1
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Wen M, Yu A, Park Y, Calarese D, Gerber HP, Yin G. Homogeneous antibody-drug conjugates with dual payloads: potential, methods and considerations. MAbs 2025; 17:2498162. [PMID: 40322862 PMCID: PMC12054377 DOI: 10.1080/19420862.2025.2498162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Revised: 04/18/2025] [Accepted: 04/21/2025] [Indexed: 05/08/2025] Open
Abstract
The development of site-specific dual-payload antibody-drug conjugates (ADCs) represents a potential advancement in targeted cancer therapy, enabling the simultaneous delivery of two distinct drugs into the same cancer cells to overcome payload resistance and enhance therapeutic efficacy. Here, we examine various methodologies for achieving site-specific dual-payload conjugation, including the use of multi-functional linkers, canonical amino acids, non-canonical amino acids, and enzyme-mediated methods, all of which facilitate precise control over payload attachment while ensuring homogeneity. We explore the implications of different conjugation techniques on drug-to-antibody ratios and the ratios of the two payloads, as well as their impact on process complexity and manufacturability. Additionally, we address the potential advantages of dual-payload ADCs compared to ADCs combined with traditional chemotherapy or single-payload ADC/ADC combinations. By evaluating these innovative methods, we aim to provide a comprehensive understanding of the current landscape in dual-payload ADC development and outline emerging directions necessary for further advancement of this promising therapeutic strategy.
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Affiliation(s)
- Miao Wen
- Sutro Biopharma Inc, South San Francisco, CA, USA
| | - Abigail Yu
- Sutro Biopharma Inc, South San Francisco, CA, USA
| | - Young Park
- Sutro Biopharma Inc, South San Francisco, CA, USA
| | | | | | - Gang Yin
- Sutro Biopharma Inc, South San Francisco, CA, USA
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2
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Eweje F, Ibrahim V, Shajii A, Walsh ML, Ahmad K, Alrefai A, Miyasato D, Davis JR, Ham H, Li K, Roehrl M, Haller CA, Liu DR, Chen J, Chaikof EL. Self-assembling protein nanoparticles for cytosolic delivery of nucleic acids and proteins. Nat Biotechnol 2025:10.1038/s41587-025-02664-2. [PMID: 40374955 DOI: 10.1038/s41587-025-02664-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Accepted: 04/01/2025] [Indexed: 05/18/2025]
Abstract
Intracellular delivery of biomacromolecules is hampered by low efficiency and cytotoxicity. Here we report the development of elastin-based nanoparticles for therapeutic delivery (ENTER), a recombinant elastin-like polypeptide (ELP)-based delivery system for effective cytosolic delivery of biomacromolecules in vitro and in vivo. Through iterative design, we developed fourth-generation ELPs fused to cationic endosomal escape peptides (EEPs) that self-assemble into pH-responsive micellar nanoparticles and enable cytosolic entry of cargo following endocytic uptake. In silico screening of α-helical peptide libraries led to the discovery of an EEP (EEP13) with 48% improved protein delivery efficiency versus a benchmark peptide. Our lead ELP-EEP13 showed similar or superior performance compared to lipid-based transfection reagents in the delivery of mRNA-encoded, DNA-encoded and protein-form Cre recombinase and CRISPR gene editors as well as short interfering RNAs to multiple cell lines and primary cell types. Intranasal administration of ELP-EEP13 combined with Cre protein achieved efficient editing of lung epithelial cells in reporter mice.
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Affiliation(s)
- Feyisayo Eweje
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Harvard and MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard/MIT MD-PhD Program, Boston, MA, USA
- Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Vanessa Ibrahim
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Aram Shajii
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Michelle L Walsh
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Harvard and MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard/MIT MD-PhD Program, Boston, MA, USA
| | - Kiran Ahmad
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Assma Alrefai
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Dominie Miyasato
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jessie R Davis
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hyunok Ham
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Kaicheng Li
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Michael Roehrl
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Carolyn A Haller
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jiaxuan Chen
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
| | - Elliot L Chaikof
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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3
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Martinusen SG, Nelson SE, Slaton EW, Long LF, Pho R, Ajayebi S, Denard CA. Protease engineering: Approaches, tools, and emerging trends. Biotechnol Adv 2025; 82:108602. [PMID: 40368116 DOI: 10.1016/j.biotechadv.2025.108602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2024] [Revised: 04/25/2025] [Accepted: 05/10/2025] [Indexed: 05/16/2025]
Abstract
Engineered proteases with bespoke substrate specificities and activities can empower broad and innovative applications in biomedicine, mass spectrometry-based proteomics, and chemical and synthetic biology. This review provides an authoritative, topical, and detailed description and discussion of the directed evolution and high-throughput strategies designed to engineer the substrate specificity of proteases in E. coli, yeast, phage, and cell-free systems. Second, we discuss emerging protease engineering strategies that complement directed evolution, including antibody-protease fusions that enable proximity catalysis, and protease substrate specificity switching driven by exogenous protein-protein interactions. Lastly, we discuss principles for engineering split and autoinhibited proteases, which are key signal-processing modules in protein circuits. Overall, readers will gain a valuable understanding of the latest advances in protease engineering, focusing on methodologies and strategies that enable precise control of protease activity and specificity.
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Affiliation(s)
| | - Sage E Nelson
- Department of Chemical Engineering, University of Florida, Gainesville 32611, USA
| | - Ethan W Slaton
- Department of Chemical Engineering, University of Florida, Gainesville 32611, USA
| | - Lawton F Long
- Department of Chemical Engineering, University of Florida, Gainesville 32611, USA
| | - Raymond Pho
- Department of Chemical Engineering, University of Florida, Gainesville 32611, USA
| | - Seyednima Ajayebi
- Department of Chemical Engineering, University of Florida, Gainesville 32611, USA
| | - Carl A Denard
- Department of Chemical Engineering, University of Florida, Gainesville 32611, USA; UF Health Cancer Center, University of Florida, Gainesville, 32611, USA.
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4
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Kopyeva I, Bretherton RC, Ayers JL, Yu M, Grady WM, DeForest CA. Matrix Stiffness and Biochemistry Govern Colorectal Cancer Cell Growth and Signaling in User-Programmable Synthetic Hydrogels. ACS Biomater Sci Eng 2025; 11:2810-2823. [PMID: 40304602 DOI: 10.1021/acsbiomaterials.4c01632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2025]
Abstract
Colorectal cancer (CRC) studies in vitro have been conducted almost exclusively on 2D cell monolayers or suspension spheroid cultures. Though these platforms have shed light on many important aspects of CRC biology, they fail to recapitulate essential cell-matrix interactions that often define in vivo function. Toward filling this knowledge gap, synthetic hydrogel biomaterials with user-programmable matrix mechanics and biochemistry have gained popularity for culturing cells in a more physiologically relevant 3D context. Here, using a poly(ethylene glycol)-based hydrogel model, we systematically assess the role of matrix stiffness and fibronectin-derived RGDS adhesive peptide presentation on CRC colony morphology and proliferation. Highlighting platform generalizability, we demonstrate that these hydrogels can support the viability and promote spontaneous spheroid or multicellular aggregate formation of six CRC cell lines that are commonly utilized in biomedical research. These gels are engineered to be fully degradable via a "biologically invisible" sortase-mediated reaction, enabling the triggered recovery of single cells and spheroids for downstream analysis. Using these platforms, we establish that substrate mechanics play a significant role in colony growth: soft conditions (∼300 Pa) encourage robust colony formation, whereas stiffer (∼2 kPa) gels severely restrict growth. Tuning the RGDS concentration did not affect the colony morphology. Additionally, we observe that epidermal growth factor receptor (EGFR) signaling in Caco-2 cells is influenced by adhesion ligand identity─whether the adhesion peptide was derived from collagen type I (DGEA) or fibronectin (RGDS)─with DGEA yielding a marked decrease in the level of downstream protein kinase phosphorylation. Taken together, this study introduces a versatile method to culture and probe CRC cell-matrix interactions within engineered 3D biomaterials.
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Affiliation(s)
- Irina Kopyeva
- Department of Bioengineering, University of Washington, Seattle 98105, Washington, United States
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle 98105, Washington, United States
| | - Ross C Bretherton
- Department of Bioengineering, University of Washington, Seattle 98105, Washington, United States
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle 98105, Washington, United States
| | - Jessica L Ayers
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle 98109, Washington, United States
| | - Ming Yu
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle 98109, Washington, United States
| | - William M Grady
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle 98109, Washington, United States
- Department of Internal Medicine, University of Washington, Seattle 98105, Washington, United States
| | - Cole A DeForest
- Department of Bioengineering, University of Washington, Seattle 98105, Washington, United States
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle 98105, Washington, United States
- Department of Chemical Engineering, University of Washington, Seattle 98105, Washington, United States
- Molecular Engineering & Sciences Institute, University of Washington, Seattle 98105, Washington, United States
- Department of Chemistry, University of Washington, Seattle 98105, Washington, United States
- Institute for Protein Design, University of Washington, Seattle 98105, Washington, United States
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5
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Wijfjes Z, Ramos Tomillero I, Le Gall CM, van Dinther EAW, Turlings F, Classens R, Manna S, van Dalen D, Peters RJRW, Schouren K, Fennemann FL, Hagemans IM, van Dalen FJ, van der Schoot JMS, Figdor CG, Esser-Kahn A, Scheeren FA, Verdoes M. Co-delivery of antigen and adjuvant by site-specific conjugation to dendritic cell-targeted Fab fragments potentiates T cell responses. RSC Chem Biol 2025:d5cb00014a. [PMID: 40343174 PMCID: PMC12057635 DOI: 10.1039/d5cb00014a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Accepted: 04/24/2025] [Indexed: 05/11/2025] Open
Abstract
The aim of therapeutic cancer vaccines is to induce tumor-specific cellular immune responses. This requires tumor antigens to be efficiently processed and presented by antigen-presenting cells, in particular dendritic cells (DCs). In addition, DCs require maturation to upregulate the surface expression and secretion of T cell costimulatory molecules, which is achieved by co-administration of adjuvants in vaccines. Peptide-based antigen vaccination is an attractive strategy due to the established biocompatibility of peptides as well as the dosing control. To enhance the efficacy of peptide-based vaccines, antigens can be targeted to DCs. Antigen-adjuvant conjugates are known to enhance T cell activation by ensuring DC maturation upon antigen delivery. In this study, we aim to combine these two approaches in a single molecule, and present a DC-targeted antibody fragment-antigen-adjuvant (AAA)-conjugate. We generate the AAA-conjugate through a combination of site-specific sortase-mediated chemoenzymatic ligation and click chemistry. Ex vivo T cell activation assays show enhanced efficacy of the AAA-conjugate compared to non-adjuvanted control conjugates. The in vivo performance of the AAA-conjugate was suboptimal, which we hypothesize to be a consequence of the hydrophobic character of the conjugate. In vivo efficacy was rescued by co-administration of antibody fragment-antigen conjugates and antibody fragment-adjuvant conjugates, in which the antigen and adjuvant were separatedly delivered using two different DC-targeting molecules. In conclusion, this study provides a proof-of-concept for effective in vivo antigen-specific T cell activation by targeted delivery of both antigen and adjuvant to DCs in a single or separate molecule using site-specific protein engineering.
