα-binding elements, Pin1 selectively enhances the binding affinity of ERα to consensus DNA elements. These studies reveal that Pin1 isomerization of phosphorylated ERα can directly regulate the function of the adjacent DNA binding domain, and this interaction is further modulated by ligand binding in the ligand-binding domain, providing evidence for Pin1-dependent allosteric regulation of ERα function.
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Affiliation(s)
- Prashant Rajbhandari
- From the McArdle Laboratories for Cancer Research, Department of Oncology and University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin, Madison, Wisconsin 53705 and
| | - Mary Szatkowski Ozers
- From the McArdle Laboratories for Cancer Research, Department of Oncology and University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin, Madison, Wisconsin 53705 and
| | - Natalia M Solodin
- From the McArdle Laboratories for Cancer Research, Department of Oncology and University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin, Madison, Wisconsin 53705 and
| | | | - Elaine T Alarid
- From the McArdle Laboratories for Cancer Research, Department of Oncology and University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin, Madison, Wisconsin 53705 and
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Protein intrinsic disorder in Arabidopsis NAC transcription factors: transcriptional activation by ANAC013 and ANAC046 and their interactions with RCD1. Biochem J 2015; 465:281-94. [DOI: 10.1042/bj20141045] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The regulatory domains of NAC [no apical meristem, ATAF (Arabidopsis transcription activation factor), cup-shaped cotyledon] transcription factors (TFs) are mostly disordered. The single molecular recognition feature (MoRF) in ANAC046 (Arabidopsis NAC domain containing protein 46) is a functional hot spot mediating interactions with RCD1 (radical-induced cell death 1), a stress-associated hub which exploits disorder and different mechanisms for interactions.
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Zhang L, Davies LJ, Elling AA. A Meloidogyne incognita effector is imported into the nucleus and exhibits transcriptional activation activity in planta. MOLECULAR PLANT PATHOLOGY 2015; 16:48-60. [PMID: 24863562 PMCID: PMC6638493 DOI: 10.1111/mpp.12160] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Root-knot nematodes are sedentary biotrophic endoparasites that maintain a complex interaction with their host plants. Nematode effector proteins are synthesized in the oesophageal glands of nematodes and secreted into plant tissue through a needle-like stylet. Effectors characterized to date have been shown to mediate processes essential for nematode pathogenesis. To gain an insight into their site of action and putative function, the subcellular localization of 13 previously isolated Meloidogyne incognita effectors was determined. Translational fusions were created between effectors and EGFP-GUS (enhanced green fluorescent protein-β-glucuronidase) reporter genes, which were transiently expressed in tobacco leaf cells. The majority of effectors localized to the cytoplasm, with one effector, 7H08, imported into the nuclei of plant cells. Deletion analysis revealed that the nuclear localization of 7H08 was mediated by two novel independent nuclear localization domains. As a result of the nuclear localization of the effector, 7H08 was tested for the ability to activate gene transcription. 7H08 was found to activate the expression of reporter genes in both yeast and plant systems. This is the first report of a plant-parasitic nematode effector with transcriptional activation activity.
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Affiliation(s)
- Lei Zhang
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
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Fattori J, Campos JLO, Doratioto TR, Assis LM, Vitorino MT, Polikarpov I, Xavier-Neto J, Figueira ACM. RXR agonist modulates TR: corepressor dissociation upon 9-cis retinoic acid treatment. Mol Endocrinol 2014; 29:258-73. [PMID: 25541638 DOI: 10.1210/me.2014-1251] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Transcriptional regulation controlled by thyroid hormone receptor (TR) drives events such as development, differentiation, and metabolism. TRs may act either as homodimers or as heterodimers with retinoid X receptor (RXR). Thyroid hormone T3 preferentially binds TR-RXR heterodimers, which activate transcription through coactivator recruitment. However, it is unclear whether TR-RXR heterodimers may also be responsive to the canonical RXR agonist 9-cis retinoic acid (9C) in the context of physiological gene regulation. New structural studies suggest that 9C promotes the displacement of bound coactivators from the heterodimer, modifying TR-RXR activity. To shed light on the molecular mechanisms that control TR-RXR function, we used biophysical approaches to characterize coregulator recruitment to TR-TR or to TR-RXR in the presence of T3 and/or 9C as well as cell-based assays to establish the functional significance of biophysical findings. Using cell-based and fluorescence assays with mutant and wild-type TR, we show that 9C does indeed have a function in the TR-RXR heterodimer context, in which it induces the release of corepressors. Furthermore, we show that 9C does not promote detectable conformational changes in the structure of the TR-RXR heterodimer and does not affect coactivator recruitment. Finally, our data support the view that DNA binding domain and Hinge regions are important to set up NR-coactivator binding interfaces. In summary, we showed that the RXR agonist 9C can regulate TR function through its modulation of corepressor dissociation.
