1
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Pereira GP, Jiménez-García B, Pellarin R, Launay G, Wu S, Martin J, Souza PCT. Rational Prediction of PROTAC-Compatible Protein-Protein Interfaces by Molecular Docking. J Chem Inf Model 2023; 63:6823-6833. [PMID: 37877240 DOI: 10.1021/acs.jcim.3c01154] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Proteolysis targeting chimeras (PROTACs) are heterobifunctional ligands that mediate the interaction between a protein target and an E3 ligase, resulting in a ternary complex, whose interaction with the ubiquitination machinery leads to target degradation. This technology is emerging as an exciting new avenue for therapeutic development, with several PROTACs currently undergoing clinical trials targeting cancer. Here, we describe a general and computationally efficient methodology combining restraint-based docking, energy-based rescoring, and a filter based on the minimal solvent-accessible surface distance to produce PROTAC-compatible PPIs suitable for when there is no a priori known PROTAC ligand. In a benchmark employing a manually curated data set of 13 ternary complex crystals, we achieved an accuracy of 92% when starting from bound structures and 77% when starting from unbound structures, respectively. Our method only requires that the ligand-bound structures of the monomeric forms of the E3 ligase and target proteins be given to run, making it general, accurate, and highly efficient, with the ability to impact early-stage PROTAC-based drug design campaigns where no structural information about the ternary complex structure is available.
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Affiliation(s)
- Gilberto P Pereira
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | | | - Riccardo Pellarin
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | - Guillaume Launay
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | - Sangwook Wu
- PharmCADD, Busan 48792, Republic of Korea
- Department of Physics, Pukyong National University, Busan 48513, Republic of Korea
| | - Juliette Martin
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
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2
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Pinch BJ, Buckley DL, Gleim S, Brittain SM, Tandeske L, D'Alessandro PL, Hauseman ZJ, Lipps J, Xu L, Harvey EP, Schirle M, Sprague ER, Forrester WC, Dovala D, McGregor LM, Thoma CR. A strategy to assess the cellular activity of E3 ligase components against neo-substrates using electrophilic probes. Cell Chem Biol 2021; 29:57-66.e6. [PMID: 34499862 DOI: 10.1016/j.chembiol.2021.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 06/17/2021] [Accepted: 08/20/2021] [Indexed: 01/12/2023]
Abstract
While there are hundreds of predicted E3 ligases, characterizing their applications for targeted protein degradation has proved challenging. Here, we report a chemical biology approach to evaluate the ability of modified recombinant E3 ligase components to support neo-substrate degradation. Bypassing the need for specific E3 ligase binders, we use maleimide-thiol chemistry for covalent functionalization followed by E3 electroporation (COFFEE) in live cells. We demonstrate that electroporated recombinant von Hippel-Lindau (VHL) protein, covalently functionalized at its ligandable cysteine with JQ1 or dasatinib, induces degradation of BRD4 or tyrosine kinases, respectively. Furthermore, by applying COFFEE to SPSB2, a Cullin-RING ligase 5 receptor, as well as to SKP1, the adaptor protein for Cullin-RING ligase 1 F box (SCF) complexes, we validate this method as a powerful approach to define the activity of previously uncharacterized ubiquitin ligase components, and provide further evidence that not only E3 ligase receptors but also adaptors can be directly hijacked for neo-substrate degradation.
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Affiliation(s)
- Benika J Pinch
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
| | - Dennis L Buckley
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Scott Gleim
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Scott M Brittain
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Laura Tandeske
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | | | | | - Jennifer Lipps
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Lei Xu
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Edward P Harvey
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | | | | | - Dustin Dovala
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA.
| | - Lynn M McGregor
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
| | - Claudio R Thoma
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
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3
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Paladino A, D'Angelo F, Noviello TMR, Iavarone A, Ceccarelli M. Structural Model for Recruitment of RIT1 to the LZTR1 E3 Ligase: Evidences from an Integrated Computational Approach. J Chem Inf Model 2021; 61:1875-1888. [PMID: 33792302 PMCID: PMC8154269 DOI: 10.1021/acs.jcim.1c00296] [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] [Indexed: 11/30/2022]
Abstract
Leucine-zipper transcription regulator 1 (LZTR1) is a highly mutated tumor suppressor gene, involved in the pathogenesis of several cancer types and developmental disorders. In proteasomal degradation, it acts as an adaptor protein responsible for the recognition and recruitment of substrates to be ubiquitinated in Cullin3-RING ligase E3 (CRL3) machinery. LZTR1 belongs to the BTB-Kelch family, a multi-domain protein where the Kelch propeller plays as the substrate recognition region and for which no experimental structure has been solved. Recently, large effort mutational analyses pointed to the role of disease-associated LZTR1 mutations in the RAS/MAPK signaling pathway and RIT1, a small Ras-related GTPase protein, has been identified by mass spectroscopy to interact with LZTR1. Hence, a better understanding of native structure, molecular mechanism, and substrate specificity would help clarifying the role of LZTR1 in pathological diseases, thus promoting advancement in the development of novel therapeutic strategies. Here, we address the interaction model between adaptor LZTR1 and substrate RIT1 by applying an integrated computational approach, including molecular modeling and docking techniques. We observe that the interaction model LZTR1-RIT1 is stabilized by an electrostatic bond network established between the two protein surfaces, which is reminiscent of homologous ubiquitin ligases complexes. Then, running MD simulations, we characterize differential conformational dynamics of the multi-domain LZTR1, offering interesting implications on the mechanistic role of specific point mutations. We identify G248R and R283Q as damaging mutations involved in the recognition process of the substrate RIT1 and R412C as a possible allosteric mutation from the Kelch to the C-term BTB-domain. Our findings provide important structural insights on targeting CRL3s for drug discovery.
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Affiliation(s)
- Antonella Paladino
- BIOGEM Istituto di Ricerche Genetiche "G. Salvatore", via Camporeale, Ariano Irpino 83031, Italy
| | - Fulvio D'Angelo
- BIOGEM Istituto di Ricerche Genetiche "G. Salvatore", via Camporeale, Ariano Irpino 83031, Italy.,Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Ave, New York, New York 10032, United States
| | - Teresa Maria Rosaria Noviello
- BIOGEM Istituto di Ricerche Genetiche "G. Salvatore", via Camporeale, Ariano Irpino 83031, Italy.,Department of Electrical Engineering and Information Technology (DIETI), University of Naples "Federico II", Via Claudio 21, Naples 80128, Italy
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Ave, New York, New York 10032, United States.,Department of Pathology and Cell Biology, Columbia University Medical Center, 1130 St Nicholas Ave, New York , New York 10032 United States.,Department of Neurology, Columbia University Medical Center, 1130 St Nicholas Ave, New York, New York 10032, United States
| | - Michele Ceccarelli
- BIOGEM Istituto di Ricerche Genetiche "G. Salvatore", via Camporeale, Ariano Irpino 83031, Italy.,Department of Electrical Engineering and Information Technology (DIETI), University of Naples "Federico II", Via Claudio 21, Naples 80128, Italy
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4
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Maneiro M, De Vita E, Conole D, Kounde CS, Zhang Q, Tate EW. PROTACs, molecular glues and bifunctionals from bench to bedside: Unlocking the clinical potential of catalytic drugs. PROGRESS IN MEDICINAL CHEMISTRY 2021; 60:67-190. [PMID: 34147206 DOI: 10.1016/bs.pmch.2021.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The vast majority of currently marketed drugs rely on small molecules with an 'occupancy-driven' mechanism of action (MOA). Therefore, the efficacy of these therapeutics depends on a high degree of target engagement, which often requires high dosages and enhanced drug exposure at the target site, thus increasing the risk of off-target toxicities (Churcher, 2018 [1]). Although small molecule drugs have been successfully used as treatments for decades, tackling a variety of disease-relevant targets with a defined binding site, many relevant therapeutic targets remain challenging to drug due, for example, to lack of well-defined binding pockets or large protein-protein interaction (PPI) interfaces which resist interference (Dang et al., 2017 [2]). In the quest for alternative therapeutic approaches to address different pathologies and achieve enhanced efficacy with reduced side effects, ligand-induced targeted protein degradation (TPD) has gained the attention of many research groups both in academia and in industry in the last two decades. This therapeutic modality represents a novel paradigm compared to conventional small-molecule inhibitors. To pursue this strategy, heterobifunctional small molecule degraders, termed PROteolysis TArgeting Chimeras (PROTACs) have been devised to artificially redirect a protein of interest (POI) to the cellular protein homeostasis machinery for proteasomal degradation (Chamberlain et al., 2019 [3]). In this chapter, the development of PROTACs will first be discussed providing a historical perspective in parallel to the experimental progress made to understand this novel therapeutic modality. Furthermore, common strategies for PROTAC design, including assays and troubleshooting tips will be provided for the reader, before presenting a compendium of all PROTAC targets reported in the literature to date. Due to the recent advancement of these molecules into clinical trials, consideration of pharmacokinetics and pharmacodynamic properties will be introduced, together with the biotech landscape that has developed from the success of PROTACs. Finally, an overview of subsequent strategies for targeted protein degradation will be presented, concluding with further scientific quests triggered by the invention of PROTACs.
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Affiliation(s)
- M Maneiro
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - E De Vita
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - D Conole
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - C S Kounde
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - Q Zhang
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - E W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom.