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Affiliation(s)
- Zacharias Wijfjes
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen The Netherlands
- Institute for Chemical Immunology Nijmegen The Netherlands
| | - Iván Ramos Tomillero
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen The Netherlands
| | - Camille M Le Gall
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen The Netherlands
| | - Eric A W van Dinther
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen The Netherlands
| | - Frederique Turlings
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen The Netherlands
- IMAGINE! Consortium Nijmegen The Netherlands
| | - René Classens
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen The Netherlands
| | - Saikat Manna
- Pritzker School of Molecular Engineering, University of Chicago Chicago USA
| | - Duco van Dalen
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen The Netherlands
| | - Ruud J R W Peters
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen The Netherlands
| | - Kayleigh Schouren
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen The Netherlands
| | - Felix L Fennemann
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen The Netherlands
| | - Iris M Hagemans
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen The Netherlands
| | - Floris J van Dalen
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen The Netherlands
- Institute for Chemical Immunology Nijmegen The Netherlands
| | | | - Carl G Figdor
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen The Netherlands
- Institute for Chemical Immunology Nijmegen The Netherlands
| | - Aaron Esser-Kahn
- Pritzker School of Molecular Engineering, University of Chicago Chicago USA
| | - Ferenc A Scheeren
- Department of Dermatology, Leiden University Medical Center Leiden The Netherlands
| | - Martijn Verdoes
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen The Netherlands
- Institute for Chemical Immunology Nijmegen The Netherlands
- IMAGINE! Consortium Nijmegen The Netherlands
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6
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El Hebieshy AF, Wijfjes Z, Le Gall CM, Middelburg J, de Roode KE, Fennemann FL, Sluijter M, van Hall T, Dijkstra DJ, Trouw LA, van Dalen FJ, Rodgers Furones A, van der Schoot JMS, Derksen I, de Haard H, van der Woning B, Talavera Ormeño CMP, van Doodewaerd BR, Figdor CG, van der Heden van Noort GJ, Parren PWHI, Heskamp S, Ovaa H, Verdoes M, Scheeren FA. Site-directed multivalent conjugation of antibodies to ubiquitinated payloads. Nat Biomed Eng 2025:10.1038/s41551-024-01342-z. [PMID: 40204992 DOI: 10.1038/s41551-024-01342-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 12/20/2024] [Indexed: 04/11/2025]
Abstract
Antibody conjugates are the foundation of a wide range of diagnostic and therapeutic applications. Although many antibody-conjugation techniques are robust and efficient, obtaining homogeneous multimeric conjugation products remains challenging. Here we report a modular and versatile technique for the site-directed multivalent conjugation of antibodies via the small-protein ubiquitin. Specifically, multiple ubiquitin fusions with antibodies, antibody fragments, nanobodies, peptides or small molecules such as fluorescent dyes can be conjugated to antibodies and nanobodies within 30 min. The technique, which we named 'ubi-tagging', allowed us to efficiently generate a bispecific T-cell engager as well as nanobodies conjugated to dendritic-cell-targeted antigens that led to potent T-cell responses. Using both recombinant ubi-tagged proteins and synthetic ubiquitin derivatives allows for the iterative, site-directed and multivalent conjugation of antibodies and nanobodies to a plethora of molecular moieties.
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Affiliation(s)
- Angela F El Hebieshy
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Zacharias Wijfjes
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Institute for Chemical Immunology, Nijmegen, the Netherlands
| | - Camille M Le Gall
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jim Middelburg
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Kim E de Roode
- Department of Medical Imaging, Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Tagworks Pharmaceuticals, Nijmegen, the Netherlands
| | - Felix L Fennemann
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marjolein Sluijter
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Thorbald van Hall
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Douwe J Dijkstra
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Leendert A Trouw
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Floris J van Dalen
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Andrea Rodgers Furones
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Ian Derksen
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
| | | | | | - Cami M P Talavera Ormeño
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Bjorn R van Doodewaerd
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Carl G Figdor
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Paul W H I Parren
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Sandra Heskamp
- Department of Medical Imaging, Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Huib Ovaa
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Martijn Verdoes
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands.
- Institute for Chemical Immunology, Nijmegen, the Netherlands.
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Ferenc A Scheeren
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands.
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7
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Cui Y, Han D, Bai X, Shi W. Development and applications of enzymatic peptide and protein ligation. J Pept Sci 2025; 31:e3657. [PMID: 39433441 DOI: 10.1002/psc.3657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 09/23/2024] [Accepted: 09/24/2024] [Indexed: 10/23/2024]
Abstract
Chemical synthesis of complex peptides and proteins continues to play increasingly important roles in industry and academia, where strategies for covalent ligation of two or more peptide fragments to produce longer peptides and proteins in convergent manners have become critical. In recent decades, efficient and site-selective ligation strategies mediated by exploiting the biocatalytic capacity of nature's diverse toolkit (i.e., enzymes) have been widely recognized as a powerful extension of existing chemical strategies. In this review, we present a chronological overview of the development of proteases, transpeptidases, transglutaminases, and ubiquitin ligases. We survey the different properties between the ligation reactions of various enzymes, including the selectivity and efficiency of the reaction, the ligation "scar" left in the product, the type of amide bond formed (natural or isopeptide), the synthetic availability of the reactants, and whether the enzymes are orthogonal to another. This review also describes how the inherent specificity of these enzymes can be exploited for peptide and protein ligation.
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Affiliation(s)
- Yan Cui
- Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Dongyang Han
- Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Xuerong Bai
- Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Weiwei Shi
- Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
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8
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Martin J, Michaelis M, Petrović S, Lehnen A, Müllers Y, Wendler P, Möller HM, Hartlieb M, Glebe U. Application of Sortase-Mediated Ligation for the Synthesis of Block Copolymers and Protein-Polymer Conjugates. Macromol Biosci 2025; 25:e2400316. [PMID: 39360589 PMCID: PMC11727822 DOI: 10.1002/mabi.202400316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 09/18/2024] [Indexed: 10/04/2024]
Abstract
Sortase-mediated ligation (SML) has become a powerful tool for site-specific protein modification. However, sortase A (SrtA) suffers from low catalytic efficiency and mediates an equilibrium reaction. Therefore, ligations with large macromolecules may be challenging. Here, the synthesis of polymeric building blocks for sortase-mediated ligation constituting peptide-polymers with either the recognition sequence for sortase A (LPX1TGX2) or its nucleophilic counterpart (Gx) is demonstrated. The peptide-polymers are synthesized by solid-phase peptide synthesis followed by photo-iniferter (PI) reversible addition-fragmentation chain-transfer (RAFT) polymerization of various monomers. The building blocks are subsequently utilized to investigate possibilities and limitations when using macromolecules in SML. In particular, diblock copolymers are obtained even when using the orthogonal building blocks in equimolar ratio by exploiting a technique to shift the reaction equilibrium. However, ligations of two polymers can not be achieved when the degree of polymerization exceeds 100. Subsequently, C-terminal protein-polymer conjugates are synthesized. Several polymers are utilized that can replace the omnipresent polyethylene glycol (PEG) in future therapeutics. The conjugation is exemplified with a nanobody that is known for efficient neutralization of SARS-CoV-2. The study demonstrates a universal approach to polymer-LPX1TGX2 and Gx-polymer building blocks and gives insight into their application in SML.
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Affiliation(s)
- Johannes Martin
- Institute of ChemistryUniversity of PotsdamKarl‐Liebknecht‐Str. 24–2514476Potsdam‐GolmGermany
- Fraunhofer Institute for Applied Polymer Research IAPGeiselbergstr. 6914476Potsdam‐GolmGermany
| | - Marcus Michaelis
- Institute of ChemistryUniversity of PotsdamKarl‐Liebknecht‐Str. 24–2514476Potsdam‐GolmGermany
| | - Saša Petrović
- Department of BiochemistryUniversity of PotsdamKarl‐Liebknecht‐Str. 24–2514476Potsdam‐GolmGermany
| | - Anne‐Catherine Lehnen
- Institute of ChemistryUniversity of PotsdamKarl‐Liebknecht‐Str. 24–2514476Potsdam‐GolmGermany
- Fraunhofer Institute for Applied Polymer Research IAPGeiselbergstr. 6914476Potsdam‐GolmGermany
| | - Yannic Müllers
- Institute of ChemistryUniversity of PotsdamKarl‐Liebknecht‐Str. 24–2514476Potsdam‐GolmGermany
- Fraunhofer Institute for Applied Polymer Research IAPGeiselbergstr. 6914476Potsdam‐GolmGermany
| | - Petra Wendler
- Department of BiochemistryUniversity of PotsdamKarl‐Liebknecht‐Str. 24–2514476Potsdam‐GolmGermany
| | - Heiko M. Möller
- Institute of ChemistryUniversity of PotsdamKarl‐Liebknecht‐Str. 24–2514476Potsdam‐GolmGermany
| | - Matthias Hartlieb
- Institute of ChemistryUniversity of PotsdamKarl‐Liebknecht‐Str. 24–2514476Potsdam‐GolmGermany
- Fraunhofer Institute for Applied Polymer Research IAPGeiselbergstr. 6914476Potsdam‐GolmGermany
| | - Ulrich Glebe
- Institute of ChemistryUniversity of PotsdamKarl‐Liebknecht‐Str. 24–2514476Potsdam‐GolmGermany
- Fraunhofer Institute for Applied Polymer Research IAPGeiselbergstr. 6914476Potsdam‐GolmGermany
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9
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Vilen Z, Pang JM, Huang ML. Proximity Labeling of Cell Surface Proteins via Cell Surface Remodeling. Methods Mol Biol 2025; 2908:33-50. [PMID: 40304901 DOI: 10.1007/978-1-0716-4434-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2025]
Abstract
Within the complex interplay of proteins, lipids and carbohydrates at the cell surface is the surfaceome, a dense layer of proteins and their posttranslationally modified counterparts that serves as a hub for cell signaling and signal transduction. The surfaceome plays crucial roles in mediating interactions between cells and the extracellular environment, which combined with their availability at the cell surface make it an attractive therapeutic target. Despite its importance, the development of technologies to selectively target cell surface proteins for empirical identification is challenged by their structural complexity. Here, we describe a proximity labeling-based technique to covalently label proteins at the cell surface with a biotin handle, enabling downstream streptavidin-based enrichment and manipulation in a variety of modalities, including fluorescence imaging, western blotting, and mass spectrometry-based proteomics.
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Affiliation(s)
- Zak Vilen
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, La Jolla, CA, USA
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - Jia Meng Pang
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, La Jolla, CA, USA
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - Mia L Huang
- Department of Chemistry, Scripps Research, La Jolla, CA, USA.
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10
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Antonenko A, Pomorski A, Singh AK, Kapczyńska K, Krężel A. Site-Specific and Fluorescently Enhanced Installation of Post-Translational Protein Modifications via Bifunctional Biarsenical Linker. ACS OMEGA 2024; 9:45127-45137. [PMID: 39554417 PMCID: PMC11561763 DOI: 10.1021/acsomega.4c05828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 09/18/2024] [Accepted: 10/21/2024] [Indexed: 11/19/2024]
Abstract
To understand how particular post-translational modifications (PTMs) affect the function of a target protein, it is essential to first prepare and investigate the target with the modification at the desired position. This drives the continuous development of site-specific protein modification technologies. Here, we present the chemical synthesis and application of the biarsenical linker SrtCrAsH-EDT2, which has a dual labeling functionality. This linker, containing a sortase A recognition motif, can be conjugated with any protein containing the LPXTG motif at the C terminus, such as ubiquitin and the SUMO tag, and then attached to a protein of interest (POI) containing a terminal or bipartite (intramolecularly placed) tetracysteine motif. This modification of the POI facilitates the straightforward and rapid incorporation of PTMs, which are further highlighted by the fluorescent biarsenical probe. Consequently, this directly correlates proteins' physical properties and cellular roles under various physiological conditions or in disease states. The proposed one-pot labeling methodology can be utilized to explore the effects of PTMs on proteins, affecting their structure, function, localization, and interactions within the cellular environment. Understanding these effects is crucial for uncovering the complex mechanisms that regulate cellular function and dysfunction.
