1
|
Freitas AI, Domingues L, Aguiar TQ. Tag-mediated single-step purification and immobilization of recombinant proteins toward protein-engineered advanced materials. J Adv Res 2022; 36:249-264. [PMID: 35127175 PMCID: PMC8799874 DOI: 10.1016/j.jare.2021.06.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022] Open
Abstract
Background The potential applications of protein-engineered functional materials are so wide and exciting that the interest in these eco-friendly advanced materials will further expand in the future. Tag-mediated protein purification/immobilization technologies have emerged as green and cost-effective approaches for the fabrication of such materials. Strategies that combine the purification and immobilization of recombinant proteins/peptides onto/into natural, synthetic or hybrid materials in a single-step are arising and attracting increasing interest. Aim of Review This review highlights the most significant advances of the last 5 years within the scope of tag-mediated protein purification/immobilization and elucidates their contributions for the development of efficient single-step purification and immobilization strategies. Recent progresses in the field of protein-engineered materials created using innovative protein-tag combinations and future opportunities created by these new technologies are also summarized and identified herein. Key Scientific Concepts of Review Protein purification/immobilization tags present a remarkable ability to establish specific non-covalent/covalent interactions between solid materials and biological elements, which prompted the creation of tailor-made and advanced functional materials, and of next-generation hybrid materials. Affinity tags can bind to a wide range of materials (of synthetic, natural or hybrid nature), being most suitable for protein purification. Covalently binding tags are most suitable for long-term protein immobilization, but can only bind naturally to protein-based materials. Hybrid affinity-covalently binding tags have allowed efficient one-step purification and immobilization of proteins onto different materials, as well as the development of innovative protein-engineered materials. Self-aggregating tags have been particularly useful in combination with other tags for generating protein-engineered materials with self-assembling, flexible and/or responsive properties. While these tags have been mainly explored for independent protein purification, immobilization or functionalization purposes, efficient strategies that combine tag-mediated purification and immobilization/functionalization in a single-step will be essential to guarantee the sustainable manufacturing of advanced protein-engineered materials.
Collapse
Affiliation(s)
- Ana I. Freitas
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Tatiana Q. Aguiar
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| |
Collapse
|
2
|
Huang Y, Nieh MP, Chen W, Lei Y. Outer membrane vesicles (OMVs) enabled bio-applications: A critical review. Biotechnol Bioeng 2021; 119:34-47. [PMID: 34698385 DOI: 10.1002/bit.27965] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 07/28/2021] [Accepted: 10/10/2021] [Indexed: 11/07/2022]
Abstract
Outer membrane vesicles (OMVs) are nanoscale spherical vesicles released from Gram-negative bacteria. The lipid bilayer membrane structure of OMVs consists of similar components as bacterial membrane and thus has attracted more and more attention in exploiting OMVs' bio-applications. Although the endotoxic lipopolysaccharide on natural OMVs may impose potential limits on their clinical applications, genetic modification can reduce their endotoxicity and decorate OMVs with multiple functional proteins. These genetically engineered OMVs have been employed in various fields including vaccination, drug delivery, cancer therapy, bioimaging, biosensing, and enzyme carrier. This review will first briefly introduce the background of OMVs followed by recent advances in functionalization and various applications of engineered OMVs with an emphasis on the working principles and their performance, and then discuss about the future trends of OMVs in biomedical applications.
Collapse
Affiliation(s)
- Yikun Huang
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut, USA
| | - Mu-Ping Nieh
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
| | - Yu Lei
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut, USA.,Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut, USA
| |
Collapse
|
3
|
Wang B, Patkar SS, Kiick KL. Application of Thermoresponsive Intrinsically Disordered Protein Polymers in Nanostructured and Microstructured Materials. Macromol Biosci 2021; 21:e2100129. [PMID: 34145967 PMCID: PMC8449816 DOI: 10.1002/mabi.202100129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/25/2021] [Indexed: 01/15/2023]
Abstract
Modulation of inter- and intramolecular interactions between bioinspired designer molecules can be harnessed for developing functional structures that mimic the complex hierarchical organization of multicomponent assemblies observed in nature. Furthermore, such multistimuli-responsive molecules offer orthogonal tunability for generating versatile multifunctional platforms via independent biochemical and biophysical cues. In this review, the remarkable physicochemical and mechanical properties of genetically engineered protein polymers derived from intrinsically disordered proteins, specifically elastin and resilin, are discussed. This review highlights emerging technologies which use them as building blocks in the fabrication of highly programmable structured biomaterials for applications in delivery of biotherapeutic cargo and regenerative medicine.