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5
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The functional analysis of Cullin 7 E3 ubiquitin ligases in cancer. Oncogenesis 2020; 9:98. [PMID: 33130829 PMCID: PMC7603503 DOI: 10.1038/s41389-020-00276-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 09/11/2020] [Accepted: 09/21/2020] [Indexed: 01/09/2023] Open
Abstract
Cullin (CUL) proteins have critical roles in development and cancer, however few studies on CUL7 have been reported due to its characteristic molecular structure. CUL7 forms a complex with the ROC1 ring finger protein, and only two F-box proteins Fbxw8 and Fbxw11 have been shown to bind to CUL7. Interestingly, CUL7 can interact with its substrates by forming a novel complex that is independent of these two F-box proteins. The biological implications of CUL-ring ligase 7 (CRL7) suggest that the CRL7 may not only perform a proteolytic function but may also play a non-proteolytic role. Among the existing studied CRL7-based E3 ligases, CUL7 exerts both tumor promotion and suppression in a context-dependent manner. Currently, the mechanism of CUL7 in cancer remains unclear, and no studies have addressed potential therapies targeting CUL7. Consistent with the roles of the various CRL7 adaptors exhibit, targeting CRL7 might be an effective strategy for cancer prevention and treatment. We systematically describe the recent major advances in understanding the role of the CUL7 E3 ligase in cancer and further summarize its potential use in clinical therapy.
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6
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Pan Y, Shlyakhtenko LS, Lyubchenko YL. High-speed atomic force microscopy directly visualizes conformational dynamics of the HIV Vif protein in complex with three host proteins. J Biol Chem 2020; 295:11995-12001. [PMID: 32587092 PMCID: PMC7443491 DOI: 10.1074/jbc.ra120.014442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/23/2020] [Indexed: 11/06/2022] Open
Abstract
Vif (viral infectivity factor) is a protein that is essential for the replication of the HIV-1 virus. The key function of Vif is to disrupt the antiviral activity of host APOBEC3 (apolipoprotein B mRNA-editing enzyme catalytic subunit 3) proteins, which mutate viral nucleic acids. Inside the cell, Vif binds to the host cell proteins Elongin-C, Elongin-B, and core-binding factor subunit β, forming a four-protein complex called VCBC. The structure of VCBC-Cullin5 has recently been solved by X-ray crystallography, and, using molecular dynamics simulations, the dynamics of VCBC have been characterized. Here, we applied time-lapse high-speed atomic force microscopy to visualize the conformational changes of the VCBC complex. We determined the three most favorable conformations of this complex, which we identified as the triangle, dumbbell, and globular structures. Moreover, we characterized the dynamics of each of these structures. Our data revealed the very dynamic behavior of all of them, with the triangle and dumbbell structures being the most dynamic. These findings provide insight into the structure and dynamics of the VCBC complex and may support efforts to improve HIV treatment, because Vif is essential for virus survival in the cell.
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Affiliation(s)
- Yangang Pan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Luda S Shlyakhtenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska, USA.
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7
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Horx P, Geyer A. Defining the mobility range of a hinge-type connection using molecular dynamics and metadynamics. PLoS One 2020; 15:e0230962. [PMID: 32282813 PMCID: PMC7153902 DOI: 10.1371/journal.pone.0230962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 03/12/2020] [Indexed: 01/29/2023] Open
Abstract
A designed disulfide-rich β-hairpin peptide that dimerizes spontaneously served as a hinge-type connection between proteins. Here, we analyze the range of dynamics of this hinge dimer with the aim of proposing new applications for the DNA-encodable peptide and establishing guidelines for the computational analysis of other disulfide hinges. A recent structural analysis based on nuclear magnetic resonance spectroscopy and ion mobility spectrometry revealed an averaged conformation in the hinge region which motivated us to investigate the dynamic behavior using a combination of molecular dynamics simulation, metadynamics and free energy surface analysis to characterize the conformational space available to the hinge. Principal component analysis uncovered two slow modes of the peptide, namely, the opening and closing motion and twisting of the two β-hairpins assembling the hinge. Applying a collective variable (CV) that mimics the first dominating mode, led to a major expansion of the conformational space. The description of the dynamics could be achieved by analysis of the opening angle and the twisting of the β-hairpins and, thus, offers a methodology that can also be transferred to other derivatives. It has been demonstrated that the hinge peptide’s lowest energy conformation consists of a large opening angle and strong twist but is separated by small energy barriers and can, thus, adopt a closed and untwisted structure. With the aim of proposing further applications for the hinge peptide, we simulated its behavior in the sterically congested environment of a four-helix bundle. Preliminary investigations show that one helix is pushed out and a three-helix bundle forms. The insights gained into the dynamics of the tetra-disulfide peptide and analytical guidelines developed in this study may contribute to the understanding of the structure and function of more complex hinge-type proteins, such as the IgG antibody family.
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Affiliation(s)
- Philip Horx
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Armin Geyer
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
- * E-mail:
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8
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Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase. Nat Commun 2019; 10:2534. [PMID: 31182716 PMCID: PMC6557900 DOI: 10.1038/s41467-019-10190-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/26/2019] [Indexed: 01/10/2023] Open
Abstract
The suppressor of cytokine signaling 2 (SOCS2) acts as substrate recognition subunit of a Cullin5 E3 ubiquitin ligase complex. SOCS2 binds to phosphotyrosine-modified epitopes as degrons for ubiquitination and proteasomal degradation, yet the molecular basis of substrate recognition has remained elusive. Here, we report co-crystal structures of SOCS2-ElonginB-ElonginC in complex with phosphorylated peptides from substrates growth hormone receptor (GHR-pY595) and erythropoietin receptor (EpoR-pY426) at 1.98 Å and 2.69 Å, respectively. Both peptides bind in an extended conformation recapitulating the canonical SH2 domain-pY pose, but capture different conformations of the EF loop via specific hydrophobic interactions. The flexible BG loop is fully defined in the electron density, and does not contact the substrate degron directly. Cancer-associated SNPs located around the pY pocket weaken substrate-binding affinity in biophysical assays. Our findings reveal insights into substrate recognition and specificity by SOCS2, and provide a blueprint for small molecule ligand design. The suppressor of cytokine signaling 2 (SOCS2) is a component of the Cullin5 E3 ubiquitin ligase complex. Here the authors provide insights into substrate recognition and specificity of SOCS2 by determining the crystal structures of the SOCS2-ElonginB-ElonginC in complex with phosphorylated peptides from two of its substrates the growth hormone receptor and erythropoietin receptor.
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9
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Ball KA, Chan LM, Stanley DJ, Tierney E, Thapa S, Ta HM, Burton L, Binning JM, Jacobson MP, Gross JD. Conformational Dynamics of the HIV-Vif Protein Complex. Biophys J 2019; 116:1432-1445. [PMID: 30961890 PMCID: PMC6486493 DOI: 10.1016/j.bpj.2019.03.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/27/2019] [Accepted: 03/02/2019] [Indexed: 12/29/2022] Open
Abstract
Human immunodeficiency virus-1 viral infectivity factor (Vif) is an intrinsically disordered protein responsible for the ubiquitination of the APOBEC3 (A3) antiviral proteins. Vif folds when it binds Cullin-RING E3 ligase 5 and the transcription cofactor CBF-β. A five-protein complex containing the substrate receptor (Vif, CBF-β, Elongin-B, Elongin-C (VCBC)) and Cullin5 (CUL5) has a published crystal structure, but dynamics of this VCBC-CUL5 complex have not been characterized. Here, we use molecular dynamics (MD) simulations and NMR to characterize the dynamics of the VCBC complex with and without CUL5 and an A3 protein bound. Our simulations show that the VCBC complex undergoes global dynamics involving twisting and clamshell opening of the complex, whereas VCBC-CUL5 maintains a more static conformation, similar to the crystal structure. This observation from MD is supported by methyl-transverse relaxation-optimized spectroscopy NMR data, which indicates that the VCBC complex without CUL5 is dynamic on the μs-ms timescale. Our NMR data also show that the VCBC complex is more conformationally restricted when bound to the antiviral APOBEC3F (one of the A3 proteins), consistent with our MD simulations. Vif contains a flexible linker region located at the hinge of the VCBC complex, which changes conformation in conjunction with the global dynamics of the complex. Like other substrate receptors, VCBC can exist alone or in complex with CUL5 and other proteins in cells. Accordingly, the VCBC complex could be a good target for therapeutics that would inhibit full assembly of the ubiquitination complex by stabilizing an alternate VCBC conformation.
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Affiliation(s)
- K Aurelia Ball
- Department of Chemistry, Skidmore College, Saratoga Springs, New York.
| | - Lieza M Chan
- Department of Chemistry, Skidmore College, Saratoga Springs, New York
| | - David J Stanley
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Elise Tierney
- Department of Chemistry, Skidmore College, Saratoga Springs, New York
| | - Sampriti Thapa
- Department of Chemistry, Skidmore College, Saratoga Springs, New York
| | - Hai M Ta
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Lily Burton
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Jennifer M Binning
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - John D Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California.
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10
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Lucas X, Van Molle I, Ciulli A. Surface Probing by Fragment-Based Screening and Computational Methods Identifies Ligandable Pockets on the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase. J Med Chem 2018; 61:7387-7393. [PMID: 30040896 PMCID: PMC6109845 DOI: 10.1021/acs.jmedchem.8b00842] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Beyond the targeting of E3 ubiquitin ligases to inhibit protein homeostasis, E3 ligase binders can be repurposed as targeted protein degraders (PROTACs or molecular glues). We sought to identify new binders of the VHL E3 ligase by biophysical fragment-based screening followed by X-ray crystallographic soaking. We identified fragments binding at the ElonginC:Cullin2 interface and a new cryptic pocket in VHL, along with other potential ligandable sites predicted computationally and found to bind solvent molecules in crystal structures. The elucidated interactions provide starting points for future ligand development.
