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A Role for the Proteasome Alpha2 Subunit N-Tail in Substrate Processing. Biomolecules 2023; 13:biom13030480. [PMID: 36979414 PMCID: PMC10046698 DOI: 10.3390/biom13030480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
The proteolytic active sites of the 26S proteasome are sequestered within the catalytic chamber of its 20S core particle (CP). Access to this chamber is through a narrow channel defined by the seven outer α subunits. In the resting state, the N-termini of neighboring α subunits form a gate blocking access to the channel. The attachment of the activators or regulatory particles rearranges the blocking α subunit N-termini facilitating the entry of substrates. By truncating or mutating each of the participating α N-termini, we report that whereas only a few N-termini are important for maintaining the closed gate, all seven N-termini participate in the open gate. Specifically, the open state is stabilized by a hydrogen bond between an invariant tyrosine (Y) in each subunit with a conserved aspartate (D) in its counterclockwise neighbor. The lone exception is the α1–α2 pair leaving a gap in the ring circumference. The third residue (X) of this YD(X) motif aligns with the open channel. Phenylalanine at this position in the α2 subunit comes in direct contact with the translocating substrate. Consequently, deletion of the α2 N-terminal tail attenuates proteolysis despite the appearance of an open gate state. In summary, the interlacing N-terminal YD(X) motifs regulate both the gating and translocation of the substrate.
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2
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Giletto MB, Osmulski PA, Jones CL, Gaczynska ME, Tepe JJ. Pipecolic esters as minimized templates for proteasome inhibition. Org Biomol Chem 2020; 17:2734-2746. [PMID: 30778435 DOI: 10.1039/c9ob00122k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Allosteric regulators of clinically important enzymes are gaining popularity as alternatives to competitive inhibitors. This is also the case for the proteasome, a major intracellular protease and a target of anti-cancer drugs. All clinically used proteasome inhibitors bind to the active sites in catalytic chamber and display a competitive mechanism. Unfortunately, inevitable resistance associated with this type of inhibition drives the search for non-competitive agents. The multisubunit and multicatalytic "proteolytic machine" such as the proteasome is occasionally found to be affected by agents with other primary targets. For example the immunosuppressive agent rapamycin has been shown to allosterically inhibit the proteasome albeit at levels far higher than its mTOR related efficacy. As part of an ongoing program to search for novel proteasome-targeting pharmacophores, we identified the binding domain of rapamycin as required for proteasome inhibition even without the macrocyclic context of the parent compound. By subsequent structure-activity relationship studies, we generated a pipecolic ester derivative compound 3 representing a new class of proteasome inhibitors. Compound 3 affects the core proteasome activities and proliferation of cancer cells with low micromolar/high nanomolar efficacy. Molecular modeling, atomic force microscopy imaging and biochemical data suggest that compound 3 binds into one of intersubunit pockets in the proteasomal α ring and destabilizes the α face and the gate. The α face is used as a docking area for proteasome-regulating protein modules and the gate is critical for controlling access to the catalytic chamber. Thus, the pipecolic ester template elicits a new and attractive mechanism for proteasome inhibition distinct from classical competitive drugs.
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Affiliation(s)
- Matthew B Giletto
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA.