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Affiliation(s)
- Anastasiia Antonenko
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Adam Pomorski
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Avinash Kumar Singh
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wrocław, Poland
- Department
of Laboratory Medicine and Pathology, Mayo
Clinic, Rochester 55901, Minnesota, United States
| | - Katarzyna Kapczyńska
- Department
of Immunology of Infectious Diseases, Hirszfeld
Institute of Immunology and Experimental Therapy, Polish Academy of
Sciences, 53-114 Wrocław, Poland
| | - Artur Krężel
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wrocław, Poland
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11
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Liu Y, Gilchrist AE, Heilshorn SC. Engineered Protein Hydrogels as Biomimetic Cellular Scaffolds. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2407794. [PMID: 39233559 PMCID: PMC11573243 DOI: 10.1002/adma.202407794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/01/2024] [Indexed: 09/06/2024]
Abstract
The biochemical and biophysical properties of the extracellular matrix (ECM) play a pivotal role in regulating cellular behaviors such as proliferation, migration, and differentiation. Engineered protein-based hydrogels, with highly tunable multifunctional properties, have the potential to replicate key features of the native ECM. Formed by self-assembly or crosslinking, engineered protein-based hydrogels can induce a range of cell behaviors through bioactive and functional domains incorporated into the polymer backbone. Using recombinant techniques, the amino acid sequence of the protein backbone can be designed with precise control over the chain-length, folded structure, and cell-interaction sites. In this review, the modular design of engineered protein-based hydrogels from both a molecular- and network-level perspective are discussed, and summarize recent progress and case studies to highlight the diverse strategies used to construct biomimetic scaffolds. This review focuses on amino acid sequences that form structural blocks, bioactive blocks, and stimuli-responsive blocks designed into the protein backbone for highly precise and tunable control of scaffold properties. Both physical and chemical methods to stabilize dynamic protein networks with defined structure and bioactivity for cell culture applications are discussed. Finally, a discussion of future directions of engineered protein-based hydrogels as biomimetic cellular scaffolds is concluded.
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Affiliation(s)
- Yueming Liu
- Department of Materials Science & Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Aidan E Gilchrist
- Department of Biomedical Engineering, University of California, Davis 451 Health Sciences Dr, GBSF 3315, Davis, CA, 95616, USA
| | - Sarah C Heilshorn
- Department of Materials Science & Engineering, 476 Lomita Mall, McCullough Room 246, Stanford, CA, 94305, USA
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12
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Kopyeva I, Goldner EC, Hoye JW, Yang S, Regier MC, Bradford JC, Vera KR, Bretherton RC, Robinson JL, DeForest CA. Stepwise Stiffening/Softening of and Cell Recovery from Reversibly Formulated Hydrogel Interpenetrating Networks. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2404880. [PMID: 39240007 PMCID: PMC11530321 DOI: 10.1002/adma.202404880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 08/06/2024] [Indexed: 09/07/2024]
Abstract
Biomechanical contributions of the extracellular matrix underpin cell growth and proliferation, differentiation, signal transduction, and other fate decisions. As such, biomaterials whose mechanics can be spatiotemporally altered- particularly in a reversible manner- are extremely valuable for studying these mechanobiological phenomena. Herein, a poly(ethylene glycol) (PEG)-based hydrogel model consisting of two interpenetrating step-growth networks is introduced that are independently formed via largely orthogonal bioorthogonal chemistries and sequentially degraded with distinct recombinant sortases, affording reversibly tunable stiffness ranges that span healthy and diseased soft tissues (e.g., 500 Pa-6 kPa) alongside terminal cell recovery for pooled and/or single-cell analysis in a near "biologically invisible" manner. Spatiotemporal control of gelation within the primary supporting network is achieved via mask-based and two-photon lithography; these stiffened patterned regions can be subsequently returned to the original soft state following sortase-based secondary network degradation. Using this approach, the effects of 4D-triggered network mechanical changes on human mesenchymal stem cell morphology and Hippo signaling, as well as Caco-2 colorectal cancer cell mechanomemory using transcriptomics and metabolic assays are investigated. This platform is expected to be of broad utility for studying and directing mechanobiological phenomena, patterned cell fate, and disease resolution in softer matrices.
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Affiliation(s)
- Irina Kopyeva
- Department of Bioengineering, University of Washington, Seattle WA 98105, USA
| | - Ethan C. Goldner
- Department of Chemical Engineering, University of Washington, Seattle WA 98105, USA
| | - Jack W. Hoye
- Department of Chemical Engineering, University of Washington, Seattle WA 98105, USA
| | - Shiyu Yang
- Department of Chemical Engineering, University of Washington, Seattle WA 98105, USA
| | - Mary C. Regier
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle WA 98105, USA
| | - John C. Bradford
- Department of Bioengineering, University of Washington, Seattle WA 98105, USA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle WA 98105, USA
| | - Kaitlyn R. Vera
- Department of Chemical Engineering, University of Washington, Seattle WA 98105, USA
| | - Ross C. Bretherton
- Department of Bioengineering, University of Washington, Seattle WA 98105, USA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle WA 98105, USA
| | - Jennifer L. Robinson
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle WA 98105, USA
- Department of Orthopedic Surgery and Sports Medicine, University of Washington, Seattle WA 98105, USA
- Department of Mechanical Engineering, University of Washington, Seattle WA 98105, USA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle WA 98105, USA
| | - Cole A. DeForest
- Department of Bioengineering, University of Washington, Seattle WA 98105, USA
- Department of Chemical Engineering, University of Washington, Seattle WA 98105, USA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle WA 98105, USA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle WA 98105, USA
- Department of Chemistry, University of Washington, Seattle WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle WA 98105, USA
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13
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Jiang H, Miller BD, Viennet T, Kim H, Lee K, Arthanari H, Cole PA. Protein semisynthesis reveals plasticity in HECT E3 ubiquitin ligase mechanisms. Nat Chem 2024; 16:1894-1905. [PMID: 39030419 DOI: 10.1038/s41557-024-01576-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/11/2024] [Indexed: 07/21/2024]
Abstract
Lys ubiquitination is catalysed by E3 ubiquitin ligases and is central to the regulation of protein stability and cell signalling in normal and disease states. There are gaps in our understanding of E3 mechanisms, and here we use protein semisynthesis, chemical rescue, microscale thermophoresis and other biochemical approaches to dissect the role of catalytic base/acid function and conformational interconversion in HECT-domain E3 catalysis. We demonstrate that there is plasticity in the use of the terminal side chain or backbone carboxylate for proton transfer in HECT E3 ubiquitin ligase reactions, with yeast Rsp5 orthologues appearing to be possible evolutionary intermediates. We also show that the HECT-domain ubiquitin covalent intermediate appears to eject the E2 conjugating enzyme, promoting catalytic turnover. These findings provide key mechanistic insights into how protein ubiquitination occurs and provide a framework for understanding E3 functions and regulation.
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Affiliation(s)
- Hanjie Jiang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Bryant D Miller
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Human Biology, Sattler College, Boston, MA, USA
| | - Thibault Viennet
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Hyojeon Kim
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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14
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Wanka V, Fottner M, Cigler M, Lang K. Genetic Code Expansion Approaches to Decipher the Ubiquitin Code. Chem Rev 2024; 124:11544-11584. [PMID: 39311880 PMCID: PMC11503651 DOI: 10.1021/acs.chemrev.4c00375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 08/05/2024] [Accepted: 08/19/2024] [Indexed: 10/25/2024]
Abstract
The covalent attachment of Ub (ubiquitin) to target proteins (ubiquitylation) represents one of the most versatile PTMs (post-translational modifications) in eukaryotic cells. Substrate modifications range from a single Ub moiety being attached to a target protein to complex Ub chains that can also contain Ubls (Ub-like proteins). Ubiquitylation plays pivotal roles in most aspects of eukaryotic biology, and cells dedicate an orchestrated arsenal of enzymes to install, translate, and reverse these modifications. The entirety of this complex system is coined the Ub code. Deciphering the Ub code is challenging due to the difficulty in reconstituting enzymatic machineries and generating defined Ub/Ubl-protein conjugates. This Review provides a comprehensive overview of recent advances in using GCE (genetic code expansion) techniques to study the Ub code. We highlight strategies to site-specifically ubiquitylate target proteins and discuss their advantages and disadvantages, as well as their various applications. Additionally, we review the potential of small chemical PTMs targeting Ub/Ubls and present GCE-based approaches to study this additional layer of complexity. Furthermore, we explore methods that rely on GCE to develop tools to probe interactors of the Ub system and offer insights into how future GCE-based tools could help unravel the complexity of the Ub code.
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Affiliation(s)
- Vera Wanka
- Laboratory
for Organic Chemistry (LOC), Department of Chemistry and Applied Biosciences
(D-CHAB), ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Maximilian Fottner
- Laboratory
for Organic Chemistry (LOC), Department of Chemistry and Applied Biosciences
(D-CHAB), ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Marko Cigler
- Department
of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Kathrin Lang
- Laboratory
for Organic Chemistry (LOC), Department of Chemistry and Applied Biosciences
(D-CHAB), ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
- Department
of Chemistry, Technical University of Munich, 85748 Garching, Germany
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15
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Xiao Y, Wu M. Robust and Irreversible Sortase-Mediated Ligation by Empolyment of Sarkosyl. Chemistry 2024; 30:e202401961. [PMID: 39046730 DOI: 10.1002/chem.202401961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/16/2024] [Accepted: 07/24/2024] [Indexed: 07/25/2024]
Abstract
Sortase-mediated ligation (SML) is a widely used method for peptide and protein ligation due to ease of substrate preparation and fast enzymatic kinetics. But there are drawbacks that limit broader applications. Sorting motif in substrates may not be exposed to sortase efficiently due to folding or aggregation. In addition, the ligation is reversible under transpeptidation equilibrium that restricts ligation yield. Here we report a simple but robust method to overcome such limitations. By employment of sarkosyl, the detergent alters substrate conformation to raise sorting motif accessibility for sortase catalysis. Moreover, transpeptidation becomes irreversible presumably by formation of micelle to shield ligation products from sortase. In consequence, excellent yields were achieved from sortase variants with different substrate specificity. Notably, this method is compatible with peptides or proteins capable of forming liquid-liquid phase separation (LLPS), presenting a powerful approach for the conjugation of aggregation-prone substrates. Therefore, we believe the sarkosyl-enhanced SML could be widely applied in peptide and protein chemistry and the unique irreversible transpeptidation mechanism offers an insight to detergent-driven equilibrium.
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Affiliation(s)
- Yihang Xiao
- Department of Chemistry, School of Science Westlake University, Hangzhou, 310030, Zhejiang Province, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, Zhejiang Province, China
| | - Mingxuan Wu
- Department of Chemistry, School of Science Westlake University, Hangzhou, 310030, Zhejiang Province, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang Province, China
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16
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Fröse J, Rowley J, Farid AS, Rakhshandehroo T, Leclerc P, Mak H, Allen H, Moravej H, Munaretto L, Millan-Barea L, Codet E, Glockner H, Jacobson C, Hemann M, Rashidian M. Development of an antigen-based approach to noninvasively image CAR T cells in real time and as a predictive tool. SCIENCE ADVANCES 2024; 10:eadn3816. [PMID: 39292778 PMCID: PMC11409975 DOI: 10.1126/sciadv.adn3816] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 08/12/2024] [Indexed: 09/20/2024]
Abstract
CAR T cell therapy has revolutionized the treatment of a spectrum of blood-related malignancies. However, treatment responses vary among cancer types and patients. Accurate monitoring of CAR T cell dynamics is crucial for understanding and evaluating treatment efficacy. Positron emission tomography (PET) offers a comprehensive view of CAR T cell homing, especially in critical organs such as lymphoid structures and bone marrow. This information will help assess treatment response and predict relapse risk. Current PET imaging methods for CAR T require genetic modifications, limiting clinical use. To overcome this, we developed an antigen-based imaging approach enabling whole-body CAR T cell imaging. The probe detects CAR T cells in vivo without affecting their function. In an immunocompetent B cell leukemia model, CAR-PET signal in the spleen predicted early mortality risk. The antigen-based CAR-PET approach allows assessment of CAR T therapy responses without altering established clinical protocols. It seamlessly integrates with FDA-approved and future CAR T cell generations, facilitating broader clinical application.