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Affiliation(s)
- Xavier Lucas
- Division of Biological Chemistry and Drug Discovery, James Black Centre, School of Life Sciences , University of Dundee , Dow Street , Dundee , DD1 5EH , United Kingdom
| | - Inge Van Molle
- Department of Chemistry , University of Cambridge , Cambridge CB2 1EW , United Kingdom
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, James Black Centre, School of Life Sciences , University of Dundee , Dow Street , Dundee , DD1 5EH , United Kingdom
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11
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Cardote TAF, Gadd MS, Ciulli A. Crystal Structure of the Cul2-Rbx1-EloBC-VHL Ubiquitin Ligase Complex. Structure 2018; 25:901-911.e3. [PMID: 28591624 PMCID: PMC5462531 DOI: 10.1016/j.str.2017.04.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/07/2017] [Accepted: 04/28/2017] [Indexed: 01/07/2023]
Abstract
Cullin RING E3 ubiquitin ligases (CRLs) function in the ubiquitin proteasome system to catalyze the transfer of ubiquitin from E2 conjugating enzymes to specific substrate proteins. CRLs are large dynamic complexes and attractive drug targets for the development of small-molecule inhibitors and chemical inducers of protein degradation. The atomic details of whole CRL assembly and interactions that dictate subunit specificity remain elusive. Here we present the crystal structure of a pentameric CRL2VHL complex, composed of Cul2, Rbx1, Elongin B, Elongin C, and pVHL. The structure traps a closed state of full-length Cul2 and a new pose of Rbx1 in a trajectory from closed to open conformation. We characterize hotspots and binding thermodynamics at the interface between Cul2 and pVHL-EloBC and identify mutations that contribute toward a selectivity switch for Cul2 versus Cul5 recognition. Our findings provide structural and biophysical insights into the whole Cul2 complex that could aid future drug targeting.
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Affiliation(s)
- Teresa A F Cardote
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Morgan S Gadd
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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12
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Shafique S, Ali W, Kanwal S, Rashid S. Structural basis for Cullins and RING component inhibition: Targeting E3 ubiquitin pathway conductors for cancer therapeutics. Int J Biol Macromol 2018; 106:532-543. [DOI: 10.1016/j.ijbiomac.2017.08.047] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/04/2017] [Accepted: 08/06/2017] [Indexed: 02/01/2023]
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13
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Conformational Dynamics and Allostery in E2:E3 Interactions Drive Ubiquitination: gp78 and Ube2g2. Structure 2017; 25:794-805.e5. [PMID: 28434917 DOI: 10.1016/j.str.2017.03.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 01/23/2017] [Accepted: 03/24/2017] [Indexed: 12/30/2022]
Abstract
Conformational dynamics plays a fundamental role in molecular recognition and activity in enzymes. The ubiquitin-conjugating enzyme (E2) Ube2g2 functions with the ubiquitin ligase (E3) gp78 to assemble poly-ubiquitin chains on target substrates. Two domains in gp78, RING and G2BR, bind to two distant regions of Ube2g2, and activate it for ubiquitin (Ub) transfer. G2BR increases the affinity between the RING and Ube2g2 by 50-fold, while the RING catalyzes the transfer of Ub from the Ube2g2∼Ub conjugate. How G2BR and RING activate Ube2g2 is unclear. In this work, conformational dynamics in Ube2g2 revealed a clear correlation of binding G2BR and RING with the sequential progression toward Ub transfer. The interrelationship of the existence and exchange between ground and excited states leads to a dynamic energy landscape model, in which redistribution of populations contributes to allostery and activation. These findings provide insight into gp78's modulation of conformational exchange in Ube2g2 to stimulate ubiquitination.
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14
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Onel M, Sumbul F, Liu J, Nussinov R, Haliloglu T. Cullin neddylation may allosterically tune polyubiquitin chain length and topology. Biochem J 2017; 474:781-795. [PMID: 28082425 PMCID: PMC7900908 DOI: 10.1042/bcj20160748] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 01/09/2017] [Accepted: 01/12/2017] [Indexed: 12/13/2022]
Abstract
Conjugation of Nedd8 (neddylation) to Cullins (Cul) in Cul-RING E3 ligases (CRLs) stimulates ubiquitination and polyubiquitination of protein substrates. CRL is made up of two Cul-flanked arms: one consists of the substrate-binding and adaptor proteins and the other consists of E2 and Ring-box protein (Rbx). Polyubiquitin chain length and topology determine the substrate fate. Here, we ask how polyubiquitin chains are accommodated in the limited space available between the two arms and what determines the polyubiquitin linkage topology. We focus on Cul5 and Rbx1 in three states: before Cul5 neddylation (closed state), after neddylation (open state), and after deneddylation, exploiting molecular dynamics simulations and the Gaussian Network Model. We observe that regulation of substrate ubiquitination and polyubiquitination takes place through Rbx1 rotations, which are controlled by Nedd8-Rbx1 allosteric communication. Allosteric propagation proceeds from Nedd8 via Cul5 dynamic hinges and hydrogen bonds between the C-terminal domain of Cul5 (Cul5CTD) and Rbx1 (Cul5CTD residues R538/R569 and Rbx1 residue E67, or Cul5CTD E474/E478/N491 and Rbx1 K105). Importantly, at each ubiquitination step (homogeneous or heterogeneous, linear or branched), the polyubiquitin linkages fit into the distances between the two arms, and these match the inherent CRL conformational tendencies. Hinge sites may constitute drug targets.
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Affiliation(s)
- Melis Onel
- Polymer Research Center and Chemical Engineering Department, Bogazici University, Istanbul, Turkey
| | - Fidan Sumbul
- Polymer Research Center and Chemical Engineering Department, Bogazici University, Istanbul, Turkey
| | - Jin Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, U.S.A
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, U.S.A.
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Turkan Haliloglu
- Polymer Research Center and Chemical Engineering Department, Bogazici University, Istanbul, Turkey
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15
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Abstract
Small-molecule drug discovery has traditionally focused on occupancy of a binding site that directly affects protein function, and this approach typically precludes targeting proteins that lack such amenable sites. Furthermore, high systemic drug exposures may be needed to maintain sufficient target inhibition in vivo, increasing the risk of undesirable off-target effects. Induced protein degradation is an alternative approach that is event-driven: upon drug binding, the target protein is tagged for elimination. Emerging technologies based on proteolysis-targeting chimaeras (PROTACs) that exploit cellular quality control machinery to selectively degrade target proteins are attracting considerable attention in the pharmaceutical industry owing to the advantages they could offer over traditional small-molecule strategies. These advantages include the potential to reduce systemic drug exposure, the ability to counteract increased target protein expression that often accompanies inhibition of protein function and the potential ability to target proteins that are not currently therapeutically tractable, such as transcription factors, scaffolding and regulatory proteins.
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Affiliation(s)
| | - Craig M. Crews
- Departments of Molecular, Cellular & Developmental Biology; Chemistry; Pharmacology, Yale University, New Haven, CT 06511, USA
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16
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Papaleo E, Saladino G, Lambrughi M, Lindorff-Larsen K, Gervasio FL, Nussinov R. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chem Rev 2016; 116:6391-423. [DOI: 10.1021/acs.chemrev.5b00623] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Elena Papaleo
- Computational
Biology Laboratory, Unit of Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Giorgio Saladino
- Department
of Chemistry, University College London, London WC1E 6BT, United Kingdom
| | - Matteo Lambrughi
- Department
of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126 Milan, Italy
| | - Kresten Lindorff-Larsen
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Ruth Nussinov
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick
National Laboratory for Cancer Research, National Cancer Institute Frederick, Frederick, Maryland 21702, United States
- 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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17
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Guharoy M, Bhowmick P, Tompa P. Design Principles Involving Protein Disorder Facilitate Specific Substrate Selection and Degradation by the Ubiquitin-Proteasome System. J Biol Chem 2016; 291:6723-31. [PMID: 26851277 DOI: 10.1074/jbc.r115.692665] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The ubiquitin-proteasome system (UPS) regulates diverse cellular pathways by the timely removal (or processing) of proteins. Here we review the role of structural disorder and conformational flexibility in the different aspects of degradation. First, we discuss post-translational modifications within disordered regions that regulate E3 ligase localization, conformation, and enzymatic activity, and also the role of flexible linkers in mediating ubiquitin transfer and reaction processivity. Next we review well studied substrates and discuss that substrate elements (degrons) recognized by E3 ligases are highly disordered: short linear motifs recognized by many E3s constitute an important class of degrons, and these are almost always present in disordered regions. Substrate lysines targeted for ubiquitination are also often located in neighboring regions of the E3 docking motifs and are therefore part of the disordered segment. Finally, biochemical experiments and predictions show that initiation of degradation at the 26S proteasome requires a partially unfolded region to facilitate substrate entry into the proteasomal core.