Collapse
Affiliation(s)
- Bin Wang
- Department of Materials Science and Engineering, University of Delaware, 201 DuPont Hall, Newark, DE, 19716, USA
| | - Sai S Patkar
- Department of Materials Science and Engineering, University of Delaware, 201 DuPont Hall, Newark, DE, 19716, USA
| | - Kristi L Kiick
- Department of Materials Science and Engineering, University of Delaware, 201 DuPont Hall, Newark, DE, 19716, USA
- Department of Biomedical Engineering, University of Delaware, 161 Colburn Laboratory, Newark, DE, 19716, USA
- Delaware Biotechnology Institute, Ammon Pinizzotto Biopharmaceutical Innovation Center, 590 Avenue 1743, Newark, DE, 19713, USA
| |
Collapse
|
4
|
Shapiro DM, Ney M, Eghtesadi SA, Chilkoti A. Protein Phase Separation Arising from Intrinsic Disorder: First-Principles to Bespoke Applications. J Phys Chem B 2021; 125:6740-6759. [PMID: 34143622 DOI: 10.1021/acs.jpcb.1c01146] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The phase separation of biomolecules has become the focus of intense research in the past decade, with a growing body of research implicating this phenomenon in essentially all biological functions, including but not limited to homeostasis, stress responses, gene regulation, cell differentiation, and disease. Excellent reviews have been published previously on the underlying physical basis of liquid-liquid phase separation (LLPS) of biological molecules (Nat. Phys. 2015, 11, 899-904) and LLPS as it occurs natively in physiology and disease (Science 2017, 357, eaaf4382; Biochemistry 2018, 57, 2479-2487; Chem. Rev. 2014, 114, 6844-6879). Here, we review how the theoretical physical basis of LLPS has been used to better understand the behavior of biomolecules that undergo LLPS in natural systems and how this understanding has also led to the development of novel synthetic systems that exhibit biomolecular phase separation, and technologies that exploit these phenomena. In part 1 of this Review, we explore the theory behind the phase separation of biomolecules and synthetic macromolecules and introduce a few notable phase-separating biomolecules. In part 2, we cover experimental and computational methods used to study phase-separating proteins and how these techniques have uncovered the mechanisms underlying phase separation in physiology and disease. Finally, in part 3, we cover the development and applications of engineered phase-separating polypeptides, ranging from control of their self-assembly to create defined supramolecular architectures to reprogramming biological processes using engineered IDPs that exhibit LLPS.
Collapse
Affiliation(s)
- Daniel Mark Shapiro
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Max Ney
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Seyed Ali Eghtesadi
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| |
Collapse
|
5
|
Mullerpatan A, Chandra D, Kane E, Karande P, Cramer S. Purification of proteins using peptide-ELP based affinity precipitation. J Biotechnol 2020; 309:59-67. [DOI: 10.1016/j.jbiotec.2019.12.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 12/13/2019] [Accepted: 12/18/2019] [Indexed: 02/06/2023]
|
6
|
Kim H, Gaynor A, Chen W. Tunable modulation of antibody-antigen interaction by protease cleavage of protein M. Biotechnol Bioeng 2019; 116:2834-2842. [PMID: 31286479 DOI: 10.1002/bit.27111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/27/2019] [Accepted: 06/30/2019] [Indexed: 12/12/2022]
Abstract
While immunoglobulins find ubiquitous use in biotechnology as static binders, recent developments have created proantibodies that enable orthogonal switch-like behavior to antibody function. Previously, peptides with low binding affinity have been genetically fused to antibodies, to proteolytically control binding function by blocking the antigen-binding site. However, development of these artificial blockers requires panning for peptide sequences that reversibly affect antigen affinity for each antibody. Instead, a more general strategy to achieve dynamic control over antibody affinity may be feasible using protein M (ProtM) from Mycoplasma genitalium, a newly identified polyspecific immunity evasion protein that is capable of blocking antigen binding for a wide range of antibodies. Using C-terminus truncation to identify ProtM variants that are still capable of binding to antibodies without the ability to block antigens, we developed a novel and universal biological switch for antibodies. Using a site-specifically placed thrombin cut site, antibody affinity can be modulated by cleavage of the two distinct antibody-binding and antigen-blocking domains of ProtM. Because of the high affinity of ProtM toward a large variety of IgG subtypes, this strategy may be used as a universal approach to create proantibodies that are conditionally activated by disease-specific proteases such as matrix metalloproteinases.