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Affiliation(s)
- Julia Fröse
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jennifer Rowley
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02215, USA
| | - Ali Salehi Farid
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Taha Rakhshandehroo
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paul Leclerc
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA 02142, USA
| | - Howard Mak
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA 02142, USA
| | - Harris Allen
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Heydar Moravej
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Leila Munaretto
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Luis Millan-Barea
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA 02142, USA
| | - Elisabeth Codet
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hannah Glockner
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Caron Jacobson
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Michael Hemann
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Mohammad Rashidian
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02215, USA
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02215, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
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17
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Nealy ES, Reed SJ, Adelmund SM, Badeau BA, Shadish JA, Girard EJ, Brasel K, Pakiam FJ, Mhyre AJ, Price JP, Sarkar S, Kalia V, DeForest CA, Olson JM. Versatile tissue-injectable hydrogels capable of the extended hydrolytic release of bioactive protein therapeutics. Bioeng Transl Med 2024; 9:e10668. [PMID: 39553428 PMCID: PMC11561820 DOI: 10.1002/btm2.10668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/25/2024] [Accepted: 03/27/2024] [Indexed: 11/19/2024] Open
Abstract
Hydrogels are extensively employed in healthcare due to their adaptable structures, high water content, and biocompatibility, with FDA-approved applications ranging from spinal cord regeneration to local therapeutic delivery. However, clinical hydrogels encounter challenges related to inconsistent therapeutic exposure, unmodifiable release windows, and difficulties in subsurface polymer insertion. Addressing these issues, we engineered injectable, biocompatible hydrogels as a local therapeutic depot, utilizing poly(ethylene glycol) (PEG)-based hydrogels functionalized with bioorthogonal SPAAC handles for network polymerization and functionalization. Our hydrogel solutions polymerize in situ in a temperature-sensitive manner, persist in tissue, and facilitate the delivery of bioactive therapeutics in subsurface locations. Demonstrating the efficacy of our approach, recombinant anti-CD47 monoclonal antibodies, when incorporated into subsurface-injected hydrogel solutions, exhibited cytotoxic activity against infiltrative high-grade glioma xenografts in the rodent brain. To enhance the gel's versatility, recombinant protein cargos can undergo site-specific modification with hydrolysable "azidoester" adapters, allowing for user-defined release profiles from the hydrogel. Hydrogel-generated gradients of murine CXCL10, linked to intratumorally injected hydrogel solutions via azidoester linkers, resulted in significant recruitment of CD8+ T-cells and the attenuation of tumor growth in a "cold" syngeneic melanoma model. This study highlights a highly customizable, hydrogel-based delivery system for local protein therapeutic administration to meet diverse clinical needs.
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Affiliation(s)
- Eric S. Nealy
- Seattle Children's Research InstituteSeattleWashingtonUSA
- Fred Hutch Cancer CenterSeattleWashingtonUSA
| | - Steven J. Reed
- Seattle Children's Research InstituteSeattleWashingtonUSA
| | - Steven M. Adelmund
- Department of Chemical EngineeringUniversity of WashingtonSeattleWashingtonUSA
| | - Barry A. Badeau
- Department of Chemical EngineeringUniversity of WashingtonSeattleWashingtonUSA
| | - Jared A. Shadish
- Department of Chemical EngineeringUniversity of WashingtonSeattleWashingtonUSA
| | - Emily J. Girard
- Seattle Children's Research InstituteSeattleWashingtonUSA
- Fred Hutch Cancer CenterSeattleWashingtonUSA
| | - Kenneth Brasel
- Seattle Children's Research InstituteSeattleWashingtonUSA
- Fred Hutch Cancer CenterSeattleWashingtonUSA
| | | | - Andrew J. Mhyre
- Seattle Children's Research InstituteSeattleWashingtonUSA
- Fred Hutch Cancer CenterSeattleWashingtonUSA
| | - Jason P. Price
- Seattle Children's Research InstituteSeattleWashingtonUSA
- Fred Hutch Cancer CenterSeattleWashingtonUSA
| | - Surojit Sarkar
- Seattle Children's Research InstituteSeattleWashingtonUSA
- Department of PathologyUniversity of WashingtonSeattleWashingtonUSA
- Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
| | - Vandana Kalia
- Seattle Children's Research InstituteSeattleWashingtonUSA
- Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
| | - Cole A. DeForest
- Department of Chemical EngineeringUniversity of WashingtonSeattleWashingtonUSA
- Department of BioengineeringUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
- Department of ChemistryUniversity of WashingtonSeattleWashingtonUSA
- Institute for Stem Cell and Regenerative Medicine, University of WashingtonSeattleWashingtonUSA
- Institute for Protein Design, University of WashingtonSeattleWashingtonUSA
| | - James M. Olson
- Seattle Children's Research InstituteSeattleWashingtonUSA
- Fred Hutch Cancer CenterSeattleWashingtonUSA
- Department of PharmacologyUniversity of WashingtonSeattleWashingtonUSA
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18
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Amacher JF, Antos JM. Sortases: structure, mechanism, and implications for protein engineering. Trends Biochem Sci 2024; 49:596-610. [PMID: 38692993 DOI: 10.1016/j.tibs.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/22/2024] [Accepted: 04/15/2024] [Indexed: 05/03/2024]
Abstract
Sortase enzymes are critical cysteine transpeptidases on the surface of bacteria that attach proteins to the cell wall and are involved in the construction of bacterial pili. Due to their ability to recognize specific substrates and covalently ligate a range of reaction partners, sortases are widely used in protein engineering applications via sortase-mediated ligation (SML) strategies. In this review, we discuss recent structural studies elucidating key aspects of sortase specificity and the catalytic mechanism. We also highlight select recent applications of SML, including examples where fundamental studies of sortase structure and function have informed the continued development of these enzymes as tools for protein engineering.
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Affiliation(s)
- Jeanine F Amacher
- Department of Chemistry, Western Washington University, Bellingham, WA 98225, USA.
| | - John M Antos
- Department of Chemistry, Western Washington University, Bellingham, WA 98225, USA.
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19
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Patel RS, Pannala NM, Das C. Reading and Writing the Ubiquitin Code Using Genetic Code Expansion. Chembiochem 2024; 25:e202400190. [PMID: 38588469 PMCID: PMC11161312 DOI: 10.1002/cbic.202400190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/10/2024]
Abstract
Deciphering ubiquitin proteoform signaling and its role in disease has been a long-standing challenge in the field. The effects of ubiquitin modifications, its relation to ubiquitin-related machineries, and its signaling output has been particularly limited by its reconstitution and means of characterization. Advances in genetic code expansion have contributed towards addressing these challenges by precision incorporation of unnatural amino acids through site selective codon suppression. This review discusses recent advances in studying the 'writers', 'readers', and 'erasers' of the ubiquitin code using genetic code expansion. Highlighting strategies towards genetically encoded protein ubiquitination, ubiquitin phosphorylation, acylation, and finally surveying ubiquitin interactions, we strive to bring attention to this unique approach towards addressing a widespread proteoform problem.
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Affiliation(s)
- Rishi S Patel
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
| | - Nipuni M Pannala
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
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20
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Braga Emidio N, Cheloha RW. Sortase-mediated labeling: Expanding frontiers in site-specific protein functionalization opens new research avenues. Curr Opin Chem Biol 2024; 80:102443. [PMID: 38503199 PMCID: PMC11164631 DOI: 10.1016/j.cbpa.2024.102443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/21/2024]
Abstract
New applications for biomolecules demand novel approaches for their synthesis and modification. Traditional methods for modifying proteins and cells using non-specific labeling chemistry are insufficiently precise to rigorously interrogate the mechanistic biological and physiological questions at the forefront of biomedical science. Site-specific catalytic modification of proteins promises to meet these challenges. Here, we describe recent applications of the enzyme sortase A in facilitating precise biomolecule labeling. We focus on describing new chemistries to broaden the scope of sortase-mediated labeling (sortagging), the development of new probes for imaging via enzymatic labeling, and the modulation of biological systems using probes and reactions mediated by sortase.
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Affiliation(s)
- Nayara Braga Emidio
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20894, United States
| | - Ross W Cheloha
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20894, United States.
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21
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Frazier CL, Deb D, Weeks AM. Engineered reactivity of a bacterial E1-like enzyme enables ATP-driven modification of protein C termini. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593989. [PMID: 38798401 PMCID: PMC11118369 DOI: 10.1101/2024.05.13.593989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
In biological systems, ATP provides an energetic driving force for peptide bond formation, but protein chemists lack tools that emulate this strategy. Inspired by the eukaryotic ubiquitination cascade, we developed an ATP-driven platform for C-terminal activation and peptide ligation based on E. coli MccB, a bacterial ancestor of ubiquitin-activating (E1) enzymes that natively catalyzes C-terminal phosphoramidate bond formation. We show that MccB can act on non-native substrates to generate an O-AMPylated electrophile that can react with exogenous nucleophiles to form diverse C-terminal functional groups including thioesters, a versatile class of biological intermediates that have been exploited for protein semisynthesis. To direct this activity towards specific proteins of interest, we developed the Thioesterification C-terminal Handle (TeCH)-tag, a sequence that enables high-yield, ATP-driven protein bioconjugation via a thioester intermediate. By mining the natural diversity of the MccB family, we developed two additional MccB/TeCH-tag pairs that are mutually orthogonal to each other and to the E. coli system, facilitating the synthesis of more complex bioconjugates. Our method mimics the chemical logic of peptide bond synthesis that is widespread in biology for high-yield in vitro manipulation of protein structure with molecular precision.
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Affiliation(s)
- Clara L. Frazier
- Department of Biochemistry, University of Wisconsin – Madison, Madison, WI, USA 53706
| | - Debashrito Deb
- Department of Biochemistry, University of Wisconsin – Madison, Madison, WI, USA 53706
| | - Amy M. Weeks
- Department of Biochemistry, University of Wisconsin – Madison, Madison, WI, USA 53706
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
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22
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Machin DC, Williamson DJ, Fisher P, Miller VJ, Arnott ZLP, Stevenson CME, Wildsmith GC, Ross JF, Wasson CW, Macdonald A, Andrews BI, Ungar D, Turnbull WB, Webb ME. Sortase-Modified Cholera Toxoids Show Specific Golgi Localization. Toxins (Basel) 2024; 16:194. [PMID: 38668619 PMCID: PMC11054894 DOI: 10.3390/toxins16040194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/18/2024] [Accepted: 04/09/2024] [Indexed: 04/29/2024] Open
Abstract
Cholera toxoid is an established tool for use in cellular tracing in neuroscience and cell biology. We use a sortase labeling approach to generate site-specific N-terminally modified variants of both the A2-B5 heterohexamer and B5 pentamer forms of the toxoid. Both forms of the toxoid are endocytosed by GM1-positive mammalian cells, and while the heterohexameric toxoid was principally localized in the ER, the B5 pentamer showed an unexpectedly specific localization in the medial/trans-Golgi. This study suggests a future role for specifically labeled cholera toxoids in live-cell imaging beyond their current applications in neuronal tracing and labeling of lipid rafts in fixed cells.
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Affiliation(s)
- Darren C. Machin
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (D.C.M.)
| | - Daniel J. Williamson
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (D.C.M.)
| | - Peter Fisher
- Department of Biology, University of York, York YO10 5DD, UK
| | | | - Zoe L. P. Arnott
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (D.C.M.)
| | - Charlotte M. E. Stevenson
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (D.C.M.)
| | - Gemma C. Wildsmith
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (D.C.M.)
| | - James F. Ross
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (D.C.M.)
| | - Christopher W. Wasson
- Faculty of Biological Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK (A.M.)
| | - Andrew Macdonald
- Faculty of Biological Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK (A.M.)
| | - Benjamin I. Andrews
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Daniel Ungar
- Department of Biology, University of York, York YO10 5DD, UK
| | - W. Bruce Turnbull
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (D.C.M.)
| | - Michael E. Webb
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (D.C.M.)
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23
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Kopyeva I, Goldner EC, Hoye JW, Yang S, Regier MC, Vera KR, Bretherton RC, DeForest CA. Stepwise Stiffening/Softening of and Cell Recovery from Reversibly Formulated Hydrogel Double Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588191. [PMID: 38645065 PMCID: PMC11030224 DOI: 10.1101/2024.04.04.588191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Biomechanical contributions of the ECM underpin cell growth and proliferation, differentiation, signal transduction, and other fate decisions. As such, biomaterials whose mechanics can be spatiotemporally altered - particularly in a reversible manner - are extremely valuable for studying these mechanobiological phenomena. Herein, we introduce a poly(ethylene glycol) (PEG)-based hydrogel model consisting of two interpenetrating step-growth networks that are independently formed via largely orthogonal bioorthogonal chemistries and sequentially degraded with distinct bacterial transpeptidases, affording reversibly tunable stiffness ranges that span healthy and diseased soft tissues (e.g., 500 Pa - 6 kPa) alongside terminal cell recovery for pooled and/or single-cell analysis in a near "biologically invisible" manner. Spatiotemporal control of gelation within the primary supporting network was achieved via mask-based and two-photon lithography; these stiffened patterned regions could be subsequently returned to the original soft state following sortase-based secondary network degradation. Using this approach, we investigated the effects of 4D-triggered network mechanical changes on human mesenchymal stem cell (hMSC) morphology and Hippo signaling, as well as Caco-2 colorectal cancer cell mechanomemory at the global transcriptome level via RNAseq. We expect this platform to be of broad utility for studying and directing mechanobiological phenomena, patterned cell fate, as well as disease resolution in softer matrices.
