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Rinaldi F, Schipani F, Balboni B, Catalano F, Marotta R, Myers SH, Previtali V, Veronesi M, Scietti L, Cecatiello V, Pasqualato S, Ortega JA, Girotto S, Cavalli A. Isolation and Characterization of Monomeric Human RAD51: A Novel Tool for Investigating Homologous Recombination in Cancer. Angew Chem Int Ed Engl 2023; 62:e202312517. [PMID: 37924230 DOI: 10.1002/anie.202312517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/06/2023]
Abstract
DNA repair protein RAD51 is a key player in the homologous recombination pathway. Upon DNA damage, RAD51 is transported into the nucleus by BRCA2, where it can repair DNA double-strand breaks. Due to the structural complexity and dynamics, researchers have not yet clarified the mechanistic details of every step of RAD51 recruitment and DNA repair. RAD51 possesses an intrinsic tendency to form oligomeric structures, which make it challenging to conduct biochemical and biophysical investigations. Here, for the first time, we report on the isolation and characterization of a human monomeric RAD51 recombinant form, obtained through a double mutation, which preserves the protein's integrity and functionality. We investigated different buffers to identify the most suitable condition needed to definitively stabilize the monomer. The monomer of human RAD51 provides the community with a unique biological tool for investigating RAD51-mediated homologous recombination, and paves the way for more reliable structural, mechanistic, and drug discovery studies.
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Affiliation(s)
- Francesco Rinaldi
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Fabrizio Schipani
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Beatrice Balboni
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Federico Catalano
- Electron Microscopy Facility, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Roberto Marotta
- Electron Microscopy Facility, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Samuel H Myers
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Viola Previtali
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Marina Veronesi
- Structural Biophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Luigi Scietti
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IRCCS European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Valentina Cecatiello
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IRCCS European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
- Current address: Structural Biology Research Centre, Human Technopole Milan, Italy Palazzo Italia Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Sebastiano Pasqualato
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IRCCS European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
- Current address: Structural Biology Research Centre, Human Technopole Milan, Italy Palazzo Italia Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Jose Antonio Ortega
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Stefania Girotto
- Structural Biophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Andrea Cavalli
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
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2
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Parolini F, Ataie Kachoie E, Leo G, Civiero L, Bubacco L, Arrigoni G, Munari F, Assfalg M, D'Onofrio M, Capaldi S. Site-Specific Ubiquitination of Tau Amyloids Promoted by the E3 Ligase CHIP. Angew Chem Int Ed Engl 2023; 62:e202310230. [PMID: 37878393 DOI: 10.1002/anie.202310230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/13/2023] [Accepted: 10/25/2023] [Indexed: 10/27/2023]
Abstract
Post-translational modifications of Tau are emerging as key players in determining the onset and progression of different tauopathies such as Alzheimer's disease, and are recognized to mediate the structural diversity of the disease-specific Tau amyloids. Here we show that the E3 ligase CHIP catalyzes the site-specific ubiquitination of Tau filaments both in vitro and in cellular models, proving that also Tau amyloid aggregates are direct substrate of PTMs. Transmission electron microscopy and mass spectrometry analysis on ubiquitin-modified Tau amyloids revealed that the conformation of the filaments restricts CHIP-mediated ubiquitination to specific positions of the repeat domain, while only minor alterations in the structure of the fibril core were inferred using seeding experiments in vitro and in a cell-based tauopathy model. Overexpression of CHIP significantly increased the ubiquitination of exogenous PHF, proving that the ligase can interact and modify Tau aggregates also in a complex cellular environment.
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Affiliation(s)
| | | | - Giulia Leo
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Laura Civiero
- Department of Biology, University of Padova, 35121, Padova, Italy
- IRCCS San Camillo Hospital, 30126, Venice, Italy
| | - Luigi Bubacco
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, 35131, Padova, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, 35131, Padova, Italy
| | - Francesca Munari
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | | | - Stefano Capaldi
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
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3
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Mi T, Siriwibool S, Burgess K. Streamlined Protein-Protein Interface Loop Mimicry. Angew Chem Int Ed Engl 2023; 62:e202307092. [PMID: 37849440 DOI: 10.1002/anie.202307092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
Abstract
Cyclic peptides comprising endocyclic organic fragments, "cyclo-organopeptides", can be probes for perturbing protein-protein interactions (PPIs). Finding loop mimics is difficult because of high conformational variability amongst targets. Backbone Matching (BM), introduced here, helps solve this problem in the illustrative cases by facilitating efficient evaluation of virtual cyclo-organopeptide core-structure libraries. Thus, 86 rigid organic fragments were selected to build a library of 602 cyclo-organopeptides comprising Ala and organic parts: "cyclo-{-(Ala)n -organo-}". The central hypothesis is "hit" library members have accessible low energy conformers corresponding to backbone structures of target protein loops, while library members which cannot attain this conformation are probably unworthy of further evaluation. BM thereby prioritizes candidate loop mimics, so that less than 10 cyclo-organopeptides are needed to be prepared to find leads for two illustrative PPIs: iNOS ⋅ SPSB2, and uPA ⋅ uPAR.
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Affiliation(s)
- Tianxiong Mi
- Department of Chemistry, Texas A & M University, 77842, College Station, TX, USA
| | - Siriwalee Siriwibool
- School of Chemistry, Institute of Science, Suranaree University of Technology, 30000, Nakhon Ratchasima, Thailand
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, 77842, College Station, TX, USA
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Dewis LI, Rudrakshula M, Williams C, Chiarparin E, Myers EL, Butts CP, Aggarwal VK. Conformationally Controlled sp 3 -Hydrocarbon-Based α-Helix Mimetics. Angew Chem Int Ed Engl 2023; 62:e202301209. [PMID: 37017133 PMCID: PMC10953326 DOI: 10.1002/anie.202301209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 04/06/2023]
Abstract
With over 60 % of protein-protein interfaces featuring an α-helix, the use of α-helix mimetics as inhibitors of these interactions is a prevalent therapeutic strategy. However, methods to control the conformation of mimetics, thus enabling maximum efficacy, can be restrictive. Alternatively, conformation can be controlled through the introduction of destabilizing syn-pentane interactions. This tactic, which is often adopted by Nature, is not a common feature of lead optimization owing to the significant synthetic effort required. Through assembly-line synthesis with NMR and computational analysis, we have shown that alternating syn-anti configured contiguously substituted hydrocarbons, by avoiding syn-pentane interactions, adopt well-defined conformations that present functional groups in an arrangement that mimics the α-helix. The design of a p53 mimetic that binds to Mdm2 with moderate to good affinity, demonstrates the therapeutic promise of these scaffolds.
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Affiliation(s)
- Lydia I. Dewis
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | | | | | | | - Eddie L. Myers
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
- School of Biological and Chemical SciencesUniversity of GalwayUniversity RoadGalwayIreland
| | - Craig P. Butts
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
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5
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Somsen BA, Sijbesma E, Leysen S, Honzejkova K, Visser EJ, Cossar PJ, Obšil T, Brunsveld L, Ottmann C. Molecular basis and dual ligand regulation of tetrameric Estrogen Receptor α/14-3-3ζ protein complex. J Biol Chem 2023:104855. [PMID: 37224961 PMCID: PMC10302166 DOI: 10.1016/j.jbc.2023.104855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/26/2023] Open
Abstract
Therapeutic strategies targeting Nuclear Receptors (NRs) beyond their endogenous ligand binding pocket have gained significant scientific interest, driven by a need to circumvent problems associated with drug resistance and pharmacological profile. The hub protein 14-3-3 is an endogenous regulator of various NRs, providing a novel entry point for small molecule modulation of NR activity. Exemplified, 14-3-3 binding to the C-terminal F-domain of the Estrogen Receptor alpha (ERα), and small molecule stabilization of the ERα/14-3-3ζ protein complex by the natural product Fusicoccin A (FC-A), was demonstrated to downregulate ERα-mediated breast cancer proliferation. This presents a novel drug discovery approach to target ERα, however, structural and mechanistic insights into ERα/14-3-3 complex formation are lacking. Here, we provide an in-depth molecular understanding of the ERα/14-3-3ζ complex by isolating 14-3-3ζ in complex with an ERα protein construct comprising its Ligand Binding Domain (LBD) and phosphorylated F-domain. Bacterial co-expression and co-purification of the ERα/14-3-3ζ complex, followed by extensive biophysical and structural characterization, revealed a tetrameric complex between the ERα homodimer and the 14-3-3ζ homodimer. 14-3-3ζ binding to ERα, and ERα/14-3-3ζ complex stabilization by FC-A, appeared to be orthogonal to ERα endogenous agonist (E2) binding, E2-induced conformational changes, and cofactor recruitment. Similarly, the ERα antagonist 4-hydroxytamoxifen inhibited cofactor recruitment to the ERα LBD while ERα was bound to 14-3-3ζ. Furthermore, stabilization of the ERα/14-3-3ζ protein complex by FC-A was not influenced by the disease-associated and 4-hydroxytamoxifen resistant ERα-Y537S mutant. Together, these molecular and mechanistic insights provide direction for targeting ERα via the ERα/14-3-3 complex as an alternative drug discovery approach.
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Affiliation(s)
- Bente A Somsen
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Eline Sijbesma
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Seppe Leysen
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Karolina Honzejkova
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Emira J Visser
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Tomáš Obšil
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands.
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands.
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Atre R, Sharma R, Vadim G, Solanki K, Wadhonkar K, Singh N, Patidar P, Khabiya R, Samaur H, Banerjee S, Baig MS. The indispensability of macrophage adaptor proteins in chronic inflammatory diseases. Int Immunopharmacol 2023; 119:110176. [PMID: 37104916 DOI: 10.1016/j.intimp.2023.110176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/06/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023]
Abstract
Adaptor proteins represent key signalling molecules involved in regulating immune responses. The host's innate immune system recognizes pathogens via various surface and intracellular receptors. Adaptor molecules are centrally involved in different receptor-mediated signalling pathways, acting as bridges between the receptors and other molecules. The presence of adaptors in major signalling pathways involved in the pathogenesis of various chronic inflammatory diseases has drawn attention toward the role of these proteins in such diseases. In this review, we summarize the importance and roles of different adaptor molecules in macrophage-mediated signalling in various chronic disease states. We highlight the mechanistic roles of adaptors and how they are involved in protein-protein interactions (PPI) via different domains to carry out signalling. Hence, we also provide insights into how targeting these adaptor proteins can be a good therapeutic strategy against various chronic inflammatory diseases.
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Affiliation(s)
- Rajat Atre
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Rahul Sharma
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Gaponenko Vadim
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Kundan Solanki
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Khandu Wadhonkar
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Neha Singh
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Pramod Patidar
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Rakhi Khabiya
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India; School of Pharmacy, Devi Ahilya Vishwavidyalaya, Indore, India
| | - Harshita Samaur
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Sreeparna Banerjee
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey.
| | - Mirza S Baig
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India.
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7
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Liu Q, Zhang D, Gao S, Cai X, Yao M, Xu Y, Gong Y, Zheng K, Mao Y, Yang L, Yang D, Molnár I, Yang X. Didepside Formation by the Nonreducing Polyketide Synthase Preu6 of Preussia isomera Requires Interaction of Starter Acyl Transferase and Thioesterase Domains. Angew Chem Int Ed Engl 2023; 62:e202214379. [PMID: 36484777 DOI: 10.1002/anie.202214379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/13/2022]
Abstract
Orsellinic acid (OA) derivatives are produced by filamentous fungi using nonreducing polyketide synthases (nrPKSs). The chain-releasing thioesterase (TE) domains of such nrPKSs were proposed to also catalyze dimerization to yield didepsides, such as lecanoric acid. Here, we use combinatorial domain exchanges, domain dissections and reconstitutions to reveal that the TE domain of the lecanoric acid synthase Preu6 of Preussia isomera must collaborate with the starter acyl transferase (SAT) domain from the same nrPKS. We show that artificial SAT-TE fusion proteins are highly effective catalysts and reprogram the ketide homologation chassis to form didepsides. We also demonstrate that dissected SAT and TE domains of Preu6 physically interact, and SAT and TE domains of OA-synthesizing nrPKSs may co-evolve. Our work highlights an unexpected domain-domain interaction in nrPKSs that must be considered for the combinatorial biosynthesis of unnatural didepsides, depsidones, and diphenyl ethers.