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3
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Santoro AM, Lanza V, Bellia F, Sbardella D, Tundo GR, Cannizzo A, Grasso G, Arizzi M, Nicoletti VG, Alcaro S, Costa G, Pietropaolo A, Malgieri G, D'Abrosca G, Fattorusso R, García‐Viñuales S, Ahmed IMM, Coletta M, Milardi D. Pyrazolones Activate the Proteasome by Gating Mechanisms and Protect Neuronal Cells from β‐Amyloid Toxicity. ChemMedChem 2019; 15:302-316. [DOI: 10.1002/cmdc.201900612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/28/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Anna Maria Santoro
- Consiglio Nazionale delle Ricerche Istituto di Cristallografia Via P. Gaifami 18 95126 Catania Italy
| | - Valeria Lanza
- Consiglio Nazionale delle Ricerche Istituto di Cristallografia Via P. Gaifami 18 95126 Catania Italy
| | - Francesco Bellia
- Consiglio Nazionale delle Ricerche Istituto di Cristallografia Via P. Gaifami 18 95126 Catania Italy
| | - Diego Sbardella
- IRCCS – Fondazione G.B. Bietti Via Livenza 3 00189 Roma Italy
- Università di Roma Tor Vergata Dipartimento di Scienze Cliniche e Medicina Traslazionale Via Montpellier 1 00133 Roma Italy
| | - Grazia R. Tundo
- Università di Roma Tor Vergata Dipartimento di Scienze Cliniche e Medicina Traslazionale Via Montpellier 1 00133 Roma Italy
| | - Alessandra Cannizzo
- Università degli Studi di Catania Dipartimento di Scienze Chimiche V.le Andrea Doria 6 95125 Catania Italy
| | - Giuseppe Grasso
- Università degli Studi di Catania Dipartimento di Scienze Chimiche V.le Andrea Doria 6 95125 Catania Italy
| | - Mariaconcetta Arizzi
- Università degli Studi di Catania Dipartimento di Scienze Chimiche V.le Andrea Doria 6 95125 Catania Italy
| | - Vincenzo G. Nicoletti
- Università degli Studi di Catania Dipartimento di Scienze Biomediche e Biotecnologiche (BIOMETEC) Università di Catania Via Santa Sofia 97 95124 Catania
| | - Stefano Alcaro
- Università degli Studi Magna Graecia di Catanzaro Dipartimento di Scienze della Salute Viale Europa 88100 Catanzaro Italy
| | - Giosuè Costa
- Università degli Studi Magna Graecia di Catanzaro Dipartimento di Scienze della Salute Viale Europa 88100 Catanzaro Italy
| | - Adriana Pietropaolo
- Università degli Studi Magna Graecia di Catanzaro Dipartimento di Scienze della Salute Viale Europa 88100 Catanzaro Italy
| | - Gaetano Malgieri
- Università della Campania “Luigi Vanvitelli” Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche Via Vivaldi 43 81100 Caserta Italy
| | - Gianluca D'Abrosca
- Università della Campania “Luigi Vanvitelli” Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche Via Vivaldi 43 81100 Caserta Italy
| | - Roberto Fattorusso
- Università della Campania “Luigi Vanvitelli” Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche Via Vivaldi 43 81100 Caserta Italy
| | - Sara García‐Viñuales
- Consiglio Nazionale delle Ricerche Istituto di Cristallografia Via P. Gaifami 18 95126 Catania Italy
| | - Ikhlas M. M. Ahmed
- Consiglio Nazionale delle Ricerche Istituto di Cristallografia Via P. Gaifami 18 95126 Catania Italy
| | - Massimiliano Coletta
- Università di Roma Tor Vergata Dipartimento di Scienze Cliniche e Medicina Traslazionale Via Montpellier 1 00133 Roma Italy
| | - Danilo Milardi
- Consiglio Nazionale delle Ricerche Istituto di Cristallografia Via P. Gaifami 18 95126 Catania Italy
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4
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Coleman RA, Trader DJ. Methods to Discover and Evaluate Proteasome Small Molecule Stimulators. Molecules 2019; 24:molecules24122341. [PMID: 31242677 PMCID: PMC6630500 DOI: 10.3390/molecules24122341] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/18/2019] [Accepted: 06/22/2019] [Indexed: 11/25/2022] Open
Abstract
Protein accumulation has been identified as a characteristic of many degenerative conditions, such as neurodegenerative diseases and aging. In most cases, these conditions also present with diminished protein degradation. The ubiquitin-proteasome system (UPS) is responsible for the degradation of the majority of proteins in cells; however, the activity of the proteasome is reduced in these disease states, contributing to the accumulation of toxic protein. It has been hypothesized that proteasome activity, both ubiquitin-dependent and -independent, can be chemically stimulated to reduce the load of protein in diseased cells. Several methods exist to identify and characterize stimulators of proteasome activity. In this review, we detail the ways in which protease activity can be enhanced and analyze the biochemical and cellular methods of identifying stimulators of both the ubiquitin-dependent and -independent proteasome activities.
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Affiliation(s)
- Rachel A Coleman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, USA.
| | - Darci J Trader
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, USA.