Collapse
Affiliation(s)
- Heejae Kim
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware
| | - Andrew Gaynor
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware
| |
Collapse
|
7
|
Lieser RM, Chen W, Sullivan MO. Controlled Epidermal Growth Factor Receptor Ligand Display on Cancer Suicide Enzymes via Unnatural Amino Acid Engineering for Enhanced Intracellular Delivery in Breast Cancer Cells. Bioconjug Chem 2019; 30:432-442. [PMID: 30615416 DOI: 10.1021/acs.bioconjchem.8b00783] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Proteins are ideal candidates for disease treatment because of their high specificity and potency. Despite this potential, delivery of proteins remains a significant challenge due to the intrinsic size, charge, and stability of proteins. Attempts to overcome these challenges have most commonly relied on direct conjugation of polymers and peptides to proteins via reactive groups on naturally occurring residues. While such approaches have shown some success, they allow limited control of the spacing and number of moieties coupled to proteins, which can hinder bioactivity and delivery capabilities of the therapeutic. Here, we describe a strategy to site-specifically conjugate delivery moieties to therapeutic proteins through unnatural amino acid (UAA) incorporation, in order to explore the effect of epidermal growth factor receptor (EGFR)-targeted ligand valency and spacing on internalization of proteins in EGFR-overexpressing inflammatory breast cancer (IBC) cells. Our results demonstrate the ability to enhance targeted protein delivery by tuning a small number of EGFR ligands per protein and clustering these ligands to promote multivalent ligand-receptor interactions. Furthermore, the tailorability of this simple approach was demonstrated through IBC-targeted cell death via the delivery of yeast cytosine deaminase (yCD), a prodrug converting enzyme.
Collapse
Affiliation(s)
- Rachel M Lieser
- Department of Chemical and Biomolecular Engineering , University of Delaware , 150 Academy Street , Newark , Delaware 19716 , United States
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering , University of Delaware , 150 Academy Street , Newark , Delaware 19716 , United States
| | - Millicent O Sullivan
- Department of Chemical and Biomolecular Engineering , University of Delaware , 150 Academy Street , Newark , Delaware 19716 , United States
| |
Collapse
|
8
|
Chen Q, Yu S, Myung N, Chen W. DNA-guided assembly of a five-component enzyme cascade for enhanced conversion of cellulose to gluconic acid and H 2 O 2. J Biotechnol 2017; 263:30-35. [DOI: 10.1016/j.jbiotec.2017.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/25/2017] [Accepted: 10/09/2017] [Indexed: 01/17/2023]
|
9
|
Swartz AR, Xu X, Traylor SJ, Li ZJ, Chen W. One‐step affinity capture and precipitation for improved purification of an industrial monoclonal antibody using Z‐ELP functionalized nanocages. Biotechnol Bioeng 2017; 115:423-432. [DOI: 10.1002/bit.26467] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/21/2017] [Accepted: 10/03/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Andrew R. Swartz
- Department of Chemical and Biomolecular EngineeringUniversity of DelawareNewarkDelaware
| | - Xuankuo Xu
- Biologics Process DevelopmentBristol Myers SquibbDevensMassachusetts
| | - Steven J. Traylor
- Biologics Process DevelopmentBristol Myers SquibbDevensMassachusetts
| | - Zheng J. Li
- Biologics Process DevelopmentBristol Myers SquibbDevensMassachusetts
| | - Wilfred Chen
- Department of Chemical and Biomolecular EngineeringUniversity of DelawareNewarkDelaware
| |
Collapse
|
10
|
Guo C, Kim H, Ovadia EM, Mourafetis CM, Yang M, Chen W, Kloxin AM. Bio-orthogonal conjugation and enzymatically triggered release of proteins within multi-layered hydrogels. Acta Biomater 2017; 56:80-90. [PMID: 28391052 PMCID: PMC5510749 DOI: 10.1016/j.actbio.2017.04.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 02/02/2023]
Abstract