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Affiliation(s)
- Qingpei Liu
- School of Pharmaceutical Sciences, South-Central Minzu University, 182 Minyuan Road, Hongshan District, Wuhan, 430074, P. R. China
| | - Dan Zhang
- School of Pharmaceutical Sciences, South-Central Minzu University, 182 Minyuan Road, Hongshan District, Wuhan, 430074, P. R. China
| | - Shuaibiao Gao
- School of Pharmaceutical Sciences, South-Central Minzu University, 182 Minyuan Road, Hongshan District, Wuhan, 430074, P. R. China
| | - Xianhua Cai
- School of Pharmaceutical Sciences, South-Central Minzu University, 182 Minyuan Road, Hongshan District, Wuhan, 430074, P. R. China
| | - Ming Yao
- School of Pharmaceutical Sciences, South-Central Minzu University, 182 Minyuan Road, Hongshan District, Wuhan, 430074, P. R. China
| | - Yao Xu
- School of Pharmaceutical Sciences, South-Central Minzu University, 182 Minyuan Road, Hongshan District, Wuhan, 430074, P. R. China
| | - Yifu Gong
- School of Pharmaceutical Sciences, South-Central Minzu University, 182 Minyuan Road, Hongshan District, Wuhan, 430074, P. R. China
| | - Ke Zheng
- School of Pharmaceutical Sciences, South-Central Minzu University, 182 Minyuan Road, Hongshan District, Wuhan, 430074, P. R. China
| | - Yigui Mao
- School of Pharmaceutical Sciences, South-Central Minzu University, 182 Minyuan Road, Hongshan District, Wuhan, 430074, P. R. China
| | - Liyan Yang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, No.98 Daling Road, Nanning, 530007, P. R. China
| | - Dengfeng Yang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, No.98 Daling Road, Nanning, 530007, P. R. China
| | - István Molnár
- VTT Technical Research Centre of Finland, Division of Industrial Biotechnology and Food Solutions, Tietotie 2, Espoo, 02150, Finland
| | - Xiaolong Yang
- School of Pharmaceutical Sciences, South-Central Minzu University, 182 Minyuan Road, Hongshan District, Wuhan, 430074, P. R. China
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Madhu P, Davey NE, Ivarsson Y. How viral proteins bind short linear motifs and intrinsically disordered domains. Essays Biochem 2022; 66:EBC20220047. [PMID: 36504386 DOI: 10.1042/ebc20220047] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 02/11/2024]
Abstract
Viruses are the obligate intracellular parasites that exploit the host cellular machinery to replicate their genome. During the viral life cycle viruses manipulate the host cell through interactions with host proteins. Many of these protein-protein interactions are mediated through the recognition of host globular domains by short linear motifs (SLiMs), or longer intrinsically disordered domains (IDD), in the disordered regions of viral proteins. However, viruses also employ their own globular domains for binding to SLiMs and IDDs present in host proteins or virus proteins. In this review, we focus on the different strategies adopted by viruses to utilize proteins or protein domains for binding to the disordered regions of human or/and viral ligands. With a set of examples, we describe viral domains that bind human SLiMs. We also provide examples of viral proteins that bind to SLiMs, or IDDs, of viral proteins as a part of complex assembly and regulation of protein functions. The protein-protein interactions are often crucial for viral replication, and may thus offer possibilities for innovative inhibitor design.
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Affiliation(s)
- Priyanka Madhu
- Department of Chemistry, BMC, Uppsala University, Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, London, U.K
| | - Ylva Ivarsson
- Department of Chemistry, BMC, Uppsala University, Uppsala, Sweden
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9
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Peng Z, Zheng Z, Gao M, Qin L, Xiong L, Li X, Xie J. Mechanisms of Compound Sophora flavescens (Kushen) Decoction for the Treatment of Ulcerative Colitis Based on Network Pharmacology and Molecular Docking Technology. Curr Comput Aided Drug Des 2022; 18:228-239. [PMID: 35388762 DOI: 10.2174/1573409918666220406103708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/19/2022] [Accepted: 02/25/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND The Compound Sophora flavescenes (Kushen) Decoction was found to reduce the inflammatory symptom of Ulcerative colitis (UC). However, there exists a very limited understanding of the molecular pharmacological mechanisms. OBJECTIVE To explore the mechanism of Compound Sophora flavescens (Kushen) Decoction in treating ulcerative colitis from the perspective of network pharmacology. METHODS Active components and potential targets of Compound Sophora flavescens (Kushen) Decoction were obtained through the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) database. GeneCards and other databases were used to predict and screen ulcerative colitis related genes. Cytoscape software was applied to construct "drug-active component-disease-target" network. GO function and KEGG pathway enrichment analysis revealed the potential pathway of the Compound Sophora flavescenes (Kushen) Decoction for UC. RESULTS After screening, a total of 124 active ingredients and 163 potential therapeutic targets for UC, were obtained for the Compound Sophora flavescens (Kushen) Decoction. Protein interaction network analysis showed that 15 key targets could be identified for the possible treatment of UC. GO and KEGG analysis showed that the active ingredients in the Compound Sophora flavescens (Kushen) Decoction were mainly enriched in 2556 biological processes and 172 signaling pathways. CONCLUSION The study showed that the Compound Sophora flavescens (Kushen) Decoction has therapeutic effects on UC through multi-component, multi-target, and multi-pathway.
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Affiliation(s)
- Zijing Peng
- Department of Pharmacy,Sixth Affiliated Hospital of Sun Yat-sen University, China
| | - Zhuoling Zheng
- Department of Pharmacy,Sixth Affiliated Hospital of Sun Yat-sen University, China
| | - Min Gao
- Department of Pharmacy,Sixth Affiliated Hospital of Sun Yat-sen University, China
| | - Li Qin
- Department of Pharmacy,Sixth Affiliated Hospital of Sun Yat-sen University, China
| | - Lixiong Xiong
- Department of Pharmacy,Sixth Affiliated Hospital of Sun Yat-sen University, China
| | - Xiaoyan Li
- Department of Pharmacy,Sixth Affiliated Hospital of Sun Yat-sen University, China
| | - Jingwen Xie
- Department of Pharmacy,Sixth Affiliated Hospital of Sun Yat-sen University, China
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10
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Goher SS, Ali F, Amin M. The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2. Med Drug Discov 2021; 13:100114. [PMID: 34901826 PMCID: PMC8650763 DOI: 10.1016/j.medidd.2021.100114] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/14/2021] [Accepted: 11/22/2021] [Indexed: 12/14/2022] Open
Abstract
Mutations in the receptor binding domain (RBD) in SARS-CoV-2 are shown to enhance its replication, transmissibility, and binding to host cells. Recently, a new strain is reported in India that includes a mutation (T478K, and L452R) in the RBD, that is possibly increasing the infection rate. Here, using Molecular Mechanics (MM) and Monte Carlo (MC) sampling, we show that the double mutant variant of SARS-CoV-2 induced conformational change in ACE2-E37, which enhanced the electrostatic interactions by the formation of a salt-bridge with SARS-CoV-2-R403. In addition, we observed that the double mutated structure induced a significant change in the salt-bridge electrostatic interaction between RBD-T500 and ACE2-D355. Where that this interaction lost more than 70% of its value compared to its value in WT protein.
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Affiliation(s)
- Shaimaa S Goher
- Nanotechnology Research Centre (NTRC), the British University in Egypt (BUE), El Sherouk City, Suez Desert Road, Cairo 1183, Egypt
| | - Fedaa Ali
- Department of Sciences, University College Groningen, University of Groningen, Hoendiepskade 23/24, 9718 BG Groningen, The Netherlands
| | - Muhamed Amin
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
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11
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Gulotta MR, De Simone G, John J, Perricone U, Brancale A. A Computer-Based Methodology to Design Non-Standard Peptides Potentially Able to Prevent HOX-PBX1-Associated Cancer Diseases. Int J Mol Sci 2021; 22:5670. [PMID: 34073517 PMCID: PMC8198631 DOI: 10.3390/ijms22115670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 11/17/2022] Open
Abstract
In the last decades, HOX proteins have been extensively studied due to their pivotal role in transcriptional events. HOX proteins execute their activity by exploiting a cooperative binding to PBX proteins and DNA. Therefore, an increase or decrease in HOX activity has been associated with both solid and haematological cancer diseases. Thus, inhibiting HOX-PBX interaction represents a potential strategy to prevent these malignancies, as demonstrated by the patented peptide HTL001 that is being studied in clinical trials. In this work, a computational study is described to identify novel potential peptides designed by employing a database of non-natural amino acids. For this purpose, residue scanning of the HOX minimal active sequence was performed to select the mutations to be further processed. According to these results, the peptides were point-mutated and used for Molecular Dynamics (MD) simulations in complex with PBX1 protein and DNA to evaluate complex binding stability. MM-GBSA calculations of the resulting MD trajectories were exploited to guide the selection of the most promising mutations that were exploited to generate twelve combinatorial peptides. Finally, the latter peptides in complex with PBX1 protein and DNA were exploited to run MD simulations and the ΔGbinding average values of the complexes were calculated. Thus, the analysis of the results highlighted eleven combinatorial peptides that will be considered for further assays.
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Affiliation(s)
- Maria Rita Gulotta
- Molecular Informatics Unit, Fondazione Ri.MED, Via Filippo Marini 14, 90128 Palermo, Italy; (G.D.S.); (U.P.)
| | - Giada De Simone
- Molecular Informatics Unit, Fondazione Ri.MED, Via Filippo Marini 14, 90128 Palermo, Italy; (G.D.S.); (U.P.)
| | - Justin John
- NRN Tech LTD, Henstaff Court, Llantrisant Road, Groesfaen CF72 8NG, UK;
| | - Ugo Perricone
- Molecular Informatics Unit, Fondazione Ri.MED, Via Filippo Marini 14, 90128 Palermo, Italy; (G.D.S.); (U.P.)
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, UK;
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12
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Mohammadi S, Davila-Velderrain J, Kellis M. Reconstruction of Cell-type-Specific Interactomes at Single-Cell Resolution. Cell Syst 2019; 9:559-568.e4. [PMID: 31786210 PMCID: PMC6943823 DOI: 10.1016/j.cels.2019.10.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/13/2019] [Accepted: 10/22/2019] [Indexed: 01/03/2023]
Abstract
The human interactome is instrumental in the systems-level study of the cell and the contextualization of disease-associated gene perturbations. However, reference organismal interactomes do not capture the cell-type-specific context in which proteins and modules preferentially act. Here, we introduce SCINET, a computational framework that reconstructs an ensemble of cell-type-specific interactomes by integrating a global, context-independent reference interactome with a single-cell gene-expression profile. SCINET addresses technical challenges of single-cell data by robustly imputing, transforming, and normalizing the initially noisy and sparse expression of data. Inferred cell-level gene interaction probabilities and group-level interaction strengths define cell-type-specific interactomes. We use SCINET to reconstruct and analyze interactomes of the major human brain and immune cell types, revealing specificity and modularity of perturbations associated with neurodegenerative, neuropsychiatric, and autoimmune disorders. We report cell-type interactomes for brain and immune cell types, together with the SCINET package.
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Affiliation(s)
- Shahin Mohammadi
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Jose Davila-Velderrain
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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13
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Kamal AHM, Aloor JJ, Fessler MB, Chowdhury SM. Cross-linking Proteomics Indicates Effects of Simvastatin on the TLR2 Interactome and Reveals ACTR1A as a Novel Regulator of the TLR2 Signal Cascade. Mol Cell Proteomics 2019; 18:1732-1744. [PMID: 31221720 PMCID: PMC6731082 DOI: 10.1074/mcp.ra119.001377] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/25/2019] [Indexed: 01/23/2023] Open
Abstract
Toll-like receptor 2 (TLR2) is a pattern recognition receptor that, upon ligation by microbial molecules, interacts with other proteins to initiate pro-inflammatory responses by the cell. Statins (hydroxymethylglutaryl coenzyme A reductase inhibitors), drugs widely prescribed to reduce hypercholesterolemia, are reported to have both pro- and anti-inflammatory effects upon cells. Some of these responses are presumed to be driven by effects on signaling proteins at the plasma membrane, but the underlying mechanisms remain obscure. We reasoned that profiling the effect of statins on the repertoire of TLR2-interacting proteins might provide novel insights into the mechanisms by which statins impact inflammation. In order to study the TLR2 interactome, we designed a coimmunoprecipitation (IP)-based cross-linking proteomics study. A hemagglutinin (HA)-tagged-TLR2 transfected HEK293 cell line was used to precipitate the TLR2 interactome upon cell exposure to the TLR2 agonist Pam3CSK4 and simvastatin, singly and in combination. To stabilize protein interactors, we used two different chemical cross-linkers with different spacer chain lengths. Proteomic analysis revealed important combinatorial effects of simvastatin and Pam3CSK4 on the TLR2 interactome. After stringent data filtering, we identified alpha-centractin (ACTR1A), an actin-related protein and subunit of the dynactin complex, as a potential interactor of TLR2. The interaction was validated using biochemical methods. RNA interference studies revealed an important role for ACTR1A in induction of pro-inflammatory cytokines. Taken together, we report that statins remodel the TLR2 interactome, and we identify ACTR1A, a part of the dynactin complex, as a novel regulator of TLR2-mediated immune signaling pathways.
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Affiliation(s)
- Abu Hena Mostafa Kamal
- ‡Department of Chemistry and Biochemistry, University of Texas at Arlington, Texas 76019
| | - Jim J Aloor
- §Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Michael B Fessler
- §Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Saiful M Chowdhury
- ‡Department of Chemistry and Biochemistry, University of Texas at Arlington, Texas 76019.
