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Maiti S, Singh A, Maji T, Saibo NV, De S. Experimental methods to study the structure and dynamics of intrinsically disordered regions in proteins. Curr Res Struct Biol 2024; 7:100138. [PMID: 38707546 PMCID: PMC11068507 DOI: 10.1016/j.crstbi.2024.100138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 05/07/2024] Open
Abstract
Eukaryotic proteins often feature long stretches of amino acids that lack a well-defined three-dimensional structure and are referred to as intrinsically disordered proteins (IDPs) or regions (IDRs). Although these proteins challenge conventional structure-function paradigms, they play vital roles in cellular processes. Recent progress in experimental techniques, such as NMR spectroscopy, single molecule FRET, high speed AFM and SAXS, have provided valuable insights into the biophysical basis of IDP function. This review discusses the advancements made in these techniques particularly for the study of disordered regions in proteins. In NMR spectroscopy new strategies such as 13C detection, non-uniform sampling, segmental isotope labeling, and rapid data acquisition methods address the challenges posed by spectral overcrowding and low stability of IDPs. The importance of various NMR parameters, including chemical shifts, hydrogen exchange rates, and relaxation measurements, to reveal transient secondary structures within IDRs and IDPs are presented. Given the high flexibility of IDPs, the review outlines NMR methods for assessing their dynamics at both fast (ps-ns) and slow (μs-ms) timescales. IDPs exert their functions through interactions with other molecules such as proteins, DNA, or RNA. NMR-based titration experiments yield insights into the thermodynamics and kinetics of these interactions. Detailed study of IDPs requires multiple experimental techniques, and thus, several methods are described for studying disordered proteins, highlighting their respective advantages and limitations. The potential for integrating these complementary techniques, each offering unique perspectives, is explored to achieve a comprehensive understanding of IDPs.
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Affiliation(s)
| | - Aakanksha Singh
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Tanisha Maji
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Nikita V. Saibo
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Soumya De
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
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2
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Ribeiro C, Cariello M, Malfait A, Bria M, Fournier D, Lyskawa J, Le Fer G, Potier J, Hoogenboom R, Cooke G, Woisel P. Synergistic topological and supramolecular control of Diels-Alder reactivity based on a tunable self-complexing host-guest molecular switch. Chemistry 2024; 30:e202302300. [PMID: 37991250 DOI: 10.1002/chem.202302300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 11/23/2023]
Abstract
Compartmentalization and binding-triggered conformational change regulate many metabolic processes in living matter. Here, we have synergistically combined these two biorelevant processes to tune the Diels-Alder (DA) reactivity of a synthetic self-complexing host-guest molecular switch CBPQT4+ -Fu, consisting of an electron-rich furan unit covalently attached to the electron-deficient cyclobis(paraquat-p-phenylene) tetrachloride (CBPQT4+ , 4Cl- ) host. This design allows CBPQT4+ -Fu to efficiently compartmentalize the furan ring inside its host cavity in water, thereby protecting it from the DA reaction with maleimide. Remarkably, the self-complexed CBPQT4+ -Fu can undergo a conformational change through intramolecular decomplexation upon the addition of a stronger binding molecular naphthalene derivative as a competitive guest, triggering the DA reaction upon addition of a chemical regulator. Remarkably, connecting the guest to a thermoresponsive lower critical solution temperature (LCST) copolymer regulator controls the DA reaction on command upon heating and cooling the reaction media beyond and below the cloud point temperature of the copolymer, representing a rare example of decreased reactivity upon increasing temperature. Altogether, this work opens up new avenues towards combined topological and supramolecular control over reactivity in synthetic constructs, enabling control over reactivity through molecular regulators or even mild temperature variations.
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Affiliation(s)
- Cédric Ribeiro
- Univ. Lille, CNRS, NRAE, Centrale Lille, UMR 8207 - UMET -, Unité Matériaux et Transformations, F-59000, Lille, France
| | - Michele Cariello
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | - Aurélie Malfait
- Univ. Lille, CNRS, NRAE, Centrale Lille, UMR 8207 - UMET -, Unité Matériaux et Transformations, F-59000, Lille, France
| | - Marc Bria
- Univ. Lille, CNRS, NRAE, Centrale Lille, UMR 8207 - UMET -, Unité Matériaux et Transformations, F-59000, Lille, France
| | - David Fournier
- Univ. Lille, CNRS, NRAE, Centrale Lille, UMR 8207 - UMET -, Unité Matériaux et Transformations, F-59000, Lille, France
| | - Joël Lyskawa
- Univ. Lille, CNRS, NRAE, Centrale Lille, UMR 8207 - UMET -, Unité Matériaux et Transformations, F-59000, Lille, France
| | - Gaëlle Le Fer
- Univ. Lille, CNRS, NRAE, Centrale Lille, UMR 8207 - UMET -, Unité Matériaux et Transformations, F-59000, Lille, France
| | - Jonathan Potier
- Univ. Lille, CNRS, NRAE, Centrale Lille, UMR 8207 - UMET -, Unité Matériaux et Transformations, F-59000, Lille, France
| | - Richard Hoogenboom
- Supramolecular Chemistry Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4-bis, 9000, Ghent, Belgium
| | - Graeme Cooke
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | - Patrice Woisel
- Univ. Lille, CNRS, NRAE, Centrale Lille, UMR 8207 - UMET -, Unité Matériaux et Transformations, F-59000, Lille, France
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3
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Sopariwala D, Nguyen H, Narkar V. Estrogen-related Receptor Signaling in Skeletal Muscle Fitness. Int J Sports Med 2023; 44:609-617. [PMID: 36787804 DOI: 10.1055/a-2035-8192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Skeletal muscle is a highly plastic tissue that can alter its metabolic and contractile features, as well as regenerative potential in response to exercise and other conditions. Multiple signaling factors including metabolites, kinases, receptors, and transcriptional factors have been studied in the regulation of skeletal muscle plasticity. Recently, estrogen-related receptors (ERRs) have emerged as a critical transcriptional hub in control of skeletal muscle homeostasis. ERRα and ERRγ - the two highly expressed ERR sub-types in the muscle respond to various extracellular cues such as exercise, hypoxia, fasting and dietary factors, in turn regulating gene expression in the skeletal muscle. On the other hand, conditions such as diabetes and muscular dystrophy suppress expression of ERRs in the skeletal muscle, likely contributing to disease progression. We highlight key functions of ERRs in the skeletal muscle including the regulation of fiber type, mitochondrial metabolism, vascularization, and regeneration. We also describe how ERRs are regulated in the skeletal muscle, and their interaction with important muscle regulators (e. g. AMPK and PGCs). Finally, we identify critical gaps in our understanding of ERR signaling in the skeletal muscle, and suggest future areas of investigation to advance ERRs as potential targets for function promoting therapeutics in muscle diseases.
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Affiliation(s)
- Danesh Sopariwala
- Institute of Molecular Medicine, University of Texas John P and Katherine G McGovern Medical School, Houston, United States
| | - Hao Nguyen
- Institute of Molecular Medicine, University of Texas John P and Katherine G McGovern Medical School, Houston, United States
| | - Vihang Narkar
- Institute of Molecular Medicine, University of Texas John P and Katherine G McGovern Medical School, Houston, United States
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4
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Santos AL, Sinha S. Ageing, Metabolic Dysfunction, and the Therapeutic Role of Antioxidants. Subcell Biochem 2023; 103:341-435. [PMID: 37120475 DOI: 10.1007/978-3-031-26576-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
The gradual ageing of the world population has been accompanied by a dramatic increase in the prevalence of obesity and metabolic diseases, especially type 2 diabetes. The adipose tissue dysfunction associated with ageing and obesity shares many common physiological features, including increased oxidative stress and inflammation. Understanding the mechanisms responsible for adipose tissue dysfunction in obesity may help elucidate the processes that contribute to the metabolic disturbances that occur with ageing. This, in turn, may help identify therapeutic targets for the treatment of obesity and age-related metabolic disorders. Because oxidative stress plays a critical role in these pathological processes, antioxidant dietary interventions could be of therapeutic value for the prevention and/or treatment of age-related diseases and obesity and their complications. In this chapter, we review the molecular and cellular mechanisms by which obesity predisposes individuals to accelerated ageing. Additionally, we critically review the potential of antioxidant dietary interventions to counteract obesity and ageing.
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Affiliation(s)
- Ana L Santos
- IdISBA - Fundación de Investigación Sanitaria de las Islas Baleares, Palma, Spain.
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5
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Melnik BC, Schmitz G. Milk Exosomal microRNAs: Postnatal Promoters of β Cell Proliferation but Potential Inducers of β Cell De-Differentiation in Adult Life. Int J Mol Sci 2022; 23:ijms231911503. [PMID: 36232796 PMCID: PMC9569743 DOI: 10.3390/ijms231911503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Pancreatic β cell expansion and functional maturation during the birth-to-weaning period is driven by epigenetic programs primarily triggered by growth factors, hormones, and nutrients provided by human milk. As shown recently, exosomes derived from various origins interact with β cells. This review elucidates the potential role of milk-derived exosomes (MEX) and their microRNAs (miRs) on pancreatic β cell programming during the postnatal period of lactation as well as during continuous cow milk exposure of adult humans to bovine MEX. Mechanistic evidence suggests that MEX miRs stimulate mTORC1/c-MYC-dependent postnatal β cell proliferation and glycolysis, but attenuate β cell differentiation, mitochondrial function, and insulin synthesis and secretion. MEX miR content is negatively affected by maternal obesity, gestational diabetes, psychological stress, caesarean delivery, and is completely absent in infant formula. Weaning-related disappearance of MEX miRs may be the critical event switching β cells from proliferation to TGF-β/AMPK-mediated cell differentiation, whereas continued exposure of adult humans to bovine MEX miRs via intake of pasteurized cow milk may reverse β cell differentiation, promoting β cell de-differentiation. Whereas MEX miR signaling supports postnatal β cell proliferation (diabetes prevention), persistent bovine MEX exposure after the lactation period may de-differentiate β cells back to the postnatal phenotype (diabetes induction).
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Affiliation(s)
- Bodo C. Melnik
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, D-49076 Osnabrück, Germany
- Correspondence: ; Tel.: +49-52-4198-8060
| | - Gerd Schmitz
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital of Regensburg, University of Regensburg, D-93053 Regensburg, Germany
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Fox SN, McMeekin LJ, Savage CH, Joyce KL, Boas SM, Simmons MS, Farmer CB, Ryan J, Pereboeva L, Becker K, Auwerx J, Sudarshan S, Ma J, Lee A, Roberts RC, Crossman DK, Kralli A, Cowell RM. Estrogen-related receptor gamma regulates mitochondrial and synaptic genes and modulates vulnerability to synucleinopathy. NPJ Parkinsons Dis 2022; 8:106. [PMID: 35982091 PMCID: PMC9388660 DOI: 10.1038/s41531-022-00369-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
Many studies implicate mitochondrial dysfunction as a key contributor to cell loss in Parkinson disease (PD). Previous analyses of dopaminergic (DAergic) neurons from patients with Lewy-body pathology revealed a deficiency in nuclear-encoded genes for mitochondrial respiration, many of which are targets for the transcription factor estrogen-related receptor gamma (Esrrg/ERRγ). We demonstrate that deletion of ERRγ from DAergic neurons in adult mice was sufficient to cause a levodopa-responsive PD-like phenotype with reductions in mitochondrial gene expression and number, that partial deficiency of ERRγ hastens synuclein-mediated toxicity, and that ERRγ overexpression reduces inclusion load and delays synuclein-mediated cell loss. While ERRγ deletion did not fully recapitulate the transcriptional alterations observed in postmortem tissue, it caused reductions in genes involved in synaptic and mitochondrial function and autophagy. Altogether, these experiments suggest that ERRγ-deficient mice could provide a model for understanding the regulation of transcription in DAergic neurons and that amplifying ERRγ-mediated transcriptional programs should be considered as a strategy to promote DAergic maintenance in PD.