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Giżyńska M, Witkowska J, Karpowicz P, Rostankowski R, Chocron ES, Pickering AM, Osmulski P, Gaczynska M, Jankowska E. Proline- and Arginine-Rich Peptides as Flexible Allosteric Modulators of Human Proteasome Activity. J Med Chem 2018; 62:359-370. [PMID: 30452262 PMCID: PMC6796967 DOI: 10.1021/acs.jmedchem.8b01025] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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Proline-
and arginine-rich peptide PR11 is an allosteric inhibitor
of 20S proteasome. We modified its sequence inter alia by introducing
HbYX, RYX, or RHbX C-terminal extensions (Hb, hydrophobic moiety;
R, arginine; Y, tyrosine; X, any residue). Consequently, we were able
to improve inhibitory potency or to convert inhibitors into strong
activators: the former with an aromatic penultimate Hb residue and
the latter with the HbYX motif. The PR peptide activator stimulated
20S proteasome in vitro to efficiently degrade protein substrates,
such as α-synuclein and enolase, but also activated proteasome
in cultured fibroblasts. The positive and negative PR modulators differently
influenced the proteasome conformational dynamics and affected opening
of the substrate entry pore. The resolved crystal structure showed
PR inhibitor bound far from the active sites, at the proteasome outer
face, in the pocket used by natural activators. Our studies indicate
the opportunity to tune proteasome activity by allosteric regulators
based on PR peptide scaffold.
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Affiliation(s)
- Małgorzata Giżyńska
- Department of Biomedical Chemistry, Faculty of Chemistry , University of Gdansk , Wita Stwosza 63 , 80-308 Gdansk , Poland
| | - Julia Witkowska
- Department of Biomedical Chemistry, Faculty of Chemistry , University of Gdansk , Wita Stwosza 63 , 80-308 Gdansk , Poland
| | - Przemysław Karpowicz
- Department of Biomedical Chemistry, Faculty of Chemistry , University of Gdansk , Wita Stwosza 63 , 80-308 Gdansk , Poland
| | - Rafał Rostankowski
- Department of Biomedical Chemistry, Faculty of Chemistry , University of Gdansk , Wita Stwosza 63 , 80-308 Gdansk , Poland
| | - Estrella S Chocron
- Department of Molecular Medicine, The Barshop Institute for Longevity and Aging Studies , University of Texas Health Science Center , 15355 Lambda Drive , San Antonio , Texas 78245 , United States
| | - Andrew M Pickering
- Department of Molecular Medicine, The Barshop Institute for Longevity and Aging Studies , University of Texas Health Science Center , 15355 Lambda Drive , San Antonio , Texas 78245 , United States
| | - Pawel Osmulski
- Department of Molecular Medicine, Institute of Biotechnology , University of Texas Health Science Center , 15355 Lambda Drive , San Antonio , Texas 78245 , United States
| | - Maria Gaczynska
- Department of Molecular Medicine, Institute of Biotechnology , University of Texas Health Science Center , 15355 Lambda Drive , San Antonio , Texas 78245 , United States
| | - Elżbieta Jankowska
- Department of Biomedical Chemistry, Faculty of Chemistry , University of Gdansk , Wita Stwosza 63 , 80-308 Gdansk , Poland
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Njomen E, Osmulski PA, Jones CL, Gaczynska M, Tepe JJ. Small Molecule Modulation of Proteasome Assembly. Biochemistry 2018; 57:4214-4224. [PMID: 29897236 DOI: 10.1021/acs.biochem.8b00579] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The 20S proteasome is the main protease that directly targets intrinsically disordered proteins (IDPs) for proteolytic degradation. Mutations, oxidative stress, or aging can induce the buildup of IDPs resulting in incorrect signaling or aggregation, associated with the pathogenesis of many cancers and neurodegenerative diseases. Drugs that facilitate 20S-mediated proteolysis therefore have many potential therapeutic applications. We report herein the modulation of proteasome assembly by the small molecule TCH-165, resulting in an increase in 20S levels. The increase in the level of free 20S corresponds to enhanced proteolysis of IDPs, including α-synuclein, tau, ornithine decarboxylase, and c-Fos, but not structured proteins. Clearance of ubiquitinated protein was largely maintained by single capped proteasome complexes (19S-20S), but accumulation occurs when all 19S capped proteasome complexes are depleted. This study illustrates the first example of a small molecule capable of targeting disordered proteins for degradation by regulating the dynamic equilibrium between different proteasome complexes.
