1
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Paiva ACF, Lemos AR, Busse P, Martins MT, Silva DO, Freitas MC, Santos SP, Freire F, Barrey EJ, Manival X, Koetzner L, Heinrich T, Wegener A, Grädler U, Bandeiras TM, Schwarz D, Sousa PMF. Extract2Chip-Bypassing Protein Purification in Drug Discovery Using Surface Plasmon Resonance. Biosensors (Basel) 2023; 13:913. [PMID: 37887106 PMCID: PMC10605449 DOI: 10.3390/bios13100913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/24/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
Modern drug discovery relies on combinatorial screening campaigns to find drug molecules targeting specific disease-associated proteins. The success of such campaigns often relies on functional and structural information of the selected therapeutic target, only achievable once its purification is mastered. With the aim of bypassing the protein purification process to gain insights on the druggability, ligand binding, and/or characterization of protein-protein interactions, herein, we describe the Extract2Chip method. This approach builds on the immobilization of site-specific biotinylated proteins of interest, directly from cellular extracts, on avidin-coated sensor chips to allow for the characterization of molecular interactions via surface plasmon resonance (SPR). The developed method was initially validated using Cyclophilin D (CypD) and subsequently applied to other drug discovery projects in which the targets of interest were difficult to express, purify, and crystallize. Extract2Chip was successfully applied to the characterization of Yes-associated protein (YAP): Transcriptional enhancer factor TEF (TEAD1) protein-protein interaction inhibitors, in the validation of a ternary complex assembly composed of Dyskerin pseudouridine synthase 1 (DKC1) and RuvBL1/RuvBL2, and in the establishment of a fast-screening platform to select the most suitable NUAK family SNF1-like kinase 2 (NUAK2) surrogate for binding and structural studies. The described method paves the way for a potential revival of the many drug discovery campaigns that have failed to deliver due to the lack of suitable and sufficient protein supply.
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Affiliation(s)
- Ana C. F. Paiva
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Ana R. Lemos
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Philipp Busse
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Madalena T. Martins
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
| | - Diana O. Silva
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Micael C. Freitas
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Sandra P. Santos
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Filipe Freire
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Evelyne J. Barrey
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Xavier Manival
- IMoPA, CNRS, Université de Lorraine, F-54000 Nancy, France;
| | - Lisa Koetzner
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Timo Heinrich
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Ansgar Wegener
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Ulrich Grädler
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Tiago M. Bandeiras
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Daniel Schwarz
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Pedro M. F. Sousa
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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2
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Dos Santos Morais R, Santo PE, Ley M, Schelcher C, Abel Y, Plassart L, Deslignière E, Chagot ME, Quinternet M, Paiva ACF, Hessmann S, Morellet N, M F Sousa P, Vandermoere F, Bertrand E, Charpentier B, Bandeiras TM, Plisson-Chastang C, Verheggen C, Cianférani S, Manival X. Deciphering cellular and molecular determinants of human DPCD protein in complex with RUVBL1/RUVBL2 AAA-ATPases. J Mol Biol 2022; 434:167760. [PMID: 35901867 DOI: 10.1016/j.jmb.2022.167760] [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: 02/04/2022] [Revised: 06/24/2022] [Accepted: 07/21/2022] [Indexed: 10/16/2022]
Abstract
DPCD is a protein that may play a role in cilia formation and whose absence leads to primary ciliary dyskinesia (PCD), a rare disease caused by impairment of ciliated cells. Except for high-throughput studies that identified DPCD as a possible RUVBL1 (R1) and RUVBL2 (R2) partner, no in-depth cellular, biochemical, and structural investigation involving DPCD have been reported so far. R1 and R2 proteins are ubiquitous highly conserved AAA+ family ATPases that assemble and mature a plethora of macromolecular complexes and are pivotal in numerous cellular processes, especially by guaranteeing a co-chaperoning function within R2TP or R2TP-like machineries. In the present study, we identified DPCD as a new R1R2 partner in vivo. We show that DPCD interacts directly with R1 and R2 in vitro and in cells. We characterized the physico-chemical properties of DPCD in solution and built a 3D model of DPCD. In addition, we used a variety of orthogonal biophysical techniques including small-angle X-ray scattering, structural mass spectrometry and electron microscopy to assess the molecular determinants of DPCD interaction with R1R2. Interestingly, DPCD disrupts the dodecameric state of R1R2 complex upon binding and this interaction occurs mainly via the DII domains of R1R2.