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Affiliation(s)
- S N Fox
- Neuroscience Department, Drug Discovery Division, Southern Research, Birmingham, AL, 35205, USA
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - L J McMeekin
- Neuroscience Department, Drug Discovery Division, Southern Research, Birmingham, AL, 35205, USA
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - C H Savage
- Neuroscience Department, Drug Discovery Division, Southern Research, Birmingham, AL, 35205, USA
| | - K L Joyce
- Neuroscience Department, Drug Discovery Division, Southern Research, Birmingham, AL, 35205, USA
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - S M Boas
- Neuroscience Department, Drug Discovery Division, Southern Research, Birmingham, AL, 35205, USA
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - M S Simmons
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - C B Farmer
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - J Ryan
- NeuroInitiative, LLC, Jacksonville, FL, 32207, USA
| | - L Pereboeva
- Department of Pediatrics, Infectious Disease, Neuroscience Vector and Virus Core, University of Alabama at Birmingham, Birmingham, AL, 35223, USA
| | - K Becker
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - J Auwerx
- Swiss Federal Institute of Technology Lausanne, Lausanne, Switzerland
| | - S Sudarshan
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - J Ma
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - A Lee
- NeuroInitiative, LLC, Jacksonville, FL, 32207, USA
| | - R C Roberts
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - D K Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - A Kralli
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - R M Cowell
- Neuroscience Department, Drug Discovery Division, Southern Research, Birmingham, AL, 35205, USA.
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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7
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Wortham M, Sander M. Transcriptional mechanisms of pancreatic β-cell maturation and functional adaptation. Trends Endocrinol Metab 2021; 32:474-487. [PMID: 34030925 PMCID: PMC8259463 DOI: 10.1016/j.tem.2021.04.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/12/2021] [Accepted: 04/19/2021] [Indexed: 12/31/2022]
Abstract
Pancreatic β-cells secrete insulin commensurate to circulating nutrient levels to maintain normoglycemia. The ability of β-cells to couple insulin secretion to nutrient stimuli is acquired during a postnatal maturation process. In mature β-cells the insulin secretory response adapts to changes in nutrient state. Both β-cell maturation and functional adaptation rely on the interplay between extracellular cues and cell type-specific transcriptional programs. Here we review emerging evidence that developmental and homeostatic regulation of β-cell function involves collaboration between lineage-determining and signal-dependent transcription factors (LDTFs and SDTFs, respectively). A deeper understanding of β-cell SDTFs and their cognate signals would delineate mechanisms of β-cell maturation and functional adaptation, which has direct implications for diabetes therapies and for generating mature β-cells from stem cells.
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Affiliation(s)
- Matthew Wortham
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Maike Sander
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92093, USA.
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8
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Di Martino O, Ferris MA, Hadwiger G, Sarkar S, Vu A, Menéndez-Gutiérrez MP, Ricote M, Welch JS. RXRA DT448/9PP generates a dominant active variant capable of inducing maturation in acute myeloid leukemia cells. Haematologica 2021; 107:417-426. [PMID: 34134472 PMCID: PMC8804561 DOI: 10.3324/haematol.2021.278603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Indexed: 11/09/2022] Open
Abstract
RARA and RXRA contribute to myeloid maturation in both mice and humans, and deletion of Rxra and Rxrb augments leukemic growth in mice. While defining the domains of RXRA that are required for anti-leukemic effects in murine KMT2A-MLLT3 leukemia cells, we unexpectedly identified RXRA DT448/9PP as a constitutively active variant capable of inducing maturation and loss of their proliferative phenotype. RXRA DT448/9PP was associated with ligand-independent activity in reporter assays, with enhanced co-activator interactions, reduced engraftment in vivo, and activation of myeloid maturation transcriptional signatures that overlapped with those of cells treated with the potent RXRA agonist bexarotene, suggestive of constitutive activity that leads to leukemic maturation. Phenotypes of RXRA DT448/9PP appear to differ from those of two other RXRA mutations with forms of constitutive activity (F318A and S427F), in that DT448/9PP activity was resistant to mutations at critical ligand-interacting amino acids (R316A/L326A) and was resistant to pharmacological antagonists, suggesting it may be ligand-independent. These data provide further evidence that activated retinoid X receptors can regulate myeloid maturation and provide a novel constitutively active variant that may be germane for broader studies of retinoid X receptors in other settings.
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Affiliation(s)
- Orsola Di Martino
- Department of Internal Medicine, Washington University, St Louis, Missouri, 63110, USA
| | - Margaret A Ferris
- Department of Pediatrics, Washington University, St Louis, Missouri, 63110, USA
| | - Gayla Hadwiger
- Department of Internal Medicine, Washington University, St Louis, Missouri, 63110, USA
| | - Soyi Sarkar
- Department of Internal Medicine, Washington University, St Louis, Missouri, 63110, USA
| | - Anh Vu
- Department of Internal Medicine, Washington University, St Louis, Missouri, 63110, USA
| | - María P Menéndez-Gutiérrez
- Myocardial Pathophysiology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, 28029, Spain
| | - Mercedes Ricote
- Myocardial Pathophysiology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, 28029, Spain
| | - John S Welch
- Department of Internal Medicine, Washington University, St Louis, Missouri, 63110, USA.
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9
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Structural Insights into the Interaction of the Intrinsically Disordered Co-activator TIF2 with Retinoic Acid Receptor Heterodimer (RXR/RAR). J Mol Biol 2021; 433:166899. [PMID: 33647291 DOI: 10.1016/j.jmb.2021.166899] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/02/2021] [Accepted: 02/22/2021] [Indexed: 12/19/2022]
Abstract
Retinoic acid receptors (RARs) and retinoid X receptors (RXRs) form heterodimers that activate target gene transcription by recruiting co-activator complexes in response to ligand binding. The nuclear receptor (NR) co-activator TIF2 mediates this recruitment by interacting with the ligand-binding domain (LBD) of NRs trough the nuclear receptor interaction domain (TIF2NRID) containing three highly conserved α-helical LxxLL motifs (NR-boxes). The precise binding mode of this domain to RXR/RAR is not clear due to the disordered nature of TIF2. Here we present the structural characterization of TIF2NRID by integrating several experimental (NMR, SAXS, Far-UV CD, SEC-MALS) and computational data. Collectively, the data are in agreement with a largely disordered protein with partially structured regions, including the NR-boxes and their flanking regions, which are evolutionary conserved. NMR and X-ray crystallographic data on TIF2NRID in complex with RXR/RAR reveal a multisite binding of the three NR-boxes as well as an active role of their flanking regions in the interaction.
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10
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Kobayashi H, Kimura M, Maruyama S, Nagayasu M, Imanaka S. Revisiting estrogen-dependent signaling pathways in endometriosis: Potential targets for non-hormonal therapeutics. Eur J Obstet Gynecol Reprod Biol 2020; 258:103-110. [PMID: 33421806 DOI: 10.1016/j.ejogrb.2020.12.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/21/2020] [Indexed: 12/22/2022]
Abstract
Endometriosis is an estrogen-dependent gynecologic disease. Endometriotic cells survive in oxidative stress and hypoxic environments. The aim of this review is to reconsider new therapeutic strategies for endometriosis by focusing on estrogen signaling, ROS production and scavenging, and mitochondrial metabolism. Each keyword alone or in combination was used to search from PubMed and Embase by applying the filters of the title and the publication years between January 2000 and May 2020. Abnormal epigenetic marks of estrogen receptors (ERs) in endometriosis cause overexpression of ERβ, progesterone resistance, inflammation, anti-apoptosis, and mitochondrial metabolic modification. In addition to hormonal action, estrogen is involved in various functions such as mitochondrial biosynthesis and energy metabolism. Estrogen works with its downstream target genes to modulate mitochondrial gene expression, regulate ROS production, and affect mitochondrial biology, including ATP production, antioxidant defenses, mitochondrial biosynthesis, quality control, and energy-transducing capacity. Endometriosis can shift mitochondrial metabolism from oxidative phosphorylation to aerobic glycolysis. This metabolic conversion suppresses ROS production and thus activates the survival signal of endometriotic cells. Therefore, molecules associated with aerobic glycolysis and mitochondrial metabolism are considered therapeutic targets for endometriosis. In conclusion, estrogen downstream target genes involved in mitochondrial metabolic biosynthesis may be potential targets for non-hormonal treatment of endometriosis.
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Affiliation(s)
- Hiroshi Kobayashi
- Department of Obstetrics and Gynecology, Nara Medical University, Kashihara, Japan; Ms.Clinic MayOne, Kashihara, Japan.
| | - Mai Kimura
- Department of Obstetrics and Gynecology, Nara Medical University, Kashihara, Japan
| | - Sachiyo Maruyama
- Department of Obstetrics and Gynecology, Nara Medical University, Kashihara, Japan
| | - Mika Nagayasu
- Department of Obstetrics and Gynecology, Nara Medical University, Kashihara, Japan
| | - Shogo Imanaka
- Department of Obstetrics and Gynecology, Nara Medical University, Kashihara, Japan; Ms.Clinic MayOne, Kashihara, Japan
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11
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Kim J, Hwang H, Yoon H, Lee JE, Oh JM, An H, Ji HD, Lee S, Cha E, Ma MJ, Kim DS, Lee SJ, Kadayat TM, Song J, Lee SW, Jeon JH, Park KG, Lee IK, Jeon YH, Chin J, Cho SJ. An orally available inverse agonist of estrogen-related receptor gamma showed expanded efficacy for the radioiodine therapy of poorly differentiated thyroid cancer. Eur J Med Chem 2020; 205:112501. [PMID: 32758860 DOI: 10.1016/j.ejmech.2020.112501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/29/2020] [Accepted: 05/22/2020] [Indexed: 12/24/2022]
Abstract
Estrogen-related receptor gamma (ERRγ) is the NR3B subgroup of associated transcription factors. In this report, a new generation of a potent and selective ERRγ inverse agonist (25) with good biocompatibility was proposed. We also explored the potential of the newly developed compound 25 in the PDTC model to expand the original indications from ATC. In addition, an X-ray crystallographic study of the ligand and ERRγ co-complex showed that 25 completely binds to the target protein (PDB 6KNR). Its medicinal chemistry, including a distinctive structural study to in vivo results, denotes that 25 may be directed towards the development of a pivotal treatment for ERRγ-related cancers.
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Affiliation(s)
- Jina Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, South Korea; College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, 41566, South Korea
| | - Hayoung Hwang
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, South Korea
| | - Heeseok Yoon
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, South Korea
| | - Jae-Eon Lee
- Department of Biomaterials Science, College of Natural Resources and Life Science/Life and Industry Convergence Research Institute, Pusan National University, Pusan, South Korea
| | - Ji Min Oh
- Department of Nuclear Medicine, School of Medicine, Kyungpook National University Hospital, Daegu, South Korea
| | - Hongchan An
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, South Korea
| | - Hyun Dong Ji
- Department of Nuclear Medicine, School of Medicine, Kyungpook National University Hospital, Daegu, South Korea
| | - Seungmi Lee
- Leading-edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu, 41404, South Korea
| | - Eunju Cha
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, South Korea
| | - Min Jung Ma
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, South Korea
| | - Dong-Su Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, South Korea
| | - Su-Jeong Lee
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, South Korea
| | - Tara Man Kadayat
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, South Korea
| | - Jaeyoung Song
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, South Korea
| | - Sang Woo Lee
- Department of Nuclear Medicine, School of Medicine, Kyungpook National University Hospital, Daegu, South Korea
| | - Jae-Han Jeon
- Leading-edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu, 41404, South Korea; Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, 41944, South Korea
| | - Keun-Gyu Park
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, 41944, South Korea
| | - In-Kyu Lee
- Leading-edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu, 41404, South Korea; Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, 41944, South Korea
| | - Yong Hyun Jeon
- Laboratory Animal Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, South Korea.
| | - Jungwook Chin
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, South Korea.
| | - Sung Jin Cho
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, South Korea; Leading-edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu, 41404, South Korea.