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Affiliation(s)
- Irina Kopyeva
- Department of Bioengineering, University of Washington, Seattle WA 98105, USA
| | - Ethan C. Goldner
- Department of Chemical Engineering, University of Washington, Seattle WA 98105, USA
| | - Jack W. Hoye
- Department of Chemical Engineering, University of Washington, Seattle WA 98105, USA
| | - Shiyu Yang
- Department of Chemical Engineering, University of Washington, Seattle WA 98105, USA
| | - Mary C. Regier
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle WA 98105, USA
| | - Kaitlyn R. Vera
- Department of Chemical Engineering, University of Washington, Seattle WA 98105, USA
| | - Ross C. Bretherton
- Department of Bioengineering, University of Washington, Seattle WA 98105, USA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle WA 98105, USA
| | - Cole A. DeForest
- Department of Bioengineering, University of Washington, Seattle WA 98105, USA
- Department of Chemical Engineering, University of Washington, Seattle WA 98105, USA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle WA 98105, USA
- Department of Chemistry, University of Washington, Seattle WA 98105, USA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle WA 98105, USA
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24
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Raniszewski NR, Beyer JN, Noel MI, Burslem GM. Sortase mediated protein ubiquitination with defined chain length and topology. RSC Chem Biol 2024; 5:321-327. [PMID: 38576722 PMCID: PMC10989510 DOI: 10.1039/d3cb00229b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/01/2024] [Indexed: 04/06/2024] Open
Abstract
Ubiquitination is a key post-translational modification on protein lysine sidechains known to impact protein stability, signal transduction cascades, protein-protein interactions, and beyond. Great strides have been made towards developing new methods to generate discrete chains of polyubiquitin and conjugate them onto proteins site-specifically, with methods ranging from chemical synthetic approaches, to enzymatic approaches and many in between. Previous work has demonstrated the utility of engineered variants of the bacterial transpeptidase enzyme sortase (SrtA) for conjugation of ubiquitin site-specifically onto target proteins. In this manuscript, we've combined the classical E1/E2-mediated polyubiquitin chain extension approach with sortase-mediated ligation and click chemistry to enable the generation of mono, di, and triubiquitinated proteins sfGFP and PCNA. We demonstrate the utility of this strategy to generate both K48-linked and K63-linked polyubiquitins and attach them both N-terminally and site-specifically to the proteins of interest. Further, we highlight differential activity between two commonly employed sortase variants, SrtA 5M and 7M, and demonstrate that while SrtA 7M can be used to conjugate these ubiquitins to substrates, SrtA 5M can be employed to release the ubiquitin from the substrates as well as to cleave C-terminal tags from the ubiquitin variants used. Overall, we envision that this approach is broadly applicable to readily generate discrete polyubiquitin chains of any linkage type that is accessible via E1/E2 systems and conjugate site-specifically onto proteins of interest, thus granting access to bespoke ubiquitinated proteins that are not currently possible.
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Affiliation(s)
- Nicole R Raniszewski
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania PA 19104 USA
| | - Jenna N Beyer
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania PA 19104 USA
| | - Myles I Noel
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania PA 19104 USA
| | - George M Burslem
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania PA 19104 USA
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25
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Zou Z, Ji Y, Schwaneberg U. Empowering Site-Specific Bioconjugations In Vitro and In Vivo: Advances in Sortase Engineering and Sortase-Mediated Ligation. Angew Chem Int Ed Engl 2024; 63:e202310910. [PMID: 38081121 DOI: 10.1002/anie.202310910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Indexed: 12/23/2023]
Abstract
Sortase-mediated ligation (SML) has emerged as a powerful and versatile methodology for site-specific protein conjugation, functionalization/labeling, immobilization, and design of biohybrid molecules and systems. However, the broader application of SML faces several challenges, such as limited activity and stability, dependence on calcium ions, and reversible reactions caused by nucleophilic side-products. Over the past decade, protein engineering campaigns and particularly directed evolution, have been extensively employed to overcome sortase limitations, thereby expanding the potential application of SML in multiple directions, including therapeutics, biorthogonal chemistry, biomaterials, and biosensors. This review provides an overview of achieved advancements in sortase engineering and highlights recent progress in utilizing SML in combination with other state-of-the-art chemical and biological methodologies. The aim is to encourage scientists to employ sortases in their conjugation experiments.
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Affiliation(s)
- Zhi Zou
- DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstraβe 50, 52074, Aachen, Germany
- RWTH Aachen University, Institute of Biotechnology, Worringerweg 3, 52074, Aachen, Germany
| | - Yu Ji
- RWTH Aachen University, Institute of Biotechnology, Worringerweg 3, 52074, Aachen, Germany
| | - Ulrich Schwaneberg
- DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstraβe 50, 52074, Aachen, Germany
- RWTH Aachen University, Institute of Biotechnology, Worringerweg 3, 52074, Aachen, Germany
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26
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Fallahee I, Hawiger D. Episomal Vectors for Stable Production of Recombinant Proteins and Engineered Antibodies. Antibodies (Basel) 2024; 13:18. [PMID: 38534208 PMCID: PMC10967652 DOI: 10.3390/antib13010018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/27/2024] [Accepted: 03/04/2024] [Indexed: 03/28/2024] Open
Abstract
There is tremendous interest in the production of recombinant proteins, particularly bispecific antibodies and antibody-drug conjugates for research and therapeutic use. Here, we demonstrate a highly versatile plasmid system that allows the rapid generation of stable Expi293 cell pools by episomal retention of transfected DNA. By linking protein expression to puromycin resistance through an attenuated internal ribosome entry site, we achieve stable cell pools producing proteins of interest. In addition, split intein-split puromycin-mediated selection of two separate protein expression cassettes allows the stable production of bispecific antibody-like molecules or antibodies with distinct C-terminal heavy chain modifications, such as an antigen on one chain and a sortase tag on the other chain. We also use this novel expression system to generate stable Expi293 cell pools that secrete sortase A Δ59 variant Srt4M. Using these reagents, we prepared a site-specific drug-to-antibody ratio of 1 antibody-siRNA conjugate. We anticipate the simple, robust, and rapid stable protein expression systems described here being useful for a wide variety of applications.
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Affiliation(s)
| | - Daniel Hawiger
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
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27
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Martinusen SG, Denard CA. Leveraging yeast sequestration to study and engineer posttranslational modification enzymes. Biotechnol Bioeng 2024; 121:903-914. [PMID: 38079116 PMCID: PMC11229454 DOI: 10.1002/bit.28621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 11/04/2023] [Accepted: 11/27/2023] [Indexed: 02/20/2024]
Abstract
Enzymes that catalyze posttranslational modifications (PTMs) of peptides and proteins (PTM-enzymes)-proteases, protein ligases, oxidoreductases, kinases, and other transferases-are foundational to our understanding of health and disease and empower applications in chemical biology, synthetic biology, and biomedicine. To fully harness the potential of PTM-enzymes, there is a critical need to decipher their enzymatic and biological mechanisms, develop molecules that can probe and modulate them, and endow them with improved and novel functions. These objectives are contingent upon implementation of high-throughput functional screens and selections that interrogate large sequence libraries to isolate desired PTM-enzyme properties. This review discusses the principles of Saccharomyces cerevisiae organelle sequestration to study and engineer PTM-enzymes. These include outer membrane sequestration, specifically methods that modify yeast surface display, and cytoplasmic sequestration based on enzyme-mediated transcription activation. Furthermore, we present a detailed discussion of yeast endoplasmic reticulum sequestration for the first time. Where appropriate, we highlight the major features and limitations of different systems, specifically how they can measure and control enzyme catalytic efficiencies. Taken together, yeast-based high-throughput sequestration approaches significantly lower the barrier to understanding how PTM-enzymes function and how to reprogram them.
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Affiliation(s)
- Samantha G Martinusen
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Carl A Denard
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
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28
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Nakandakari-Higa S, Walker S, Canesso MCC, van der Heide V, Chudnovskiy A, Kim DY, Jacobsen JT, Parsa R, Bilanovic J, Parigi SM, Fiedorczuk K, Fuchs E, Bilate AM, Pasqual G, Mucida D, Kamphorst AO, Pritykin Y, Victora GD. Universal recording of immune cell interactions in vivo. Nature 2024; 627:399-406. [PMID: 38448581 PMCID: PMC11078586 DOI: 10.1038/s41586-024-07134-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024]
Abstract
Immune cells rely on transient physical interactions with other immune and non-immune populations to regulate their function1. To study these 'kiss-and-run' interactions directly in vivo, we previously developed LIPSTIC (labelling immune partnerships by SorTagging intercellular contacts)2, an approach that uses enzymatic transfer of a labelled substrate between the molecular partners CD40L and CD40 to label interacting cells. Reliance on this pathway limited the use of LIPSTIC to measuring interactions between CD4+ T helper cells and antigen-presenting cells, however. Here we report the development of a universal version of LIPSTIC (uLIPSTIC), which can record physical interactions both among immune cells and between immune and non-immune populations irrespective of the receptors and ligands involved. We show that uLIPSTIC can be used, among other things, to monitor the priming of CD8+ T cells by dendritic cells, reveal the steady-state cellular partners of regulatory T cells and identify germinal centre-resident T follicular helper cells on the basis of their ability to interact cognately with germinal centre B cells. By coupling uLIPSTIC with single-cell transcriptomics, we build a catalogue of the immune populations that physically interact with intestinal epithelial cells at the steady state and profile the evolution of the interactome of lymphocytic choriomeningitis virus-specific CD8+ T cells in multiple organs following systemic infection. Thus, uLIPSTIC provides a broadly useful technology for measuring and understanding cell-cell interactions across multiple biological systems.
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Affiliation(s)
| | - Sarah Walker
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Quantitative and Computational Biology, Princeton University, Princeton, NJ, USA
| | - Maria C C Canesso
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Verena van der Heide
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aleksey Chudnovskiy
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Dong-Yoon Kim
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Johanne T Jacobsen
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
- Institute for Immunology and Transfusion Medicine, Rikshospitalet, University of Oslo, Oslo, Norway
| | - Roham Parsa
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Jana Bilanovic
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - S Martina Parigi
- Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Karol Fiedorczuk
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Elaine Fuchs
- Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Angelina M Bilate
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Giulia Pasqual
- Laboratory of Synthetic Immunology, Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Alice O Kamphorst
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuri Pritykin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Computer Science, Princeton University, Princeton, NJ, USA.
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA.
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29
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Arnott ZLP, Morgan HE, Hollingsworth K, Stevenson CME, Collins LJ, Tamasanu A, Machin DC, Dolan JP, Kamiński TP, Wildsmith GC, Williamson DJ, Pickles IB, Warriner SL, Turnbull WB, Webb ME. Quantitative N- or C-Terminal Labelling of Proteins with Unactivated Peptides by Use of Sortases and a d-Aminopeptidase. Angew Chem Int Ed Engl 2024; 63:e202310862. [PMID: 38072831 DOI: 10.1002/anie.202310862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 01/13/2024]
Abstract
Quantitative and selective labelling of proteins is widely used in both academic and industrial laboratories, and catalytic labelling of proteins using transpeptidases, such as sortases, has proved to be a popular strategy for such selective modification. A major challenge for this class of enzymes is that the majority of procedures require an excess of the labelling reagent or, alternatively, activated substrates rather than simple commercially sourced peptides. We report the use of a coupled enzyme strategy which enables quantitative N- and C-terminal labelling of proteins using unactivated labelling peptides. The use of an aminopeptidase in conjunction with a transpeptidase allows sequence-specific degradation of the peptide by-product, shifting the equilibrium to favor product formation, which greatly enhances the reaction efficiency. Subsequent optimisation of the reaction allows N-terminal labelling of proteins using essentially equimolar ratios of peptide label to protein and C-terminal labelling with only a small excess. Minimizing the amount of substrate required for quantitative labelling has the potential to improve industrial processes and facilitate the use of transpeptidation as a method for protein labelling.