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Affiliation(s)
| | - Paulo E Santo
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Marie Ley
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg 67000, France; Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, 67087 Strasbourg, France
| | | | - Yoann Abel
- IGH, CNRS, Univ Montpellier, Montpellier, France; Equipe labélisée Ligue Nationale Contre le Cancer, 34293 Montpellier, France
| | - Laura Plassart
- MCD, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Evolène Deslignière
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg 67000, France; Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, 67087 Strasbourg, France
| | | | - Marc Quinternet
- Université de Lorraine, CNRS, INSERM, IBSLor, Biophysics and Structural Biology Core Facility, F-54000, France
| | - Ana C F Paiva
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Steve Hessmann
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg 67000, France; Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, 67087 Strasbourg, France
| | - Nelly Morellet
- Très Grandes Infrastructures de Recherche, Institut de Chimie des Substances Naturelles - CNRS, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Pedro M F Sousa
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | | | - Edouard Bertrand
- IGH, CNRS, Univ Montpellier, Montpellier, France; Equipe labélisée Ligue Nationale Contre le Cancer, 34293 Montpellier, France
| | | | - Tiago M Bandeiras
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Célia Plisson-Chastang
- MCD, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Céline Verheggen
- IGH, CNRS, Univ Montpellier, Montpellier, France; Equipe labélisée Ligue Nationale Contre le Cancer, 34293 Montpellier, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg 67000, France; Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, 67087 Strasbourg, France
| | - Xavier Manival
- IMoPA, CNRS, Université de Lorraine, Nancy F-54000, France
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3
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Abel Y, Paiva ACF, Bizarro J, Chagot ME, Santo PE, Robert MC, Quinternet M, Vandermoere F, Sousa PMF, Fort P, Charpentier B, Manival X, Bandeiras TM, Bertrand E, Verheggen C. NOPCHAP1 is a PAQosome cofactor that helps loading NOP58 on RUVBL1/2 during box C/D snoRNP biogenesis. Nucleic Acids Res 2021; 49:1094-1113. [PMID: 33367824 PMCID: PMC7826282 DOI: 10.1093/nar/gkaa1226] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 11/13/2020] [Accepted: 12/11/2020] [Indexed: 12/15/2022] Open
Abstract
The PAQosome is a large complex composed of the HSP90/R2TP chaperone and a prefoldin-like module. It promotes the biogenesis of cellular machineries but it is unclear how it discriminates closely related client proteins. Among the main PAQosome clients are C/D snoRNPs and in particular their core protein NOP58. Using NOP58 mutants and proteomic experiments, we identify different assembly intermediates and show that C12ORF45, which we rename NOPCHAP1, acts as a bridge between NOP58 and PAQosome. NOPCHAP1 makes direct physical interactions with the CC-NOP domain of NOP58 and domain II of RUVBL1/2 AAA+ ATPases. Interestingly, NOPCHAP1 interaction with RUVBL1/2 is disrupted upon ATP binding. Moreover, while it robustly binds both yeast and human NOP58, it makes little interactions with NOP56 and PRPF31, two other closely related CC-NOP proteins. Expression of NOP58, but not NOP56 or PRPF31, is decreased in NOPCHAP1 KO cells. We propose that NOPCHAP1 is a client-loading PAQosome cofactor that selects NOP58 to promote box C/D snoRNP assembly.