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Affiliation(s)
- Mainak Guharoy
- From the VIB Structural Biology Research Center (SBRC), Vlaams Instituut voor Biotechnologie, 1050 Brussel, Belgium, the Structural Biology Brussels (SBB), Vrije Universiteit Brussel, 1050 Brussels, Belgium, and
| | - Pallab Bhowmick
- From the VIB Structural Biology Research Center (SBRC), Vlaams Instituut voor Biotechnologie, 1050 Brussel, Belgium, the Structural Biology Brussels (SBB), Vrije Universiteit Brussel, 1050 Brussels, Belgium, and
| | - Peter Tompa
- From the VIB Structural Biology Research Center (SBRC), Vlaams Instituut voor Biotechnologie, 1050 Brussel, Belgium, the Structural Biology Brussels (SBB), Vrije Universiteit Brussel, 1050 Brussels, Belgium, and the Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, 1117 Budapest, Hungary
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18
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Chandra Dantu S, Nathubhai Kachariya N, Kumar A. Molecular dynamics simulations elucidate the mode of protein recognition by Skp1 and the F-box domain in the SCF complex. Proteins 2015; 84:159-71. [PMID: 26573739 DOI: 10.1002/prot.24963] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/07/2015] [Accepted: 11/09/2015] [Indexed: 11/09/2022]
Abstract
Polyubiquitination of the target protein by a ubiquitin transferring machinery is key to various cellular processes. E3 ligase Skp1-Cul1-F-box (SCF) is one such complex which plays crucial role in substrate recognition and transfer of the ubiquitin molecule. Previous computational studies have focused on S-phase kinase-associated protein 2 (Skp2), cullin, and RING-finger proteins of this complex, but the roles of the adapter protein Skp1 and F-box domain of Skp2 have not been determined. Using sub-microsecond molecular dynamics simulations of full-length Skp1, unbound Skp2, Skp2-Cks1 (Cks1: Cyclin-dependent kinases regulatory subunit 1), Skp1-Skp2, and Skp1-Skp2-Cks1 complexes, we have elucidated the function of Skp1 and the F-box domain of Skp2. We found that the L16 loop of Skp1, which was deleted in previous X-ray crystallography studies, can offer additional stability to the ternary complex via its interactions with the C-terminal tail of Skp2. Moreover, Skp1 helices H6, H7, and H8 display vivid conformational flexibility when not bound to Skp2, suggesting that these helices can recognize and lock the F-box proteins. Furthermore, we observed that the F-box domain could rotate (5°-129°), and that the binding partner determined the degree of conformational flexibility. Finally, Skp1 and Skp2 were found to execute a domain motion in Skp1-Skp2 and Skp1-Skp2-Cks1 complexes that could decrease the distance between ubiquitination site of the substrate and the ubiquitin molecule by 3 nm. Thus, we propose that both the F-box domain of Skp2 and Skp1-Skp2 domain motions displaying preferential conformational control can together facilitate polyubiquitination of a wide variety of substrates.
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Affiliation(s)
- Sarath Chandra Dantu
- Cactus Communications Pvt. Ltd, Andheri (W), Mumbai, 400053, India.,Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Nitin Nathubhai Kachariya
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
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19
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Chen P, Yao GD. The role of cullin proteins in gastric cancer. Tumour Biol 2015; 37:29-37. [PMID: 26472722 DOI: 10.1007/s13277-015-4154-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/23/2015] [Indexed: 01/09/2023] Open
Abstract
The cullin proteins are a family of scaffolding proteins that associate with RING proteins and ubiquitin E3 ligases and mediate substrate-receptor bindings. Thus, cullin proteins regulate the specificity of ubiquitin targeting in the regulation of proteins involved in various cellular processes, including proliferation, differentiation, and apoptosis. There are seven cullin proteins that have been identified in eukaryotes: CUL1, CUL2, CUL3, CUL4A, CUL4B, CUL5, and CUL7/p53-associated parkin-like cytoplasmic protein. All of these proteins contain a conserved cullin homology domain that binds to RING box proteins. Cullin-RING ubiquitin ligase complexes are activated upon post-translational modification by neural precursor cell-expressed, developmentally downregulated protein 8. The aberrant expression of several cullin proteins has been implicated in many cancers though the significance in gastric cancer has been less well investigated. This review provides the first systematic discussion of the associations between all members of the cullin protein family and gastric cancer. Functional and regulatory mechanisms of cullin proteins in gastric carcinoma progression are also summarized along with a discussion concerning future research areas. Accumulating evidence suggests a critical role of cullin proteins in tumorigenesis, and a better understanding of the function of these individual cullin proteins and their targets will help identify potential biomarkers and therapeutic targets.
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Affiliation(s)
- Peng Chen
- Department of General Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Tong-Dao-Bei Street, Hohhot, Inner Mongolia, 010050, People's Republic of China
| | - Guo-Dong Yao
- Department of General Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Tong-Dao-Bei Street, Hohhot, Inner Mongolia, 010050, People's Republic of China.
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20
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Kumanomidou T, Nishio K, Takagi K, Nakagawa T, Suzuki A, Yamane T, Tokunaga F, Iwai K, Murakami A, Yoshida Y, Tanaka K, Mizushima T. The Structural Differences between a Glycoprotein Specific F-Box Protein Fbs1 and Its Homologous Protein FBG3. PLoS One 2015; 10:e0140366. [PMID: 26460611 PMCID: PMC4603797 DOI: 10.1371/journal.pone.0140366] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/24/2015] [Indexed: 02/02/2023] Open
Abstract
The Skp1-Cul1-F-box protein (SCF) complex catalyzes protein ubiquitination in diverse cellular processes and is one of the best-characterized ubiquitin ligases. F-box proteins determine the substrate specificities of SCF ubiquitin ligases. Among these, Fbs1/FBG1/FBXO2, Fbs2/FBG2/FBXO6, and Fbs3/FBG5/FBXO27 recognize the N-glycans of glycoproteins, whereas FBG3/FBXO44 has no sugar-binding activity, despite the high sequence homology and conservation of the residues necessary for oligosaccharide binding between Fbs1–3 and FBG3. Here we determined the crystal structure of the Skp1–FBG3 complex at a resolution of 2.6 Å. The substrate-binding domain of FBG3 is composed of a 10-stranded antiparallel β-sandwich with three helices. Although the overall structure of FBG3 is similar to that of Fbs1, the residues that form the Fbs1 carbohydrate-binding pocket failed to be superposed with the corresponding residues of FBG3. Structure-based mutational analysis shows that distinct hydrogen bond networks of four FBG3 loops, i.e., β2-β3, β5-β6, β7-β8, and β9-β10, prevent the formation of the carbohydrate-binding pocket shown in Fbs1.
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Affiliation(s)
- Taichi Kumanomidou
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, Japan
| | - Kazuya Nishio
- Picobiology Institute, Department of Life Science, Graduate School of Life Science, University of Hyogo, Kouto, Kamigori-cho, Ako-gun, Hyogo, Japan
| | - Kenji Takagi
- Picobiology Institute, Department of Life Science, Graduate School of Life Science, University of Hyogo, Kouto, Kamigori-cho, Ako-gun, Hyogo, Japan
| | - Tomomi Nakagawa
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, Japan
| | - Atsuo Suzuki
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, Japan
| | - Takashi Yamane
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, Japan
| | - Fuminori Tokunaga
- Laboratory of Molecular Cell Biology, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
| | - Kazuhiro Iwai
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - Arisa Murakami
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Yukiko Yoshida
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo, Japan
- * E-mail: (TM); (YY)
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Tsunehiro Mizushima
- Picobiology Institute, Department of Life Science, Graduate School of Life Science, University of Hyogo, Kouto, Kamigori-cho, Ako-gun, Hyogo, Japan
- * E-mail: (TM); (YY)
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21
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Saritas-Yildirim B, Pliner HA, Ochoa A, Silva EM. Genome-Wide Identification and Expression of Xenopus F-Box Family of Proteins. PLoS One 2015; 10:e0136929. [PMID: 26327321 PMCID: PMC4556705 DOI: 10.1371/journal.pone.0136929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 08/11/2015] [Indexed: 02/05/2023] Open
Abstract
Protein degradation via the multistep ubiquitin/26S proteasome pathway is a rapid way to alter the protein profile and drive cell processes and developmental changes. Many key regulators of embryonic development are targeted for degradation by E3 ubiquitin ligases. The most studied family of E3 ubiquitin ligases is the SCF ubiquitin ligases, which use F-box adaptor proteins to recognize and recruit target proteins. Here, we used a bioinformatics screen and phylogenetic analysis to identify and annotate the family of F-box proteins in the Xenopus tropicalis genome. To shed light on the function of the F-box proteins, we analyzed expression of F-box genes during early stages of Xenopus development. Many F-box genes are broadly expressed with expression domains localized to diverse tissues including brain, spinal cord, eye, neural crest derivatives, somites, kidneys, and heart. All together, our genome-wide identification and expression profiling of the Xenopus F-box family of proteins provide a foundation for future research aimed to identify the precise role of F-box dependent E3 ubiquitin ligases and their targets in the regulatory circuits of development.