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Affiliation(s)
- Evert Njomen
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Pawel A Osmulski
- Institute of Biotechnology , University of Texas Health Science Center at San Antonio , 15355 Lambda Drive , San Antonio , Texas 78245 , United States
| | - Corey L Jones
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Maria Gaczynska
- Institute of Biotechnology , University of Texas Health Science Center at San Antonio , 15355 Lambda Drive , San Antonio , Texas 78245 , United States
| | - Jetze J Tepe
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
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7
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Jones CL, Njomen E, Sjögren B, Dexheimer TS, Tepe JJ. Small Molecule Enhancement of 20S Proteasome Activity Targets Intrinsically Disordered Proteins. ACS Chem Biol 2017; 12:2240-2247. [PMID: 28719185 DOI: 10.1021/acschembio.7b00489] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 20S proteasome is the main protease for the degradation of oxidatively damaged and intrinsically disordered proteins. When accumulation of disordered or oxidatively damaged proteins exceeds proper clearance in neurons, imbalanced pathway signaling or aggregation occurs, which have been implicated in the pathogenesis of several neurological disorders. Screening of the NIH Clinical Collection and Prestwick libraries identified the neuroleptic agent chlorpromazine as a lead agent capable of enhancing 20S proteasome activity. Chemical manipulation of chlorpromazine abrogated its D2R receptor binding affinity while retaining its ability to enhance 20S mediated proteolysis at low micromolar concentrations. The resulting small molecule enhancers of 20S proteasome activity induced the degradation of intrinsically disordered proteins, α-synuclein, and tau but not structured proteins. These small molecule 20S agonists can serve as leads to explore the therapeutic potential of 20S activation or as new tools to provide insight into the yet unclear mechanics of 20S-gate regulation.
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Affiliation(s)
- Corey L. Jones
- Department
of Chemistry and ‡Department of Pharmacology and Toxicology, Michigan State University, East
Lansing, Michigan 48824, United States
| | - Evert Njomen
- Department
of Chemistry and ‡Department of Pharmacology and Toxicology, Michigan State University, East
Lansing, Michigan 48824, United States
| | - Benita Sjögren
- Department
of Chemistry and ‡Department of Pharmacology and Toxicology, Michigan State University, East
Lansing, Michigan 48824, United States
| | - Thomas S. Dexheimer
- Department
of Chemistry and ‡Department of Pharmacology and Toxicology, Michigan State University, East
Lansing, Michigan 48824, United States
| | - Jetze J. Tepe
- Department
of Chemistry and ‡Department of Pharmacology and Toxicology, Michigan State University, East
Lansing, Michigan 48824, United States
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8
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Gaczynska M, Karpowicz P, Stuart CE, Norton MG, Teckman JH, Marszal E, Osmulski PA. AFM Imaging Reveals Topographic Diversity of Wild Type and Z Variant Polymers of Human α1-Proteinase Inhibitor. PLoS One 2016; 11:e0151902. [PMID: 27008547 PMCID: PMC4805282 DOI: 10.1371/journal.pone.0151902] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 03/04/2016] [Indexed: 12/17/2022] Open
Abstract
α1-Proteinase inhibitor (antitrypsin) is a canonical example of the serpin family member that binds and inhibits serine proteases. The natural metastability of serpins is crucial to carry out structural rearrangements necessary for biological activity. However, the enhanced metastability of the mutant Z variant of antitrypsin, in addition to folding defect, may substantially contribute to its polymerization, a process leading to incurable serpinopathy. The metastability also impedes structural studies on the polymers. There are no crystal structures of Z monomer or any kind of polymers larger than engineered wild type (WT) trimer. Our understanding of polymerization mechanisms is based on biochemical data using in vitro generated WT oligomers and molecular simulations. Here we applied atomic force microscopy (AFM) to compare topography of monomers, in vitro formed WT oligomers, and Z type polymers isolated from transgenic mouse liver. We found the AFM images of monomers closely resembled an antitrypsin outer shell modeled after the crystal structure. We confirmed that the Z variant demonstrated higher spontaneous propensity to dimerize than WT monomers. We also detected an unexpectedly broad range of different types of polymers with periodicity and topography depending on the applied method of polymerization. Short linear oligomers of unit arrangement similar to the Z polymers were especially abundant in heat-treated WT preparations. Long linear polymers were a prominent and unique component of liver extracts. However, the liver preparations contained also multiple types of oligomers of topographies undistinguishable from those found in WT samples polymerized with heat, low pH or guanidine hydrochloride treatments. In conclusion, we established that AFM is an excellent technique to assess morphological diversity of antitrypsin polymers, which is important for etiology of serpinopathies. These data also support previous, but controversial models of in vivo polymerization showing a surprising diversity of polymer topography.