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12
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Dobrovolska O, Brilkov M, Madeleine N, Ødegård-Fougner Ø, Strømland Ø, Martin SR, De Marco V, Christodoulou E, Teigen K, Isaksson J, Underhaug J, Reuter N, Aalen RB, Aasland R, Halskau Ø. The Arabidopsis (ASHH2) CW domain binds monomethylated K4 of the histone H3 tail through conformational selection. FEBS J 2020; 287:4458-4480. [PMID: 32083791 DOI: 10.1111/febs.15256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 12/17/2019] [Accepted: 02/20/2020] [Indexed: 12/27/2022]
Abstract
Chromatin post-translational modifications are thought to be important for epigenetic effects on gene expression. Methylation of histone N-terminal tail lysine residues constitutes one of many such modifications, executed by families of histone lysine methyltransferase (HKMTase). One such protein is ASHH2 from the flowering plant Arabidopsis thaliana, equipped with the interaction domain, CW, and the HKMTase domain, SET. The CW domain of ASHH2 is a selective binder of monomethylation at lysine 4 on histone H3 (H3K4me1) and likely helps the enzyme dock correctly onto chromatin sites. The study of CW and related interaction domains has so far been emphasizing lock-key models, missing important aspects of histone-tail CW interactions. We here present an analysis of the ASHH2 CW-H3K4me1 complex using NMR and molecular dynamics, as well as mutation and affinity studies of flexible coils. β-augmentation and rearrangement of coils coincide with changes in the flexibility of the complex, in particular the η1, η3 and C-terminal coils, but also in the β1 and β2 strands and the C-terminal part of the ligand. Furthermore, we show that mutating residues with outlier dynamic behaviour affect the complex binding affinity despite these not being in direct contact with the ligand. Overall, the binding process is consistent with conformational selection. We propose that this binding mechanism presents an advantage when searching for the correct post-translational modification state among the highly modified and flexible histone tails, and also that the binding shifts the catalytic SET domain towards the nucleosome. DATABASES: Structural data are available in the PDB database under the accession code 6QXZ. Resonance assignments for CW42 in its apo- and holo-forms are available in the BMRB database under the accession code 27251.
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Affiliation(s)
- Olena Dobrovolska
- Department of Biological Sciences, University of Bergen, Norway, Bergen
| | - Maxim Brilkov
- Department of Biological Sciences, University of Bergen, Norway, Bergen
| | - Noelly Madeleine
- Department of Biological Sciences, University of Bergen, Norway, Bergen.,Department of Biomedicine, University of Bergen, Norway, Bergen
| | - Øyvind Ødegård-Fougner
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Stephen R Martin
- Structural Biology Science Technology Platform, Francis Crick Institute, London, UK
| | | | | | - Knut Teigen
- Department of Biomedicine, University of Bergen, Norway, Bergen
| | - Johan Isaksson
- Department of Chemistry, The Arctic University of Tromsø, Norway
| | - Jarl Underhaug
- Department of Chemistry, University of Bergen, Norway, Bergen
| | - Nathalie Reuter
- Department of Chemistry, University of Bergen, Norway, Bergen
| | | | - Rein Aasland
- Department of Biosciences, University of Oslo, Norway, Oslo
| | - Øyvind Halskau
- Department of Biological Sciences, University of Bergen, Norway, Bergen
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13
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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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14
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Melnik BC. Milk exosomal miRNAs: potential drivers of AMPK-to-mTORC1 switching in β-cell de-differentiation of type 2 diabetes mellitus. Nutr Metab (Lond) 2019; 16:85. [PMID: 31827573 PMCID: PMC6898964 DOI: 10.1186/s12986-019-0412-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 11/22/2019] [Indexed: 12/15/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) steadily increases in prevalence since the 1950's, the period of widespread distribution of refrigerated pasteurized cow's milk. Whereas breastfeeding protects against the development of T2DM in later life, accumulating epidemiological evidence underlines the role of cow's milk consumption in T2DM. Recent studies in rodent models demonstrate that during the breastfeeding period pancreatic β-cells are metabolically immature and preferentially proliferate by activation of mechanistic target of rapamycin complex 1 (mTORC1) and suppression of AMP-activated protein kinase (AMPK). Weaning determines a metabolic switch of β-cells from a proliferating, immature phenotype with low insulin secretion to a differentiated mature phenotype with glucose-stimulated insulin secretion, less proliferation, reduced mTORC1- but increased AMPK activity. Translational evidence presented in this perspective implies for the first time that termination of milk miRNA transfer is the driver of this metabolic switch. miRNA-148a is a key inhibitor of AMPK and phosphatase and tensin homolog, crucial suppressors of mTORC1. β-Cells of diabetic patients return to the postnatal phenotype with high mTORC1 and low AMPK activity, explained by continuous transfer of bovine milk miRNAs to the human milk consumer. Bovine milk miRNA-148a apparently promotes β-cell de-differentiation to the immature mTORC1-high/AMPK-low phenotype with functional impairments in insulin secretion, increased mTORC1-driven endoplasmic reticulum stress, reduced autophagy and early β-cell apoptosis. In contrast to pasteurized cow's milk, milk's miRNAs are inactivated by bacterial fermentation, boiling and ultra-heat treatment and are missing in current infant formula. Persistent milk miRNA signaling adds a new perspective to the pathogenesis of T2DM and explains the protective role of breastfeeding but the diabetogenic effect of continued milk miRNA signaling by persistent consumption of pasteurized cow's milk.
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Affiliation(s)
- Bodo C. Melnik
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, Am Finkenhügel 7A, D-49076 Osnabrück, Germany
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15
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Barbosa ÉDAA, Seraphim TV, Gandin CA, Teixeira LF, da Silva RAG, Righetto GL, Goncalves KDA, Vasconcellos RDS, Almeida MR, Silva Júnior A, Fietto JLR, Kobarg J, Gileadi C, Massirer KB, Borges JC, de Oliveira Neto M, Bressan GC. Insights into the full-length SRPK2 structure and its hydrodynamic behavior. Int J Biol Macromol 2019; 137:205-214. [PMID: 31229549 DOI: 10.1016/j.ijbiomac.2019.06.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/04/2019] [Accepted: 06/19/2019] [Indexed: 11/30/2022]
Abstract
The serine/arginine-rich protein kinase 2 (SRPK2) has been reported as upregulated in several cancer types, with roles in hallmarks such as cell migration, growth, and apoptosis. These findings have indicated that SRPK2 is a promising emerging target in drug discovery initiatives. Although high-resolution models are available for SRPK2 (PDB 2X7G), they have been obtained with a heavily truncated recombinant protein version (~50% of the primary structure), due to the presence of long intrinsically unstructured regions. In the present work, we sought to characterize the structure of a full-length recombinant version of SRPK2 in solution. Low-resolution Small-Angle X-ray Scattering data were obtained for both versions of SRPK2. The truncated ΔNΔS-SRPK2 presented a propensity to dimerize at higher concentrations whereas the full-length SRPK2 was mainly found as dimers. The hydrodynamic behavior of the full-length SRPK2 was further investigated by analytical size exclusion chromatography and sedimentation velocity analytical ultracentrifugation experiments. SRPK2 behaved as a monomer-dimer equilibrium and both forms have an elongated shape in solution, pointing to a stretched-to-closed tendency among the conformational plasticity observed. Taken together, these findings allowed us to define unique structural features of the SRPK2 within SRPK family, characterized by its flexible regions outside the bipartite kinase domain.
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Affiliation(s)
| | | | - César Augusto Gandin
- Departamento de Física e Biofísica, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | | | | | - Germanna L Righetto
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Kaliandra De Almeida Goncalves
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | | | - Márcia Rogéria Almeida
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | | | | | - Jörg Kobarg
- Instituto de Biologia, Departamento de Bioquímica e Biologia Tecidual e Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Carina Gileadi
- Structural Genomics Consortium, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, Av. Dr. André Tosello, 550, Barão Geraldo, Campinas, SP, Brazil; Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Katlin B Massirer
- Structural Genomics Consortium, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, Av. Dr. André Tosello, 550, Barão Geraldo, Campinas, SP, Brazil; Center for Molecular Biology and Genetic Engineering, CBMEG, Universidade Estadual de Campinas, Campinas, SPUniversidade Estadual de Campinas, Campinas, Brazil
| | - Julio César Borges
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Mario de Oliveira Neto
- Departamento de Física e Biofísica, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Gustavo Costa Bressan
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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16
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De Vitto H, Bode AM, Dong Z. The PGC-1/ERR network and its role in precision oncology. NPJ Precis Oncol 2019; 3:9. [PMID: 30911677 PMCID: PMC6428848 DOI: 10.1038/s41698-019-0081-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
Transcriptional regulators include a superfamily of nuclear proteins referred to as co-activators and co-repressors, both of which are involved in controlling the functions of several nuclear receptors (NRs). The Nuclear Receptor Signaling Atlas (NURSA) has cataloged the composition of NRs, co-regulators, and ligands present in the human cell and their effort has been identified in more than 600 potential molecules. Given the importance of co-regulators in steroid, retinoid, and thyroid hormone signaling networks, hypothesizing that NRs/co-regulators are implicated in a wide range of pathologies are tempting. The co-activators known as peroxisome proliferator-activated receptor gamma co-activator 1 (PGC-1) and their key nuclear partner, the estrogen-related receptor (ERR), are emerging as pivotal transcriptional signatures that regulate an extremely broad repertoire of mitochondrial and metabolic genes, making them very attractive drug targets for cancer. Several studies have provided an increased understanding of the functional and structural biology of nuclear complexes. However, more comprehensive work is needed to create different avenues to explore the therapeutic potential of NRs/co-activators in precision oncology. Here, we discuss the emerging data associated with the structure, function, and molecular biology of the PGC-1/ERR network and address how the concepts evolving from these studies have deepened our understanding of how to develop more effective treatment strategies. We present an overview that underscores new biological insights into PGC-1/ERR to improve cancer outcomes against therapeutic resistance. Finally, we discuss the importance of exploiting new technologies such as single-particle cryo-electron microscopy (cryo-EM) to develop a high-resolution biological structure of PGC-1/ERR, focusing on novel drug discovery for precision oncology.
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Affiliation(s)
- Humberto De Vitto
- The Hormel Institute, University of Minnesota, 801 16th Avenue, Austin, NE 55912 USA
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, 801 16th Avenue, Austin, NE 55912 USA
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, 801 16th Avenue, Austin, NE 55912 USA
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17
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Bauzá-Thorbrügge M, Rodríguez-Cuenca S, Vidal-Puig A, Galmés-Pascual BM, Sbert-Roig M, Gianotti M, Lladó I, Proenza AM. GPER and ERα mediate estradiol enhancement of mitochondrial function in inflamed adipocytes through a PKA dependent mechanism. J Steroid Biochem Mol Biol 2019; 185:256-267. [PMID: 30253224 DOI: 10.1016/j.jsbmb.2018.09.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 08/31/2018] [Accepted: 09/17/2018] [Indexed: 01/16/2023]
Abstract
Obesity is associated with inflammation, dysregulated adipokine secretion, and disrupted adipose tissue mitochondrial function. Estradiol (E2) has been previously reported to increase mitochondrial function and biogenesis in several cell lines, but neither the type of oestrogen receptor (ERα, ERβ and GPER) involved nor the mechanism whereby such effects are exerted have been fully described. Considering the anti-inflammatory activity of E2 as well as its effects in enhancing mitochondrial biogenesis, the aim of this study was to investigate the contribution of ERα, ERβ, and GPER signaling to the E2-mediated enhancement of adipocyte mitochondrial function in a pro-inflammatory situation. 3T3-L1 cells were treated for 24 h with ER agonists (PPT, DPN, and G1) and antagonists (MPP, PHTPP, and G15) in the presence or absence of interleukin 6 (IL6), as a pro-inflammatory stimulus. Inflammation, mitochondrial function and biogenesis markers were analyzed. To confirm the involvement of the PKA pathway, cells were treated with a GPER agonist, a PKA inhibitor, and IL6. Mitochondrial function markers were analyzed. Our results showed that activation of ERα and GPER, but not ERβ, was able to counteract the proinflammatory effects of IL6 treatment, as well as mitochondrial biogenesis and function indicators. Inhibition of PKA prevented the E2- and G1-associated increase in mitochondrial function markers. In conclusion E2 prevents IL6 induced inflammation in adipocytes and promotes mitochondrial function through the combined activation of both GPER and ERα. These findings expand our understanding of ER interactions under inflammatory conditions in female rodent white adipose tissue.