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Affiliation(s)
- Banu Saritas-Yildirim
- Department of Biology, Georgetown University, Washington, DC, United States of America
| | - Hannah A. Pliner
- Department of Biology, Georgetown University, Washington, DC, United States of America
| | - Angelica Ochoa
- Department of Biology, Georgetown University, Washington, DC, United States of America
| | - Elena M. Silva
- Department of Biology, Georgetown University, Washington, DC, United States of America
- * E-mail:
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22
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Gadd MS, Bulatov E, Ciulli A. Serendipitous SAD Solution for DMSO-Soaked SOCS2-ElonginC-ElonginB Crystals Using Covalently Incorporated Dimethylarsenic: Insights into Substrate Receptor Conformational Flexibility in Cullin RING Ligases. PLoS One 2015; 10:e0131218. [PMID: 26121586 PMCID: PMC4486172 DOI: 10.1371/journal.pone.0131218] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 05/29/2015] [Indexed: 11/18/2022] Open
Abstract
Suppressor of cytokine signalling 2 (SOCS2) is the substrate-binding component of a Cullin-RING E3 ubiquitin ligase (CRL) complex that targets phosphorylated hormone receptors for degradation by the ubiquitin-proteasome system. As a key regulator of the transcriptional response to growth signals, SOCS2 and its protein complex partners are potential targets for small molecule development. We found that crystals of SOCS2 in complex with its adaptor proteins, Elongin C and Elongin B, underwent a change in crystallographic parameters when treated with dimethyl sulfoxide during soaking experiments. To solve the phase problem for the new crystal form we identified the presence of arsenic atoms in the crystals, a result of covalent modification of cysteines by cacodylate, and successfully extracted anomalous signal from these atoms for experimental phasing. The resulting structure provides a means for solving future structures where the crystals must be treated with DMSO for ligand soaking approaches. Additionally, the conformational changes induced in this structure reveal flexibility within SOCS2 that match those postulated by previous molecular dynamics simulations. This conformational flexibility illustrates how SOCS2 can orient its substrates for successful ubiquitination by other elements of the CRL complex.
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Affiliation(s)
- Morgan S. Gadd
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, United Kingdom
| | - Emil Bulatov
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, United Kingdom
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, United Kingdom
- * E-mail:
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23
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Nussinov R, Tsai CJ, Liu J. Principles of allosteric interactions in cell signaling. J Am Chem Soc 2014; 136:17692-701. [PMID: 25474128 PMCID: PMC4291754 DOI: 10.1021/ja510028c] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Indexed: 02/07/2023]
Abstract
Linking cell signaling events to the fundamental physicochemical basis of the conformational behavior of single molecules and ultimately to cellular function is a key challenge facing the life sciences. Here we outline the emerging principles of allosteric interactions in cell signaling, with emphasis on the following points. (1) Allosteric efficacy is not a function of the chemical composition of the allosteric pocket but reflects the extent of the population shift between the inactive and active states. That is, the allosteric effect is determined by the extent of preferred binding, not by the overall binding affinity. (2) Coupling between the allosteric and active sites does not decide the allosteric effect; however, it does define the propagation pathways, the allosteric binding sites, and key on-path residues. (3) Atoms of allosteric effectors can act as "driver" or "anchor" and create attractive "pulling" or repulsive "pushing" interactions. Deciphering, quantifying, and integrating the multiple co-occurring events present daunting challenges to our scientific community.
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Affiliation(s)
- Ruth Nussinov
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research,
National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler
Institute of Molecular Medicine, Department of Human Genetics and
Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chung-Jung Tsai
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research,
National Cancer Institute, Frederick, Maryland 21702, United States
| | - Jin Liu
- Department
of Biophysics, University of Texas Southwestern
Medical Center, 5323
Harry Hines Boulevard, Dallas, Texas 75390, United
States
- Department
of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4),
and Center for Scientific Computation, Southern
Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275, United
States
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24
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Couvé S, Ladroue C, Laine E, Mahtouk K, Guégan J, Gad S, Le Jeune H, Le Gentil M, Nuel G, Kim WY, Lecomte B, Pagès JC, Collin C, Lasne F, Benusiglio PR, Bressac-de Paillerets B, Feunteun J, Lazar V, Gimenez-Roqueplo AP, Mazure NM, Dessen P, Tchertanov L, Mole DR, Kaelin W, Ratcliffe P, Richard S, Gardie B. Genetic evidence of a precisely tuned dysregulation in the hypoxia signaling pathway during oncogenesis. Cancer Res 2014; 74:6554-64. [PMID: 25371412 PMCID: PMC5555745 DOI: 10.1158/0008-5472.can-14-1161] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The classic model of tumor suppression implies that malignant transformation requires full "two-hit" inactivation of a tumor-suppressor gene. However, more recent work in mice has led to the proposal of a "continuum" model that involves more fluid concepts such as gene dosage-sensitivity and tissue specificity. Mutations in the tumor-suppressor gene von Hippel-Lindau (VHL) are associated with a complex spectrum of conditions. Homozygotes or compound heterozygotes for the R200W germline mutation in VHL have Chuvash polycythemia, whereas heterozygous carriers are free of disease. Individuals with classic, heterozygous VHL mutations have VHL disease and are at high risk of multiple tumors (e.g., CNS hemangioblastomas, pheochromocytoma, and renal cell carcinoma). We report here an atypical family bearing two VHL gene mutations in cis (R200W and R161Q), together with phenotypic analysis, structural modeling, functional, and transcriptomic studies of these mutants in comparison with classical mutants involved in the different VHL phenotypes. We demonstrate that the complex pattern of disease manifestations observed in VHL syndrome is perfectly correlated with a gradient of VHL protein (pVHL) dysfunction in hypoxia signaling pathways. Thus, by studying naturally occurring familial mutations, our work validates in humans the "continuum" model of tumor suppression.
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Affiliation(s)
- Sophie Couvé
- Laboratoire de Génétique Oncologique de l'Ecole Pratique des Hautes Etudes (EPHE), Villejuif, France. Institut National de la Santé et de la Recherche Medicale (INSERM) U753, Gustave Roussy Cancer Campus, Villejuif, France. Centre Expert National Cancers Rares INCa "PREDIR" and Réseau National INCa "Maladie de VHL et prédispositions au cancer du rein," Service d'Urologie, Assistance publique, Hôpitaux de Paris, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Charline Ladroue
- Laboratoire de Génétique Oncologique de l'Ecole Pratique des Hautes Etudes (EPHE), Villejuif, France. Institut National de la Santé et de la Recherche Medicale (INSERM) U753, Gustave Roussy Cancer Campus, Villejuif, France
| | - Elodie Laine
- Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), CNRS-ENS de Cachan, LabEx LERMIT, Cachan, France. Equipe de Génomique Analytique, Laboratoire de Biologie Computationnelle et Quantitative, CNRS-UPMC, UMR 7238, Paris, France
| | - Karène Mahtouk
- Laboratoire de Génétique Oncologique de l'Ecole Pratique des Hautes Etudes (EPHE), Villejuif, France. Institut National de la Santé et de la Recherche Medicale (INSERM) U753, Gustave Roussy Cancer Campus, Villejuif, France
| | - Justine Guégan
- Plate-forme de Génomique, Gustave Roussy Cancer Campus, Villejuif, France
| | - Sophie Gad
- Laboratoire de Génétique Oncologique de l'Ecole Pratique des Hautes Etudes (EPHE), Villejuif, France. Institut National de la Santé et de la Recherche Medicale (INSERM) U753, Gustave Roussy Cancer Campus, Villejuif, France. Centre Expert National Cancers Rares INCa "PREDIR" and Réseau National INCa "Maladie de VHL et prédispositions au cancer du rein," Service d'Urologie, Assistance publique, Hôpitaux de Paris, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Hélène Le Jeune
- Laboratoire de Génétique Oncologique de l'Ecole Pratique des Hautes Etudes (EPHE), Villejuif, France. Institut National de la Santé et de la Recherche Medicale (INSERM) U753, Gustave Roussy Cancer Campus, Villejuif, France
| | - Marion Le Gentil
- Plate-forme de Génomique, Gustave Roussy Cancer Campus, Villejuif, France
| | - Gregory Nuel
- Mathématiques Appliquées à Paris 5 (MAP5), UMR CNRS 8145, Université Paris Descartes, Paris, France
| | - William Y Kim
- Lineberger Comprehensive Cancer Center University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - Jean-Christophe Pagès
- INSERM U966, Université François Rabelais de Tours, Faculté de Médecine, Tours, France
| | - Christine Collin
- INSERM U966, Université François Rabelais de Tours, Faculté de Médecine, Tours, France
| | - Françoise Lasne
- Département des analyses, Agence Française de Lutte contre le Dopage (AFLD), Chatenay-Malabry, France
| | - Patrick R Benusiglio
- Département de Médecine Oncologique, Gustave Roussy Cancer Campus, Villejuif, France. Centre Expert National Cancers Rares INCa "PREDIR" and Réseau National INCa "Maladie de VHL et prédispositions au cancer du rein," Service d'Urologie, Assistance publique, Hôpitaux de Paris, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Brigitte Bressac-de Paillerets
- Centre Expert National Cancers Rares INCa "PREDIR" and Réseau National INCa "Maladie de VHL et prédispositions au cancer du rein," Service d'Urologie, Assistance publique, Hôpitaux de Paris, Hôpital Bicêtre, Le Kremlin-Bicêtre, France. Service de Génétique, Gustave Roussy Cancer Campus, Villejuif, France
| | - Jean Feunteun
- Laboratoire Stabilité génétique et Oncogénèse, UMR CNRS 8200, Gustave Roussy Cancer Campus, Villejuif, France
| | - Vladimir Lazar
- Plate-forme de Génomique, Gustave Roussy Cancer Campus, Villejuif, France
| | - Anne-Paule Gimenez-Roqueplo
- Centre Expert National Cancers Rares INCa "PREDIR" and Réseau National INCa "Maladie de VHL et prédispositions au cancer du rein," Service d'Urologie, Assistance publique, Hôpitaux de Paris, Hôpital Bicêtre, Le Kremlin-Bicêtre, France. Assistance Publique, Hôpitaux de Paris, Hôpital européen Georges Pompidou, Service de Génétique, Paris, France. INSERM UMR970, Paris-Cardiovascular Research Center at HEGP, Paris, France. Université Paris Descartes, Faculté de Médecine, Paris, France
| | - Nathalie M Mazure
- Institute for Research on Cancer and Ageing of Nice (IRCAN), UMR CNRS 7284, INSERM U1081, UNS, Nice, France
| | - Philippe Dessen
- Plate-forme de Génomique, Gustave Roussy Cancer Campus, Villejuif, France
| | - Luba Tchertanov
- Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), CNRS-ENS de Cachan, LabEx LERMIT, Cachan, France
| | - David R Mole
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | | | - Peter Ratcliffe
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Stéphane Richard
- Laboratoire de Génétique Oncologique de l'Ecole Pratique des Hautes Etudes (EPHE), Villejuif, France. Institut National de la Santé et de la Recherche Medicale (INSERM) U753, Gustave Roussy Cancer Campus, Villejuif, France. Centre Expert National Cancers Rares INCa "PREDIR" and Réseau National INCa "Maladie de VHL et prédispositions au cancer du rein," Service d'Urologie, Assistance publique, Hôpitaux de Paris, Hôpital Bicêtre, Le Kremlin-Bicêtre, France. Faculté de Médecine Paris-Sud, Le Kremlin-Bicêtre, Paris, France.