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Affiliation(s)
- Maria Gaczynska
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Przemyslaw Karpowicz
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Christine E. Stuart
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Malgorzata G. Norton
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Jeffrey H. Teckman
- Department of Pediatrics and Biochemistry, Saint Louis University School of Medicine, Cardinal Glennon Children’s Medical Center, St. Louis, Missouri, United States of America
| | - Ewa Marszal
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Pawel A. Osmulski
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
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9
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Gaczynska M, Osmulski PA. Harnessing proteasome dynamics and allostery in drug design. Antioxid Redox Signal 2014; 21:2286-301. [PMID: 24410482 PMCID: PMC4241894 DOI: 10.1089/ars.2013.5816] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 01/12/2014] [Indexed: 12/14/2022]
Abstract
SIGNIFICANCE The proteasome is the essential protease that is responsible for regulated cleavage of the bulk of intracellular proteins. Its central role in cellular physiology has been exploited in therapies against aggressive cancers where proteasome-specific competitive inhibitors that block proteasome active centers are very effectively used. However, drugs regulating this essential protease are likely to have broader clinical usefulness. The non-catalytic sites of the proteasome emerge as an attractive alternative target in search of highly specific and diverse proteasome regulators. RECENT ADVANCES Crystallographic models of the proteasome leave the false impression of fixed structures with minimal molecular dynamics lacking long-distance allosteric signaling. However, accumulating biochemical and structural observations strongly support the notion that the proteasome is regulated by precise allosteric interactions arising from protein dynamics, encouraging the active search for allosteric regulators. Here, we discuss properties of several promising compounds that affect substrate gating and processing in antechambers, and interactions of the catalytic core with regulatory proteins. CRITICAL ISSUES Given the structural complexity of proteasome assemblies, it is a painstaking process to better understand their allosteric regulation and molecular dynamics. Here, we discuss the challenges and achievements in this field. We place special emphasis on the role of atomic force microscopy imaging in probing the allostery and dynamics of the proteasome, and in dissecting the mechanisms involving small-molecule allosteric regulators. FUTURE DIRECTIONS New small-molecule allosteric regulators may become a next generation of drugs targeting the proteasome, which is critical to the development of new therapies in cancers and other diseases.
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Affiliation(s)
- Maria Gaczynska
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio , San Antonio, Texas
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10
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Rodriguez KA, Osmulski PA, Pierce A, Weintraub ST, Gaczynska M, Buffenstein R. A cytosolic protein factor from the naked mole-rat activates proteasomes of other species and protects these from inhibition. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1842:2060-72. [PMID: 25018089 PMCID: PMC4829350 DOI: 10.1016/j.bbadis.2014.07.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/11/2014] [Accepted: 07/03/2014] [Indexed: 10/25/2022]
Abstract
The naked mole-rat maintains robust proteostasis and high levels of proteasome-mediated proteolysis for most of its exceptional (~31years) life span. Here, we report that the highly active proteasome from the naked mole-rat liver resists attenuation by a diverse suite of proteasome-specific small molecule inhibitors. Moreover, mouse, human, and yeast proteasomes exposed to the proteasome-depleted, naked mole-rat cytosolic fractions, recapitulate the observed inhibition resistance, and mammalian proteasomes also show increased activity. Gel filtration coupled with mass spectrometry and atomic force microscopy indicates that these traits are supported by a protein factor that resides in the cytosol. This factor interacts with the proteasome and modulates its activity. Although Heat shock protein 72 kDa (HSP72) and Heat shock protein 40 kDa (Homolog of bacterial DNAJ1) (HSP40(Hdj1)) are among the constituents of this factor, the observed phenomenon, such as increasing peptidase activity and protecting against inhibition cannot be reconciled with any known chaperone functions. This novel function may contribute to the exceptional protein homeostasis in the naked mole-rat and allow it to successfully defy aging.