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Affiliation(s)
- Marco Bauzá-Thorbrügge
- Grup Metabolisme Energètic i Nutrició, Departament de Biologia Fonamental i Ciències de la Salut, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, Palma de Mallorca, Spain; Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Sergio Rodríguez-Cuenca
- Metabolic Research Laboratories, Wellcome Trust MRC-Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Antonio Vidal-Puig
- Metabolic Research Laboratories, Wellcome Trust MRC-Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Bel M Galmés-Pascual
- Grup Metabolisme Energètic i Nutrició, Departament de Biologia Fonamental i Ciències de la Salut, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, Palma de Mallorca, Spain; Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Miquel Sbert-Roig
- Grup Metabolisme Energètic i Nutrició, Departament de Biologia Fonamental i Ciències de la Salut, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, Palma de Mallorca, Spain; Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Magdalena Gianotti
- Grup Metabolisme Energètic i Nutrició, Departament de Biologia Fonamental i Ciències de la Salut, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, Palma de Mallorca, Spain; Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBERobn, CB06/03/0043), Instituto de Salud Carlos III, Spain; Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain.
| | - Isabel Lladó
- Grup Metabolisme Energètic i Nutrició, Departament de Biologia Fonamental i Ciències de la Salut, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, Palma de Mallorca, Spain; Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBERobn, CB06/03/0043), Instituto de Salud Carlos III, Spain; Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Ana M Proenza
- Grup Metabolisme Energètic i Nutrició, Departament de Biologia Fonamental i Ciències de la Salut, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, Palma de Mallorca, Spain; Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBERobn, CB06/03/0043), Instituto de Salud Carlos III, Spain; Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
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18
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Benhaim M, Lee KK, Guttman M. Tracking Higher Order Protein Structure by Hydrogen-Deuterium Exchange Mass Spectrometry. Protein Pept Lett 2019; 26:16-26. [PMID: 30543159 PMCID: PMC6386625 DOI: 10.2174/0929866526666181212165037] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/30/2018] [Accepted: 11/17/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND Structural biology has provided a fundamental understanding of protein structure and mechanistic insight into their function. However, high-resolution structures alone are insufficient for a complete understanding of protein behavior. Higher energy conformations, conformational changes, and subtle structural fluctuations that underlie the proper function of proteins are often difficult to probe using traditional structural approaches. Hydrogen/Deuterium Exchange with Mass Spectrometry (HDX-MS) provides a way to probe the accessibility of backbone amide protons under native conditions, which reports on local structural dynamics of solution protein structure that can be used to track complex structural rearrangements that occur in the course of a protein's function. CONCLUSION In the last 20 years the advances in labeling techniques, sample preparation, instrumentation, and data analysis have enabled HDX to gain insights into very complex biological systems. Analysis of challenging targets such as membrane protein complexes is now feasible and the field is paving the way to the analysis of more and more complex systems.
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Affiliation(s)
- Mark Benhaim
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
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19
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Broekema MF, Hollman DAA, Koppen A, van den Ham HJ, Melchers D, Pijnenburg D, Ruijtenbeek R, van Mil SWC, Houtman R, Kalkhoven E. Profiling of 3696 Nuclear Receptor-Coregulator Interactions: A Resource for Biological and Clinical Discovery. Endocrinology 2018; 159:2397-2407. [PMID: 29718163 DOI: 10.1210/en.2018-00149] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/24/2018] [Indexed: 12/13/2022]
Abstract
Nuclear receptors (NRs) are ligand-inducible transcription factors that play critical roles in metazoan development, reproduction, and physiology and therefore are implicated in a broad range of pathologies. The transcriptional activity of NRs critically depends on their interaction(s) with transcriptional coregulator proteins, including coactivators and corepressors. Short leucine-rich peptide motifs in these proteins (LxxLL in coactivators and LxxxIxxxL in corepressors) are essential and sufficient for NR binding. With 350 different coregulator proteins identified to date and with many coregulators containing multiple interaction motifs, an enormous combinatorial potential is present for selective NR-mediated gene regulation. However, NR-coregulator interactions have often been determined experimentally on a one-to-one basis across diverse experimental conditions. In addition, NR-coregulator interactions are difficult to predict because the molecular determinants that govern specificity are not well established. Therefore, many biologically and clinically relevant NR-coregulator interactions may remain to be discovered. Here, we present a comprehensive overview of 3696 NR-coregulator interactions by systematically characterizing the binding of 24 nuclear receptors with 154 coregulator peptides. We identified unique ligand-dependent NR-coregulator interaction profiles for each NR, confirming many well-established NR-coregulator interactions. Hierarchical clustering based on the NR-coregulator interaction profiles largely recapitulates the classification of NR subfamilies based on the primary amino acid sequences of the ligand-binding domains, indicating that amino acid sequence is an important, although not the only, molecular determinant in directing and fine-tuning NR-coregulator interactions. This NR-coregulator peptide interactome provides an open data resource for future biological and clinical discovery as well as NR-based drug design.
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Affiliation(s)
- Marjoleine F Broekema
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
| | - Danielle A A Hollman
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
| | - Arjen Koppen
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
| | | | - Diana Melchers
- PamGene International B. V., BJ 's-Hertogenbosch, Netherlands
| | - Dirk Pijnenburg
- PamGene International B. V., BJ 's-Hertogenbosch, Netherlands
| | - Rob Ruijtenbeek
- PamGene International B. V., BJ 's-Hertogenbosch, Netherlands
| | - Saskia W C van Mil
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
| | - René Houtman
- PamGene International B. V., BJ 's-Hertogenbosch, Netherlands
| | - Eric Kalkhoven
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
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20
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Wang X, Yu C, Feng J, Chen J, Jiang Q, Kuang S, Wang Y. Depot-specific differences in fat mass expansion in WT and ob/ob mice. Oncotarget 2018; 8:46326-46336. [PMID: 28564636 PMCID: PMC5542270 DOI: 10.18632/oncotarget.17938] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/13/2017] [Indexed: 12/19/2022] Open
Abstract
The study was designed to investigate the cellular mechanisms underlying the differential fat expansion in different fat depots in wild type (WT) and ob/ob (OB) mice. At 6 weeks old, no differences in fat mass were found between SAT and VAT in WT mice, while O-SAT showed significantly higher weight than that of O-VAT. The average adipocyte size of SAT (~ 4133.47 μm2) was smaller than that of VAT (~ 7438.91 μm2) in OB mice. O-SAT preadipocytes gained higher triglyceride contents and higher levels of PPARγ and C/EBPα than did O-VAT preadipocytes upon in vitro differentiation. W-SAT and W-VAT displayed no significant differences in fatty acid uptake, while 1.36 fold significantly higher fatty acid uptake was found in O-SAT compared to O-VAT. Approximately 52% of the radioactivity recovered in cellular lipids was found in TAG in O-SAT, which was significantly higher than the other three adipocyte types. Significantly more radiolabelled oleic acid was β-oxidized to CO2 in adipocytes from O-VAT than that from O-SAT. ATP production was significantly lower in W-SAT compared with W-VAT, whereas no significantly ATP level was observed between O-SAT and O-VAT. Expression of UCP-1 in SAT from either WT or OB mice was significantly higher than the counterpart of VAT, which demonstrated higher uncoupled respiration and lower oxidative phosphorylation in SAT. Together, a combined increase in adipogenesis and FA uptake, and decreases in β-oxidation and ATP production, contributed to greater expansion of SAT compared to VAT in obese mice.
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Affiliation(s)
- Xinxia Wang
- College of Animal Sciences, Zhejiang University, Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, Zhejiang Provincial Laboratory of Feed and Animal Nutrition, Hangzhou, Zhejiang 310058, P. R. China
| | - Caihua Yu
- College of Animal Sciences, Zhejiang University, Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, Zhejiang Provincial Laboratory of Feed and Animal Nutrition, Hangzhou, Zhejiang 310058, P. R. China
| | - Jie Feng
- College of Animal Sciences, Zhejiang University, Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, Zhejiang Provincial Laboratory of Feed and Animal Nutrition, Hangzhou, Zhejiang 310058, P. R. China
| | - Jin Chen
- College of Animal Sciences, Zhejiang University, Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, Zhejiang Provincial Laboratory of Feed and Animal Nutrition, Hangzhou, Zhejiang 310058, P. R. China
| | - Qin Jiang
- College of Animal Sciences, Zhejiang University, Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, Zhejiang Provincial Laboratory of Feed and Animal Nutrition, Hangzhou, Zhejiang 310058, P. R. China
| | - Shihuan Kuang
- Department of Animal Sciences and Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Yizhen Wang
- College of Animal Sciences, Zhejiang University, Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, Zhejiang Provincial Laboratory of Feed and Animal Nutrition, Hangzhou, Zhejiang 310058, P. R. China
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21
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Vandenbeek R, Khan NP, Estall JL. Linking Metabolic Disease With the PGC-1α Gly482Ser Polymorphism. Endocrinology 2018; 159:853-865. [PMID: 29186342 DOI: 10.1210/en.2017-00872] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/20/2017] [Indexed: 12/11/2022]
Abstract
Peroxisome proliferator-activated receptor γ coactivator 1-α (PGC-1α) is a highly conserved transcriptional coactivator enriched in metabolically active tissues including liver, adipose, pancreas, and muscle. It plays a role in regulating whole body energy metabolism and its deregulation has been implicated in type 2 diabetes (T2D). A single nucleotide variant of the PPARGC1A gene (rs8192678) is associated with T2D susceptibility, relative risk of obesity and insulin resistance, and lower indices of β cell function. This common polymorphism is within a highly conserved region of the bioactive protein and leads to a single amino acid substitution (glycine 482 to serine). Its prevalence and effects on metabolic parameters appear to vary depending on factors including ethnicity and sex, suggesting important interactions between genetics and cultural/environmental factors and associated disease risk. Interestingly, carriers of the serine allele respond better to some T2D interventions, illustrating the importance of understanding functional impacts of genetic variance on PGC-1α when targeting this pathway for personalized medicine. This review summarizes a growing body of literature surrounding possible links between the PGC-1α Gly482Ser single nucleotide polymorphism and diabetes, with focus on key clinical findings, affected metabolic systems, potential molecular mechanisms, and the influence of geographical or ethnic background on associated risk.