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14
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Kobayashi D, Tokuda T, Sato K, Okanishi H, Nagayama M, Hirayama-Kurogi M, Ohtsuki S, Araki N. Identification of a Specific Translational Machinery via TCTP-EF1A2 Interaction Regulating NF1-associated Tumor Growth by Affinity Purification and Data-independent Mass Spectrometry Acquisition (AP-DIA). Mol Cell Proteomics 2019; 18:245-262. [PMID: 30381327 PMCID: PMC6356078 DOI: 10.1074/mcp.ra118.001014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/17/2018] [Indexed: 11/06/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant disease that predisposes individuals to developing benign neurofibromas and malignant peripheral nerve sheath tumors (MPNST). The mechanism of NF1-tumorigenesis or the curatives have not been established. Using unique trascriptome and proteome integration method, iPEACH (1), we previously identified translationally controlled tumor protein (TCTP) as a novel biological target for NF1-associated tumors (2). Here, we identified specific TCTP-interacting proteins by sequential affinity purification and data-independent mass spectrometry acquisition (AP-DIA/SWATH) to investigate the role of TCTP in NF1-associated malignant tumors. TCTP mainly interacts with proteins related to protein synthesis and especially to elongation factor complex components, including EF1A2, EF1B, EF1D, EF1G, and valyl-tRNA synthetase (VARS), in NF1-deficient malignant tumor cells. Interestingly, TCTP preferentially binds to EF1A2 (normally found only in neural and skeletal-muscle cells and several cancer cells), rather than EF1A1 despite the high homologies (98%) in their sequences. The docking simulation and further validations to study the interaction between TCTP and EF1A2 revealed that TCTP directly binds with EF1A2 via the contact areas of EF1A2 dimerization. Using unique and common sequences between EF1A2 and EF1A1 in AP-DIA/SWATH, we quantitatively validated the interaction of EF1A2 and TCTP/other elongation factors and found that TCTP coordinates the translational machinery of elongation factors via the association with EF1A2. These data suggest that TCTP activates EF1A2-dependent translation by mediating complex formation with other elongation factors. Inhibiting the TCTP-EF1A2 interaction with EF1A2 siRNAs or a TCTP inhibitor, artesunate, significantly down-regulated the factors related to protein translation and caused dramatic suppression of growth/translation in NF1-associated tumors. Our findings demonstrate that a specific protein translation machinery related to the TCTP-EF1A2 interaction is functionally implicated in the tumorigenesis and progression of NF1-associated tumors and could represent a therapeutic target.
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Affiliation(s)
- Daiki Kobayashi
- Department of Tumor Genetics and Biology, Graduate School of Medical Sciences, Faculty of Life Sciences
| | - Takaho Tokuda
- Department of Tumor Genetics and Biology, Graduate School of Medical Sciences, Faculty of Life Sciences
| | - Kyosuke Sato
- Department of Molecular Physiology, Faculty of Life Sciences
| | - Hiroki Okanishi
- Department of Tumor Genetics and Biology, Graduate School of Medical Sciences, Faculty of Life Sciences
| | - Megumi Nagayama
- Department of Tumor Genetics and Biology, Graduate School of Medical Sciences, Faculty of Life Sciences
| | - Mio Hirayama-Kurogi
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University
| | - Norie Araki
- Department of Tumor Genetics and Biology, Graduate School of Medical Sciences, Faculty of Life Sciences,.
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15
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Trcka F, Durech M, Vankova P, Chmelik J, Martinkova V, Hausner J, Kadek A, Marcoux J, Klumpler T, Vojtesek B, Muller P, Man P. Human Stress-inducible Hsp70 Has a High Propensity to Form ATP-dependent Antiparallel Dimers That Are Differentially Regulated by Cochaperone Binding. Mol Cell Proteomics 2019; 18:320-337. [PMID: 30459217 PMCID: PMC6356074 DOI: 10.1074/mcp.ra118.001044] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/09/2018] [Indexed: 12/23/2022] Open
Abstract
Eukaryotic protein homeostasis (proteostasis) is largely dependent on the action of highly conserved Hsp70 molecular chaperones. Recent evidence indicates that, apart from conserved molecular allostery, Hsp70 proteins have retained and adapted the ability to assemble as functionally relevant ATP-bound dimers throughout evolution. Here, we have compared the ATP-dependent dimerization of DnaK, human stress-inducible Hsp70, Hsc70 and BiP Hsp70 proteins, showing that their dimerization propensities differ, with stress-inducible Hsp70 being predominantly dimeric in the presence of ATP. Structural analyses using hydrogen/deuterium exchange mass spectrometry, native electrospray ionization mass spectrometry and small-angle X-ray scattering revealed that stress-inducible Hsp70 assembles in solution as an antiparallel dimer with the intermolecular interface closely resembling the ATP-bound dimer interfaces captured in DnaK and BiP crystal structures. ATP-dependent dimerization of stress-inducible Hsp70 is necessary for its efficient interaction with Hsp40, as shown by experiments with dimerization-deficient mutants. Moreover, dimerization of ATP-bound Hsp70 is required for its participation in high molecular weight protein complexes detected ex vivo, supporting its functional role in vivo As human cytosolic Hsp70 can interact with tetratricopeptide repeat (TPR) domain containing cochaperones, we tested the interaction of Hsp70 ATP-dependent dimers with Chip and Tomm34 cochaperones. Although Chip associates with intact Hsp70 dimers to form a larger complex, binding of Tomm34 disrupts the Hsp70 dimer and this event plays an important role in Hsp70 activity regulation. In summary, this study provides structural evidence of robust ATP-dependent antiparallel dimerization of human inducible Hsp70 protein and suggests a novel role of TPR domain cochaperones in multichaperone complexes involving Hsp70 ATP-bound dimers.
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Affiliation(s)
- Filip Trcka
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - Michal Durech
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - Pavla Vankova
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50 Vestec, Czech Republic;; Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43 Prague, Czech Republic
| | - Josef Chmelik
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50 Vestec, Czech Republic;; Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43 Prague, Czech Republic
| | - Veronika Martinkova
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - Jiri Hausner
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50 Vestec, Czech Republic;; Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43 Prague, Czech Republic
| | - Alan Kadek
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50 Vestec, Czech Republic;; Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43 Prague, Czech Republic
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Tomas Klumpler
- CEITEC-Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Borivoj Vojtesek
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - Petr Muller
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic;.
| | - Petr Man
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50 Vestec, Czech Republic;; Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43 Prague, Czech Republic;.
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16
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Wei R, Kaneko T, Liu X, Liu H, Li L, Voss C, Liu E, He N, Li SSC. Interactome Mapping Uncovers a General Role for Numb in Protein Kinase Regulation. Mol Cell Proteomics 2018; 17:2216-2228. [PMID: 29217616 PMCID: PMC6210222 DOI: 10.1074/mcp.ra117.000114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 12/04/2017] [Indexed: 12/24/2022] Open
Abstract
Cellular functions are frequently regulated by protein-protein interactions involving the binding of a modular domain in one protein to a specific peptide sequence in another. This mechanism may be explored to identify binding partners for proteins harboring a peptide-recognition domain. Here we report a proteomic strategy combining peptide and protein microarray screening with biochemical and cellular assays to identify modular domain-mediated protein-protein interactions in a systematic manner. We applied this strategy to Numb, a multi-functional protein containing a phosphotyrosine-binding (PTB) domain. Through the screening of a protein microarray, we identified >100 protein kinases, including both Tyr and Ser/Thr kinases, that could potentially interact with the Numb PTB domain, suggesting a general role for Numb in regulating kinase function. The putative interactions between Numb and several tyrosine kinases were subsequently validated by GST pull-down and/or co-immunoprecipitation assays. Furthermore, using the Oriented Peptide Array Library approach, we defined the specificity of the Numb PTB domain which, in turn, allowed us to predict binding partners for Numb at the genome level. The combination of the protein microarray screening with computer-aided prediction produced the most expansive interactome for Numb to date, implicating Numb in regulating phosphorylation signaling through protein kinases and phosphatases. Not only does the data generated from this study provide an important resource for hypothesis-driven research to further define the function of Numb, the proteomic strategy described herein may be employed to uncover the interactome for other peptide-recognition domains whose consensus motifs are known or can be determined.
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Affiliation(s)
- Ran Wei
- From the ‡Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Tomonori Kaneko
- From the ‡Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Xuguang Liu
- From the ‡Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Huadong Liu
- From the ‡Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
- §Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shanxi, China
| | - Lei Li
- From the ‡Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
- ¶School of Basic Medical Sciences, Qingdao University, Qingdao 266021, Shangdong, China
- ‖College of Pharmacy, Qingdao University, Qingdao 26601, Shangdong, China
| | - Courtney Voss
- From the ‡Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Eric Liu
- From the ‡Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Ningning He
- ¶School of Basic Medical Sciences, Qingdao University, Qingdao 266021, Shangdong, China
- ‖College of Pharmacy, Qingdao University, Qingdao 26601, Shangdong, China
| | - Shawn S-C Li
- From the ‡Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada;
- **Department of Oncology and Child Health Research Institute, Western University
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17
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Lyons SP, Jenkins NP, Nasa I, Choy MS, Adamo ME, Page R, Peti W, Moorhead GB, Kettenbach AN. A Quantitative Chemical Proteomic Strategy for Profiling Phosphoprotein Phosphatases from Yeast to Humans. Mol Cell Proteomics 2018; 17:2448-2461. [PMID: 30228194 DOI: 10.1074/mcp.ra118.000822] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/21/2018] [Indexed: 11/06/2022] Open
Abstract
A "tug-of-war" between kinases and phosphatases establishes the phosphorylation states of proteins. While serine and threonine phosphorylation can be catalyzed by more than 400 protein kinases, the majority of serine and threonine dephosphorylation is carried out by seven phosphoprotein phosphatases (PPPs). The PPP family consists of protein phosphatases 1 (PP1), 2A (PP2A), 2B (PP2B), 4 (PP4), 5 (PP5), 6 (PP6), and 7 (PP7). The imbalance in numbers between serine- and threonine-directed kinases and phosphatases led to the early belief that PPPs are unspecific and that kinases are the primary determinants of protein phosphorylation. However, it is now clear that PPPs achieve specificity through association with noncatalytic subunits to form multimeric holoenzymes, which expands the number of functionally distinct signaling entities to several hundred. Although there has been great progress in deciphering signaling by kinases, much less is known about phosphatases.We have developed a chemical proteomic strategy for the systematic interrogation of endogenous PPP catalytic subunits and their interacting proteins, including regulatory and scaffolding subunits (the "PPPome"). PP1, PP2A, PP4, PP5, and PP6 were captured using an immobilized, specific but nonselective PPP inhibitor microcystin-LR (MCLR), followed by protein identification by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in a single analysis. Here, we combine this approach of phosphatase inhibitor bead profiling and mass spectrometry (PIB-MS) with label-free and tandem mass tag (TMT) quantification to map the PPPome in human cancer cell lines, mouse tissues, and yeast species, through which we identify cell- and tissue-type-specific PPP expression patterns and discover new PPP interacting proteins.
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Affiliation(s)
- Scott P Lyons
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Nicole P Jenkins
- Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center at Dartmouth, Lebanon, NH, USA
| | - Isha Nasa
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA; Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center at Dartmouth, Lebanon, NH, USA
| | - Meng S Choy
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Mark E Adamo
- Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center at Dartmouth, Lebanon, NH, USA
| | - Rebecca Page
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Wolfgang Peti
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Greg B Moorhead
- Department of Biological Science, University of Calgary, Alberta, Canada
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA; Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center at Dartmouth, Lebanon, NH, USA.
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18
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Schiza C, Korbakis D, Panteleli E, Jarvi K, Drabovich AP, Diamandis EP. Discovery of a Human Testis-specific Protein Complex TEX101-DPEP3 and Selection of Its Disrupting Antibodies. Mol Cell Proteomics 2018; 17:2480-2495. [PMID: 30097533 DOI: 10.1074/mcp.ra118.000749] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/11/2018] [Indexed: 01/01/2023] Open
Abstract
TEX101 is a testis-specific protein expressed exclusively in male germ cells and is a validated biomarker of male infertility. Studies in mice suggest that TEX101 is a cell-surface chaperone which regulates, through protein-protein interactions, the maturation of proteins involved in spermatozoa transit and oocyte binding. Male TEX101-null mice are sterile. Here, we identified by co-immunoprecipitation-mass spectrometry the interactome of human TEX101 in testicular tissues and spermatozoa. The testis-specific cell-surface dipeptidase 3 (DPEP3) emerged as the top hit. We further validated the TEX101-DPEP3 complex by using hybrid immunoassays. Combinations of antibodies recognizing different epitopes of TEX101 and DPEP3 facilitated development of a simple immunoassay to screen for disruptors of TEX101-DPEP3 complex. As a proof-of-a-concept, we demonstrated that anti-TEX101 antibody T4 disrupted the native TEX101-DPEP3 complex. Disrupting antibodies may be used to study the human TEX101-DPEP3 complex, and to develop modulators for male fertility.
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Affiliation(s)
- Christina Schiza
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Dimitrios Korbakis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Efstratia Panteleli
- Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Keith Jarvi
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada; Department of Surgery, Division of Urology, Mount Sinai Hospital, Toronto, Canada
| | - Andrei P Drabovich
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada; Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada; Department of Clinical Biochemistry, University Health Network, Toronto, Canada.
