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Boone M, Ramasamy P, Zuallaert J, Bouwmeester R, Van Moer B, Maddelein D, Turan D, Hulstaert N, Eeckhaut H, Vandermarliere E, Martens L, Degroeve S, De Neve W, Vranken W, Callewaert N. Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit. Nat Commun 2021; 12:6414. [PMID: 34741024 PMCID: PMC8571348 DOI: 10.1038/s41467-021-26720-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 10/15/2021] [Indexed: 11/09/2022] Open
Abstract
While transcriptome- and proteome-wide technologies to assess processes in protein biogenesis are now widely available, we still lack global approaches to assay post-ribosomal biogenesis events, in particular those occurring in the eukaryotic secretory system. We here develop a method, SECRiFY, to simultaneously assess the secretability of >105 protein fragments by two yeast species, S. cerevisiae and P. pastoris, using custom fragment libraries, surface display and a sequencing-based readout. Screening human proteome fragments with a median size of 50-100 amino acids, we generate datasets that enable datamining into protein features underlying secretability, revealing a striking role for intrinsic disorder and chain flexibility. The SECRiFY methodology generates sufficient amounts of annotated data for advanced machine learning methods to deduce secretability patterns. The finding that secretability is indeed a learnable feature of protein sequences provides a solid base for application-focused studies.
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Affiliation(s)
- Morgane Boone
- Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium. .,Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium. .,Department of Biochemistry and Biophysics, UCSF, San Francisco, CA, USA.
| | - Pathmanaban Ramasamy
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium ,grid.8767.e0000 0001 2290 8069Structural Biology Brussels, VUB, Brussels, Belgium ,grid.11486.3a0000000104788040Structural Biology Research Center, VIB, Brussels, Belgium ,Interuniversity Institute of Bioinformatics in Brussels (IB)2, ULB-VUB, Brussels, Belgium
| | - Jasper Zuallaert
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium ,grid.510328.dCenter for Biotech Data Science, Ghent University Global Campus, Songdo, Incheon, South Korea ,grid.5342.00000 0001 2069 7798IDLab, ELIS, UGent, Ghent, Belgium
| | - Robbin Bouwmeester
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Berre Van Moer
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Davy Maddelein
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Demet Turan
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Niels Hulstaert
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Hannah Eeckhaut
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Elien Vandermarliere
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Lennart Martens
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Sven Degroeve
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Wesley De Neve
- grid.510328.dCenter for Biotech Data Science, Ghent University Global Campus, Songdo, Incheon, South Korea ,grid.5342.00000 0001 2069 7798IDLab, ELIS, UGent, Ghent, Belgium
| | - Wim Vranken
- grid.8767.e0000 0001 2290 8069Structural Biology Brussels, VUB, Brussels, Belgium ,grid.11486.3a0000000104788040Structural Biology Research Center, VIB, Brussels, Belgium ,Interuniversity Institute of Bioinformatics in Brussels (IB)2, ULB-VUB, Brussels, Belgium
| | - Nico Callewaert
- Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium. .,Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium.
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Raeeszadeh-Sarmazdeh M, Greene KA, Sankaran B, Downey GP, Radisky DC, Radisky ES. Directed evolution of the metalloproteinase inhibitor TIMP-1 reveals that its N- and C-terminal domains cooperate in matrix metalloproteinase recognition. J Biol Chem 2019; 294:9476-9488. [PMID: 31040180 DOI: 10.1074/jbc.ra119.008321] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/23/2019] [Indexed: 01/04/2023] Open
Abstract
Tissue inhibitors of metalloproteinases (TIMPs) are natural inhibitors of matrix metalloproteinases (MMPs), enzymes that contribute to cancer and many inflammatory and degenerative diseases. The TIMP N-terminal domain binds and inhibits an MMP catalytic domain, but the role of the TIMP C-terminal domain in MMP inhibition is poorly understood. Here, we employed yeast surface display for directed evolution of full-length human TIMP-1 to develop MMP-3-targeting ultrabinders. By simultaneously incorporating diversity into both domains, we identified TIMP-1 variants that were up to 10-fold improved in binding MMP-3 compared with WT TIMP-1, with inhibition constants (Ki ) in the low picomolar range. Analysis of individual and paired mutations from the selected TIMP-1 variants revealed cooperative effects between distant residues located on the N- and C-terminal TIMP domains, positioned on opposite sides of the interaction interface with MMP-3. Crystal structures of MMP-3 complexes with TIMP-1 variants revealed conformational changes in TIMP-1 near the cooperative mutation sites. Affinity was strengthened by cinching of a reciprocal "tyrosine clasp" formed between the N-terminal domain of TIMP-1 and proximal MMP-3 interface and by changes in secondary structure within the TIMP-1 C-terminal domain that stabilize interdomain interactions and improve complementarity to MMP-3. Our protein engineering and structural studies provide critical insight into the cooperative function of TIMP domains and the significance of peripheral TIMP epitopes in MMP recognition. Our findings suggest new strategies to engineer TIMP proteins for therapeutic applications, and our directed evolution approach may also enable exploration of functional domain interactions in other protein systems.
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Affiliation(s)
| | - Kerrie A Greene
- From the Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida 32224
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Gregory P Downey
- Departments of Medicine, Pediatrics, and Biomedical Research, National Jewish Health, Denver, Colorado 80206, and.,Departments of Medicine, Immunology, and Microbiology, University of Colorado, Aurora, Colorado 80045
| | - Derek C Radisky
- From the Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida 32224
| | - Evette S Radisky
- From the Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida 32224,
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