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Affiliation(s)
- Roxanne Vandenbeek
- Institut de recherches cliniques de Montreal, Montreal, Quebec, Canada
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Naveen P Khan
- Institut de recherches cliniques de Montreal, Montreal, Quebec, Canada
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Jennifer L Estall
- Institut de recherches cliniques de Montreal, Montreal, Quebec, Canada
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
- Faculty of Medicine, University of Montreal, Montréal, Québec, Canada
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A metabolic function of FGFR3-TACC3 gene fusions in cancer. Nature 2018; 553:222-227. [PMID: 29323298 PMCID: PMC5771419 DOI: 10.1038/nature25171] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 11/24/2017] [Indexed: 12/22/2022]
Abstract
Chromosomal translocations that generate in-frame oncogenic gene fusions are powerful examples of success of targeted cancer therapies1–3. We discovered FGFR3-TACC3 (F3-T3) gene fusions in 3% of human glioblastoma4. Subsequent studies reported similar frequencies of F3-T3 in many other cancers, thus qualifying F3-T3 as one of the most recurrent fusions across all tumor types5,6. F3-T3 fusions are potent oncogenes that confer sensitivity to FGFR inhibitors but the downstream oncogenic signaling remains largely unknown2,4–6. Here, we report that tumors harboring F3-T3 cluster within transcriptional subgroups characterized by activation of mitochondrial functions. F3-T3 activates oxidative phosphorylation and mitochondrial biogenesis and induces sensitivity to inhibitors of oxidative metabolism. We show that phosphorylation of PIN4 is the signaling intermediate for the activation of mitochondrial metabolism. The F3-T3-PIN4 axis triggers peroxisome biogenesis and new protein synthesis. The anabolic response converges on PGC1α through intracellular ROS, enabling mitochondrial respiration and tumor growth. Our analyses uncover the oncogenic circuit engaged by F3-T3, expose reliance on mitochondrial respiration as unexpected therapeutic opportunity for F3-T3-positive tumors and provide a clue to the genetic alterations that initiate the chain of metabolic responses driving mitochondrial metabolism in cancer.
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Bhaskaran S, Unnikrishnan A, Ranjit R, Qaisar R, Pharaoh G, Matyi S, Kinter M, Deepa SS. A fish oil diet induces mitochondrial uncoupling and mitochondrial unfolded protein response in epididymal white adipose tissue of mice. Free Radic Biol Med 2017; 108:704-714. [PMID: 28455142 DOI: 10.1016/j.freeradbiomed.2017.04.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 04/19/2017] [Accepted: 04/20/2017] [Indexed: 01/14/2023]
Abstract
White adipose tissue (WAT) mitochondrial dysfunction is linked to the pathogenesis of obesity driven insulin resistance. Dietary conditions that alter fat mass are known to affect white adipocyte mitochondrial function, however, the impact of high calorie diets on white adipocyte mitochondria is not fully understood. The aim of this study is to assess the effect of a diet rich in saturated or polyunsaturated fat on mitochondrial unfolded protein response (UPRmt), a retrograde signaling response that maintains mitochondrial homeostasis, in epididymal WAT (eWAT). Mice were fed a low fat diet (LFD), saturated fat diet (SFD) or fish oil (unsaturated fat diet, UFD) and assessed changes in eWAT mitochondria. Compared to mice fed a LFD, SFD-fed mice have reduced mitochondrial biogenesis markers, mitochondrial fatty acid oxidation enzymes and TCA cycle enzymes, suggesting an impaired mitochondrial function that could contribute to increased fat mass. In contrast, isocaloric UFD-fed mice have increased expression of mitochondrial uncoupling protein 1 (UCP1) and peroxisomal fatty acid oxidation enzymes suggesting that elevated mitochondrial uncoupling and peroxisomal fatty acid oxidation could contribute to the reduction in fat mass. Interestingly, expression of UPRmt-associated proteins caseinolytic peptidase (ClpP) and heat shock protein 60 (Hsp60) are induced by UFD, whereas SFD reduced the expression of ClpP. Based on our data, we propose that induction of UPRmt helps to preserve a functional mitochondria and efficient utilization of fat by UFD whereas a dampened UPRmt response might impair mitochondrial function and promote fat accumulation by SFD. Thus, our findings suggest a potential role of UPRmt in mediating the beneficial effects of fish oil.
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Affiliation(s)
- Shylesh Bhaskaran
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Archana Unnikrishnan
- Department of Geriatric Medicine and the Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Rojina Ranjit
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Rizwan Qaisar
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Gavin Pharaoh
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Stephanie Matyi
- Department of Geriatric Medicine and the Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Michael Kinter
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Sathyaseelan S Deepa
- Department of Geriatric Medicine and the Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
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Misra J, Kim DK, Choi HS. ERRγ: a Junior Orphan with a Senior Role in Metabolism. Trends Endocrinol Metab 2017; 28:261-272. [PMID: 28209382 DOI: 10.1016/j.tem.2016.12.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/18/2016] [Accepted: 12/22/2016] [Indexed: 01/01/2023]
Abstract
Estrogen-related receptor (ERR)γ is an orphan nuclear hormone receptor that belongs to the ERR subfamily of transcription factors. No endogenous ligand has been identified to date. ERRγ possesses ligand-independent transcriptional activity that is regulated by co-regulator interactions, and post-translational modifications (PTMs). Recent data from animal models have established ERRγ as a crucial mediator of multiple endocrine and metabolic signals. ERRγ plays important roles in pathological conditions such as insulin resistance, alcoholic liver injury, and cardiac hypertrophy, and controls energy metabolism in the heart, skeletal muscle, and pancreatic β cells. These findings corroborate the importance of ERRγ in metabolic homeostasis, and suggest that ERRγ is a good target for the treatment of metabolic diseases.
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Affiliation(s)
- Jagannath Misra
- National Creative Research Initiatives Center for Nuclear Receptor Signals and Hormone Research Center, School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Don-Kyu Kim
- Department of Molecular Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hueng-Sik Choi
- National Creative Research Initiatives Center for Nuclear Receptor Signals and Hormone Research Center, School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea.
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25
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Mays SG, Okafor CD, Tuntland ML, Whitby RJ, Dharmarajan V, Stec J, Griffin PR, Ortlund EA. Structure and Dynamics of the Liver Receptor Homolog 1-PGC1 α Complex. Mol Pharmacol 2017; 92:1-11. [PMID: 28363985 DOI: 10.1124/mol.117.108514] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/29/2017] [Indexed: 12/20/2022] Open
Abstract
Peroxisome proliferator-activated gamma coactivator 1-α (PGC1α) regulates energy metabolism by directly interacting with transcription factors to modulate gene expression. Among the PGC1α binding partners is liver receptor homolog 1 (LRH-1; NR5A2), an orphan nuclear hormone receptor that controls lipid and glucose homeostasis. Although PGC1α is known to bind and activate LRH-1, mechanisms through which PGC1α changes LRH-1 conformation to drive transcription are unknown. Here, we used biochemical and structural methods to interrogate the LRH-1-PGC1α complex. Purified, full-length LRH-1, as well as isolated ligand binding domain, bound to PGC1α with higher affinity than to the coactivator, nuclear receptor coactivator-2 (Tif2), in coregulator peptide recruitment assays. We present the first crystal structure of the LRH-1-PGC1α complex, which depicts several hydrophobic contacts and a strong charge clamp at the interface between these partners. In molecular dynamics simulations, PGC1α induced correlated atomic motion throughout the entire LRH-1 activation function surface, which was dependent on charge-clamp formation. In contrast, Tif2 induced weaker signaling at the activation function surface than PGC1α but promoted allosteric signaling from the helix 6/β-sheet region of LRH-1 to the activation function surface. These studies are the first to probe mechanisms underlying the LRH-1-PGC1α interaction and may illuminate strategies for selective therapeutic targeting of PGC1α-dependent LRH-1 signaling pathways.
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Affiliation(s)
- Suzanne G Mays
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia (S.G.M., C.D.O., M.L.T., E.A.O.); School of Chemistry, University of Southampton, Southampton, United Kingdom (R.J.W., J.S.); and Department of Molecular Medicine, Scripps Research Institute, Jupiter, Florida (V.D., P.R.G.)
| | - C Denise Okafor
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia (S.G.M., C.D.O., M.L.T., E.A.O.); School of Chemistry, University of Southampton, Southampton, United Kingdom (R.J.W., J.S.); and Department of Molecular Medicine, Scripps Research Institute, Jupiter, Florida (V.D., P.R.G.)
| | - Micheal L Tuntland
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia (S.G.M., C.D.O., M.L.T., E.A.O.); School of Chemistry, University of Southampton, Southampton, United Kingdom (R.J.W., J.S.); and Department of Molecular Medicine, Scripps Research Institute, Jupiter, Florida (V.D., P.R.G.)
| | - Richard J Whitby
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia (S.G.M., C.D.O., M.L.T., E.A.O.); School of Chemistry, University of Southampton, Southampton, United Kingdom (R.J.W., J.S.); and Department of Molecular Medicine, Scripps Research Institute, Jupiter, Florida (V.D., P.R.G.)
| | - Venkatasubramanian Dharmarajan
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia (S.G.M., C.D.O., M.L.T., E.A.O.); School of Chemistry, University of Southampton, Southampton, United Kingdom (R.J.W., J.S.); and Department of Molecular Medicine, Scripps Research Institute, Jupiter, Florida (V.D., P.R.G.)
| | - Józef Stec
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia (S.G.M., C.D.O., M.L.T., E.A.O.); School of Chemistry, University of Southampton, Southampton, United Kingdom (R.J.W., J.S.); and Department of Molecular Medicine, Scripps Research Institute, Jupiter, Florida (V.D., P.R.G.)
| | - Patrick R Griffin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia (S.G.M., C.D.O., M.L.T., E.A.O.); School of Chemistry, University of Southampton, Southampton, United Kingdom (R.J.W., J.S.); and Department of Molecular Medicine, Scripps Research Institute, Jupiter, Florida (V.D., P.R.G.)
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia (S.G.M., C.D.O., M.L.T., E.A.O.); School of Chemistry, University of Southampton, Southampton, United Kingdom (R.J.W., J.S.); and Department of Molecular Medicine, Scripps Research Institute, Jupiter, Florida (V.D., P.R.G.).
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26
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Cordeiro TN, Herranz-Trillo F, Urbanek A, Estaña A, Cortés J, Sibille N, Bernadó P. Structural Characterization of Highly Flexible Proteins by Small-Angle Scattering. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:107-129. [DOI: 10.1007/978-981-10-6038-0_7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Cordeiro TN, Herranz-Trillo F, Urbanek A, Estaña A, Cortés J, Sibille N, Bernadó P. Small-angle scattering studies of intrinsically disordered proteins and their complexes. Curr Opin Struct Biol 2016; 42:15-23. [PMID: 27794210 DOI: 10.1016/j.sbi.2016.10.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 12/01/2022]
Abstract
Intrinsically Disordered Proteins (IDPs) perform a broad range of biological functions. Their relevance has motivated intense research activity seeking to characterize their sequence/structure/function relationships. However, the conformational plasticity of these molecules hampers the application of traditional structural approaches, and new tools and concepts are being developed to address the challenges they pose. Small-Angle Scattering (SAS) is a structural biology technique that probes the size and shape of disordered proteins and their complexes with other biomolecules. The low-resolution nature of SAS can be compensated with specially designed computational tools and its combined interpretation with complementary structural information. In this review, we describe recent advances in the application of SAS to disordered proteins and highly flexible complexes and discuss current challenges.
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Affiliation(s)
- Tiago N Cordeiro
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France
| | - Fátima Herranz-Trillo
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France; Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Annika Urbanek
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France
| | - Alejandro Estaña
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France; LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
| | - Nathalie Sibille
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France.
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Carnesecchi J, Vanacker JM. Estrogen-Related Receptors and the control of bone cell fate. Mol Cell Endocrinol 2016; 432:37-43. [PMID: 26206717 DOI: 10.1016/j.mce.2015.07.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 06/23/2015] [Accepted: 07/17/2015] [Indexed: 11/17/2022]
Abstract
Bone loss is naturally occurring in aging males and females and exacerbated in the latter after menopause, altogether leading to cumulative skeleton fragility and increased fracture risk. Two types of therapeutic strategies can be envisioned to counteract age- or menopause-associated bone loss, aiming at either reducing bone resorption exerted by osteoclasts or, alternatively, promoting bone formation by osteoblasts. We here summarize data suggesting that inhibition of the Estrogen-Related Receptors α and/or γ could promote bone formation and compensate for bone loss induced by ageing or estrogen-deficiency.