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19
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Coyaud E, Ranadheera C, Cheng D, Gonçalves J, Dyakov BJA, Laurent EMN, St-Germain J, Pelletier L, Gingras AC, Brumell JH, Kim PK, Safronetz D, Raught B. Global Interactomics Uncovers Extensive Organellar Targeting by Zika Virus. Mol Cell Proteomics 2018; 17:2242-2255. [PMID: 30037810 DOI: 10.1074/mcp.tir118.000800] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/06/2018] [Indexed: 11/06/2022] Open
Abstract
Zika virus (ZIKV) is a membrane enveloped Flavivirus with a positive strand RNA genome, transmitted by Aedes mosquitoes. The geographical range of ZIKV has dramatically expanded in recent decades resulting in increasing numbers of infected individuals, and the spike in ZIKV infections has been linked to significant increases in both Guillain-Barré syndrome and microcephaly. Although a large number of host proteins have been physically and/or functionally linked to other Flaviviruses, very little is known about the virus-host protein interactions established by ZIKV. Here we map host cell protein interaction profiles for each of the ten polypeptides encoded in the ZIKV genome, generating a protein topology network comprising 3033 interactions among 1224 unique human polypeptides. The interactome is enriched in proteins with roles in polypeptide processing and quality control, vesicle trafficking, RNA processing and lipid metabolism. >60% of the network components have been previously implicated in other types of viral infections; the remaining interactors comprise hundreds of new putative ZIKV functional partners. Mining this rich data set, we highlight several examples of how ZIKV may usurp or disrupt the function of host cell organelles, and uncover an important role for peroxisomes in ZIKV infection.
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Affiliation(s)
- Etienne Coyaud
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Charlene Ranadheera
- §Public Health Agency of Canada, Zoonotic Diseases and Special Pathogens Program, Winnipeg, Manitoba, Canada
| | - Derrick Cheng
- ¶Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,‖Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - João Gonçalves
- **Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Boris J A Dyakov
- **Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,‡‡Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Estelle M N Laurent
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jonathan St-Germain
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Laurence Pelletier
- **Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,‡‡Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- **Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,‡‡Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - John H Brumell
- ¶Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,‡‡Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,§§Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,¶¶Sick Kids IBD Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Peter K Kim
- ¶Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,‖Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - David Safronetz
- §Public Health Agency of Canada, Zoonotic Diseases and Special Pathogens Program, Winnipeg, Manitoba, Canada
| | - Brian Raught
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; .,‖‖Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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20
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Fasci D, van Ingen H, Scheltema RA, Heck AJR. Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. Mol Cell Proteomics 2018; 17:2018-2033. [PMID: 30021884 DOI: 10.1074/mcp.ra118.000924] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 07/17/2018] [Indexed: 02/03/2023] Open
Abstract
Cells organize their actions partly through tightly controlled protein-protein interactions-collectively termed the interactome. Here we use crosslinking mass spectrometry (XL-MS) to chart the protein-protein interactions in intact human nuclei. Overall, we identified ∼8,700 crosslinks, of which 2/3 represent links connecting distinct proteins. From these data, we gain insights on interactions involving histone proteins. We observed that core histones on the nucleosomes expose well-defined interaction hot spots. For several nucleosome-interacting proteins, such as USF3 and Ran GTPase, the data allowed us to build low-resolution models of their binding mode to the nucleosome. For HMGN2, the data guided the construction of a refined model of the interaction with the nucleosome, based on complementary NMR, XL-MS, and modeling. Excitingly, the analysis of crosslinks carrying posttranslational modifications allowed us to extract how specific modifications influence nucleosome interactions. Overall, our data depository will support future structural and functional analysis of cell nuclei, including the nucleoprotein assemblies they harbor.
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Affiliation(s)
- Domenico Fasci
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences.,§Netherlands Proteomics Centre, and
| | - Hugo van Ingen
- ¶NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Richard A Scheltema
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; .,§Netherlands Proteomics Centre, and
| | - Albert J R Heck
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; .,§Netherlands Proteomics Centre, and
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21
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Jacquet K, Banerjee SL, Chartier FJM, Elowe S, Bisson N. Proteomic Analysis of NCK1/2 Adaptors Uncovers Paralog-specific Interactions That Reveal a New Role for NCK2 in Cell Abscission During Cytokinesis. Mol Cell Proteomics 2018; 17:1979-1990. [PMID: 30002203 DOI: 10.1074/mcp.ra118.000689] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 07/11/2018] [Indexed: 12/31/2022] Open
Abstract
Signals from cell surface receptors are often relayed via adaptor proteins. NCK1 and NCK2 are Src-Homology (SH) 2 and 3 domain adaptors that regulate processes requiring a remodeling of the actin cytoskeleton. Evidence from gene inactivation in mouse suggests that NCK1 and NCK2 are functionally redundant, although recent reports support the idea of unique functions for NCK1 and NCK2. We sought to examine this question further by delineating NCK1- and NCK2-specific signaling networks. We used both affinity purification-mass spectrometry and BioID proximity labeling to identify NCK1/2 signaling networks comprised of 98 proteins. Strikingly, we found 30 proteins restricted to NCK1 and 28 proteins specifically associated with NCK2, suggesting differences in their function. We report that Nck2 -/-, but not Nck1 -/- mouse embryo fibroblasts (MEFs) are multinucleated and display extended protrusions reminiscent of intercellular bridges, which correlate with an extended time spent in cytokinesis as well as a failure of a significant proportion of cells to complete abscission. Our data also show that the midbody of NCK2-deficient cells is not only increased in length, but also altered in composition, as judged by the mislocalization of AURKB, PLK1 and ECT2. Finally, we show that NCK2 function during cytokinesis requires its SH2 domain. Taken together, our data delineate the first high-confidence interactome for NCK1/2 adaptors and highlight several proteins specifically associated with either protein. Thus, contrary to what is generally accepted, we demonstrate that NCK1 and NCK2 are not completely redundant, and shed light on a previously uncharacterized function for the NCK2 adaptor protein in cell division.
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Affiliation(s)
- Kévin Jacquet
- From the ‡Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec G1R 2J6, QC, Canada.,§Centre de recherche sur le cancer de l'Université Laval, Québec G1R 2J6, QC, Canada.,¶PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec G1V 0A6, QC, Canada
| | - Sara L Banerjee
- From the ‡Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec G1R 2J6, QC, Canada.,§Centre de recherche sur le cancer de l'Université Laval, Québec G1R 2J6, QC, Canada.,¶PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec G1V 0A6, QC, Canada
| | - François J M Chartier
- From the ‡Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec G1R 2J6, QC, Canada.,§Centre de recherche sur le cancer de l'Université Laval, Québec G1R 2J6, QC, Canada.,¶PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec G1V 0A6, QC, Canada
| | - Sabine Elowe
- §Centre de recherche sur le cancer de l'Université Laval, Québec G1R 2J6, QC, Canada.,¶PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec G1V 0A6, QC, Canada.,‖Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Reproduction, santé de la mère et de l'enfant, Québec G1V 4G2, QC, Canada.,**Department of Pediatrics, Université Laval, Québec, QC, Canada
| | - Nicolas Bisson
- From the ‡Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec G1R 2J6, QC, Canada; .,§Centre de recherche sur le cancer de l'Université Laval, Québec G1R 2J6, QC, Canada.,¶PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec G1V 0A6, QC, Canada.,‡‡Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec G1V 0A6, QC, Canada
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22
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Chen F, Fu Q, Pu L, Zhang P, Huang Y, Hou Z, Xu Z, Chen D, Huang F, Deng T, Liang X, Lu Y, Zhang M. Integrated Analysis of Quantitative Proteome and Transcriptional Profiles Reveals the Dynamic Function of Maternally Expressed Proteins After Parthenogenetic Activation of Buffalo Oocyte. Mol Cell Proteomics 2018; 17:1875-1891. [PMID: 30002204 DOI: 10.1074/mcp.ra118.000556] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 05/16/2018] [Indexed: 01/09/2023] Open
Abstract
Maternal-effect genes are especially critical for early embryonic development after fertilization and until massive activation of the embryonic genome occurs. By applying a tandem mass tag (TMT)-labeled quantitative proteomics combined with RNA sequencing approach, the proteome of the buffalo was quantitatively analyzed during parthenogenesis of mature oocytes and the two-cell stage embryo. Of 1908 quantified proteins, 123 differed significantly. The transcriptome was analyzed eight stages (GV, MII, 2-cell, 4-cell, 8-cell, 16-cell, morula, blastocyst) of Buffalo using the RNA sequencing approach, and a total of 3567 unique genes were identified to be differently expressed between all consecutive stages of pre-implantation development. Validation of proteomics results (TUBB3, CTNNA1, CDH3, MAP2K1), which are involved in tight junction and gap junction, revealing that the maternal expression of the proteins possibly plays a role in the formation of cellular junctions firstly after parthenogenetic activation. Correlation and hierarchical analyses of transcriptional profiles and the expression of NPM2 and NLRP5 mRNA of buffalo in vitro developed oocytes and parthenogenetic embryos indicated that the "maternal-to-zygotic transition" (MZT) process might exist in the model of parthenogenesis, which is similar to a normally fertilized embryo, and may occur between the 8-cell to 16-cell stage. These data provide a rich resource for further studies on maternal proteins and genes and are conducive to improving nuclear transfer technology.
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Affiliation(s)
- Fumei Chen
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Qiang Fu
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Liping Pu
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Pengfei Zhang
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Yulin Huang
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Zhen Hou
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Zhuangzhuang Xu
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Dongrong Chen
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Fengling Huang
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Tingxian Deng
- §Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Buffalo Research Institute, Chinese Academy of Agricultural Science, Nanning, Guangxi 530001, China
| | - Xianwei Liang
- §Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Buffalo Research Institute, Chinese Academy of Agricultural Science, Nanning, Guangxi 530001, China
| | - Yangqing Lu
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China;
| | - Ming Zhang
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China;
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23
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Samavarchi-Tehrani P, Abdouni H, Samson R, Gingras AC. A Versatile Lentiviral Delivery Toolkit for Proximity-dependent Biotinylation in Diverse Cell Types. Mol Cell Proteomics 2018; 17:2256-2269. [PMID: 29991506 DOI: 10.1074/mcp.tir118.000902] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Indexed: 11/06/2022] Open
Abstract
Proximity-dependent biotinylation strategies have emerged as powerful tools to characterize the subcellular context of proteins in living cells. The popular BioID approach employs an abortive E. coli biotin ligase mutant (R118G; denoted as BirA*), which when fused to a bait protein enables the covalent biotinylation of endogenous proximal polypeptides. This approach has been mainly applied to the study of protein proximity in immortalized mammalian cell lines. To expand the application space of BioID, here we describe a set of lentiviral vectors that enable the inducible expression of BirA*-tagged bait fusion proteins for performing proximity-dependent biotinylation in diverse experimental systems. We benchmark this highly adaptable toolkit across immortalized and primary cell systems, demonstrating the ease, versatility and robustness of the system. We also provide guidelines to perform BioID using these reagents.
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Affiliation(s)
| | - Hala Abdouni
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Reuben Samson
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.,§Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Anne-Claude Gingras
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada; .,§Department of Molecular Genetics, University of Toronto, Toronto, Canada
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24
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Rosas-Salvans M, Cavazza T, Espadas G, Sabido E, Vernos I. Proteomic Profiling of Microtubule Self-organization in M-phase. Mol Cell Proteomics 2018; 17:1991-2004. [PMID: 29970457 DOI: 10.1074/mcp.ra118.000745] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/11/2018] [Indexed: 01/08/2023] Open
Abstract
Microtubules (MTs) and associated proteins can self-organize into complex structures such as the bipolar spindle, a process in which RanGTP plays a major role. Addition of RanGTP to M-phase Xenopus egg extracts promotes the nucleation and self-organization of MTs into asters and bipolar-like structures in the absence of centrosomes or chromosomes. We show here that the complex proteome of these RanGTP-induced MT assemblies is similar to that of mitotic spindles. Using proteomic profiling we show that MT self-organization in the M-phase cytoplasm involves the non-linear and non-stoichiometric recruitment of proteins from specific functional groups. Our study provides for the first time a temporal understanding of the protein dynamics driving MT self-organization in M-phase.
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Affiliation(s)
- Miquel Rosas-Salvans
- From the ‡Cell and Developmental Biology Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Tommaso Cavazza
- From the ‡Cell and Developmental Biology Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Guadalupe Espadas
- **Proteomics Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.,§Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Eduard Sabido
- **Proteomics Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.,§Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Isabelle Vernos
- From the ‡Cell and Developmental Biology Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; .,§Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain.,‡‡Institució Catalana de Recerca I Estudis Avançats (ICREA), Passeig de Lluis Companys 23, 08010 Barcelona, Spain
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25
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Hutchins JRA, Traver S, Coulombe P, Peiffer I, Kitzmann M, Latreille D, Méchali M. Proteomic data on the nuclear interactome of human MCM9. Data Brief 2015; 6:410-5. [PMID: 26870752 PMCID: PMC4712314 DOI: 10.1016/j.dib.2015.11.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 11/17/2015] [Accepted: 11/23/2015] [Indexed: 11/24/2022] Open
Abstract
We present data relating to the interactome of MCM9 from the nuclei of human cells. MCM9 belongs to the AAA+ superfamily, and contains an MCM domain and motifs that may confer DNA helicase activity. MCM9 has been shown to bind MCM8, and has been implicated in DNA replication and homologous recombination. However, the mechanistic basis of MCM9’s role in DNA repair is poorly understood, and proteins with which it interacts were hitherto unknown. We performed tandem affinity purification of MCM9 and its interacting proteins from nuclear extracts of human cells, followed by proteomic analysis, thereby generating a set of mass spectrometry data corresponding to the MCM9 interactome [1]. The proteomic data set comprises 29 mass spectrometry RAW files, deposited to the ProteomeXchange Consortium, and freely available from the PRIDE partner repository with the data set identifier PXD000212. A set of 22 interacting proteins identified from the proteomic data was used to create an MCM9-centered interactive network diagram, using the Cytoscape program. These data allow the scientific community to access, mine and explore the human nuclear MCM9 interactome.