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Affiliation(s)
- Yoann Abel
- IGMM, CNRS, Univ Montpellier, Montpellier, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Montpellier, France.,IGH, CNRS, Univ Montpellier, Montpellier, France
| | - Ana C F Paiva
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2781-901, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Jonathan Bizarro
- IGMM, CNRS, Univ Montpellier, Montpellier, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Montpellier, France
| | | | - Paulo E Santo
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2781-901, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Marie-Cécile Robert
- IGMM, CNRS, Univ Montpellier, Montpellier, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Montpellier, France.,IGH, CNRS, Univ Montpellier, Montpellier, France
| | - Marc Quinternet
- Université de Lorraine, CNRS, INSERM, IBSLor, Biophysics and Structural Biology Core Facility, F-54000, Nancy, France
| | | | - Pedro M F Sousa
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2781-901, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | | | | | - Xavier Manival
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | - Tiago M Bandeiras
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2781-901, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Edouard Bertrand
- IGMM, CNRS, Univ Montpellier, Montpellier, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Montpellier, France.,IGH, CNRS, Univ Montpellier, Montpellier, France
| | - Céline Verheggen
- IGMM, CNRS, Univ Montpellier, Montpellier, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Montpellier, France.,IGH, CNRS, Univ Montpellier, Montpellier, France
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4
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Maurizy C, Quinternet M, Abel Y, Verheggen C, Santo PE, Bourguet M, C F Paiva A, Bragantini B, Chagot ME, Robert MC, Abeza C, Fabre P, Fort P, Vandermoere F, M F Sousa P, Rain JC, Charpentier B, Cianférani S, Bandeiras TM, Pradet-Balade B, Manival X, Bertrand E. The RPAP3-Cterminal domain identifies R2TP-like quaternary chaperones. Nat Commun 2018; 9:2093. [PMID: 29844425 PMCID: PMC5974087 DOI: 10.1038/s41467-018-04431-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 04/19/2018] [Indexed: 12/22/2022] Open
Abstract
R2TP is an HSP90 co-chaperone that assembles important macro-molecular machineries. It is composed of an RPAP3-PIH1D1 heterodimer, which binds the two essential AAA+ATPases RUVBL1/RUVBL2. Here, we resolve the structure of the conserved C-terminal domain of RPAP3, and we show that it directly binds RUVBL1/RUVBL2 hexamers. The human genome encodes two other proteins bearing RPAP3-C-terminal-like domains and three containing PIH-like domains. Systematic interaction analyses show that one RPAP3-like protein, SPAG1, binds PIH1D2 and RUVBL1/2 to form an R2TP-like complex termed R2SP. This co-chaperone is enriched in testis and among 68 of the potential clients identified, some are expressed in testis and others are ubiquitous. One substrate is liprin-α2, which organizes large signaling complexes. Remarkably, R2SP is required for liprin-α2 expression and for the assembly of liprin-α2 complexes, indicating that R2SP functions in quaternary protein folding. Effects are stronger at 32 °C, suggesting that R2SP could help compensating the lower temperate of testis. R2TP is an HSP90 co-chaperone composed of an RPAP3-PIH1D1 heterodimer, which binds two essential AAA+ ATPases RUVBL1/RUVBL2. Here authors use a structural approach to study RPAP3 and find an RPAP3-like protein (SPAG1) which also forms a co-chaperone complex with PIH1D2 and RUVBL1/2 enriched in testis.
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Affiliation(s)
- Chloé Maurizy
- IGMM, CNRS, Université de Montpellier, Montpellier, 34293, France.,Equipe labélisée Ligue Nationale Contre le Cancer, 34293, Montpellier, France
| | - Marc Quinternet
- CNRS, INSERM, IBSLOR, Université de Lorraine, Nancy, F-54000, France
| | - Yoann Abel
- IGMM, CNRS, Université de Montpellier, Montpellier, 34293, France.,Equipe labélisée Ligue Nationale Contre le Cancer, 34293, Montpellier, France
| | - Céline Verheggen
- IGMM, CNRS, Université de Montpellier, Montpellier, 34293, France.,Equipe labélisée Ligue Nationale Contre le Cancer, 34293, Montpellier, France
| | - Paulo E Santo
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2781-901, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Maxime Bourguet
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, 67000, France
| | - Ana C F Paiva
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2781-901, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | | | | | - Marie-Cécile Robert
- IGMM, CNRS, Université de Montpellier, Montpellier, 34293, France.,Equipe labélisée Ligue Nationale Contre le Cancer, 34293, Montpellier, France
| | - Claire Abeza
- IGMM, CNRS, Université de Montpellier, Montpellier, 34293, France.,Equipe labélisée Ligue Nationale Contre le Cancer, 34293, Montpellier, France
| | - Philippe Fabre
- CNRS, IMoPA, Université de Lorraine, Nancy, F-54000, France
| | - Philippe Fort
- CRBM, University of Montpellier, CNRS, 1919 Route de Mende, Montpellier, 34090, France
| | | | - Pedro M F Sousa
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2781-901, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | | | | | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, 67000, France
| | - Tiago M Bandeiras
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2781-901, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | | | - Xavier Manival
- CNRS, IMoPA, Université de Lorraine, Nancy, F-54000, France.
| | - Edouard Bertrand
- IGMM, CNRS, Université de Montpellier, Montpellier, 34293, France. .,Equipe labélisée Ligue Nationale Contre le Cancer, 34293, Montpellier, France.
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