Hydrogels are facile architectures for the controlled presentation of proteins with far-reaching applications, from fundamental biological studies in three-dimensional culture to new regenerative medicine and therapeutic delivery strategies. Here, we demonstrate a versatile approach for spatially-defined presentation of engineered proteins within hydrogels through i) immobilization using bio-orthogonal strain-promoted alkyne-azide click chemistry and ii) dynamic protease-driven protein release using exogenously applied enzyme. Model fluorescent proteins were expressed using nonsense codon replacement to incorporate azide-containing unnatural amino acids in a site-specific manner toward maintaining protein activity: here, cyan fluorescent protein (AzCFP), mCherry fluorescent protein (AzmCh), and mCh decorated with a thrombin cut-site. (AzTMBmCh). Eight-arm poly(ethylene glycol) (PEG) was modified with dibenzylcyclooctyne (DBCO) groups and reacted with azide functionalized PEG in aqueous solution for rapid formation of hydrogels. Azide functionalized full-length fluorescent proteins were successfully incorporated into the hydrogel network by reaction with PEG-DBCO prior to gel formation. Temporal release and removal of select proteins (AzTMBmCh) was triggered with the application of thrombin and monitored in real-time with confocal microscopy, providing a responsive handle for controlling matrix properties. Hydrogels with regions of different protein compositions were created using a layering technique with thicknesses of hundreds of micrometers, affording opportunities for the creation of complex geometries on size scales relevant for controlling cellular microenvironments. STATEMENT OF SIGNIFICANCE Controlling protein presentation within biomaterials is important for modulating interactions with biological systems. For example, native tissues are composed of subunits with different matrix compositions (proteins, stiffness) that dynamically interact with cells, influencing function and fate. Toward mimicking such temporally-regulated and spatially-defined microenvironments, we utilize bio-orthogonal click chemistry and protein engineering to create hydrogels with distinct regions of proteins and modify them over time. Through nonsense codon replacement, we site-specifically functionalize large proteins with i) azides for covalent conjugation and ii) an enzymatic cleavage site for user-defined release from hydrogels. Our results exemplify not only the ability to create unique bio-functionalized hydrogels with controlled mechanical properties, but also the potential for creating interesting interfaces for cell culture and tissue engineering applications.
Collapse
Affiliation(s)
- Chen Guo
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States
| | - Heejae Kim
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States
| | - Elisa M Ovadia
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States
| | - Christine M Mourafetis
- Department of Chemical and Biomolecular Engineering, New York University, Brooklyn, NY 11201, United States
| | - Mingrui Yang
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States
| | - April M Kloxin
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States; Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, United States.
| |
Collapse
|
11
|
Swartz AR, Sun Q, Chen W. Ligand-Induced Cross-Linking of Z-Elastin-like Polypeptide-Functionalized E2 Protein Nanoparticles for Enhanced Affinity Precipitation of Antibodies. Biomacromolecules 2017; 18:1654-1659. [DOI: 10.1021/acs.biomac.7b00275] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Andrew R. Swartz
- Department of Chemical and
Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Qing Sun
- Department of Chemical and
Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Wilfred Chen
- Department of Chemical and
Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| |
Collapse
|
12
|
Yadav DK, Yadav N, Yadav S, Haque S, Tuteja N. An insight into fusion technology aiding efficient recombinant protein production for functional proteomics. Arch Biochem Biophys 2016; 612:57-77. [DOI: 10.1016/j.abb.2016.10.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/15/2016] [Accepted: 10/18/2016] [Indexed: 11/27/2022]
|