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Affiliation(s)
- Zoe L P Arnott
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- Present address: Centre for Process Innovation, Central Park, The Nigel Perry Building, 1 Union St, Darlington, DL1 1GL, United Kingdom
| | - Holly E Morgan
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- Present Address: Ashfield MedComms, City Tower, Piccadilly Plaza, Manchester, M1 4BT, United Kingdom
| | - Kristian Hollingsworth
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Charlotte M E Stevenson
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Lawrence J Collins
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Alexandra Tamasanu
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Darren C Machin
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Jonathan P Dolan
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- Present Address: School of Chemical and Physical Sciences & Centre for Glycoscience Research and Training, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom
| | - Tomasz P Kamiński
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Gemma C Wildsmith
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Daniel J Williamson
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- Present Address: Iksuda Therapeutics, The Biosphere, Draymans Way, Newcastle upon Tyne, NE4 5BX, United Kingdom
| | - Isabelle B Pickles
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- Present Address: York Structural Biology Laboratory, Department of Biology, University of York, Heslington, York, YO10 5DD, United Kingdom
| | - Stuart L Warriner
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - W Bruce Turnbull
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Michael E Webb
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
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30
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Fallahee I, Hawiger D. EPISOMAL VECTORS FOR STABLE PRODUCTION OF RECOMBINANT PROTEINS AND ENGINEERED ANTIBODIES. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.574076. [PMID: 38260603 PMCID: PMC10802304 DOI: 10.1101/2024.01.03.574076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
There is tremendous interest in the production of recombinant proteins, particularly bispecific antibodies and antibody-drug conjugates for research and therapeutic use. Here, we demonstrate a highly versatile plasmid system that allows rapid generation of stable Expi293 cell pools by episomal retention of transfected DNA. By linking protein expression to puromycin resistance though an attenuated internal ribosome entry site, we achieve stable cell pools producing proteins of interest. In addition, split intein-split puromycin-mediated selection of two separate protein expression cassettes allows the stable production of bispecific antibody-like molecules or antibodies with distinct C-terminal heavy chain modifications, such as an antigen on one chain and a sortase tag on the other chain. We also use this novel expression system to generate stable Expi293 cell pools that secrete sortase A Δ59 variant Srt4M. Using these reagents, we prepared a site-specific drug-to-antibody ratio of 1 antibody-siRNA conjugate. We anticipate the simple, robust, and rapid stable protein expression systems described here being useful for a wide variety of applications.
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31
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Vilen Z, Joeh E, Lee E, Huang ML. Surfaceome Profiling Identifies Basigin-Chaperoned Protein Clients. Chembiochem 2023; 24:e202300073. [PMID: 36973167 PMCID: PMC10424708 DOI: 10.1002/cbic.202300073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/21/2023] [Accepted: 03/25/2023] [Indexed: 03/29/2023]
Abstract
The surface proteome or "surfaceome" is a critical mediator of cellular biology, facilitating cell-to-cell interactions and communication with extracellular biomolecules. Constituents of the surfaceome can serve as biomarkers for changing cell states and as targets for pharmacological intervention. While some pathways of cell surface trafficking are well characterized to allow prediction of surface localization, some non-canonical trafficking mechanisms do not. Basigin (Bsg), a cell surface glycoprotein, has been shown to chaperone protein clients to the cell surface. However, understanding which proteins are served by Bsg is not always straightforward. To accelerate such identification, we applied a surfaceome proximity labeling method that is integrated with quantitative mass spectrometry-based proteomics to discern changes in the surfaceome of hepatic stellate cells that occur in response to the genetic loss of Bsg. Using this strategy, we observed that the loss of Bsg leads to corresponding reductions in the cell surface expression of monocarboxylate transporters MCT1 and MCT4. We also found that these relationships were unique to Bsg and not found in neuroplastin (Nptn), a related family member. These results establish the utility of the surfaceome proximity labeling method to determine clients of cell surface chaperone proteins.
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Affiliation(s)
- Zak Vilen
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- Department of Molecular Medicine, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Eugene Joeh
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- Department of Molecular Medicine, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Elizabeth Lee
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- Department of Molecular Medicine, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Mia L. Huang
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- Department of Molecular Medicine, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
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32
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Ebberink E, Fernandes S, Hatzopoulos G, Agashe N, Chang PH, Guidotti N, Reichart TM, Reymond L, Velluz MC, Schneider F, Pourroy C, Janke C, Gönczy P, Fierz B, Aumeier C. Tubulin engineering by semi-synthesis reveals that polyglutamylation directs detyrosination. Nat Chem 2023:10.1038/s41557-023-01228-8. [PMID: 37386282 DOI: 10.1038/s41557-023-01228-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 04/28/2023] [Indexed: 07/01/2023]
Abstract
Microtubules, a critical component of the cytoskeleton, carry post-translational modifications (PTMs) that are important for the regulation of key cellular processes. Long-lived microtubules, in neurons particularly, exhibit both detyrosination of α-tubulin and polyglutamylation. Dysregulation of these PTMs can result in developmental defects and neurodegeneration. Owing to a lack of tools to study the regulation and function of these PTMs, the mechanisms that govern such PTM patterns are not well understood. Here we produce fully functional tubulin carrying precisely defined PTMs within its C-terminal tail. We ligate synthetic α-tubulin tails-which are site-specifically glutamylated-to recombinant human tubulin heterodimers by applying a sortase- and intein-mediated tandem transamidation strategy. Using microtubules reconstituted with these designer tubulins, we find that α-tubulin polyglutamylation promotes its detyrosination by enhancing the activity of the tubulin tyrosine carboxypeptidase vasohibin/small vasohibin-binding protein in a manner dependent on the length of polyglutamyl chains. We also find that modulating polyglutamylation levels in cells results in corresponding changes in detyrosination, corroborating the link between the detyrosination cycle to polyglutamylation.
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Affiliation(s)
- Eduard Ebberink
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland
| | - Simon Fernandes
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Georgios Hatzopoulos
- Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland
| | - Ninad Agashe
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland
| | - Po-Han Chang
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland
| | - Nora Guidotti
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland
| | - Timothy M Reichart
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland
| | - Luc Reymond
- Biomolecular Screening Facility, EPFL, Lausanne, Switzerland
| | | | - Fabian Schneider
- Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland
| | - Cédric Pourroy
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland
| | - Carsten Janke
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France
- Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland
| | - Beat Fierz
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland.
| | - Charlotte Aumeier
- Department of Biochemistry, University of Geneva, Geneva, Switzerland.
- National Center for Competence in Research Chemical Biology, University of Geneva, Geneva, Switzerland.
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33
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Debon A, Siirola E, Snajdrova R. Enzymatic Bioconjugation: A Perspective from the Pharmaceutical Industry. JACS AU 2023; 3:1267-1283. [PMID: 37234110 PMCID: PMC10207132 DOI: 10.1021/jacsau.2c00617] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 05/27/2023]
Abstract
Enzymes have firmly established themselves as bespoke catalysts for small molecule transformations in the pharmaceutical industry, from early research and development stages to large-scale production. In principle, their exquisite selectivity and rate acceleration can also be leveraged for modifying macromolecules to form bioconjugates. However, available catalysts face stiff competition from other bioorthogonal chemistries. In this Perspective, we seek to illuminate applications of enzymatic bioconjugation in the face of an expanding palette of new drug modalities. With these applications, we wish to highlight some examples of current successes and pitfalls of using enzymes for bioconjugation along the pipeline and try to illustrate opportunities for further development.
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Affiliation(s)
- Aaron Debon
- Global
Discovery Chemistry, Novartis Institute
for Biomedical Research, Basel 4108, Switzerland
| | - Elina Siirola
- Global
Discovery Chemistry, Novartis Institute
for Biomedical Research, Basel 4108, Switzerland
| | - Radka Snajdrova
- Global
Discovery Chemistry, Novartis Institute
for Biomedical Research, Basel 4108, Switzerland
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34
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Obeng EM, Fulcher AJ, Wagstaff KM. Harnessing sortase A transpeptidation for advanced targeted therapeutics and vaccine engineering. Biotechnol Adv 2023; 64:108108. [PMID: 36740026 DOI: 10.1016/j.biotechadv.2023.108108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
The engineering of potent prophylactic and therapeutic complexes has always required careful protein modification techniques with seamless capabilities. In this light, methods that favor unobstructed multivalent targeting and correct antigen presentations remain essential and very demanding. Sortase A (SrtA) transpeptidation has exhibited these attributes in various settings over the years. However, its applications for engineering avidity-inspired therapeutics and potent vaccines have yet to be significantly noticed, especially in this era where active targeting and multivalent nanomedications are in great demand. This review briefly presents the SrtA enzyme and its associated transpeptidation activity and describes interesting sortase-mediated protein engineering and chemistry approaches for achieving multivalent therapeutic and antigenic responses. The review further highlights advanced applications in targeted delivery systems, multivalent therapeutics, adoptive cellular therapy, and vaccine engineering. These innovations show the potential of sortase-mediated techniques in facilitating the development of simple plug-and-play nanomedicine technologies against recalcitrant diseases and pandemics such as cancer and viral infections.
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Affiliation(s)
- Eugene M Obeng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
| | - Alex J Fulcher
- Monash Micro Imaging, Monash University, Clayton, VIC 3800, Australia
| | - Kylie M Wagstaff
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
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35
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Bretherton RC, Haack AJ, Kopyeva I, Rahman F, Kern JD, Bugg D, Theberge AB, Davis J, DeForest CA. User-Controlled 4D Biomaterial Degradation with Substrate-Selective Sortase Transpeptidases for Single-Cell Biology. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2209904. [PMID: 36808641 PMCID: PMC10175157 DOI: 10.1002/adma.202209904] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/08/2023] [Indexed: 05/12/2023]
Abstract
Stimuli-responsive biomaterials show great promise for modeling disease dynamics ex vivo with spatiotemporal control over the cellular microenvironment. However, harvesting cells from such materials for downstream analysis without perturbing their state remains an outstanding challenge in 3/4-dimensional (3D/4D) culture and tissue engineering. In this manuscript, a fully enzymatic strategy for hydrogel degradation that affords spatiotemporal control over cell release while maintaining cytocompatibility is introduced. Exploiting engineered variants of the sortase transpeptidase evolved to recognize and selectively cleave distinct peptide sequences largely absent from the mammalian proteome, many limitations implicit to state-of-the-art methods to liberate cells from gels are sidestepped. It is demonstrated that evolved sortase exposure has minimal impact on the global transcriptome of primary mammalian cells and that proteolytic cleavage proceeds with high specificity; incorporation of substrate sequences within hydrogel crosslinkers permits rapid and selective cell recovery with high viability. In composite multimaterial hydrogels, it is shown that sequential degradation of hydrogel layers enables highly specific retrieval of single-cell suspensions for phenotypic analysis. It is expected that the high bioorthogonality and substrate selectivity of the evolved sortases will lead to their broad adoption as an enzymatic material dissociation cue and that their multiplexed use will enable newfound studies in 4D cell culture.