| | - Betty Gardie
- Laboratoire de Génétique Oncologique de l'Ecole Pratique des Hautes Etudes (EPHE), Villejuif, France. Unité Mixte de Recherche (UMR) INSERM U892, CNRS 6299, Centre de Recherche en Cancérologie Nantes/Angers (CRCNA), Université de Nantes, Nantes, France.
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Cullin E3 ligases and their rewiring by viral factors. Biomolecules 2014; 4:897-930. [PMID: 25314029 PMCID: PMC4279162 DOI: 10.3390/biom4040897] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 08/20/2014] [Accepted: 09/15/2014] [Indexed: 02/06/2023] Open
Abstract
The ability of viruses to subvert host pathways is central in disease pathogenesis. Over the past decade, a critical role for the Ubiquitin Proteasome System (UPS) in counteracting host immune factors during viral infection has emerged. This counteraction is commonly achieved by the expression of viral proteins capable of sequestering host ubiquitin E3 ligases and their regulators. In particular, many viruses hijack members of the Cullin-RING E3 Ligase (CRL) family. Viruses interact in many ways with CRLs in order to impact their ligase activity; one key recurring interaction involves re-directing CRL complexes to degrade host targets that are otherwise not degraded within host cells. Removal of host immune factors by this mechanism creates a more amenable cellular environment for viral propagation. To date, a small number of target host factors have been identified, many of which are degraded via a CRL-proteasome pathway. Substantial effort within the field is ongoing to uncover the identities of further host proteins targeted in this fashion and the underlying mechanisms driving their turnover by the UPS. Elucidation of these targets and mechanisms will provide appealing anti-viral therapeutic opportunities. This review is focused on the many methods used by viruses to perturb host CRLs, focusing on substrate sequestration and viral regulation of E3 activity.
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Nussinov R, Jang H, Tsai CJ. The structural basis for cancer treatment decisions. Oncotarget 2014; 5:7285-302. [PMID: 25277176 PMCID: PMC4202123 DOI: 10.18632/oncotarget.2439] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 09/03/2014] [Indexed: 12/31/2022] Open
Abstract
Cancer treatment decisions rely on genetics, large data screens and clinical pharmacology. Here we point out that genetic analysis and treatment decisions may overlook critical elements in cancer development, progression and drug resistance. Two critical structural elements are missing in genetics-based decision-making: the mechanisms of oncogenic mutations and the cellular network which is rewired in cancer. These lay the foundation for the structural basis for cancer treatment decisions, which is rooted in the physical principles of the molecular conformational behavior of single molecules and their interactions. Improved tumor mutational analysis platforms and knowledge of the redundant pathways which can take over in cancer, may not only supplement known actionable findings, but forecast possible cancer progression and resistance. Such forward-looking can be powerful, endowing the oncologist with mechanistic insight and cancer prognosis, and consequently more informed treatment options. Examples include redundant pathways taking over after inhibition of EGFR constitutive activation, mutations in PIK3CA p110α and p85, and the non-hotspot AKT1 mutants conferring constitutive membrane localization.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, U.S.A
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, U.S.A
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, U.S.A
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Abstract
A key issue in drug discovery is how to reduce drug dosage and increase specificity while retaining or increasing efficacy, as high dosage is often linked to toxicity. There are two types of drugs on the market: orthosteric and allosteric. Orthosteric drugs can be noncovalent or covalent. The latter are advantageous because they may be prescribed in lower doses, but their potential off-target toxicity is a primary concern. The chief advantages of allosteric drugs are their higher specificity and their consequently lower chance of toxic side effects. Covalent allosteric drugs combine the pharmacological merits of covalent drugs with the additional benefit of the higher specificity of allosteric drugs. In a recent promising step in therapeutic drug development, allosteric, disulfide-tethered fragments successfully modulated the activity of a protein kinase and K-Ras.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland 21702;
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28
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Nussinov R, Ma B, Tsai CJ. Multiple conformational selection and induced fit events take place in allosteric propagation. Biophys Chem 2014; 186:22-30. [PMID: 24239303 PMCID: PMC6361548 DOI: 10.1016/j.bpc.2013.10.002] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/07/2013] [Accepted: 10/09/2013] [Indexed: 12/16/2022]
Abstract
The fact that we observe a single conformational selection event during binding does not necessarily mean that only a single conformational selection event takes place, even though this is the common assumption. Here we suggest that conformational selection takes place not once in a given binding/allosteric event, but at every step along the allosteric pathway. This view generalizes conformational selection and makes it applicable also to other allosteric events, such as post-translational modifications (PTMs) and photon absorption. Similar to binding, at each step along a propagation pathway, conformational selection is coupled with induced fit which optimizes the interactions. Thus, as in binding, the allosteric effects induced by PTMs and light relate not only to population shift; but to conformational selection as well. Conformational selection and population shift take place conjointly.
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Affiliation(s)
- Ruth Nussinov
- Leidos Biomedical Research, Inc., Frederick National Laboratory, Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States; Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Buyong Ma
- Leidos Biomedical Research, Inc., Frederick National Laboratory, Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States
| | - Chung-Jung Tsai
- Leidos Biomedical Research, Inc., Frederick National Laboratory, Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States
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29
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Nussinov R, Tsai CJ, Mattos C. 'Pathway drug cocktail': targeting Ras signaling based on structural pathways. Trends Mol Med 2013; 19:695-704. [PMID: 23953481 DOI: 10.1016/j.molmed.2013.07.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 07/12/2013] [Accepted: 07/22/2013] [Indexed: 01/07/2023]
Abstract
Tumors bearing Ras mutations are notoriously difficult to treat. Drug combinations targeting the Ras protein or its pathway have also not met with success. 'Pathway drug cocktails', which are combinations aiming at parallel pathways, appear more promising; however, to be usefully exploited, a repertoire of classified pathway combinations is desirable. This challenge would be facilitated by the availability of the structural network of signaling pathways. When integrated with functional and systems level clinical data, they can be powerful in advancing novel therapeutic platforms. Based on structural knowledge, drug cocktails may tear into multiple cellular processes that drive tumorigenesis, and help in deciphering the interrelationship between Ras mutations and the rewired Ras network. The pathway drug cocktail paradigm can be applied to other signaling protein targets.
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Affiliation(s)
- Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc., Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Sackler Institute of Molecular Medicine, Department of Human Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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30
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Abstract
The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and microclusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell organization also organizes signaling and coordinates cellular behavior. We propose a new view of the spatial structure of cell signaling systems. This new view describes cell signaling in terms of dynamic allosteric interactions within and among distinct, spatially organized transient clusters. The clusters vary over time and space and are on length scales from nanometers to micrometers. When considered across these length scales, primary factors in the spatial organization are cell membrane domains and the actin cytoskeleton, both also highly dynamic. A key challenge is to understand the interplay across these multiple scales, link it to the physicochemical basis of the conformational behavior of single molecules and ultimately relate it to cellular function. Overall, our premise is that at these scales, cell signaling should be thought of not primarily as a sequence of diffusion-controlled molecular collisions, but instead transient, allostery-driven cluster re-forming interactions.