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Affiliation(s)
- Juliana Fattori
- Centro Nacional de Pesquisa em Energia e Materiais (J.F., J.L.O.C., T.R.D., L.M.A., M.T.V., J.X.-N., A.C.M.F.), Laboratório Nacional de Biociências, Campinas SP, 13083-970, Brazil; and Instituto de Física de São Carlos (I.P.), Universidade de São Paulo, São Carlos SP, 13560-970, Brazil
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Dunker AK, Bondos SE, Huang F, Oldfield CJ. Intrinsically disordered proteins and multicellular organisms. Semin Cell Dev Biol 2014; 37:44-55. [PMID: 25307499 DOI: 10.1016/j.semcdb.2014.09.025] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 09/15/2014] [Accepted: 09/30/2014] [Indexed: 12/12/2022]
Abstract
Intrinsically disordered proteins (IDPs) and IDP regions lack stable tertiary structure yet carry out numerous biological functions, especially those associated with signaling, transcription regulation, DNA condensation, cell division, and cellular differentiation. Both post-translational modifications (PTMs) and alternative splicing (AS) expand the functional repertoire of IDPs. Here we propose that an "IDP-based developmental toolkit," which is comprised of IDP regions, PTMs, especially multiple PTMs, within these IDP regions, and AS events within segments of pre-mRNA that code for these same IDP regions, allows functional diversification and environmental responsiveness for molecules that direct the development of complex metazoans.
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Affiliation(s)
- A Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, United States.
| | - Sarah E Bondos
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, United States.
| | - Fei Huang
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, United States.
| | - Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, United States.
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Firestone GL, Kapadia BJ. Minireview: Steroid/nuclear receptor-regulated dynamics of occluding and anchoring junctions. Mol Endocrinol 2014; 28:1769-84. [PMID: 25203673 DOI: 10.1210/me.2014-1037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A diverse set of physiological signals control intercellular interactions by regulating the structure and function of occluding junctions (tight junctions) and anchoring junctions (adherens junctions and desmosomes). These plasma membrane junctions are comprised of multiprotein complexes of transmembrane and cytoplasmic peripheral plasma membrane proteins. Evidence from many hormone-responsive tissues has shown that expression, modification, molecular interactions, stability, and localization of junctional complex-associated proteins can be targeted by nuclear hormone receptors and their ligands through transcriptional and nontranscriptional mechanisms. The focus of this minireview is to discuss molecular, cellular, and physiological studies that directly link nuclear receptor- and ligand-triggered signaling pathways to the regulation of occluding and anchoring junction dynamics.
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Affiliation(s)
- Gary L Firestone
- Department of Molecular and Cell Biology and The Cancer Research Laboratory, University of California at Berkeley, Berkeley, California 94720-3200
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Arroyo V, García-Martinez R, Salvatella X. Human serum albumin, systemic inflammation, and cirrhosis. J Hepatol 2014; 61:396-407. [PMID: 24751830 DOI: 10.1016/j.jhep.2014.04.012] [Citation(s) in RCA: 353] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/04/2014] [Accepted: 04/06/2014] [Indexed: 12/16/2022]
Abstract
Human serum albumin (HSA) is one of the most frequent treatments in patients with decompensated cirrhosis. Prevention of paracentesis-induced circulatory dysfunction, prevention of type-1 HRS associated with bacterial infections, and treatment of type-1 hepatorenal syndrome are the main indications. In these indications treatment with HSA is associated with improvement in survival. Albumin is a stable and very flexible molecule with a heart shape, 585 residues, and three domains of similar size, each one containing two sub-domains. Many of the physiological functions of HSA rely on its ability to bind an extremely wide range of endogenous and exogenous ligands, to increase their solubility in plasma, to transport them to specific tissues and organs, or to dispose of them when they are toxic. The chemical structure of albumin can be altered by some specific processes (oxidation, glycation) leading to rapid clearance and catabolism. An outstanding feature of HSA is its capacity to bind lipopolysaccharide and other bacterial products (lipoteichoic acid and peptidoglycan), reactive oxygen species, nitric oxide and other nitrogen reactive species, and prostaglandins. Binding to NO and prostaglandins are reversible, so they can be transferred to other molecules at different sites from their synthesis. Through these functions, HSA modulates the inflammatory reaction. Decompensated cirrhosis is a disease associated systemic inflammation, which plays an important role in the pathogenesis of organ or system dysfunction/failure. Although, the beneficial effects of HAS have been traditionally attributed to plasma volume expansion, they could also relate to its effects modulating systemic and organ inflammation.