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Affiliation(s)
- Karl A Rodriguez
- Sam and Ann Barshop Institute for Aging and Longevity Studies, University of Texas Health Science Center at San Antonio, 15355 Lambda Dr., San Antonio, TX 78245, USA; Department of Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Pawel A Osmulski
- Sam and Ann Barshop Institute for Aging and Longevity Studies, University of Texas Health Science Center at San Antonio, 15355 Lambda Dr., San Antonio, TX 78245, USA; Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 15355 Lambda Dr., San Antonio, TX 78245, USA
| | - Anson Pierce
- Mitchell Center for Neurodegenerative Diseases, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Susan T Weintraub
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Maria Gaczynska
- Sam and Ann Barshop Institute for Aging and Longevity Studies, University of Texas Health Science Center at San Antonio, 15355 Lambda Dr., San Antonio, TX 78245, USA; Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 15355 Lambda Dr., San Antonio, TX 78245, USA
| | - Rochelle Buffenstein
- Sam and Ann Barshop Institute for Aging and Longevity Studies, University of Texas Health Science Center at San Antonio, 15355 Lambda Dr., San Antonio, TX 78245, USA; Department of Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA; Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
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11
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Abstract
Rapamycin is a canonical allosteric inhibitor of the mammalian tarpet of rapamycin (mTOR) kinase with immunosuppressive and proapoptotic activities. We found that in vitro rapamycin also regulates the proteasome, which is an essential intracellular protease of the ubiquitin-proteasome pathway. Rapamycin inhibits proteinase and selected peptidase activities of the catalytic core proteasome at low micromolar concentrations. Moreover, the drug interferes with binding of the 19S cap essential for processing of polyubiquitinylated substrates and with the PA200 proteasome activator to the 20S catalytic core proteasome. These protein complexes are known to bind to specific grooves on the α face region of the 20S core. Treatment with rapamycin affects the conformational dynamics of the proteasomal gate, which is centrally positioned within the α face and allosterically regulated element responsible for the intake of substrates. We showed that rapamycin shares all the proteasome targeting properties not only with other two-domain, closed-ring analogs (rapalogs) but also with its single domain mimics and seco-rapamycin, which is the first in vivo open-ring metabolite of rapamycin that does not affect mTOR. We hypothesize that rapamycin and related compounds bind to the α face and allosterically impact proteasome function. This article discusses the implications of our findings for the mechanism of in vivo actions of rapamycin and for the design of novel allosteric drugs targeting the proteasome.
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Affiliation(s)
- Pawel A Osmulski
- University of Texas Health Science Center at San Antonio, Department of Molecular Medicine, Institute of Biotechnology, 15355 Lambda Drive, San Antonio, TX 78245, USA
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12
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Abstract
The ubiquitin-proteasome system (UPS) is involved in many cellular processes including protein degradation. Degradation of a protein via this system involves two successive steps: ubiquitination and degradation. Ubiquitination tags the target protein with ubiquitin-like proteins (UBLs), such as ubiquitin, small ubiquitin-like modifier (SUMO) and NEDD8, via a cascade involving three enzymes: activating enzyme E1, conjugating enzyme E2 and E3 ubiquitin ligases. The proteasomes recognize the UBL-tagged substrate proteins and degrade them. Accumulating evidence indicates that allostery is a central player in the regulation of ubiquitination, as well as deubiquitination and degradation. Here, we provide an overview of the key mechanistic roles played by allostery in all steps of these processes, and highlight allosteric drugs targeting them. Throughout the review, we emphasize the crucial mechanistic role played by linkers in allosterically controlling the UPS action by biasing the sampling of the conformational space, which facilitate the catalytic reactions of the ubiquitination and degradation. Finally, we propose that allostery may similarly play key roles in the regulation of molecular machines in the cell, and as such allosteric drugs can be expected to be increasingly exploited in therapeutic regimes.
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Affiliation(s)
- Jin Liu
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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