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Affiliation(s)
- Julie Carnesecchi
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon I, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jean-Marc Vanacker
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon I, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France.
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29
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Gong W, Yu J, Wang Q, Li S, Song J, Jia Z, Huang S, Zhang A. Estrogen-related receptor (ERR) γ protects against puromycin aminonucleoside-induced podocyte apoptosis by targeting PI3K/Akt signaling. Int J Biochem Cell Biol 2016; 78:75-86. [PMID: 27417234 DOI: 10.1016/j.biocel.2016.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 07/06/2016] [Accepted: 07/08/2016] [Indexed: 12/21/2022]
Abstract
Accumulating evidence has shown that podocyte apoptosis is of vital importance for the development of glomerulosclerosis and progressive loss of renal function. However, the molecular mechanisms leading to podocyte apoptosis are still elusive. In this study, we investigated the role of estrogen-related receptor (ERR) γ in podocyte apoptosis, as well as the underlying mechanisms. Treatment of PAN caused a dose- and time-dependent podocyte apoptosis in line with a significant downregulation of ERRγ. Interestingly, the occurrence of ERRγ downregulation appeared earlier than the onset of cell apoptosis, suggesting a potential that ERRγ reduction triggered apoptotic response in podocyte. To test this hypothesis, ERRγ siRNA was administered to the podocytes. Strikingly, ERRγ silencing resulted in a significant cell apoptosis accompanied with increased injury markers of B7-1 and cathepsin L and decreased podocyte protein nephrin. In contrast, overexpression of ERRγ remarkably attenuated PAN-induced cell apoptosis. Moreover, ERRγ overexpression stimulated PI3K/Akt signaling pathway evidenced by increased expression of PI3K subunits p85α and p110α and phosphorylated Akt. Importantly, a specific PI3K inhibitor LY294002 entirely reversed the anti-apoptotic effect of ERRγ following PAN treatment. Finally, we observed a striking downregulation of ERRγ in PAN-treated rat kidneys, suggesting that our cell model replicated the in vivo condition. Taken together, these data highly suggested that ERRγ played a novel role in modulating podocyte apoptosis by targeting PI3K/Akt signaling pathway.
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Affiliation(s)
- Wei Gong
- Department of Nephrology, Nanjing Children's Hospital Affiliated to Nanjing Medical University, Nanjing 210008, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China; Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing 210029, China
| | - Jing Yu
- Department of Nephrology, Nanjing Children's Hospital Affiliated to Nanjing Medical University, Nanjing 210008, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China; Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing 210029, China
| | - Qilei Wang
- Department of Nephrology, Nanjing Children's Hospital Affiliated to Nanjing Medical University, Nanjing 210008, China; Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing 210029, China
| | - Shuzhen Li
- Department of Nephrology, Nanjing Children's Hospital Affiliated to Nanjing Medical University, Nanjing 210008, China; Nanjing Key Laboratory of Pediatrics, Nanjing 210008, China
| | - Jiayu Song
- Department of Nephrology, Nanjing Children's Hospital Affiliated to Nanjing Medical University, Nanjing 210008, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China; Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing 210029, China
| | - Zhanjun Jia
- Department of Nephrology, Nanjing Children's Hospital Affiliated to Nanjing Medical University, Nanjing 210008, China; Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing 210029, China; Nanjing Key Laboratory of Pediatrics, Nanjing 210008, China
| | - Songming Huang
- Department of Nephrology, Nanjing Children's Hospital Affiliated to Nanjing Medical University, Nanjing 210008, China; Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing 210029, China; Nanjing Key Laboratory of Pediatrics, Nanjing 210008, China
| | - Aihua Zhang
- Department of Nephrology, Nanjing Children's Hospital Affiliated to Nanjing Medical University, Nanjing 210008, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China; Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing 210029, China; Nanjing Key Laboratory of Pediatrics, Nanjing 210008, China.
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30
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Grimm SL, Hartig SM, Edwards DP. Progesterone Receptor Signaling Mechanisms. J Mol Biol 2016; 428:3831-49. [PMID: 27380738 DOI: 10.1016/j.jmb.2016.06.020] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 06/25/2016] [Accepted: 06/27/2016] [Indexed: 12/27/2022]
Abstract
Progesterone receptor (PR) is a master regulator in female reproductive tissues that controls developmental processes and proliferation and differentiation during the reproductive cycle and pregnancy. PR also plays a role in progression of endocrine-dependent breast cancer. As a member of the nuclear receptor family of ligand-dependent transcription factors, the main action of PR is to regulate networks of target gene expression in response to binding its cognate steroid hormone, progesterone. This paper summarizes recent advances in understanding the structure-function properties of the receptor protein and the tissue/cell-type-specific PR signaling pathways that contribute to the biological actions of progesterone in the normal breast and in breast cancer.
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Affiliation(s)
- Sandra L Grimm
- Department of Molecular and Cellular Biology, Baylor College of Medicine,Houston, TX 77030, USA
| | - Sean M Hartig
- Department of Molecular and Cellular Biology, Baylor College of Medicine,Houston, TX 77030, USA
| | - Dean P Edwards
- Department of Molecular and Cellular Biology, Baylor College of Medicine,Houston, TX 77030, USA.
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31
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Cummins DJ, Espada A, Novick SJ, Molina-Martin M, Stites RE, Espinosa JF, Broughton H, Goswami D, Pascal BD, Dodge JA, Chalmers MJ, Griffin PR. Two-Site Evaluation of the Repeatability and Precision of an Automated Dual-Column Hydrogen/Deuterium Exchange Mass Spectrometry Platform. Anal Chem 2016; 88:6607-14. [PMID: 27224086 DOI: 10.1021/acs.analchem.6b01650] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) is an information-rich biophysical method for the characterization of protein dynamics. Successful applications of differential HDX-MS include the characterization of protein-ligand binding. A single differential HDX-MS data set (protein ± ligand) is often comprised of more than 40 individual HDX-MS experiments. To eliminate laborious manual processing of samples, and to minimize random and gross errors, automated systems for HDX-MS analysis have become routine in many laboratories. However, an automated system, while less prone to random errors introduced by human operators, may have systematic errors that go unnoticed without proper detection. Although the application of automated (and manual) HDX-MS has become common, there are only a handful of studies reporting the systematic evaluation of the performance of HDX-MS experiments, and no reports have been published describing a cross-site comparison of HDX-MS experiments. Here, we describe an automated HDX-MS platform that operates with a parallel, two-trap, two-column configuration that has been installed in two remote laboratories. To understand the performance of the system both within and between laboratories, we have designed and completed a test-retest repeatability study for differential HDX-MS experiments implemented at each of two laboratories, one in Florida and the other in Spain. This study provided sufficient data to do both within and between laboratory variability assessments. Initial results revealed a systematic run-order effect within one of the two systems. Therefore, the study was repeated, and this time the conclusion was that the experimental conditions were successfully replicated with minimal systematic error.
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Affiliation(s)
- David J Cummins
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Alfonso Espada
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Scott J Novick
- The Scripps Research Institute , Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Manuel Molina-Martin
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Ryan E Stites
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Juan Felix Espinosa
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Howard Broughton
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Devrishi Goswami
- The Scripps Research Institute , Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Bruce D Pascal
- The Scripps Research institute, Informatics Core, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jeffrey A Dodge
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Michael J Chalmers
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Patrick R Griffin
- The Scripps Research Institute , Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, Florida 33458, United States
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Caloric restriction and exercise "mimetics'': Ready for prime time? Pharmacol Res 2015; 103:158-66. [PMID: 26658171 DOI: 10.1016/j.phrs.2015.11.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 12/19/2022]
Abstract
Exercise and diet are powerful interventions to prevent and ameliorate various pathologies. The development of pharmacological agents that confer exercise- or caloric restriction-like phenotypic effects is thus an appealing therapeutic strategy in diseases or even when used as life-style and longevity drugs. Such so-called exercise or caloric restriction "mimetics" have so far mostly been described in pre-clinical, experimental settings with limited translation into humans. Interestingly, many of these compounds activate related signaling pathways, most often postulated to act on the common downstream effector peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) in skeletal muscle. In this review, resveratrol and other exercise- and caloric restriction "mimetics" are discussed with a special focus on feasibility, chances and limitations of using such compounds in patients as well as in healthy individuals.
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Conformational kinetics reveals affinities of protein conformational states. Proc Natl Acad Sci U S A 2015; 112:9352-7. [PMID: 26162682 DOI: 10.1073/pnas.1502084112] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Most biological reactions rely on interplay between binding and changes in both macromolecular structure and dynamics. Practical understanding of this interplay requires detection of critical intermediates and determination of their binding and conformational characteristics. However, many of these species are only transiently present and they have often been overlooked in mechanistic studies of reactions that couple binding to conformational change. We monitored the kinetics of ligand-induced conformational changes in a small protein using six different ligands. We analyzed the kinetic data to simultaneously determine both binding affinities for the conformational states and the rate constants of conformational change. The approach we used is sufficiently robust to determine the affinities of three conformational states and detect even modest differences in the protein's affinities for relatively similar ligands. Ligand binding favors higher-affinity conformational states by increasing forward conformational rate constants and/or decreasing reverse conformational rate constants. The amounts by which forward rate constants increase and reverse rate constants decrease are proportional to the ratio of affinities of the conformational states. We also show that both the affinity ratio and another parameter, which quantifies the changes in conformational rate constants upon ligand binding, are strong determinants of the mechanism (conformational selection and/or induced fit) of molecular recognition. Our results highlight the utility of analyzing the kinetics of conformational changes to determine affinities that cannot be determined from equilibrium experiments. Most importantly, they demonstrate an inextricable link between conformational dynamics and the binding affinities of conformational states.
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35
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Tria G, Mertens HDT, Kachala M, Svergun DI. Advanced ensemble modelling of flexible macromolecules using X-ray solution scattering. IUCRJ 2015; 2:207-17. [PMID: 25866658 PMCID: PMC4392415 DOI: 10.1107/s205225251500202x] [Citation(s) in RCA: 434] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 01/30/2015] [Indexed: 05/19/2023]
Abstract
Dynamic ensembles of macromolecules mediate essential processes in biology. Understanding the mechanisms driving the function and molecular interactions of 'unstructured' and flexible molecules requires alternative approaches to those traditionally employed in structural biology. Small-angle X-ray scattering (SAXS) is an established method for structural characterization of biological macromolecules in solution, and is directly applicable to the study of flexible systems such as intrinsically disordered proteins and multi-domain proteins with unstructured regions. The Ensemble Optimization Method (EOM) [Bernadó et al. (2007 ▶). J. Am. Chem. Soc. 129, 5656-5664] was the first approach introducing the concept of ensemble fitting of the SAXS data from flexible systems. In this approach, a large pool of macromolecules covering the available conformational space is generated and a sub-ensemble of conformers coexisting in solution is selected guided by the fit to the experimental SAXS data. This paper presents a series of new developments and advancements to the method, including significantly enhanced functionality and also quantitative metrics for the characterization of the results. Building on the original concept of ensemble optimization, the algorithms for pool generation have been redesigned to allow for the construction of partially or completely symmetric oligomeric models, and the selection procedure was improved to refine the size of the ensemble. Quantitative measures of the flexibility of the system studied, based on the characteristic integral parameters of the selected ensemble, are introduced. These improvements are implemented in the new EOM version 2.0, and the capabilities as well as inherent limitations of the ensemble approach in SAXS, and of EOM 2.0 in particular, are discussed.