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Affiliation(s)
- Ross C Bretherton
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
| | - Amanda J Haack
- Department of Chemistry, University of Washington, Seattle, WA, 98105, USA
| | - Irina Kopyeva
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Fariha Rahman
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Jonah D Kern
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Darrian Bugg
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, 98109, USA
| | | | - Jennifer Davis
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, 98109, USA
| | - Cole A DeForest
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Department of Chemistry, University of Washington, Seattle, WA, 98105, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98105, USA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98109, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98105, USA
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36
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Nakandakari-Higa S, Canesso MCC, Walker S, Chudnovskiy A, Jacobsen JT, Bilanovic J, Parigi SM, Fiedorczuk K, Fuchs E, Bilate AM, Pasqual G, Mucida D, Pritykin Y, Victora GD. Universal recording of cell-cell contacts in vivo for interaction-based transcriptomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.533003. [PMID: 36993443 PMCID: PMC10055214 DOI: 10.1101/2023.03.16.533003] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Cellular interactions are essential for tissue organization and functionality. In particular, immune cells rely on direct and usually transient interactions with other immune and non-immune populations to specify and regulate their function. To study these "kiss-and-run" interactions directly in vivo, we previously developed LIPSTIC (Labeling Immune Partnerships by SorTagging Intercellular Contacts), an approach that uses enzymatic transfer of a labeled substrate between the molecular partners CD40L and CD40 to label interacting cells. Reliance on this pathway limited the use of LIPSTIC to measuring interactions between CD4+ helper T cells and antigen presenting cells, however. Here, we report the development of a universal version of LIPSTIC (uLIPSTIC), which can record physical interactions both among immune cells and between immune and non-immune populations irrespective of the receptors and ligands involved. We show that uLIPSTIC can be used, among other things, to monitor the priming of CD8+ T cells by dendritic cells, reveal the cellular partners of regulatory T cells in steady state, and identify germinal center (GC)-resident T follicular helper (Tfh) cells based on their ability to interact cognately with GC B cells. By coupling uLIPSTIC with single-cell transcriptomics, we build a catalog of the immune populations that physically interact with intestinal epithelial cells (IECs) and find evidence of stepwise acquisition of the ability to interact with IECs as CD4+ T cells adapt to residence in the intestinal tissue. Thus, uLIPSTIC provides a broadly useful technology for measuring and understanding cell-cell interactions across multiple biological systems.
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Affiliation(s)
| | - Maria C C Canesso
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Sarah Walker
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Quantitative and Computational Biology Graduate Program, Princeton University, Princeton, NJ, USA
| | - Aleksey Chudnovskiy
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Johanne T Jacobsen
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Jana Bilanovic
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - S Martina Parigi
- Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Karol Fiedorczuk
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Elaine Fuchs
- Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Angelina M Bilate
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Giulia Pasqual
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Yuri Pritykin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
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37
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Abstract
The ability to manipulate the chemical composition of proteins and peptides has been central to the development of improved polypeptide-based therapeutics and has enabled researchers to address fundamental biological questions that would otherwise be out of reach. Protein ligation, in which two or more polypeptides are covalently linked, is a powerful strategy for generating semisynthetic products and for controlling polypeptide topology. However, specialized tools are required to efficiently forge a peptide bond in a chemoselective manner with fast kinetics and high yield. Fortunately, nature has addressed this challenge by evolving enzymatic mechanisms that can join polypeptides using a diverse set of chemical reactions. Here, we summarize how such nature-inspired protein ligation strategies have been repurposed as chemical biology tools that afford enhanced control over polypeptide composition.
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Affiliation(s)
- Rasmus Pihl
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA.
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, USA.
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
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38
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Wee LM, Tong AB, Florez Ariza AJ, Cañari-Chumpitaz C, Grob P, Nogales E, Bustamante CJ. A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery. Cell 2023; 186:1244-1262.e34. [PMID: 36931247 PMCID: PMC10135430 DOI: 10.1016/j.cell.2023.02.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 03/18/2023]
Abstract
In prokaryotes, translation can occur on mRNA that is being transcribed in a process called coupling. How the ribosome affects the RNA polymerase (RNAP) during coupling is not well understood. Here, we reconstituted the E. coli coupling system and demonstrated that the ribosome can prevent pausing and termination of RNAP and double the overall transcription rate at the expense of fidelity. Moreover, we monitored single RNAPs coupled to ribosomes and show that coupling increases the pause-free velocity of the polymerase and that a mechanical assisting force is sufficient to explain the majority of the effects of coupling. Also, by cryo-EM, we observed that RNAPs with a terminal mismatch adopt a backtracked conformation, while a coupled ribosome allosterically induces these polymerases toward a catalytically active anti-swiveled state. Finally, we demonstrate that prolonged RNAP pausing is detrimental to cell viability, which could be prevented by polymerase reactivation through a coupled ribosome.
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Affiliation(s)
- Liang Meng Wee
- QB3-Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Alexander B Tong
- QB3-Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Alfredo Jose Florez Ariza
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - Cristhian Cañari-Chumpitaz
- QB3-Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Patricia Grob
- QB3-Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Eva Nogales
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Carlos J Bustamante
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Department of Physics, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Kavli Energy Nanoscience Institute, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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39
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Dunleavy R, Chandrasekaran S, Crane BR. Enzymatic Spin-Labeling of Protein N- and C-Termini for Electron Paramagnetic Resonance Spectroscopy. Bioconjug Chem 2023:10.1021/acs.bioconjchem.3c00029. [PMID: 36921260 PMCID: PMC10502183 DOI: 10.1021/acs.bioconjchem.3c00029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for investigating the structure and dynamics of proteins. The introduction of paramagnetic moieties at specific positions in a protein enables precise measurement of local structure and dynamics. This technique, termed site-directed spin-labeling, has traditionally been performed using cysteine-reactive radical-containing probes. However, large proteins are more likely to contain multiple cysteine residues and cysteine labeling at specific sites may be infeasible or impede function. To address this concern, we applied three peptide-ligating enzymes (sortase, asparaginyl endopeptidase, and inteins) for nitroxide labeling of N- and C-termini of select monomeric and dimeric proteins. Continuous wave and pulsed EPR (double electron electron resonance) experiments reveal specific attachment of nitroxide probes to ether N-termini (OaAEP1) or C-termini (sortase and intein) across three test proteins (CheY, CheA, and iLOV), thereby enabling a straightforward, highly specific, and general method for protein labeling. Importantly, the linker length (3, 5, and 9 residues for OaAEP1, intein, and sortase reactions, respectively) between the probe and the target protein has a large impact on the utility of distance measurements by pulsed EPR, with longer linkers leading to broader distributions. As these methods are only dependent on accessible N- and C-termini, we anticipate application to a wide range of protein targets for biomolecular EPR spectroscopy.
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Affiliation(s)
- Robert Dunleavy
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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40
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Morgan H, Arnott ZLP, Kamiński TP, Turnbull WB, Webb ME. Combined Application of Orthogonal Sortases and Depsipeptide Substrates for Dual Protein Labeling. Bioconjug Chem 2022; 33:2341-2347. [PMID: 36356167 PMCID: PMC9782347 DOI: 10.1021/acs.bioconjchem.2c00411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Staphylococcus aureus sortase A is a transpeptidase that has been extensively exploited for site-specific modification of proteins and was originally used to attach a labeling reagent containing an LPXTG recognition sequence to a protein or peptide with an N-terminal glycine. Sortase mutants with other recognition sequences have also been reported, but in all cases, the reversibility of the transpeptidation reaction limits the efficiency of sortase-mediated labeling reactions. For the wildtype sortase, depsipeptide substrates, in which the scissile peptide bond is replaced with an ester, allow effectively irreversible sortase-mediated labeling as the alcohol byproduct is a poor competing nucleophile. In this paper, the use of depsipeptide substrates for evolved sortase variants is reported. Substrate specificities of three sortases have been investigated allowing identification of an orthogonal pair of enzymes accepting LPEToG and LPESoG depsipeptides, which have been applied to dual N-terminal labeling of a model protein mutant containing a second, latent N-terminal glycine residue. The method provides an efficient orthogonal site-specific labeling technique that further expands the biochemical protein labeling toolkit.
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41
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Britton BM, London JA, Martin-Lopez J, Jones ND, Liu J, Lee JB, Fishel R. Exploiting the distinctive properties of the bacterial and human MutS homolog sliding clamps on mismatched DNA. J Biol Chem 2022; 298:102505. [PMID: 36126773 PMCID: PMC9597889 DOI: 10.1016/j.jbc.2022.102505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 12/30/2022] Open
Abstract
MutS homologs (MSHs) are highly conserved core components of DNA mismatch repair. Mismatch recognition provokes ATP-binding by MSH proteins that drives a conformational transition from a short-lived lesion-searching clamp to an extremely stable sliding clamp on the DNA. Here, we have expanded on previous bulk biochemical studies to examine the stability, lifetime, and kinetics of bacterial and human MSH sliding clamps on mismatched DNA using surface plasmon resonance and single-molecule analysis of fluorescently labeled proteins. We found that ATP-bound MSH complexes bound to blocked-end or very long mismatched DNAs were extremely stable over a range of ionic conditions. These observations underpinned the development of a high-throughput Förster resonance energy transfer system that specifically detects the formation of MSH sliding clamps on mismatched DNA. The Förster resonance energy transfer system is capable of distinguishing between HsMSH2-HsMSH3 and HsMSH2-HsMSH6 and appears suitable for chemical inhibitor screens. Taken together, our results provide additional insight into MSH sliding clamps as well as methods to distinguish their functions in mismatch repair.
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Affiliation(s)
- Brooke M Britton
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - James A London
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Juana Martin-Lopez
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Nathan D Jones
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Jiaquan Liu
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Korea; Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Korea
| | - Richard Fishel
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA.
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42
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Structures of Streptococcus pyogenes Class A sortase in complex with substrate and product mimics provide key details of target recognition. J Biol Chem 2022; 298:102446. [PMID: 36055407 PMCID: PMC9520033 DOI: 10.1016/j.jbc.2022.102446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 12/02/2022] Open
Abstract
The cell wall is a critical extracellular barrier for bacteria and many other organisms. In bacteria, this structural layer consists of peptidoglycan, which maintains cell shape and structural integrity and provides a scaffold for displaying various protein factors. To attach proteins to the cell wall, Gram-positive bacteria utilize sortase enzymes, which are cysteine transpeptidases that recognize and cleave a specific sorting signal, followed by ligation of the sorting signal–containing protein to the peptidoglycan precursor lipid II (LII). This mechanism is the subject of considerable interest as a target for therapeutic intervention and as a tool for protein engineering, where sortases have enabled sortase-mediated ligation or sortagging strategies. Despite these uses, there remains an incomplete understanding of the stereochemistry of substrate recognition and ligation product formation. Here, we solved the first structures of sortase A from Streptococcus pyogenes bound to two substrate sequences, LPATA and LPATS. In addition, we synthesized a mimetic of the product of sortase-mediated ligation involving LII (LPAT-LII) and solved the complex structure in two ligand conformations. These structures were further used as the basis for molecular dynamics simulations to probe sortase A-ligand dynamics and to construct a model of the acyl–enzyme intermediate, thus providing a structural view of multiple key states in the catalytic mechanism. Overall, this structural information provides new insights into the recognition of the sortase substrate motif and LII ligation partner and will support the continued development of sortases for protein engineering applications.
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43
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Assignment of structural transitions during mechanical unwrapping of nucleosomes and their disassembly products. Proc Natl Acad Sci U S A 2022; 119:e2206513119. [PMID: 35939666 PMCID: PMC9388122 DOI: 10.1073/pnas.2206513119] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Nucleosomes, the fundamental structural unit of chromatin, consists of ∼147 DNA base pairs wrapped around a histone protein octamer. To characterize the strength of the nucleosomal barrier and its contribution as a mechanism of control of gene expression, it is essential to determine the forces required to unwrap the DNA from the core particle and the stepwise transitions involved. In this study, we performed combined optical tweezers and single-molecule fluorescence measurements to identify the specific DNA segments unwrapped during the force transitions observed in mechanical stretching of nucleosomes. Furthermore, we characterize the mechanical signatures of subnucleosomal hexasomes and tetrasomes. The characterization performed in this work is essential for the interpretation of ongoing studies of chromatin remodelers, polymerases, and histone chaperones. Nucleosome DNA unwrapping and its disassembly into hexasomes and tetrasomes is necessary for genomic access and plays an important role in transcription regulation. Previous single-molecule mechanical nucleosome unwrapping revealed a low- and a high-force transitions, and force-FRET pulling experiments showed that DNA unwrapping is asymmetric, occurring always first from one side before the other. However, the assignment of DNA segments involved in these transitions remains controversial. Here, using high-resolution optical tweezers with simultaneous single-molecule FRET detection, we show that the low-force transition corresponds to the undoing of the outer wrap of one side of the nucleosome (∼27 bp), a process that can occur either cooperatively or noncooperatively, whereas the high-force transition corresponds to the simultaneous unwrapping of ∼76 bp from both sides. This process may give rise stochastically to the disassembly of nucleosomes into hexasomes and tetrasomes whose unwrapping/rewrapping trajectories we establish. In contrast, nucleosome rewrapping does not exhibit asymmetry. To rationalize all previous nucleosome unwrapping experiments, it is necessary to invoke that mechanical unwrapping involves two nucleosome reorientations: one that contributes to the change in extension at the low-force transition and another that coincides but does not contribute to the high-force transition.