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Affiliation(s)
- Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702
- Sackler Inst. 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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Bhowmick P, Pancsa R, Guharoy M, Tompa P. Functional diversity and structural disorder in the human ubiquitination pathway. PLoS One 2013; 8:e65443. [PMID: 23734257 PMCID: PMC3667038 DOI: 10.1371/journal.pone.0065443] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/24/2013] [Indexed: 02/04/2023] Open
Abstract
The ubiquitin-proteasome system plays a central role in cellular regulation and protein quality control (PQC). The system is built as a pyramid of increasing complexity, with two E1 (ubiquitin activating), few dozen E2 (ubiquitin conjugating) and several hundred E3 (ubiquitin ligase) enzymes. By collecting and analyzing E3 sequences from the KEGG BRITE database and literature, we assembled a coherent dataset of 563 human E3s and analyzed their various physical features. We found an increase in structural disorder of the system with multiple disorder predictors (IUPred – E1: 5.97%, E2: 17.74%, E3: 20.03%). E3s that can bind E2 and substrate simultaneously (single subunit E3, ssE3) have significantly higher disorder (22.98%) than E3s in which E2 binding (multi RING-finger, mRF, 0.62%), scaffolding (6.01%) and substrate binding (adaptor/substrate recognition subunits, 17.33%) functions are separated. In ssE3s, the disorder was localized in the substrate/adaptor binding domains, whereas the E2-binding RING/HECT-domains were structured. To demonstrate the involvement of disorder in E3 function, we applied normal modes and molecular dynamics analyses to show how a disordered and highly flexible linker in human CBL (an E3 that acts as a regulator of several tyrosine kinase-mediated signalling pathways) facilitates long-range conformational changes bringing substrate and E2-binding domains towards each other and thus assisting in ubiquitin transfer. E3s with multiple interaction partners (as evidenced by data in STRING) also possess elevated levels of disorder (hubs, 22.90% vs. non-hubs, 18.36%). Furthermore, a search in PDB uncovered 21 distinct human E3 interactions, in 7 of which the disordered region of E3s undergoes induced folding (or mutual induced folding) in the presence of the partner. In conclusion, our data highlights the primary role of structural disorder in the functions of E3 ligases that manifests itself in the substrate/adaptor binding functions as well as the mechanism of ubiquitin transfer by long-range conformational transitions.
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Affiliation(s)
- Pallab Bhowmick
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Rita Pancsa
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Mainak Guharoy
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Tompa
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
- * E-mail:
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Albin JS, Anderson JS, Johnson JR, Harjes E, Matsuo H, Krogan NJ, Harris RS. Dispersed sites of HIV Vif-dependent polyubiquitination in the DNA deaminase APOBEC3F. J Mol Biol 2013; 425:1172-82. [PMID: 23318957 PMCID: PMC3602375 DOI: 10.1016/j.jmb.2013.01.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 11/20/2022]
Abstract
APOBEC3F (A3F) and APOBEC3G (A3G) are DNA cytosine deaminases that potently restrict human immunodeficiency virus type 1 replication when the virus is deprived of its accessory protein Vif (virion infectivity factor). Vif counteracts these restriction factors by recruiting A3F and A3G to an E3 ubiquitin (Ub) ligase complex that mediates their polyubiquitination (polyUb) and proteasomal degradation. While previous efforts have identified single amino acid residues in APOBEC3 proteins required for Vif recognition, less is known about the downstream Ub acceptor sites that are targeted. One prior report identified a cluster of polyubiquitinated residues in A3G and proposed an antiparallel model of A3G interaction with the Vif-E3 Ub ligase complex wherein Vif binding at one terminus of A3G orients the opposite terminus for polyUb [Iwatani et al. (2009). Proc. Natl. Acad. Sci. USA, 106, 19539-19544]. To test the generalizability of this model, we carried out a complete mutagenesis of the lysine residues in A3F and used a complementary, unbiased proteomic approach to identify Ub acceptor sites targeted by Vif. Our data indicate that internal lysines are the dominant Ub acceptor sites in both A3F and A3G. In contrast with the proposed antiparallel model, however, we find that the Vif-dependent polyUb of A3F and A3G can occur at multiple acceptor sites dispersed along predicted lysine-enriched surfaces of both the N- and C-terminal deaminase domains. These data suggest an alternative model for binding of APOBEC3 proteins to the Vif-E3 Ub ligase complex and diminish enthusiasm for the amenability of APOBEC3 Ub acceptor sites to therapeutic intervention.
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Affiliation(s)
- John S. Albin
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455
| | - John S. Anderson
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455
| | - Jeffrey R. Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
- J. David Gladstone Institutes, San Francisco, CA 94158
| | - Elena Harjes
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455
| | - Hiroshi Matsuo
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455
| | - Nevan J. Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
- J. David Gladstone Institutes, San Francisco, CA 94158
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455
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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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Nussinov R, Ma B, Tsai CJ. A broad view of scaffolding suggests that scaffolding proteins can actively control regulation and signaling of multienzyme complexes through allostery. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:820-9. [PMID: 23291467 DOI: 10.1016/j.bbapap.2012.12.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 12/19/2012] [Accepted: 12/21/2012] [Indexed: 10/27/2022]
Abstract
Enzymes often work sequentially in pathways; and consecutive reaction steps are typically carried out by molecules associated in the same multienzyme complex. Localization confines the enzymes; anchors them; increases the effective concentration of substrates and products; and shortens pathway timescales; however, it does not explain enzyme coordination or pathway branching. Here, we distinguish between metabolic and signaling multienzyme complexes. We argue for a central role of scaffolding proteins in regulating multienzyme complexes signaling and suggest that metabolic multienzyme complexes are less dependent on scaffolding because they undergo conformational control through direct subunit-subunit contacts. In particular, we propose that scaffolding proteins have an essential function in controlling branching in signaling pathways. This new broadened definition of scaffolding proteins goes beyond cases such as the classic yeast mitogen-activated protein kinase Ste5 and encompasses proteins such as E3 ligases which lack active sites and work via allostery. With this definition, we classify the mechanisms of multienzyme complexes based on whether the substrates are transferred through the involvement of scaffolding proteins, and outline the functional merits to metabolic or signaling pathways. Overall, while co-localization topography helps multistep pathways non-specifically, allosteric regulation requires precise multienzyme organization and interactions and works via population shift, either through direct enzyme subunit-subunit interactions or through active involvement of scaffolding proteins. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.
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Affiliation(s)
- Ruth Nussinov
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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Elgin ES, Sökmen N, Peterson FC, Volkman BF, Dağ C, Haas AL. E2-binding surface on Uba3 β-grasp domain undergoes a conformational transition. Proteins 2012; 80:2482-7. [PMID: 22821745 DOI: 10.1002/prot.24148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 06/22/2012] [Accepted: 07/05/2012] [Indexed: 11/05/2022]
Abstract
The covalent attachment of ubiquitin (Ub) and ubiquitin-like (Ubl) proteins to various eukaryotic targets plays critical roles in regulating numerous cellular processes. E1-activating enzymes are critical, because they catalyze activation of their cognate Ub/Ubl protein and are responsible for its transfer to the correct E2-conjugating enzyme(s). The activating enzyme for neural-precursor-cell-expressed developmentally downregulated 8 (NEDD8) is a heterodimer composed of APPBP1 and Uba3 subunits. The carboxyl terminal ubiquitin-like β-grasp domain of human Uba3 (Uba3-βGD) has been suggested as a key E2-binding site defining E2 specificity. In crystal structures of free E1 and the NEDD8-E1 complex, the E2-binding surface on the domain was missing from the electron density. However, when complexed with various E2s, this missing segment adopts a kinked α-helix. Here, we demonstrate that Uba3-βGD is an independently folded domain in solution and that residues involved in E2 binding are absent from the NMR spectrum, indicating that the E2-binding surface on Uba3-βGD interconverts between multiple conformations, analogous to a similar conformational transition observed in the E2-binding surface of SUMO E1. These results suggest that access to multiple conformational substates is an important feature of the E1-E2 interaction.
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Affiliation(s)
- E Sonay Elgin
- Department of Chemistry, Muğla Sıtkı Koçman University, Muğla 48000, Turkey.
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36
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Harnessing glycosylation to improve cellulase activity. Curr Opin Biotechnol 2012; 23:338-45. [DOI: 10.1016/j.copbio.2011.11.030] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 11/24/2011] [Accepted: 11/26/2011] [Indexed: 11/17/2022]
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Liu J, Nussinov R. Flexible cullins in cullin-RING E3 ligases allosterically regulate ubiquitination. J Biol Chem 2011; 286:40934-42. [PMID: 21937436 PMCID: PMC3220518 DOI: 10.1074/jbc.m111.277236] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 09/08/2011] [Indexed: 12/20/2022] Open
Abstract
How do the cullins, with conserved structures, accommodate substrate-binding proteins with distinct shapes and sizes? Cullin-RING E3 ubiquitin ligases facilitate ubiquitin transfer from E2 to the substrate, tagging the substrate for degradation. They contain substrate-binding, adaptor, cullin, and Rbx proteins. Previously, we showed that substrate-binding and Rbx proteins are flexible. This allows shortening of the E2-substrate distance for initiation of ubiquitination or increasing the distance to accommodate the polyubiquitin chain. However, the role of the cullin remained unclear. Is cullin a rigid scaffold, or is it flexible and actively assists in the ubiquitin transfer reaction? Why are there different cullins, and how do these cullins specifically facilitate ubiquitination for different substrates? To answer these questions, we performed structural analysis and molecular dynamics simulations based on Cul1, Cul4A, and Cul5 crystal structures. Our results show that these three cullins are not rigid scaffolds but are flexible with conserved hinges in the N-terminal domain. However, the degrees of flexibilities are distinct among the different cullins. Of interest, Cul1 flexibility can also be changed by deletion of the long loop (which is absent in Cul4A) in the N-terminal domain, suggesting that the loop may have an allosteric functional role. In all three cases, these conformational changes increase the E2-substrate distance to a specific range to facilitate polyubiquitination, suggesting that rather than being inert scaffold proteins, cullins allosterically regulate ubiquitination.