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Affiliation(s)
- Giancarlo Tria
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg, 22603, Germany
| | - Haydyn D. T. Mertens
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg, 22603, Germany
| | - Michael Kachala
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg, 22603, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg, 22603, Germany
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Membrane-enabled dimerization of the intrinsically disordered cytoplasmic domain of ADAM10. Proc Natl Acad Sci U S A 2014; 111:15987-92. [PMID: 25349418 DOI: 10.1073/pnas.1409354111] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Intrinsically disordered protein regions are widely distributed in the cytoplasmic domains of many transmembrane receptors. The cytoplasmic domain of a disintegrin and metalloprotease (ADAM)10, a transmembrane metalloprotease mediating ectodomain shedding of diverse membrane proteins, was recently suggested to mediate the homodimerization of ADAM10. Here we show that a recombinant cytoplasmic domain of ADAM10 (A10Cp) is unstructured as judged by its susceptibility to limited trypsin digestion and its circular dichroism spectrum. In comparison, recombinant transmembrane-cytoplasmic domain of ADAM10 (A10TmCp) reconstituted in dodecylphosphocholine (DPC) micelles exhibits much greater resistance to trypsin digestion, with its cytoplasmic domain taking on a significant ordered structure. FRET analysis demonstrates that, although A10Cp remains monomeric, A10TmCp forms a tight homodimer (K(d) ∼ 7 nM) in DPC micelles. Phospholipid-conjugated A10Cp dose-dependently inhibits formation of A10TmCp homodimer, whereas A10Cp achieves only limited inhibition. Placing the transmembrane and cytoplasmic domains of ADAM10, but not the transmembrane domain alone, in their native orientation in the inner membrane of Escherichia coli produces specific and strong dimerization signal in the AraC-based transcriptional reporter assay. A chimeric construct containing the otherwise monomeric transmembrane domain of L-selectin and the cytoplasmic domain of ADAM10 produces a similar dimerization signal. Overall, these results demonstrate that a transmembrane domain imparts a stable structure to the adjacent and intrinsically disordered cytoplasmic domain of ADAM10 to form a homodimer in the membrane. This finding advances our understanding of the regulatory mechanism of ADAMs and has general implications for membrane-protein interactions in the process of transmembrane signaling.
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Rey M, Sarpe V, Burns KM, Buse J, Baker CAH, van Dijk M, Wordeman L, Bonvin AMJJ, Schriemer DC. Mass spec studio for integrative structural biology. Structure 2014; 22:1538-48. [PMID: 25242457 DOI: 10.1016/j.str.2014.08.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/30/2014] [Accepted: 08/06/2014] [Indexed: 02/01/2023]
Abstract
The integration of biophysical data from multiple sources is critical for developing accurate structural models of large multiprotein systems and their regulators. Mass spectrometry (MS) can be used to measure the insertion location for a wide range of topographically sensitive chemical probes, and such insertion data provide a rich, but disparate set of modeling restraints. We have developed a software platform that integrates the analysis of label-based MS and tandem MS (MS(2)) data with protein modeling activities (Mass Spec Studio). Analysis packages can mine any labeling data from any mass spectrometer in a proteomics-grade manner, and link labeling methods with data-directed protein interaction modeling using HADDOCK. Support is provided for hydrogen/deuterium exchange (HX) and covalent labeling chemistries, including novel acquisition strategies such as targeted HX-MS(2) and data-independent HX-MS(2). The latter permits the modeling of highly complex systems, which we demonstrate by the analysis of microtubule interactions.
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Affiliation(s)
- Martial Rey
- Department of Biochemistry and Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Vladimir Sarpe
- Department of Biochemistry and Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Kyle M Burns
- Department of Biochemistry and Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Joshua Buse
- Department of Biochemistry and Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | | | - Marc van Dijk
- Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Padualaan 8, Utrecht CH 3584, the Netherlands
| | - Linda Wordeman
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, WA 98195-7290, USA
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Padualaan 8, Utrecht CH 3584, the Netherlands
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada.
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Mackinnon JAG, Gallastegui N, Osguthorpe DJ, Hagler AT, Estébanez-Perpiñá E. Allosteric mechanisms of nuclear receptors: insights from computational simulations. Mol Cell Endocrinol 2014; 393:75-82. [PMID: 24911885 DOI: 10.1016/j.mce.2014.05.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 05/15/2014] [Accepted: 05/19/2014] [Indexed: 01/07/2023]
Abstract
The traditional structural view of allostery defines this key regulatory mechanism as the ability of one conformational event (allosteric site) to initiate another in a separate location (active site). In recent years computational simulations conducted to understand how this phenomenon occurs in nuclear receptors (NRs) has gained significant traction. These results have yield insights into allosteric changes and communication mechanisms that underpin ligand binding, coactivator binding site formation, post-translational modifications, and oncogenic mutations. Moreover, substantial efforts have been made in understanding the dynamic processes involved in ligand binding and coregulator recruitment to different NR conformations in order to predict cell/tissue-selective pharmacological outcomes of drugs. They also have improved the accuracy of in silico screening protocols so that nowadays they are becoming part of optimisation protocols for novel therapeutics. Here we summarise the important contributions that computational simulations have made towards understanding the structure/function relationships of NRs and how these can be exploited for rational drug design.
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Affiliation(s)
- Jonathan A G Mackinnon
- Institute of Biomedicine of the University of Barcelona (IBUB), Department of Biochemistry and Molecular Biology, University of Barcelona (UB), Baldiri-Reixac 15-21, 08028 Barcelona, Spain
| | - Nerea Gallastegui
- Institute of Biomedicine of the University of Barcelona (IBUB), Department of Biochemistry and Molecular Biology, University of Barcelona (UB), Baldiri-Reixac 15-21, 08028 Barcelona, Spain
| | - David J Osguthorpe
- Shifa Biomedical, 1 Great Valley Parkway, Suite 8, Malvern, PA 19355, USA
| | - Arnold T Hagler
- Department of Chemistry, University of Massachusetts, 701 Lederle, Graduate Research Tower, 710 North Pleasant Street, Amherst, MA 01003-9336, USA.
| | - Eva Estébanez-Perpiñá
- Institute of Biomedicine of the University of Barcelona (IBUB), Department of Biochemistry and Molecular Biology, University of Barcelona (UB), Baldiri-Reixac 15-21, 08028 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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Abstract
Skeletal muscle is the largest organ in the body and contributes to innumerable aspects of organismal biology. Muscle dysfunction engenders numerous diseases, including diabetes, cachexia, and sarcopenia. At the same time, skeletal muscle is also the main engine of exercise, one of the most efficacious interventions for prevention and treatment of a wide variety of diseases. The transcriptional coactivator PGC-1α has emerged as a key driver of metabolic programming in skeletal muscle, both in health and in disease. We review here the many aspects of PGC-1α function in skeletal muscle, with a focus on recent developments.
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Affiliation(s)
- Mun Chun Chan
- Cardiovascular Institute and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center and Harvard Medical School
| | - Zolt Arany
- Cardiovascular Institute and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center and Harvard Medical School.
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Rastinejad F, Huang P, Chandra V, Khorasanizadeh S. Understanding nuclear receptor form and function using structural biology. J Mol Endocrinol 2013; 51:T1-T21. [PMID: 24103914 PMCID: PMC3871882 DOI: 10.1530/jme-13-0173] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nuclear receptors (NRs) are a major transcription factor family whose members selectively bind small-molecule lipophilic ligands and transduce those signals into specific changes in gene programs. For over two decades, structural biology efforts were focused exclusively on the individual ligand-binding domains (LBDs) or DNA-binding domains of NRs. These analyses revealed the basis for both ligand and DNA binding and also revealed receptor conformations representing both the activated and repressed states. Additionally, crystallographic studies explained how NR LBD surfaces recognize discrete portions of transcriptional coregulators. The many structural snapshots of LBDs have also guided the development of synthetic ligands with therapeutic potential. Yet, the exclusive structural focus on isolated NR domains has made it difficult to conceptualize how all the NR polypeptide segments are coordinated physically and functionally in the context of receptor quaternary architectures. Newly emerged crystal structures of the peroxisome proliferator-activated receptor-γ-retinoid X receptor α (PPARγ-RXRα) heterodimer and hepatocyte nuclear factor (HNF)-4α homodimer have recently revealed the higher order organizations of these receptor complexes on DNA, as well as the complexity and uniqueness of their domain-domain interfaces. These emerging structural advances promise to better explain how signals in one domain can be allosterically transmitted to distal receptor domains, also providing much better frameworks for guiding future drug discovery efforts.
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Affiliation(s)
- Fraydoon Rastinejad
- Metabolic Signaling and Disease Program, Sanford-Burnham Medical Research Institute, Orlando, Florida 32827, USA
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42
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Simons SS, Edwards DP, Kumar R. Minireview: dynamic structures of nuclear hormone receptors: new promises and challenges. Mol Endocrinol 2013; 28:173-82. [PMID: 24284822 DOI: 10.1210/me.2013-1334] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Therapeutic targeting of nuclear receptors (NRs) is presently restricted due to 2 constraints: 1) a limited knowledge of the structural dynamics of intact receptor when complexed to DNA and coregulatory proteins; and 2) the inability to more selectively modulate NR actions at specific organ/gene targets. A major obstacle has been the current lack of understanding about the function and structure of the intrinsically disordered N-terminal domain that contains a major regulatory transcriptional activation function (AF1). Current studies of both mechanism of action and small molecule-selective receptor modulators for clinical uses target the structured pocket of the ligand-binding domain to modulate coregulatory protein interactions with the other activation function AF2. However, these approaches overlook AF1 activity. Recent studies have shown that highly flexible intrinsically disordered regions of transcription factors, including that of the N-terminal domain AF1 of NRs, not only are critical for several aspects of NR action but also can be exploited as drug targets, thereby opening unique opportunities for endocrine-based therapies. In this review article, we discuss the role of structural flexibilities in the allosteric modulation of NR activity and future perspectives for therapeutic interventions.
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Affiliation(s)
- S Stoney Simons
- Steroid Hormones Section (S.S.S.), Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892; Departments of Molecular & Cellular Biology and Pathology & Immunology (D.P.E.), Baylor College of Medicine, Houston, Texas 77030; and Department of Basic Sciences (R.K.), The Commonwealth Medical College, Scranton, Pennsylvania 18510
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Goswami D, Devarakonda S, Chalmers MJ, Pascal BD, Spiegelman BM, Griffin PR. Time window expansion for HDX analysis of an intrinsically disordered protein. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1584-92. [PMID: 23884631 PMCID: PMC3773365 DOI: 10.1007/s13361-013-0669-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Revised: 05/07/2013] [Accepted: 05/08/2013] [Indexed: 05/16/2023]
Abstract
Application of typical HDX methods to examine intrinsically disordered proteins (IDP), proteins that are natively unstructured and highly dynamic at physiological pH, is limited because of the rapid exchange of unprotected amide hydrogens with solvent. The exchange rates of these fast exchanging amides are usually faster than the shortest time scale (10 s) employed in typical automated HDX-MS experiments. Considering the functional importance of IDPs and their association with many diseases, it is valuable to develop methods that allow the study of solution dynamics of these proteins as well as the ability to probe the interaction of IDPs with their wide range of binding partners. Here, we report the application of time window expansion to the millisecond range by altering the on-exchange pH of the HDX experiment to study a well-characterized IDP; the activation domain of the nuclear receptor coactivator, peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α). This method enabled mapping the regions of PGC-1α that are stabilized upon binding the ligand binding domain (LBD) of the nuclear receptor peroxisome proliferator-activated receptor gamma (PPARγ). We further demonstrate the method's applicability to other binding partners of the IDP PGC-1α and pave the way for characterizing many other biologically important ID proteins.