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Affiliation(s)
- Vicente Arroyo
- Liver Unit, Hospital Clinic, Centre Esther Koplowitz, IDIBAPS, University of Barcelona, Barcelona, Spain; EASL-Cronic Liver Failure Consortium, Fundació Clinic, Barcelona, Spain.
| | | | - Xavier Salvatella
- ICREA and BSC-CRG-IRB Research Programme in Computational Biology, IRB Barcelona (IRB), Barcelona, Spain
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Influence of domain interactions on conformational mobility of the progesterone receptor detected by hydrogen/deuterium exchange mass spectrometry. Structure 2014; 22:961-73. [PMID: 24909783 DOI: 10.1016/j.str.2014.04.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 03/31/2014] [Accepted: 04/22/2014] [Indexed: 11/22/2022]
Abstract
Structural and functional details of the N-terminal activation function 1 (AF1) of most nuclear receptors are poorly understood due to the highly dynamic intrinsically disordered nature of this domain. A hydrogen/deuterium exchange (HDX) mass-spectrometry-based investigation of TATA box-binding protein (TBP) interaction with various domains of progesterone receptor (PR) demonstrate that agonist-bound PR interaction with TBP via AF1 impacts the mobility of the C-terminal AF2. Results from HDX and other biophysical studies involving agonist- and antagonist-bound full-length PR and isolated PR domains reveal the molecular mechanism underlying synergistic transcriptional activation mediated by AF1 and AF2, dominance of PR-B isoform over PR-A, and the necessity of AF2 for full AF1-mediated transcriptional activity. These results provide a comprehensive picture elaborating the underlying mechanism of PR-TBP interactions as a model for studying nuclear receptor (NR)-transcription factor functional interactions.
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Protective epitopes of the Plasmodium falciparum SERA5 malaria vaccine reside in intrinsically unstructured N-terminal repetitive sequences. PLoS One 2014; 9:e98460. [PMID: 24886718 PMCID: PMC4041889 DOI: 10.1371/journal.pone.0098460] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 05/04/2014] [Indexed: 01/27/2023] Open
Abstract
The malaria vaccine candidate antigen, SE36, is based on the N-terminal 47 kDa domain of Plasmodium falciparum serine repeat antigen 5 (SERA5). In epidemiological studies, we have previously shown the inhibitory effects of SE36 specific antibodies on in vitro parasite growth and the negative correlation between antibody level and malaria symptoms. A phase 1 b trial of the BK-SE36 vaccine in Uganda elicited 72% protective efficacy against symptomatic malaria in children aged 6–20 years during the follow-up period 130–365 days post–second vaccination. Here, we performed epitope mapping with synthetic peptides covering the whole sequence of SE36 to identify and map dominant epitopes in Ugandan adult serum presumed to have clinical immunity to P. falciparum malaria. High titer sera from the Ugandan adults predominantly reacted with peptides corresponding to two successive N-terminal regions of SERA5 containing octamer repeats and serine rich sequences, regions of SERA5 that were previously reported to have limited polymorphism. Affinity purified antibodies specifically recognizing the octamer repeats and serine rich sequences exhibited a high antibody-dependent cellular inhibition (ADCI) activity that inhibited parasite growth. Furthermore, protein structure predictions and structural analysis of SE36 using spectroscopic methods indicated that N-terminal regions possessing inhibitory epitopes are intrinsically unstructured. Collectively, these results suggest that strict tertiary structure of SE36 epitopes is not required to elicit protective antibodies in naturally immune Ugandan adults.
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