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Affiliation(s)
- James R A Hutchins
- Laboratory of DNA Replication and Genome Dynamics, Institute of Human Genetics, CNRS, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Sabine Traver
- Laboratory of DNA Replication and Genome Dynamics, Institute of Human Genetics, CNRS, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Philippe Coulombe
- Laboratory of DNA Replication and Genome Dynamics, Institute of Human Genetics, CNRS, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Isabelle Peiffer
- Laboratory of DNA Replication and Genome Dynamics, Institute of Human Genetics, CNRS, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Magali Kitzmann
- Laboratory of DNA Replication and Genome Dynamics, Institute of Human Genetics, CNRS, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Daniel Latreille
- Laboratory of Gene Regulation, Institute of Human Genetics, CNRS, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Marcel Méchali
- Laboratory of DNA Replication and Genome Dynamics, Institute of Human Genetics, CNRS, 141 rue de la Cardonille, 34396 Montpellier, France
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26
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Yasuda S, Sato T, Maekawa S, Aoyama S, Fukao Y, Yamaguchi J. Phosphorylation of Arabidopsis ubiquitin ligase ATL31 is critical for plant carbon/nitrogen nutrient balance response and controls the stability of 14-3-3 proteins. J Biol Chem 2014; 289:15179-93. [PMID: 24722992 PMCID: PMC4140878 DOI: 10.1074/jbc.m113.533133] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 04/02/2014] [Indexed: 12/22/2022] Open
Abstract
Ubiquitin ligase plays a fundamental role in regulating multiple cellular events in eukaryotes by fine-tuning the stability and activity of specific target proteins. We have previously shown that ubiquitin ligase ATL31 regulates plant growth in response to nutrient balance between carbon and nitrogen (C/N) in Arabidopsis. Subsequent study demonstrated that ATL31 targets 14-3-3 proteins for ubiquitination and modulates the protein abundance in response to C/N-nutrient status. However, the underlying mechanism for the targeting of ATL31 to 14-3-3 proteins remains unclear. Here, we show that ATL31 interacts with 14-3-3 proteins in a phosphorylation-dependent manner. We identified Thr(209), Ser(247), Ser(270), and Ser(303) as putative 14-3-3 binding sites on ATL31 by motif analysis. Mutation of these Ser/Thr residues to Ala in ATL31 inhibited the interaction with 14-3-3 proteins, as demonstrated by yeast two-hybrid and co-immunoprecipitation analyses. Additionally, we identified in vivo phosphorylation of Thr(209) and Ser(247) on ATL31 by MS analysis. A peptide competition assay showed that the application of synthetic phospho-Thr(209) peptide, but not the corresponding unphosphorylated peptide, suppresses the interaction between ATL31 and 14-3-3 proteins. Moreover, Arabidopsis plants overexpressing mutated ATL31, which could not bind to 14-3-3 proteins, showed accumulation of 14-3-3 proteins and growth arrest in disrupted C/N-nutrient conditions similar to wild-type plants, although overexpression of intact ATL31 resulted in repression of 14-3-3 accumulation and tolerance to the conditions. Together, these results demonstrate that the physiological role of phosphorylation at 14-3-3 binding sites on ATL31 is to modulate the binding ability and stability of 14-3-3 proteins to control plant C/N-nutrient response.
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Affiliation(s)
- Shigetaka Yasuda
- From the Faculty of Science and Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan and
| | - Takeo Sato
- From the Faculty of Science and Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan and
| | - Shugo Maekawa
- From the Faculty of Science and Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan and
| | - Shoki Aoyama
- From the Faculty of Science and Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan and
| | - Yoichiro Fukao
- the Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Junji Yamaguchi
- From the Faculty of Science and Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan and
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27
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Qadota H, Luo Y, Matsunaga Y, Park AS, Gernert KM, Benian GM. Suppressor mutations suggest a surface on PAT-4 (Integrin-linked Kinase) that interacts with UNC-112 (Kindlin). J Biol Chem 2014; 289:14252-62. [PMID: 24692564 PMCID: PMC4022890 DOI: 10.1074/jbc.m114.556308] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/20/2014] [Indexed: 11/06/2022] Open
Abstract
Caenorhabditis elegans striated muscle cells attach to basement membrane and transmit the force of muscle contraction through integrin adhesion complexes. The cytoplasmic tail of β-integrin (PAT-3) is associated with a conserved four-protein complex that includes UNC-112 (kindlin), PAT-4 (integrin-linked kinase), PAT-6 (α-parvin/actopaxin), and UNC-97 (PINCH). The proper localization of UNC-112 to muscle integrin adhesion sites requires PAT-4. A recent report (Qadota, H., Moerman, D. G., and Benian, G. M. (2012) A molecular mechanism for the requirement of PAT-4 (integrin-linked kinase (ILK)) for the localization of UNC-112 (kindlin) to integrin adhesion sites. J. Biol. Chem. 287, 28537-28551) suggests a possible molecular mechanism for this requirement: that UNC-112 exists in closed inactive and open active conformations, and conversion to the open active form is promoted by binding to PAT-4 (ILK). Previously, we also reported identification of a single missense mutation in UNC-112, D382V, which abolishes both binding to PAT-4 and normal localization to integrin adhesion sites in vivo. In this report, we describe isolation and characterization of PAT-4 missense mutations that permit binding with UNC-112 D382V and place nine affected residues on a homology model of PAT-4. These nine residues cluster in two regions on the surface of PAT-4, do not overlap the likely binding surface for PAT-6 (α-parvin), and therefore may reside along the interaction surface of PAT-4 for UNC-112 (kindlin). We also show that one of these PAT-4 mutations restores the ability of UNC-112 D382V to localize to integrin adhesions and participate in complex formation.
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Affiliation(s)
- Hiroshi Qadota
- From the Department of Pathology, Emory University, Atlanta, Georgia 30322 and
| | - Yating Luo
- From the Department of Pathology, Emory University, Atlanta, Georgia 30322 and
| | - Yohei Matsunaga
- From the Department of Pathology, Emory University, Atlanta, Georgia 30322 and
| | - Angela S Park
- From the Department of Pathology, Emory University, Atlanta, Georgia 30322 and
| | - Kim M Gernert
- the Biomolecular Computing Resource, Emory University, Atlanta, Georgia 30322
| | - Guy M Benian
- From the Department of Pathology, Emory University, Atlanta, Georgia 30322 and
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28
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Han H, Kursula P. Periaxin and AHNAK nucleoprotein 2 form intertwined homodimers through domain swapping. J Biol Chem 2014; 289:14121-31. [PMID: 24675079 PMCID: PMC4022880 DOI: 10.1074/jbc.m114.554816] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/24/2014] [Indexed: 11/06/2022] Open
Abstract
Periaxin (PRX) is an abundant protein in the peripheral nervous system, with an important role in myelination. PRX participates in large molecular complexes, most likely through the interactions of its N-terminal PSD-95/Discs-large/ZO-1 (PDZ)-like domain. We present the crystal structures of the PDZ-like domains from PRX and its homologue AHNAK nucleoprotein 2 (AHNAK2). The unique intertwined, domain-swapped dimers provide a structural basis for the homodimerization of both proteins. The core of the homodimer is formed by a 6-stranded antiparallel β sheet, with every other strand from a different chain. The AHNAK2 PDZ domain structure contains a bound class III ligand peptide. The binding pocket is preformed, and the peptide-PDZ interactions have unique aspects, including two salt bridges and weak recognition of the peptide C terminus. Tight homodimerization may be central to the scaffolding functions of PRX and AHNAK2 in molecular complexes linking the extracellular matrix to the cytoskeletal network.
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Affiliation(s)
- Huijong Han
- From the Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, 90014 Oulu, Finland, the German Electron Synchrotron (DESY), 22607 Hamburg, Germany, and
| | - Petri Kursula
- From the Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, 90014 Oulu, Finland, the German Electron Synchrotron (DESY), 22607 Hamburg, Germany, and the Department of Chemistry, University of Hamburg, 22607 Hamburg, Germany
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29
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Cubillos-Rojas M, Amair-Pinedo F, Peiró-Jordán R, Bartrons R, Ventura F, Rosa JL. The E3 ubiquitin protein ligase HERC2 modulates the activity of tumor protein p53 by regulating its oligomerization. J Biol Chem 2014; 289:14782-95. [PMID: 24722987 DOI: 10.1074/jbc.m113.527978] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The tumor suppressor p53 is a transcription factor that coordinates the cellular response to several kinds of stress. p53 inactivation is an important step in tumor progression. Oligomerization of p53 is critical for its posttranslational modification and its ability to regulate the transcription of target genes necessary to inhibit tumor growth. Here we report that the HECT E3 ubiquitin ligase HERC2 interacts with p53. This interaction involves the CPH domain of HERC2 (a conserved domain within Cul7, PARC, and HERC2 proteins) and the last 43 amino acid residues of p53. Through this interaction, HERC2 regulates p53 activity. RNA interference experiments showed how HERC2 depletion reduces the transcriptional activity of p53 without affecting its stability. This regulation of p53 activity by HERC2 is independent of proteasome or MDM2 activity. Under these conditions, up-regulation of cell growth and increased focus formation were observed, showing the functional relevance of the HERC2-p53 interaction. This interaction was maintained after DNA damage caused by the chemotherapeutic drug bleomycin. In these stressed cells, p53 phosphorylation was not impaired by HERC2 knockdown. Interestingly, p53 mutations that affect its tetramerization domain disrupted the HERC2-p53 interaction, suggesting a role for HERC2 in p53 oligomerization. This regulatory role was shown using cross-linking assays. Thus, the inhibition of p53 activity after HERC2 depletion can be attributed to a reduction in p53 oligomerization. Ectopic expression of HERC2 (residues 2292-2923) confirmed these observations. Together, these results identify HERC2 as a novel regulator of p53 signaling.
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Affiliation(s)
- Monica Cubillos-Rojas
- From the Departament de Ciències Fisiològiques II, Campus de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona 08907, Spain
| | - Fabiola Amair-Pinedo
- From the Departament de Ciències Fisiològiques II, Campus de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona 08907, Spain
| | - Roser Peiró-Jordán
- From the Departament de Ciències Fisiològiques II, Campus de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona 08907, Spain
| | - Ramon Bartrons
- From the Departament de Ciències Fisiològiques II, Campus de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona 08907, Spain
| | - Francesc Ventura
- From the Departament de Ciències Fisiològiques II, Campus de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona 08907, Spain
| | - Jose Luis Rosa
- From the Departament de Ciències Fisiològiques II, Campus de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona 08907, Spain
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Abstract
Neurogranin (Ng) is a member of the IQ motif class of calmodulin (CaM)-binding proteins, and interactions with CaM are its only known biological function. In this report we demonstrate that the binding affinity of Ng for CaM is weakened by Ca(2+) but to a lesser extent (2-3-fold) than that previously suggested from qualitative observations. We also show that Ng induced a >10-fold decrease in the affinity of Ca(2+) binding to the C-terminal domain of CaM with an associated increase in the Ca(2+) dissociation rate. We also discovered a modest, but potentially important, increase in the cooperativity in Ca(2+) binding to the C-lobe of CaM in the presence of Ng, thus sharpening the threshold for the C-domain to become Ca(2+)-saturated. Domain mapping using synthetic peptides indicated that the IQ motif of Ng is a poor mimetic of the intact protein and that the acidic sequence just N-terminal to the IQ motif plays an important role in reproducing Ng-mediated decreases in the Ca(2+) binding affinity of CaM. Using NMR, full-length Ng was shown to make contacts largely with residues in the C-domain of CaM, although contacts were also detected in residues in the N-terminal domain. Together, our results can be consolidated into a model where Ng contacts residues in the N- and C-lobes of both apo- and Ca(2+)-bound CaM and that although Ca(2+) binding weakens Ng interactions with CaM, the most dramatic biochemical effect is the impact of Ng on Ca(2+) binding to the C-terminal lobe of CaM.