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Affiliation(s)
- Jin Liu
- From the Basic Science Program, SAIC-Frederick, Incorporated, Center for Cancer Research Nanobiology Program, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702 and
| | - Ruth Nussinov
- From the Basic Science Program, SAIC-Frederick, Incorporated, Center for Cancer Research Nanobiology Program, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702 and
- the 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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Ma B, Tsai CJ, Haliloğlu T, Nussinov R. Dynamic allostery: linkers are not merely flexible. Structure 2011; 19:907-17. [PMID: 21742258 PMCID: PMC6361528 DOI: 10.1016/j.str.2011.06.002] [Citation(s) in RCA: 179] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 06/05/2011] [Accepted: 06/07/2011] [Indexed: 12/19/2022]
Abstract
Most proteins consist of multiple domains. How do linkers efficiently transfer information between sites that are on different domains to activate the protein? Mere flexibility only implies that the conformations would be sampled. For fast timescales between triggering events and cellular response, which often involves large conformational change, flexibility on its own may not constitute a good solution. We posit that successive conformational states along major allosteric propagation pathways are pre-encoded in linker sequences where each state is encoded by the previous one. The barriers between these states that are hierarchically populated are lower, achieving faster timescales even for large conformational changes. We further propose that evolution has optimized the linker sequences and lengths for efficiency, which explains why mutations in linkers may affect protein function and review the literature in this light.
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Affiliation(s)
- Buyong Ma
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA
| | - Chung-Jung Tsai
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA
| | - Türkan Haliloğlu
- Polymer Research Center and Chemical Engineering Department, Bogazici University, Bebek-Istanbul 34342, Turkey
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA
- 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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Abstract
Proteins provide much of the scaffolding for life, as well as undertaking a variety of essential catalytic reactions. These characteristic functions have led us to presuppose that proteins are in general functional only when well structured and correctly folded. As we begin to explore the repertoire of possible protein sequences inherent in the human and other genomes, two stark facts that belie this supposition become clear: firstly, the number of apparent open reading frames in the human genome is significantly smaller than appears to be necessary to code for all of the diverse proteins in higher organisms, and secondly that a significant proportion of the protein sequences that would be coded by the genome would not be expected to form stable three-dimensional (3D) structures. Clearly the genome must include coding for a multitude of alternative forms of proteins, some of which may be partly or fully disordered or incompletely structured in their functional states. At the same time as this likelihood was recognized, experimental studies also began to uncover examples of important protein molecules and domains that were incompletely structured or completely disordered in solution, yet remained perfectly functional. In the ensuing years, we have seen an explosion of experimental and genome-annotation studies that have mapped the extent of the intrinsic disorder phenomenon and explored the possible biological rationales for its widespread occurrence. Answers to the question 'why would a particular domain need to be unstructured?' are as varied as the systems where such domains are found. This review provides a survey of recent new directions in this field, and includes an evaluation of the role not only of intrinsically disordered proteins but also of partially structured and highly dynamic members of the disorder-order continuum.
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40
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Leonardi E, Martella M, Tosatto SC, Murgia A. Identification and In Silico Analysis of Novel von Hippel-Lindau (VHL) Gene Variants from a Large Population. Ann Hum Genet 2011; 75:483-96. [DOI: 10.1111/j.1469-1809.2011.00647.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Liu J, Nussinov R. Rbx1 flexible linker facilitates cullin-RING ligase function before neddylation and after deneddylation. Biophys J 2010; 99:736-44. [PMID: 20682250 PMCID: PMC2913186 DOI: 10.1016/j.bpj.2010.05.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 04/27/2010] [Accepted: 05/12/2010] [Indexed: 12/31/2022] Open
Abstract
In ubiquitination, cullin-RING E3 ubiquitin ligases (CRLs) assist in ubiquitin transfer from ubiquitin-conjugating enzyme E2 to the substrate. Neddylation, which involves NEDD8 transfer from E2 to E3-cullin, stimulates ubiquitination by inducing conformational change in CRLs. However, deneddylation, which removes NEDD8 from cullin, does not suppress ubiquitination in vivo, raising the question of how neddylation/deneddylation exerts its effects. Using molecular-dynamics simulations, we demonstrate that before neddylation occurs, the linker flexibility of Rbx1, a CRL component, leads to conformational changes in CRLs that allow neddylation and initiation of ubiquitination. These large NEDD8-induced conformational changes are retained after deneddylation, allowing both initiation of the ubiquitination process and ubiquitin chain elongation after deneddylation. Furthermore, mutation of lysine, the cullin residue to which NEDD8 covalently attaches, dramatically reduces CRL conformational changes, suggesting that the acceptor lysine allosterically regulates CRLs. Thus, our results imply that neddylation stimulates ubiquitination by CRL conformational control via lysine modification.
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Affiliation(s)
- Jin Liu
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, Maryland
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, Maryland
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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Mittag T, Marsh J, Grishaev A, Orlicky S, Lin H, Sicheri F, Tyers M, Forman-Kay JD. Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase. Structure 2010; 18:494-506. [PMID: 20399186 DOI: 10.1016/j.str.2010.01.020] [Citation(s) in RCA: 211] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 01/22/2010] [Accepted: 01/26/2010] [Indexed: 01/19/2023]
Abstract
Intrinsically disordered proteins can form highly dynamic complexes with partner proteins. One such dynamic complex involves the intrinsically disordered Sic1 with its partner Cdc4 in regulation of yeast cell cycle progression. Phosphorylation of six N-terminal Sic1 sites leads to equilibrium engagement of each phosphorylation site with the primary binding pocket in Cdc4, the substrate recognition subunit of a ubiquitin ligase. ENSEMBLE calculations using experimental nuclear magnetic resonance and small-angle X-ray scattering data reveal significant transient structure in both phosphorylation states of the isolated ensembles (Sic1 and pSic1) that modulates their electrostatic potential, suggesting a structural basis for the proposed strong contribution of electrostatics to binding. A structural model of the dynamic pSic1-Cdc4 complex demonstrates the spatial arrangements in the ubiquitin ligase complex. These results provide a physical picture of a protein that is predominantly disordered in both its free and bound states, enabling aspects of its structure/function relationship to be elucidated.
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Affiliation(s)
- Tanja Mittag
- Program in Molecular Structure and Function, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada
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43
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Shen A. Allosteric regulation of protease activity by small molecules. MOLECULAR BIOSYSTEMS 2010; 6:1431-43. [PMID: 20539873 DOI: 10.1039/c003913f] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Proteases regulate a plethora of biological processes. Because they irreversibly cleave peptide bonds, the activity of proteases is strictly controlled. While there are many ways to regulate protease activity, an emergent mechanism is the modulation of protease function by small molecules acting at allosteric sites. This mode of regulation holds the potential to allow for the specific and temporal control of a given biological process using small molecules. These compounds also serve as useful tools for studying protein dynamics and function. This review highlights recent advances in identifying and characterizing natural and synthetic small molecule allosteric regulators of proteases and discusses their utility in studies of protease function, drug discovery and protein engineering.
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Affiliation(s)
- Aimee Shen
- Department of Pathology, Stanford School of Medicine, Stanford, California 94305, USA.
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Liu J, Nussinov R. Molecular dynamics reveal the essential role of linker motions in the function of cullin-RING E3 ligases. J Mol Biol 2010; 396:1508-23. [PMID: 20083119 PMCID: PMC2824043 DOI: 10.1016/j.jmb.2010.01.022] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 01/10/2010] [Accepted: 01/12/2010] [Indexed: 11/30/2022]
Abstract
Tagging proteins by polyubiquitin is a key step in protein degradation. Cullin-RING E3 ubiquitin ligases facilitate ubiquitin transfer from the E2-conjugating enzyme to the substrate, yet crystallography indicates a large distance between the E2 and the substrate, raising the question of how this distance is bridged in the ubiquitin transfer reaction. Here, we demonstrate that the linker motions in the substrate binding proteins can allosterically shorten this distance to facilitate this crucial ubiquitin transfer step and increase this distance to allow polyubiquitination. We performed molecular dynamics simulations for five substrate binding proteins, Skp2, Fbw7, beta-TrCP1, Cdc4, and pVHL, in two forms: bound to their substrates and bound to both substrate and adaptor. The adaptor connects the substrate binding proteins to the cullin. In the bound-to-both forms of all cases, we observed rotations of the substrate binding domain, shortening the gap between the tip of the substrate peptide and the E2 active site by 7-12 A compared with the crystal structures. Overall, together with our earlier simulations of the unbound forms and the bound-to-adaptor forms, the emerging picture is that the maximum distance of 51-73 A between the substrate binding domain and the E2 active site in the modeled unbound forms of these five proteins shrinks to a minimum of 39-49 A in the bound-to-both forms. This large distance range, the result of allosterically controlled linker motions, facilitates ubiquitin transfer and polyubiquitination and as such argues that the cullin-RING E3 ubiquitin ligase is under conformational control. We further observed that substrate binding proteins with multiple substrate acceptor lysines have a larger distance range between the substrate and the E2 as compared with beta-TrCP1, with only one acceptor lysine.
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Affiliation(s)
- Jin Liu
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, 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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45
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Pan Y, Tsai CJ, Ma B, Nussinov R. How do transcription factors select specific binding sites in the genome? Nat Struct Mol Biol 2009; 16:1118-20. [PMID: 19888307 PMCID: PMC6416780 DOI: 10.1038/nsmb1109-1118] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
How does a transcription factor select a specific DNA response element given the presence of degenerate sequences? To date, this question has largely been viewed from the standpoint of DNA sequence variability and transcription factor binding affinity under steady-state conditions. Here we propose that to address this problem, it is also necessary to account for fluctuating cellular conditions. These lead to dynamic changes in the ensemble of protein (and DNA) conformational states via allosteric effects.
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Affiliation(s)
- Yongping Pan
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, National Cancer Institute-Frederick, Frederick, Maryland, USA
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