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Affiliation(s)
- Devrishi Goswami
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, 33458, USA
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Marsh JJ, Guan HS, Li S, Chiles PG, Tran D, Morris TA. Structural insights into fibrinogen dynamics using amide hydrogen/deuterium exchange mass spectrometry. Biochemistry 2013; 52:5491-502. [PMID: 23875785 DOI: 10.1021/bi4007995] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We determined the amide hydrogen/deuterium exchange profile of native human fibrinogen under physiologic conditions. After optimization of the quench and proteolysis conditions, more than 1,200 peptides were identified by mass spectrometry, spanning more than 90% of the constituent Aα, Bβ, and γ chain amino acid sequences. The compact central and distal globular regions of fibrinogen were well protected from deuterium exchange, with the exception of the unfolded amino-terminal segments of the Aα and Bβ chains extending from the central region, and the short γ chain "tail" extending from each distal globular region. The triple-helical coiled-coil regions, which bridge the central region to each distal region, were also well protected with the exception of a moderately fast-exchanging area in the middle of each coiled-coil adjacent to the γ chain carbohydrate attachment site. These dynamic regions appear to provide flexibility to the fibrinogen molecule. The γ chain "out loop" contained within each coiled-coil also exchanged rapidly. The αC domain (Aα 392-610) exchanged rapidly, with the exception of a short segment sandwiched between a conserved disulfide linkage in the N-terminal αC subdomain. This latter finding is consistent with a mostly disordered structure for the αC domain in native fibrinogen. Analysis of the dysfibrinogen Bβ 235 Pro/Leu, which exhibits abnormal fibrin structure, revealed enhanced deuterium exchange surrounding the Pro/Leu substitution site as well as in the vicinity of the high affinity calcium binding site and the A knob polymerization pocket within the γC domain. The implication of these changes with respect to fibrin structure is discussed.
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Affiliation(s)
- James J Marsh
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA.
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45
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Takacs M, Petoukhov MV, Atkinson RA, Roblin P, Ogi FX, Demeler B, Potier N, Chebaro Y, Dejaegere A, Svergun DI, Moras D, Billas IML. The asymmetric binding of PGC-1α to the ERRα and ERRγ nuclear receptor homodimers involves a similar recognition mechanism. PLoS One 2013; 8:e67810. [PMID: 23874451 PMCID: PMC3706463 DOI: 10.1371/journal.pone.0067810] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 05/22/2013] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND PGC-1α is a crucial regulator of cellular metabolism and energy homeostasis that functionally acts together with the estrogen-related receptors (ERRα and ERRγ) in the regulation of mitochondrial and metabolic gene networks. Dimerization of the ERRs is a pre-requisite for interactions with PGC-1α and other coactivators, eventually leading to transactivation. It was suggested recently (Devarakonda et al) that PGC-1α binds in a strikingly different manner to ERRγ ligand-binding domains (LBDs) compared to its mode of binding to ERRα and other nuclear receptors (NRs), where it interacts directly with the two ERRγ homodimer subunits. METHODS/PRINCIPAL FINDINGS Here, we show that PGC-1α receptor interacting domain (RID) binds in an almost identical manner to ERRα and ERRγ homodimers. Microscale thermophoresis demonstrated that the interactions between PGC-1α RID and ERR LBDs involve a single receptor subunit through high-affinity, ERR-specific L3 and low-affinity L2 interactions. NMR studies further defined the limits of PGC-1α RID that interacts with ERRs. Consistent with these findings, the solution structures of PGC-1α/ERRα LBDs and PGC-1α/ERRγ LBDs complexes share an identical architecture with an asymmetric binding of PGC-1α to homodimeric ERR. CONCLUSIONS/SIGNIFICANCE These studies provide the molecular determinants for the specificity of interactions between PGC-1α and the ERRs, whereby negative cooperativity prevails in the binding of the coactivators to these receptors. Our work indicates that allosteric regulation may be a general mechanism controlling the binding of the coactivators to homodimers.
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Affiliation(s)
- Maria Takacs
- Department of Integrative Structural Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Université de Strasbourg (UdS), Illkirch, France
| | - Maxim V. Petoukhov
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL DESY, Hamburg, Germany
| | - R. Andrew Atkinson
- Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | - Pierre Roblin
- SOLEIL Synchrotron, L'Orme des Merisiers Saint-Aubin, Gif-sur-Yvette, France
- INRA-URBIA, Nantes, France
| | | | - Borries Demeler
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas, United States of America
| | - Noelle Potier
- Institut de Chimie LC3, Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), UMR 7177, Strasbourg, France
| | - Yassmine Chebaro
- Department of Integrative Structural Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Université de Strasbourg (UdS), Illkirch, France
| | - Annick Dejaegere
- Department of Integrative Structural Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Université de Strasbourg (UdS), Illkirch, France
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL DESY, Hamburg, Germany
| | - Dino Moras
- Department of Integrative Structural Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Université de Strasbourg (UdS), Illkirch, France
| | - Isabelle M. L. Billas
- Department of Integrative Structural Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Université de Strasbourg (UdS), Illkirch, France
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Sheff JG, Rey M, Schriemer DC. Peptide-column interactions and their influence on back exchange rates in hydrogen/deuterium exchange-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1006-15. [PMID: 23649779 DOI: 10.1007/s13361-013-0639-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 04/04/2013] [Accepted: 04/05/2013] [Indexed: 05/11/2023]
Abstract
Hydrogen/deuterium exchange (HDX) methods generate useful information on protein structure and dynamics, ideally at the individual residue level. Most MS-based HDX methods involve a rapid proteolytic digestion followed by LC/MS analysis, with exchange kinetics monitored at the peptide level. Localizing specific sites of HDX is usually restricted to a resolution the size of the host peptide because gas-phase processes can scramble deuterium throughout the peptide. Subtractive methods may improve resolution, where deuterium levels of overlapping and nested peptides are used in a subtractive manner to localize exchange to smaller segments. In this study, we explore the underlying assumption of the subtractive method, namely, that the measured back exchange kinetics of a given residue is independent of its host peptide. Using a series of deuterated peptides, we show that secondary structure can be partially retained under quenched conditions, and that interactions between peptides and reversed-phase LC columns may both accelerate and decelerate residue HDX, depending upon peptide sequence and length. Secondary structure is induced through column interactions in peptides with a solution-phase propensity for structure, which has the effect of slowing HDX rates relative to predicted random coil values. Conversely, column interactions can orient random-coil peptide conformers to accelerate HDX, the degree to which correlates with peptide charge in solution, and which can be reversed by using stronger ion pairing reagents. The dependency of these effects on sequence and length suggest that subtractive methods for improving structural resolution in HDX-MS will not offer a straightforward solution for increasing exchange site resolution.
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Affiliation(s)
- Joey G Sheff
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada
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The protein level of PGC-1α, a key metabolic regulator, is controlled by NADH-NQO1. Mol Cell Biol 2013; 33:2603-13. [PMID: 23648480 DOI: 10.1128/mcb.01672-12] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
PGC-1α is a key transcription coactivator regulating energy metabolism in a tissue-specific manner. PGC-1α expression is tightly regulated, it is a highly labile protein, and it interacts with various proteins--the known attributes of intrinsically disordered proteins (IDPs). In this study, we characterize PGC-1α as an IDP and demonstrate that it is susceptible to 20S proteasomal degradation by default. We further demonstrate that PGC-1α degradation is inhibited by NQO1, a 20S gatekeeper protein. NQO1 binds and protects PGC-1α from degradation in an NADH-dependent manner. Using different cellular physiological settings, we also demonstrate that NQO1-mediated PGC-1α protection plays an important role in controlling both basal and physiologically induced PGC-1α protein level and activity. Our findings link NQO1, a cellular redox sensor, to the metabolite-sensing network that tunes PGC-1α expression and activity in regulating energy metabolism.
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48
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Reichmann D, Jakob U. The roles of conditional disorder in redox proteins. Curr Opin Struct Biol 2013; 23:436-42. [PMID: 23477949 DOI: 10.1016/j.sbi.2013.02.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 02/13/2013] [Accepted: 02/15/2013] [Indexed: 11/18/2022]
Abstract
Cells are constantly exposed to various oxidants, either generated endogenously due to metabolic activity or exogenously. One way that cells respond to oxidants is through the action of redox-regulated proteins. These proteins also play important roles in oxidant signaling and protein biogenesis events. The key sensors built into redox-regulated proteins are cysteines, which undergo reversible thiol oxidation in response to changes in the oxidation status of the cellular environment. In this review, we discuss three examples of redox-regulated proteins found in bacteria, mitochondria, and chloroplasts. These proteins use oxidation of their redox-sensitive cysteines to reversibly convert large structural domains into more disordered regions or vice versa. These massive structural rearrangements are directly implicated in the functions of these proteins.
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Affiliation(s)
- Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem 91904, Israel.
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Rey M, Yang M, Burns KM, Yu Y, Lees-Miller SP, Schriemer DC. Nepenthesin from monkey cups for hydrogen/deuterium exchange mass spectrometry. Mol Cell Proteomics 2012. [PMID: 23197791 DOI: 10.1074/mcp.m112.025221] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Studies of protein dynamics, structure and interactions using hydrogen/deuterium exchange mass spectrometry (HDX-MS) have sharply increased over the past 5-10 years. The predominant technology requires fast digestion at pH 2-3 to retain deuterium label. Pepsin is used almost exclusively, but it provides relatively low efficiency under the constraints of the experiment, and a selectivity profile that renders poor coverage of intrinsically disordered regions. In this study we present nepenthesin-containing secretions of the pitcher plant Nepenthes, commonly called monkey cups, for use in HDX-MS. We show that nepenthesin is at least 1400-fold more efficient than pepsin under HDX-competent conditions, with a selectivity profile that mimics pepsin in part, but also includes efficient cleavage C-terminal to "forbidden" residues K, R, H, and P. High efficiency permits a solution-based analysis with no detectable autolysis, avoiding the complication of immobilized enzyme reactors. Relaxed selectivity promotes high coverage of disordered regions and the ability to "tune" the mass map for regions of interest. Nepenthesin-enriched secretions were applied to an analysis of protein complexes in the nonhomologous end-joining DNA repair pathway. The analysis of XRCC4 binding to the BRCT domains of Ligase IV points to secondary interactions between the disordered C-terminal tail of XRCC4 and remote regions of the BRCT domains, which could only be identified with a nepenthesin-based workflow. HDX data suggest that stalk-binding to XRCC4 primes a BRCT conformation in these remote regions to support tail interaction, an event which may be phosphoregulated. We conclude that nepenthesin is an effective alternative to pepsin for all HDX-MS applications, and especially for the analysis of structural transitions among intrinsically disordered proteins and their binding partners.
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Affiliation(s)
- Martial Rey
- Department of Biochemistry and Molecular Biology and the Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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Kusminski CM, Scherer PE. Mitochondrial dysfunction in white adipose tissue. Trends Endocrinol Metab 2012; 23:435-43. [PMID: 22784416 PMCID: PMC3430798 DOI: 10.1016/j.tem.2012.06.004] [Citation(s) in RCA: 256] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 06/06/2012] [Accepted: 06/11/2012] [Indexed: 12/14/2022]
Abstract
Although mitochondria in brown adipose tissue and their role in non-shivering thermogenesis have been widely studied, we have only a limited understanding of the relevance of mitochondria in white adipose tissue (WAT) for cellular homeostasis of the adipocyte and their impact upon systemic energy homeostasis. A better understanding of the regulatory role that white adipocyte mitochondria play in the regulation of whole-body physiology becomes increasingly important. WAT mitochondrial biogenesis can effectively be induced pharmacologically using a number of agents, including PPARγ agonists. Through their ability to influence key biochemical processes central to the adipocyte, such as fatty acid (FA) esterification and lipogenesis, as well as their impact upon the production and release of key adipokines, mitochondria play a crucial role in determining systemic insulin sensitivity.
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Affiliation(s)
| | - Philipp E. Scherer
- Touchstone Diabetes Center, Department of Internal Medicine, Dallas, Texas 75390-8549
- Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390-8549
- corresponding author: , Telephone: (214) 648-8715, Fax: (214) 648-8720
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