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Affiliation(s)
| | | | - Xu Wang
- Biochemistry and Molecular Biology, University of Texas Medical School at Houston, Houston, Texas 77030
| | - John A Putkey
- Biochemistry and Molecular Biology, University of Texas Medical School at Houston, Houston, Texas 77030
| | - M Neal Waxham
- From the Departments of Neurobiology and Anatomy and
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31
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Korneeva VA, Trubetskov MM, Korshunova AV, Lushchekina SV, Kolyadko VN, Sergienko OV, Lunin VG, Panteleev MA, Ataullakhanov FI. Interactions outside the proteinase-binding loop contribute significantly to the inhibition of activated coagulation factor XII by its canonical inhibitor from corn. J Biol Chem 2014; 289:14109-20. [PMID: 24706752 PMCID: PMC4022879 DOI: 10.1074/jbc.m114.553735] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Activated factor XII (FXIIa) is selectively inhibited by corn Hageman factor inhibitor (CHFI) among other plasma proteases. CHFI is considered a canonical serine protease inhibitor that interacts with FXIIa through its protease-binding loop. Here we examined whether the protease-binding loop alone is sufficient for the selective inhibition of serine proteases or whether other regions of a canonical inhibitor are involved. Six CHFI mutants lacking different N- and C-terminal portions were generated. CHFI-234, which lacks the first and fifth disulfide bonds and 11 and 19 amino acid residues at the N and C termini, respectively, exhibited no significant changes in FXIIa inhibition (Ki = 3.2 ± 0.4 nm). CHFI-123, which lacks 34 amino acid residues at the C terminus and the fourth and fifth disulfide bridges, inhibited FXIIa with a Ki of 116 ± 16 nm. To exclude interactions outside the FXIIa active site, a synthetic cyclic peptide was tested. The peptide contained residues 20–45 (Protein Data Bank code 1BEA), and a C29D substitution was included to avoid unwanted disulfide bond formation between unpaired cysteines. Surprisingly, the isolated protease-binding loop failed to inhibit FXIIa but retained partial inhibition of trypsin (Ki = 11.7 ± 1.2 μm) and activated factor XI (Ki = 94 ± 11 μm). Full-length CHFI inhibited trypsin with a Ki of 1.3 ± 0.2 nm and activated factor XI with a Ki of 5.4 ± 0.2 μm. Our results suggest that the protease-binding loop is not sufficient for the interaction between FXIIa and CHFI; other regions of the inhibitor also contribute to specific inhibition.
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Affiliation(s)
- Vera A Korneeva
- From the Laboratory of the Molecular Mechanisms of Hemostasis, Center for Theoretical Problems of Physicochemical Pharmacology of Russian Academy of Sciences, Moscow 119991, Russia
| | - Mikhail M Trubetskov
- From the Laboratory of the Molecular Mechanisms of Hemostasis, Center for Theoretical Problems of Physicochemical Pharmacology of Russian Academy of Sciences, Moscow 119991, Russia, the Department of Physics, Moscow State University, Moscow 119992, Russia
| | | | - Sofya V Lushchekina
- the Laboratory of Computer Modeling of Biomolecular Systems and Nanomaterials, Emanuel Institute of Biochemical Physics of Russian Academy of Sciences, Moscow 119334, Russia
| | - Vladimir N Kolyadko
- From the Laboratory of the Molecular Mechanisms of Hemostasis, Center for Theoretical Problems of Physicochemical Pharmacology of Russian Academy of Sciences, Moscow 119991, Russia
| | - Olga V Sergienko
- the Laboratory of Molecular Diagnostics and Genetic Engineering, Institute of Agricultural Biotechnology of Russian Academy of Agricultural Sciences, Moscow 127550, Russia
| | - Vladimir G Lunin
- the Laboratory of Molecular Diagnostics and Genetic Engineering, Institute of Agricultural Biotechnology of Russian Academy of Agricultural Sciences, Moscow 127550, Russia, the Laboratory of Biologically Active Nanostructures, Gamaleya Institute of Epidemiology and Microbiology of Russian Federation Ministry of Health and Social Development, Moscow 123098, Russia
| | - Mikhail A Panteleev
- From the Laboratory of the Molecular Mechanisms of Hemostasis, Center for Theoretical Problems of Physicochemical Pharmacology of Russian Academy of Sciences, Moscow 119991, Russia, the Department of Physics, Moscow State University, Moscow 119992, Russia, the Research Department, HemaCore LLC, Moscow 125319, Russia, the Research Division, Scientific Clinical Centre of Pediatric Hematology, Oncology, and Immunology Named after Dmitry Rogachev of Ministry of Health of Russian Federation, Moscow 117997, Russia, and the Department of Translational and Regenerative Medicine, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141700, Russia
| | - Fazoil I Ataullakhanov
- From the Laboratory of the Molecular Mechanisms of Hemostasis, Center for Theoretical Problems of Physicochemical Pharmacology of Russian Academy of Sciences, Moscow 119991, Russia, the Department of Physics, Moscow State University, Moscow 119992, Russia, the Research Department, HemaCore LLC, Moscow 125319, Russia, the Research Division, Scientific Clinical Centre of Pediatric Hematology, Oncology, and Immunology Named after Dmitry Rogachev of Ministry of Health of Russian Federation, Moscow 117997, Russia, and the Department of Translational and Regenerative Medicine, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141700, Russia
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32
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Lee JH, Kwon JH, Jeon YH, Ko KY, Lee SR, Kim IY. Pro178 and Pro183 of selenoprotein S are essential residues for interaction with p97(VCP) during endoplasmic reticulum-associated degradation. J Biol Chem 2014; 289:13758-68. [PMID: 24700463 DOI: 10.1074/jbc.m113.534529] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
During endoplasmic reticulum (ER)-associated degradation, p97(VCP) is recruited to the ER membrane through interactions with transmembrane proteins, such as selenoprotein S (SelS), selenoprotein K (SelK), hrd1, and gp78. SelS has a single-spanning transmembrane domain and protects cells from ER stress-induced apoptosis through interaction with p97(VCP). The cytosolic tail of SelS consists of a coiled-coil domain, a putative VCP-interacting motif (VIM), and an unpronounced glycine- and proline-rich secondary structure. To understand the regulatory mechanism of SelS during ER stress, we investigated the interaction of the protein with p97(VCP) using mouse neuroblastoma cells and human embryonic kidney 293 cells. The SelS expression level increased when ER stress was induced. In addition, the effect of ER stress was enhanced, and recruitment of p97(VCP) to the ER membrane was inhibited in SelS knockdown cells. The effect of SelS knockdown was rescued by ectopic expression of SelS U188C. p97(VCP) interacted with SelS U188C and was recruited to the ER membrane. The expression of SelS[ΔVIM], which is a VIM deletion mutant of SelS, also showed both a recovery effect and an interaction with p97(VCP) in cells. However, mutants in which the proline residue positions 178 or 183 of SelS were changed to alanine or were deleted did not interact with p97(VCP). The proline mutants did not rescue ER stress in SelS knockdown cells. These results suggest that both Pro(178) and Pro(183) of SelS play important roles in the translocation of p97(VCP) to the ER membrane and protect cells from ER stress.
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Affiliation(s)
- Jea Hwang Lee
- From the Laboratory of Cellular and Molecular Biochemistry, Division of Life Sciences, Korea University, 1, 5-Ka, Anam-Dong, Sungbuk-Ku, Seoul 136-701, Republic of Korea and
| | - Joon Hyun Kwon
- From the Laboratory of Cellular and Molecular Biochemistry, Division of Life Sciences, Korea University, 1, 5-Ka, Anam-Dong, Sungbuk-Ku, Seoul 136-701, Republic of Korea and
| | - Yeong Ha Jeon
- From the Laboratory of Cellular and Molecular Biochemistry, Division of Life Sciences, Korea University, 1, 5-Ka, Anam-Dong, Sungbuk-Ku, Seoul 136-701, Republic of Korea and
| | - Kwan Young Ko
- From the Laboratory of Cellular and Molecular Biochemistry, Division of Life Sciences, Korea University, 1, 5-Ka, Anam-Dong, Sungbuk-Ku, Seoul 136-701, Republic of Korea and
| | - Seung-Rock Lee
- the Department of Biochemistry, Department of Biomedical Science, Research Center for Aging and Geriatrics, Research Institute of Medical Science, Chonnam National University Medical School, Gwangju 501-190, Republic of Korea
| | - Ick Young Kim
- From the Laboratory of Cellular and Molecular Biochemistry, Division of Life Sciences, Korea University, 1, 5-Ka, Anam-Dong, Sungbuk-Ku, Seoul 136-701, Republic of Korea and
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Abstract
Previously, Smad ubiquitination regulatory factor 1 (Smurf1)-mediated Lys29 (K29)-linked poly-ubiquitination of Axin has been identified as a novel regulatory process in Wnt/β-catenin signaling. In this work, we discovered that the C2 domain of Smurf1 is critical for targeting Axin for ubiquitination. We found that the C2 domain-mediated plasma membrane localization of Smurf1 is required for Axin ubiquitination, and interfering with that disturbs the co-localization of Smurf1 and Axin around the plasma membrane. Moreover, the C2 domain of Smurf1, rather than its WW domains, is involved in Smurf1's interaction with Axin; and the putative PPXY motifs (PY motif) of Axin are not essential for such an interaction, indicating that Smurf1 binds to Axin in a non-canonical way independent of WW-PY interaction. Further, we found that Smurf1-Axin interaction and Axin ubiquitination are attenuated in the G2/M phase of cell cycle, contributing to an increased cell response to Wnt stimulation at that stage. Collectively, we uncovered a dual role of Smurf1 C2 domain, recruiting Smurf1 to membrane for accessing Axin and mediating its interaction with Axin, and that Smurf1-mediated Axin ubiquitination is subjected to the regulation of cell cycle.
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Affiliation(s)
- Cong Fei
- From the State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaoli He
- From the State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Sichun Xie
- From the State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Haofei Miao
- From the State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhilei Zhou
- From the State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lin Li
- From the State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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34
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Abstract
Protein splicing is a posttranslational modification where intervening proteins (inteins) cleave themselves from larger precursor proteins and ligate their flanking polypeptides (exteins) through a multistep chemical reaction. First thought to be an anomaly found in only a few organisms, protein splicing by inteins has since been observed in microorganisms from all domains of life. Despite this broad phylogenetic distribution, all inteins share common structural features such as a horseshoe-like pseudo two-fold symmetric fold, several canonical sequence motifs, and similar splicing mechanisms. Intriguingly, the splicing efficiencies and substrate specificity of different inteins vary considerably, reflecting subtle changes in the chemical mechanism of splicing, linked to their local structure and dynamics. As intein chemistry has widespread use in protein chemistry, understanding the structural and dynamical aspects of inteins is crucial for intein engineering and the improvement of intein-based technologies.
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Affiliation(s)
- Ertan Eryilmaz
- From the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461 and
| | - Neel H Shah
- the Department of Chemistry, Frick Laboratory, Princeton University, Princeton, New Jersey 08544
| | - Tom W Muir
- the Department of Chemistry, Frick Laboratory, Princeton University, Princeton, New Jersey 08544
| | - David Cowburn
- From the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461 and
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35
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Tonkin ML, Beck JR, Bradley PJ, Boulanger MJ. The inner membrane complex sub-compartment proteins critical for replication of the apicomplexan parasite Toxoplasma gondii adopt a pleckstrin homology fold. J Biol Chem 2014; 289:13962-73. [PMID: 24675080 DOI: 10.1074/jbc.m114.548891] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Toxoplasma gondii, an apicomplexan parasite prevalent in developed nations, infects up to one-third of the human population. The success of this parasite depends on several unique structures including an inner membrane complex (IMC) that lines the interior of the plasma membrane and contains proteins important for gliding motility and replication. Of these proteins, the IMC sub-compartment proteins (ISPs) have recently been shown to play a role in asexual T. gondii daughter cell formation, yet the mechanism is unknown. Complicating mechanistic characterization of the ISPs is a lack of sequence identity with proteins of known structure or function. In support of elucidating the function of ISPs, we first determined the crystal structures of representative members TgISP1 and TgISP3 to a resolution of 2.10 and 2.32 Å, respectively. Structural analysis revealed that both ISPs adopt a pleckstrin homology fold often associated with phospholipid binding or protein-protein interactions. Substitution of basic for hydrophobic residues in the region that overlays with phospholipid binding in related pleckstrin homology domains, however, suggests that ISPs do not retain phospholipid binding activity. Consistent with this observation, biochemical assays revealed no phospholipid binding activity. Interestingly, mapping of conserved surface residues combined with crystal packing analysis indicates that TgISPs have functionally repurposed the phospholipid-binding site likely to coordinate protein partners. Recruitment of larger protein complexes may also be aided through avidity-enhanced interactions resulting from multimerization of the ISPs. Overall, we propose a model where TgISPs recruit protein partners to the IMC to ensure correct progression of daughter cell formation.