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44
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Fottner M, Heimgärtner J, Gantz M, Mühlhofer R, Nast-Kolb T, Lang K. Site-Specific Protein Labeling and Generation of Defined Ubiquitin-Protein Conjugates Using an Asparaginyl Endopeptidase. J Am Chem Soc 2022; 144:13118-13126. [PMID: 35850488 PMCID: PMC9335880 DOI: 10.1021/jacs.2c02191] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
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Asparaginyl endopeptidases
(AEPs) have recently been widely utilized
for peptide and protein modification. Labeling is however restricted
to protein termini, severely limiting flexibility and scope in creating
diverse conjugates as needed for therapeutic and diagnostic applications.
Here, we use genetic code expansion to site-specifically modify target
proteins with an isopeptide-linked glycylglycine moiety that serves
as an acceptor nucleophile in AEP-mediated transpeptidation with various
probes containing a tripeptidic recognition motif. Our approach allows
simple and flexible labeling of recombinant proteins at any internal
site and leaves a minimal, entirely peptidic footprint (NGG) in the
conjugation product. We show site-specific labeling of diverse target
proteins with various biophysical probes, including dual labeling
at an internal site and the N-terminus. Furthermore, we harness AEP-mediated
transpeptidation for generation of ubiquitin- and ubiquitin-like-modifier
conjugates bearing a native isopeptide bond and only one point mutation
in the linker region.
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Affiliation(s)
- Maximilian Fottner
- Laboratory for Organic Chemistry (LOC), Department of Chemistry and Applied Biosciences (D-CHAB), ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Johannes Heimgärtner
- Laboratory for Organic Chemistry (LOC), Department of Chemistry and Applied Biosciences (D-CHAB), ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Maximilian Gantz
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Rahel Mühlhofer
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Timon Nast-Kolb
- Center for Protein Assemblies (CPA) and Lehrstuhl für Biophysik (E27), Physics Department, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Kathrin Lang
- Laboratory for Organic Chemistry (LOC), Department of Chemistry and Applied Biosciences (D-CHAB), ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland.,Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
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45
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Zuo C, Ding R, Wu X, Wang Y, Chu GC, Liang LJ, Ai H, Tong ZB, Mao J, Zheng Q, Wang T, Li Z, Liu L, Sun D. Thioester-Assisted Sortase-A-Mediated Ligation. Angew Chem Int Ed Engl 2022; 61:e202201887. [PMID: 35514243 DOI: 10.1002/anie.202201887] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Indexed: 11/12/2022]
Abstract
Sortase A (SrtA)-mediated ligation, a popular method for protein labeling and semi-synthesis, is limited by its reversibility and dependence on the LPxTG motif, where "x" is any amino acid. Here, we report that SrtA can mediate the efficient and irreversible ligation of a protein/peptide containing a C-terminal thioester with another protein/peptide bearing an N-terminal Gly, with broad tolerance for a wide variety of LPxT-derived sequences. This strategy, the thioester-assisted SrtA-mediated ligation, enabled the expedient preparation of proteins bearing various N- or C-terminal labels, including post-translationally modified proteins such as the Ser139-phosphorylated histone H2AX and Lys9-methylated histone H3, with less dependence on the LPxTG motif. Our study validates the chemical modification of substrates as an effective means of augmenting the synthetic capability of existing enzymatic methods.
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Affiliation(s)
- Chong Zuo
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Ruichao Ding
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Xiangwei Wu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yuanxia Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Guo-Chao Chu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Lu-Jun Liang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Huasong Ai
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Ze-Bin Tong
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Junxiong Mao
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Qingyun Zheng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Tian Wang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Zichen Li
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Demeng Sun
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230001, China
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46
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He G, Lei H, Sun W, Gu J, Yu W, Zhang D, Chen H, Li Y, Qin M, Xue B, Wang W, Cao Y. Strong and Reversible Covalent Double Network Hydrogel Based on Force-Coupled Enzymatic Reactions. Angew Chem Int Ed Engl 2022; 61:e202201765. [PMID: 35419931 DOI: 10.1002/anie.202201765] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Indexed: 12/12/2022]
Abstract
Biological load-bearing tissues are strong, tough, and recoverable under periodic mechanical loads. However, such features have rarely been achieved simultaneously in the same synthetic hydrogels. Here, we use a force-coupled enzymatic reaction to tune a strong covalent peptide linkage to a reversible bond. Based on this concept we engineered double network hydrogels that combine high mechanical strength and reversible mechanical recovery in the same hydrogels. Specifically, we found that a peptide ligase, sortase A, can promote the proteolysis of peptides under force. The peptide bond can be re-ligated by the same enzyme in the absence of force. This allows the sacrificial network in the double-network hydrogels to be ruptured and rebuilt reversibly. Our results demonstrate a general approach for precisely controlling the mechanical and dynamic properties of hydrogels at the molecular level.
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Affiliation(s)
- Guangxiao He
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing, 210093, China.,Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250021, China.,School of Public Health and Management, Hubei University of Medicine, Shiyan, 442000, China
| | - Hai Lei
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing, 210093, China
| | - Wenxu Sun
- School of Public Health and Management, Hubei University of Medicine, Shiyan, 442000, China
| | - Jie Gu
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing, 210093, China
| | - Wenting Yu
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing, 210093, China
| | - Di Zhang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing, 210093, China
| | - Huiyan Chen
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing, 210093, China
| | - Ying Li
- School of Science, Nantong University, Nantong, 226019, China
| | - Meng Qin
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing, 210093, China
| | - Bin Xue
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing, 210093, China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing, 210093, China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing, 210093, China.,Institute of Advanced Materials and Flexible Electronics (IAMFE), School of Chemistry and Materials Science, Nanjing University of Information Science & Technology, Nanjing, 210044, China.,Institute for Brain Sciences, Nanjing University, Nanjing, 210093, China
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47
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Zuo C, Ding R, Wu X, Wang Y, Chu GC, Liang LJ, Ai H, Tong ZB, Mao J, Zheng Q, Wang T, Li Z, Liu L, Sun D. Thioester‐Assisted Sortase‐A ‐ Mediated Ligation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Chong Zuo
- Tsinghua University Tsinghua-Peking Center for Life Sciences CHINA
| | - Ruichao Ding
- Tsinghua University Tsinghua-Peking Center for Life Sciences CHINA
| | - Xiangwei Wu
- Tsinghua University Tsinghua-Peking Center for Life Sciences CHINA
| | - Yuanxia Wang
- University of Science and Technology of China School of Life Sciences CHINA
| | - Guo-Chao Chu
- Tsinghua University Department of Chemistry CHINA
| | - Lu-Jun Liang
- Tsinghua University Department of Chemistry CHINA
| | - Huasong Ai
- Tsinghua University Department of Chemistry CHINA
| | - Ze-Bin Tong
- Tsinghua University Department of Chemistry CHINA
| | - Junxiong Mao
- Tsinghua University Department of Chemistry CHINA
| | | | - Tian Wang
- Tsinghua University Tsinghua-Peking Center for Life Sciences CHINA
| | - Zichen Li
- Tsinghua University Department of Chemistry CHINA
| | - Lei Liu
- Tsinghua University Department of Chemistry CHINA
| | - Demeng Sun
- University of Science and Technology of China School of Life Sciences 96 Jinzhai Road 230026 Hefei CHINA
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48
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Morgan HE, Turnbull WB, Webb ME. Challenges in the use of sortase and other peptide ligases for site-specific protein modification. Chem Soc Rev 2022; 51:4121-4145. [PMID: 35510539 PMCID: PMC9126251 DOI: 10.1039/d0cs01148g] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Site-specific protein modification is a widely-used biochemical tool. However, there are many challenges associated with the development of protein modification techniques, in particular, achieving site-specificity, reaction efficiency and versatility. The engineering of peptide ligases and their substrates has been used to address these challenges. This review will focus on sortase, peptidyl asparaginyl ligases (PALs) and variants of subtilisin; detailing how their inherent specificity has been utilised for site-specific protein modification. The review will explore how the engineering of these enzymes and substrates has led to increased reaction efficiency mainly due to enhanced catalytic activity and reduction of reversibility. It will also describe how engineering peptide ligases to broaden their substrate scope is opening up new opportunities to expand the biochemical toolkit, particularly through the development of techniques to conjugate multiple substrates site-specifically onto a protein using orthogonal peptide ligases. We highlight chemical and biochemical strategies taken to optimise peptide and protein modification using peptide ligases.![]()
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Affiliation(s)
- Holly E Morgan
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - W Bruce Turnbull
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - Michael E Webb
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
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49
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Vilen Z, Reeves AE, O’Leary TR, Joeh E, Kamasawa N, Huang ML. Cell Surface Engineering Enables Surfaceome Profiling. ACS Chem Biol 2022; 18:701-710. [PMID: 35443134 PMCID: PMC9901301 DOI: 10.1021/acschembio.1c00865] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cell surface proteins (CSPs) are vital molecular mediators for cells and their extracellular environment. Thus, understanding which CSPs are displayed on cells, especially in different cell states, remains an important endeavor in cell biology. Here, we describe the integration of cell surface engineering with radical-mediated protein biotinylation to profile CSPs. This method relies on the prefunctionalization of cells with cholesterol lipid groups, followed by sortase-catalyzed conjugation with an APEX2 ascorbate peroxidase enzyme. In the presence of biotin-phenol and H2O2, APEX2 catalyzes the formation of highly reactive biotinyl radicals that covalently tag electron-rich residues within CSPs for subsequent streptavidin-based enrichment and analysis by quantitative mass spectrometry. While APEX2 is traditionally used to capture proximity-based interactomes, we envisioned using it in a "baitless" manner on cell surfaces to capture CSPs. We evaluate this strategy in light of another CSP labeling method that relies on the presence of cell surface sialic acid. Using the APEX2 strategy, we describe the CSPs found in three mammalian cell lines and compare CSPs in adherent versus three-dimensional pancreatic adenocarcinoma cells.
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Affiliation(s)
- Zak Vilen
- Department of Molecular Medicine, Scripps Research, 120 Scripps Way, Jupiter, FL 33458-5284,Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037,Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037
| | - Abigail E. Reeves
- Department of Molecular Medicine, Scripps Research, 120 Scripps Way, Jupiter, FL 33458-5284,Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037,Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037
| | - Timothy R. O’Leary
- Department of Molecular Medicine, Scripps Research, 120 Scripps Way, Jupiter, FL 33458-5284
| | - Eugene Joeh
- Department of Molecular Medicine, Scripps Research, 120 Scripps Way, Jupiter, FL 33458-5284,Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037,Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037
| | - Naomi Kamasawa
- The Imaging Center and Electron Microscopy Core Facility, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL, 33458
| | - Mia L. Huang
- Department of Molecular Medicine, Scripps Research, 120 Scripps Way, Jupiter, FL 33458-5284,Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037,Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037,Corresponding author:
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50
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He G, Lei H, Sun W, Gu J, Yu W, Zhang D, Chen H, Li Y, Qin M, Xue B, Wang W, Cao Y. Strong and Reversible Covalent Double Network Hydrogel Based on Force‐coupled Enzymatic Reactions. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Hai Lei
- Nanjing University Physics CHINA
| | - Wenxu Sun
- Nantong University School of Science CHINA
| | - Jie Gu
- Nanjing University Physics CHINA
| | | | - Di Zhang
- Nanjing University Physics CHINA
| | | | - Ying Li
- Nanjing University of Information Science and Technology School of Environmental Science and Engineering CHINA
| | - Meng Qin
- Nanjing University Physics CHINA
| | - Bin Xue
- Nanjing University Physics CHINA
| | - Wei Wang
- Nanjing University Physics CHINA
| | - Yi Cao
- Nanjing University Department of Physics 22 Hankou Road 210093 Nanjing CHINA
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