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Affiliation(s)
- Michelle L Tonkin
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and
| | - Josh R Beck
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, California 90095
| | - Peter J Bradley
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, California 90095
| | - Martin J Boulanger
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and
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36
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Yamashiro S, Gokhin DS, Sui Z, Bergeron SE, Rubenstein PA, Fowler VM. Differential actin-regulatory activities of Tropomodulin1 and Tropomodulin3 with diverse tropomyosin and actin isoforms. J Biol Chem 2014; 289:11616-11629. [PMID: 24644292 DOI: 10.1074/jbc.m114.555128] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Tropomodulins (Tmods) are F-actin pointed end capping proteins that interact with tropomyosins (TMs) and cap TM-coated filaments with higher affinity than TM-free filaments. Here, we tested whether differences in recognition of TM or actin isoforms by Tmod1 and Tmod3 contribute to the distinct cellular functions of these Tmods. We found that Tmod3 bound ~5-fold more weakly than Tmod1 to α/βTM, TM5b, and TM5NM1. However, surprisingly, Tmod3 was as effective as Tmod1 at capping pointed ends of skeletal muscle α-actin (αsk-actin) filaments coated with α/βTM, TM5b, or TM5NM1. Tmod3 only capped TM-coated αsk-actin filaments more weakly than Tmod1 in the presence of recombinant αTM2, which is unacetylated at its NH2 terminus, binds F-actin weakly, and has a disabled Tmod-binding site. Moreover, both Tmod1 and Tmod3 were similarly effective at capping pointed ends of platelet β/cytoplasmic γ (γcyto)-actin filaments coated with TM5NM1. In the absence of TMs, both Tmod1 and Tmod3 had similarly weak abilities to nucleate β/γcyto-actin filament assembly, but only Tmod3 could sequester cytoplasmic β- and γcyto-actin (but not αsk-actin) monomers and prevent polymerization under physiological conditions. Thus, differences in TM binding by Tmod1 and Tmod3 do not appear to regulate the abilities of these Tmods to cap TM-αsk-actin or TM-β/γcyto-actin pointed ends and, thus, are unlikely to determine selective co-assembly of Tmod, TM, and actin isoforms in different cell types and cytoskeletal structures. The ability of Tmod3 to sequester β- and γcyto-actin (but not αsk-actin) monomers in the absence of TMs suggests a novel function for Tmod3 in regulating actin remodeling or turnover in cells.
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Affiliation(s)
- Sawako Yamashiro
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037; Laboratory of Single-Molecule Cell Biology, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - David S Gokhin
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Zhenhua Sui
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Sarah E Bergeron
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242
| | | | - Velia M Fowler
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037.
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37
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Hendrix J, van Heertum B, Vanstreels E, Daelemans D, De Rijck J. Dynamics of the ternary complex formed by c-Myc interactor JPO2, transcriptional co-activator LEDGF/p75, and chromatin. J Biol Chem 2014; 289:12494-506. [PMID: 24634210 DOI: 10.1074/jbc.m113.525964] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Lens epithelium-derived growth factor (LEDGF/p75) is a transcriptional co-activator involved in targeting human immunodeficiency virus (HIV) integration and the development of MLL fusion-mediated acute leukemia. A previous study revealed that LEDGF/p75 dynamically scans the chromatin, and upon interaction with HIV-1 integrase, their complex is locked on chromatin. At present, it is not known whether LEDGF/p75-mediated chromatin locking is typical for interacting proteins. Here, we employed continuous photobleaching and fluorescence correlation and cross-correlation spectroscopy to investigate in vivo chromatin binding of JPO2, a LEDGF/p75- and c-Myc-interacting protein involved in transcriptional regulation. In the absence of LEDGF/p75, JPO2 performs chromatin scanning inherent to transcription factors. However, whereas the dynamics of JPO2 chromatin binding are decelerated upon interaction with LEDGF/p75, very strong locking of their complex onto chromatin is absent. Similar results were obtained with the domesticated transposase PogZ, another cellular interaction partner of LEDGF/p75. We furthermore show that diffusive JPO2 can oligomerize; that JPO2 and LEDGF/p75 interact directly and specifically in vivo through the specific interaction domain of JPO2 and the C-terminal domain of LEDGF/p75, comprising the integrase-binding domain; and that modulation of JPO2 dynamics requires a functional PWWP domain in LEDGF/p75. Our results suggest that the dynamics of the LEDGF/p75-chromatin interaction depend on the specific partner and that strong chromatin locking is not a property of all LEDGF/p75-binding proteins.
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Affiliation(s)
- Jelle Hendrix
- From the Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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Anamika, Markin CJ, Rout MK, Spyracopoulos L. Molecular basis for impaired DNA damage response function associated with the RAP80 ΔE81 defect. J Biol Chem 2014; 289:12852-62. [PMID: 24627472 DOI: 10.1074/jbc.m113.538280] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Signal transduction within the DNA damage response is driven by the flux of protein-protein interaction cascades that ultimately recruit repair complexes to sites of damage. The protein RAP80 plays a central role in the damage response by targeting BRCA1/BRCA2 tumor suppressors to DNA damage foci through multivalent binding of Lys-63-linked polyubiquitin chains. Mutations within the high penetrance BRCA1/BRCA2 genes account for ∼20% of familial breast cancers. The genetic basis for the remaining cancers remains unknown, but may involve defects in binding partners for BRCA1 and BRCA2 that lead to impaired targeting to foci and a concomitant role in the pathogenesis of cancer. Recently, an in-frame deletion mutation (ΔE81) in a conserved region from the first ubiquitin interaction motif of RAP80 has been linked to an increase in chromosomal abnormalities. Using NMR spectroscopy, we demonstrate that the N-cap motif within the α-helix of the first ubiquitin interaction motif from ΔE81 undergoes a structural frameshift that leads to abolishment of multivalent binding of polyubiquitin chains. Loss of this single glutamate residue disrupts favorable electrostatic interactions between RAP80 and ubiquitin, establishing a plausible molecular basis for a potential predisposition to cancer unrelated to mutations within BRCA1/BRCA2 genes.
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Affiliation(s)
- Anamika
- From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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Pohane AA, Joshi H, Jain V. Molecular dissection of phage endolysin: an interdomain interaction confers host specificity in Lysin A of Mycobacterium phage D29. J Biol Chem 2014; 289:12085-12095. [PMID: 24627486 DOI: 10.1074/jbc.m113.529594] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mycobacterium tuberculosis has always been recognized as one of the most successful pathogens. Bacteriophages that attack and kill mycobacteria offer an alternate mechanism for the curtailment of this bacterium. Upon infection, mycobacteriophages produce lysins that catalyze cell wall peptidoglycan hydrolysis and mycolic acid layer breakdown of the host resulting in bacterial cell rupture and virus release. The ability to lyse bacterial cells make lysins extremely significant. We report here a detailed molecular dissection of the function and regulation of mycobacteriophage D29 Lysin A. Several truncated versions of Lysin A were constructed, and their activities were analyzed by zymography and by expressing them in both Escherichia coli and Mycobacterium smegmatis. Our experiments establish that Lysin A harbors two catalytically active domains, both of which show E. coli cell lysis upon their expression exclusively in the periplasmic space. However, the expression of only one of these domains and the full-length Lysin A caused M. smegmatis cell lysis. Interestingly, full-length protein remained inactive in E. coli periplasm. Our data suggest that the inactivity is ensued by a C-terminal domain that interacts with the N-terminal domain. This interaction was affirmed by surface plasmon resonance. Our experiments also demonstrate that the C-terminal domain of Lysin A selectively binds to M. tuberculosis and M. smegmatis peptidoglycans. Our methodology of studying E. coli cell lysis by Lysin A and its truncations after expressing these proteins in the bacterial periplasm with the help of signal peptide paves the way for a large scale identification and analysis of such proteins obtained from other bacteriophages.
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Affiliation(s)
- Amol Arunrao Pohane
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462023, India
| | - Himanshu Joshi
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462023, India
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462023, India.
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Kim SJ, Cho J, Song EJ, Kim SJ, Kim HM, Lee KE, Suh SW, Kim EE. Structural basis for ovarian tumor domain-containing protein 1 (OTU1) binding to p97/valosin-containing protein (VCP). J Biol Chem 2014; 289:12264-74. [PMID: 24610782 DOI: 10.1074/jbc.m113.523936] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Valosin-containing protein (VCP), also known as p97, is an AAA(+) ATPase that plays an essential role in a broad array of cellular processes including the endoplasmic reticulum-associated degradation (ERAD) pathway. Recently, ERAD-specific deubiquitinating enzymes have been reported to be physically associated with VCP, although the exact mechanism is not yet clear. Among these enzymes is ovarian tumor domain-containing protein 1 (OTU1). Here, we report the structural basis for interaction between VCP and OTU1. The crystal structure of the ubiquitin regulatory X-like (UBXL) domain of OTU1 (UBXLOTU1) complexed to the N-terminal domain of VCP (NVCP) at 1.8-Å resolution reveals that UBXLOTU1 adopts a ubiquitin-like fold and binds at the interface of two subdomains of NVCP using the (39)GYPP(42) loop of UBXLOTU1 with the two prolines in cis- and trans-configurations, respectively. A mutagenesis study shows that this loop is not only critical for the interaction with VCP but also for its role in the ERAD pathway. Negative staining EM shows that one molecule of OTU1 binds to one VCP hexamer, and isothermal titration calorimetry suggests that the two proteins bind with a KD of 0.71 μM. Analytical size exclusion chromatography and isothermal titration calorimetry demonstrates that OTU1 can bind VCP in both the presence and absence of a heterodimer formed by ubiquitin fusion degradation protein 1 and nuclear localization protein 4.
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Affiliation(s)
- Su Jin Kim
- From the Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
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41
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Slavoff SA, Heo J, Budnik BA, Hanakahi LA, Saghatelian A. A human short open reading frame (sORF)-encoded polypeptide that stimulates DNA end joining. J Biol Chem 2014; 289:10950-10957. [PMID: 24610814 DOI: 10.1074/jbc.c113.533968] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The recent discovery of numerous human short open reading frame (sORF)-encoded polypeptides (SEPs) has raised important questions about the functional roles of these molecules in cells. Here, we show that a 69-amino acid SEP, MRI-2, physically interacts with the Ku heterodimer to stimulate DNA double-strand break ligation via nonhomologous end joining. The characterization of MRI-2 suggests that this SEP may participate in DNA repair and underscores the potential of SEPs to serve important biological functions in mammalian cells.
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Affiliation(s)
- Sarah A Slavoff
- Department of Chemistry and Chemical Biology and Harvard University, Cambridge, Massachusetts 02138
| | - Jinho Heo
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois College of Pharmacy, Rockford, Illinois 60612
| | - Bogdan A Budnik
- Faculty of Arts and Sciences (FAS) Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138 and
| | - Leslyn A Hanakahi
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois College of Pharmacy, Rockford, Illinois 60612.
| | - Alan Saghatelian
- Department of Chemistry and Chemical Biology and Harvard University, Cambridge, Massachusetts 02138.
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42
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Fitzpatrick P, Shattil SJ, Ablooglu AJ. C-terminal COOH of integrin β1 is necessary for β1 association with the kindlin-2 adapter protein. J Biol Chem 2014; 289:11183-11193. [PMID: 24599960 DOI: 10.1074/jbc.m113.535369] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein-protein interactions are driving forces in cellular processes. As a prime example, transmembrane integrins link extracellular matrix and intracellular proteins, resulting in bidirectional signaling that regulates cell migration, proliferation, differentiation, and survival. Here we provide the first evidence that interaction between the integrin β1 cytoplasmic tail and kindlin-2, a member of a family of adapters implicated in human disease pathogenesis, is mainly governed by the β1 C-terminal carboxylate moiety and is required for laterality organ development in zebrafish. Affinity measurements indicate that this unusual protein-protein interaction mode is coordinated by a putative carboxylate-binding motif in the kindlin-2 FERM subdomain F3. Contrary to the C terminus of proteins that engage PDZ domains, the C-terminal three residues of β1, per se, do not contribute to kindlin-2 binding or to laterality organ development. Thus, by employing zebrafish as an in situ physiological tool to correlate protein structure and function, we have discovered an unexpected association chemistry between an integrin and a key adapter involved in integrin signaling.
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Affiliation(s)
- Paul Fitzpatrick
- Department of Medicine, University of California San Diego, La Jolla, California 92093-0726
| | - Sanford J Shattil
- Department of Medicine, University of California San Diego, La Jolla, California 92093-0726
| | - Ararat J Ablooglu
- Department of Medicine, University of California San Diego, La Jolla, California 92093-0726.
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43
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Kan W, Adjobo-Hermans M, Burroughs M, Faibis G, Malik S, Tall GG, Smrcka AV. M3 muscarinic receptor interaction with phospholipase C β3 determines its signaling efficiency. J Biol Chem 2014; 289:11206-11218. [PMID: 24596086 DOI: 10.1074/jbc.m113.538546] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Phospholipase Cβ (PLCβ) enzymes are activated by G protein-coupled receptors through receptor-catalyzed guanine nucleotide exchange on Gαβγ heterotrimers containing Gq family G proteins. Here we report evidence for a direct interaction between M3 muscarinic receptor (M3R) and PLCβ3. Both expressed and endogenous M3R interacted with PLCβ in coimmunoprecipitation experiments. Stimulation of M3R with carbachol significantly increased this association. Expression of M3R in CHO cells promoted plasma membrane localization of YFP-PLCβ3. Deletion of the PLCβ3 C terminus or deletion of the PLCβ3 PDZ ligand inhibited coimmunoprecipitation with M3R and M3R-dependent PLCβ3 plasma membrane localization. Purified PLCβ3 bound directly to glutathione S-transferase (GST)-fused M3R intracellular loops 2 and 3 (M3Ri2 and M3Ri3) as well as M3R C terminus (M3R/H8-CT). PLCβ3 binding to M3Ri3 was inhibited when the PDZ ligand was removed. In assays using reconstituted purified components in vitro, M3Ri2, M3Ri3, and M3R/H8-CT potentiated Gαq-dependent but not Gβγ-dependent PLCβ3 activation. Disruption of key residues in M3Ri3N and of the PDZ ligand in PLCβ3 inhibited M3Ri3-mediated potentiation. We propose that the M3 muscarinic receptor maximizes the efficiency of PLCβ3 signaling beyond its canonical role as a guanine nucleotide exchange factor for Gα.
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Affiliation(s)
- Wei Kan
- Departments of Pharmacology and Physiology and University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Merel Adjobo-Hermans
- Department of Biochemistry, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Michael Burroughs
- Departments of Pharmacology and Physiology and University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Guy Faibis
- Departments of Pharmacology and Physiology and University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Sundeep Malik
- Departments of Pharmacology and Physiology and University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Gregory G Tall
- Departments of Pharmacology and Physiology and University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Alan V Smrcka
- Departments of Pharmacology and Physiology and University of Rochester School of Medicine and Dentistry, Rochester, New York 14642; Biochemistry and Biophysics and University of Rochester School of Medicine and Dentistry, Rochester, New York 14642; Aab Institute of Cardiovascular Research, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642 and.
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44
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Wallez Y, Riedl SJ, Pasquale EB. Association of the breast cancer antiestrogen resistance protein 1 (BCAR1) and BCAR3 scaffolding proteins in cell signaling and antiestrogen resistance. J Biol Chem 2014; 289:10431-10444. [PMID: 24584939 DOI: 10.1074/jbc.m113.541839] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Most breast cancers are estrogen receptor-positive and treated with antiestrogens, but aberrant signaling networks can induce drug resistance. One of these networks involves the scaffolding protein BCAR1/p130CAS, which regulates cell growth and migration/invasion. A less investigated scaffolding protein that also confers antiestrogen resistance is the SH2 domain-containing protein BCAR3. BCAR1 and BCAR3 bind tightly to each other through their C-terminal domains, thus potentially connecting their associated signaling networks. However, recent studies using BCAR1 and BCAR3 interaction mutants concluded that association between the two proteins is not critical for many of their interrelated activities regulating breast cancer malignancy. We report that these previously used BCAR mutations fail to cause adequate loss-of-function of the complex. By using structure-based BCAR1 and BCAR3 mutants that lack the ability to interact, we show that BCAR3-induced antiestrogen resistance in MCF7 breast cancer cells critically depends on its ability to bind BCAR1. Interaction with BCAR3 increases the levels of phosphorylated BCAR1, ultimately potentiating BCAR1-dependent antiestrogen resistance. Furthermore, antiestrogen resistance in cells overexpressing BCAR1/BCAR3 correlates with increased ERK1/2 activity. Inhibiting ERK1/2 through overexpression of the regulatory protein PEA15 negates the resistance, revealing a key role for ERK1/2 in BCAR1/BCAR3-induced antiestrogen resistance. Reverse-phase protein array data show that PEA15 levels in invasive breast cancers correlate with patient survival, suggesting that PEA15 can override ERK1/2 activation by BCAR1/BCAR3 and other upstream regulators. We further uncovered that the BCAR3-related NSP3 can also promote antiestrogen resistance. Thus, strategies to disrupt BCAR1-BCAR3/NSP3 complexes and associated signaling networks could ultimately lead to new breast cancer therapies.
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Affiliation(s)
- Yann Wallez
- Sanford-Burnham Medical Research Institute, La Jolla, California 92037
| | - Stefan J Riedl
- Sanford-Burnham Medical Research Institute, La Jolla, California 92037
| | - Elena B Pasquale
- Sanford-Burnham Medical Research Institute, La Jolla, California 92037; Department of Pathology, University of California, San Diego California 92093.
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Trcka F, Durech M, Man P, Hernychova L, Muller P, Vojtesek B. The assembly and intermolecular properties of the Hsp70-Tomm34-Hsp90 molecular chaperone complex. J Biol Chem 2014; 289:9887-901. [PMID: 24567332 DOI: 10.1074/jbc.m113.526046] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Maintenance of protein homeostasis by molecular chaperones Hsp70 and Hsp90 requires their spatial and functional coordination. The cooperation of Hsp70 and Hsp90 is influenced by their interaction with the network of co-chaperone proteins, some of which contain tetratricopeptide repeat (TPR) domains. Critical to these interactions are TPR domains that target co-chaperone binding to the EEVD-COOH motif that terminates Hsp70/Hsp90. Recently, the two-TPR domain-containing protein, Tomm34, was reported to bind both Hsp70 and Hsp90. Here we characterize the structural basis of Tomm34-Hsp70/Hsp90 interactions. Using multiple methods, including pull-down assays, fluorescence polarization, hydrogen/deuterium exchange, and site-directed mutagenesis, we defined the binding activities and specificities of Tomm34 TPR domains toward Hsp70 and Hsp90. We found that Tomm34 TPR1 domain specifically binds Hsp70. This interaction is partly mediated by a non-canonical TPR1 two-carboxylate clamp and is strengthened by so far unidentified additional intermolecular contacts. The two-carboxylate clamp of the isolated TPR2 domain has affinity for both chaperones, but as part of the full-length Tomm34 protein, the TPR2 domain binds specifically Hsp90. These binding properties of Tomm34 TPR domains thus enable simultaneous binding of Hsp70 and Hsp90. Importantly, we provide evidence for the existence of an Hsp70-Tomm34-Hsp90 tripartite complex. In addition, we defined the basic conformational demands of the Tomm34-Hsp90 interaction. These results suggest that Tomm34 represents a novel scaffolding co-chaperone of Hsp70 and Hsp90, which may facilitate Hsp70/Hsp90 cooperation during protein folding.
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Affiliation(s)
- Filip Trcka
- From the Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Zluty kopec 7, 656 53 Brno, Czech Republic
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46
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Vild CJ, Xu Z. Vfa1 binds to the N-terminal microtubule-interacting and trafficking (MIT) domain of Vps4 and stimulates its ATPase activity. J Biol Chem 2014; 289:10378-10386. [PMID: 24567329 DOI: 10.1074/jbc.m113.532960] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The endosomal sorting complexes required for transport (ESCRT) are responsible for multivesicular body biogenesis, membrane abscission during cytokinesis, and retroviral budding. They function as transiently assembled molecular complexes on the membrane, and their disassembly requires the action of the AAA-ATPase Vps4. Vps4 is regulated by a multitude of ESCRT and ESCRT-related proteins. Binding of these proteins to Vps4 is often mediated via the microtubule-interacting and trafficking (MIT) domain of Vps4. Recently, a new Vps4-binding protein Vfa1 was identified in a yeast genetic screen, where overexpression of Vfa1 caused defects in vacuolar morphology. However, the function of Vfa1 and its role in vacuolar biology were largely unknown. Here, we provide the first detailed biochemical and biophysical study of Vps4-Vfa1 interaction. The MIT domain of Vps4 binds to the C-terminal 17 residues of Vfa1. This interaction is of high affinity and greatly stimulates the ATPase activity of Vps4. The crystal structure of the Vps4-Vfa1 complex shows that Vfa1 adopts a canonical MIT-interacting motif 2 structure that has been observed previously in other Vps4-ESCRT interactions. These findings suggest that Vfa1 is a novel positive regulator of Vps4 function.
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Affiliation(s)
- Cody J Vild
- Life Sciences Institute and Department of Biological Chemistry, Medical School, University of Michigan, Ann Arbor, Michigan 48109
| | - Zhaohui Xu
- Life Sciences Institute and Department of Biological Chemistry, Medical School, University of Michigan, Ann Arbor, Michigan 48109.
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47
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Zimmermann J, Latta L, Beck A, Leidinger P, Fecher-Trost C, Schlenstedt G, Meese E, Wissenbach U, Flockerzi V. Trans-activation response (TAR) RNA-binding protein 2 is a novel modulator of transient receptor potential canonical 4 (TRPC4) protein. J Biol Chem 2014; 289:9766-80. [PMID: 24563462 DOI: 10.1074/jbc.m114.557066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
TRPC4 proteins function as Ca(2+) conducting, non-selective cation channels in endothelial, smooth muscle, and neuronal cells. To further characterize the roles of TRPC4 in vivo, detailed information about the molecular composition of native channel complexes and their association with cellular signaling networks is needed. Therefore, a mouse brain cDNA library was searched for novel TRPC4-interacting proteins using a modified yeast two-hybrid assay. This screen identified Trans-activation Response RNA-binding protein 2 (Tarpb2), a protein that recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Tarbp2 was found to bind to the C terminus of TRPC4 and TRPC5 and to modulate agonist-dependent TRPC4-induced Ca(2+) entry. A stretch of basic residues within the Tarbp2 protein is required for these actions. Tarbp2 binding to and modulation of TRPC4 occurs in the presence of endogenously expressed Dicer but is no longer detectable when the Dicer cDNA is overexpressed. Dicer activity in crude cell lysates is increased in the presence of Ca(2+), most probably by Ca(2+)-dependent proteolytic activation of Dicer. Apparently, Tarbp2 binding to TRPC4 promotes changes of cytosolic Ca(2+) and, thereby, leads to a dynamic regulation of Dicer activity, essentially at low endogenous Dicer concentrations.
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Affiliation(s)
- Jasmin Zimmermann
- From the Institut für Experimentelle und Klinische Pharmakologie und Toxikologie
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48
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Abstract
The estrogen receptor (ER) is a steroid hormone receptor that acts as a transcription factor, modulating genes that regulate a vast range of cellular functions. IQGAP1 interacts with several signaling proteins, cytoskeletal components, and transmembrane receptors, thereby serving as a scaffold to integrate signaling pathways. Both ERα and IQGAP1 contribute to breast cancer. In this study, we report that IQGAP1 binds ERα and ERβ. In vitro analysis with pure proteins revealed a direct interaction between IQGAP1 and ERα. Investigation with multiple short fragments of each protein showed that ERα binds to the IQ domain of IQGAP1, whereas the hinge region of ERα is responsible for binding IQGAP1. In addition, IQGAP1 and ERα co-immunoprecipitated from cells, and the association was modulated by estradiol. The interaction has functional effects. Knockdown of endogenous IQGAP1 attenuated the ability of estradiol to induce transcription of the estrogen-responsive genes pS2, progesterone receptor, and cyclin D1. These data reveal that IQGAP1 binds to ERα and modulates its transcriptional function, suggesting that IQGAP1 might be a target for therapy in patients with breast carcinoma.
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Affiliation(s)
- Huseyin H Erdemir
- From the Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland 20892
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49
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Abu-Odeh M, Bar-Mag T, Huang H, Kim T, Salah Z, Abdeen SK, Sudol M, Reichmann D, Sidhu S, Kim PM, Aqeilan RI. Characterizing WW domain interactions of tumor suppressor WWOX reveals its association with multiprotein networks. J Biol Chem 2014; 289:8865-80. [PMID: 24550385 DOI: 10.1074/jbc.m113.506790] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
WW domains are small modules present in regulatory and signaling proteins that mediate specific protein-protein interactions. The WW domain-containing oxidoreductase (WWOX) encodes a 46-kDa tumor suppressor that contains two N-terminal WW domains and a central short-chain dehydrogenase/reductase domain. Based on its ligand recognition motifs, the WW domain family is classified into four groups. The largest one, to which WWOX belongs, recognizes ligands with a PPXY motif. To pursue the functional properties of the WW domains of WWOX, we employed mass spectrometry and phage display experiments to identify putative WWOX-interacting partners. Our analysis revealed that the first WW (WW1) domain of WWOX is the main functional interacting domain. Furthermore, our study uncovered well known and new PPXY-WW1-interacting partners and shed light on novel LPXY-WW1-interacting partners of WWOX. Many of these proteins are components of multiprotein complexes involved in molecular processes, including transcription, RNA processing, tight junction, and metabolism. By utilizing GST pull-down and immunoprecipitation assays, we validated that WWOX is a substrate of the E3 ubiquitin ligase ITCH, which contains two LPXY motifs. We found that ITCH mediates Lys-63-linked polyubiquitination of WWOX, leading to its nuclear localization and increased cell death. Our data suggest that the WW1 domain of WWOX provides a versatile platform that links WWOX with individual proteins associated with physiologically important networks.
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Affiliation(s)
- Mohammad Abu-Odeh
- From the Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel 91120
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50
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Xu X, Yu T, Shi J, Chen X, Zhang W, Lin T, Liu Z, Wang Y, Zeng Z, Wang C, Li M, Liu C. Thymine DNA glycosylase is a positive regulator of Wnt signaling in colorectal cancer. J Biol Chem 2014; 289:8881-90. [PMID: 24532795 DOI: 10.1074/jbc.m113.538835] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Wnt signaling plays an important role in colorectal cancer (CRC). Although the mechanisms of β-catenin degradation have been well studied, the mechanism by which β-catenin activates transcription is still not fully understood. While screening a panel of DNA demethylases, we found that thymine DNA glycosylase (TDG) up-regulated Wnt signaling. TDG interacts with the transcription factor TCF4 and coactivator CREB-binding protein/p300 in the Wnt pathway. Knocking down TDG by shRNAs inhibited the proliferation of CRC cells in vitro and in vivo. In CRC patients, TDG levels were significantly higher in tumor tissues than in the adjacent normal tissues. These results suggest that TDG warrants consideration as a potential biomarker for CRC and as a target for CRC treatment.
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Affiliation(s)
- Xuehe Xu
- From the Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40506
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