1
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Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024; 124:8740-8786. [PMID: 38959423 PMCID: PMC11273360 DOI: 10.1021/acs.chemrev.4c00120] [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: 02/09/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
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Affiliation(s)
| | | | | | | | - Anthony P. Green
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
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2
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Cao L, Wang L. Biospecific Chemistry for Covalent Linking of Biomacromolecules. Chem Rev 2024; 124:8516-8549. [PMID: 38913432 PMCID: PMC11240265 DOI: 10.1021/acs.chemrev.4c00066] [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] [Indexed: 06/26/2024]
Abstract
Interactions among biomacromolecules, predominantly noncovalent, underpin biological processes. However, recent advancements in biospecific chemistry have enabled the creation of specific covalent bonds between biomolecules, both in vitro and in vivo. This Review traces the evolution of biospecific chemistry in proteins, emphasizing the role of genetically encoded latent bioreactive amino acids. These amino acids react selectively with adjacent natural groups through proximity-enabled bioreactivity, enabling targeted covalent linkages. We explore various latent bioreactive amino acids designed to target different protein residues, ribonucleic acids, and carbohydrates. We then discuss how these novel covalent linkages can drive challenging protein properties and capture transient protein-protein and protein-RNA interactions in vivo. Additionally, we examine the application of covalent peptides as potential therapeutic agents and site-specific conjugates for native antibodies, highlighting their capacity to form stable linkages with target molecules. A significant focus is placed on proximity-enabled reactive therapeutics (PERx), a pioneering technology in covalent protein therapeutics. We detail its wide-ranging applications in immunotherapy, viral neutralization, and targeted radionuclide therapy. Finally, we present a perspective on the existing challenges within biospecific chemistry and discuss the potential avenues for future exploration and advancement in this rapidly evolving field.
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Affiliation(s)
- Li Cao
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
| | - Lei Wang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
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3
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Cao L, Yu B, Li S, Zhang P, Li Q, Wang L. Genetically Enabling Phosphorus Fluoride Exchange Click Chemistry in Proteins. Chem 2024; 10:1868-1884. [PMID: 38975291 PMCID: PMC11225796 DOI: 10.1016/j.chempr.2024.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Phosphorus Fluoride Exchange (PFEx), recently debuted in small molecules, represents the forefront of click chemistry. To explore PFEx's potential in biological settings, we developed amino acids PFY and PFK featuring phosphoramidofluoridates and incorporated them into proteins through genetic code expansion. PFY/PFK selectively reacted with nearby His, Tyr, Lys, or Cys in proteins, both in vitro and in living cells, demonstrating that proximity enabled PFEx reactivity without external reagents. The reaction with His showed unique pH-dependent properties and created thermally sensitive linkages. Additionally, Na2SiO3 enhanced PFEx reactions with Tyr and Cys. PFEx, by generating defined covalent P-N/O linkages, extends the utility of phosphorus linkages in proteins, aligning with nature's use of phosphate connectors in other biomolecules. More versatile and durable than SuFEx, PFEx in proteins expands the latent bioreactive arsenal for covalent protein engineering and will facilitate the broad application of this potent click chemistry in biological and biomedical fields.
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Affiliation(s)
- Li Cao
- Department of Pharmaceutical Chemistry, the Cardiovascular Research Institute, and Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- These authors contributed equally
| | - Bingchen Yu
- Department of Pharmaceutical Chemistry, the Cardiovascular Research Institute, and Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- These authors contributed equally
| | - Shanshan Li
- Department of Pharmaceutical Chemistry, the Cardiovascular Research Institute, and Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Pan Zhang
- Department of Pharmaceutical Chemistry, the Cardiovascular Research Institute, and Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Qingke Li
- Department of Pharmaceutical Chemistry, the Cardiovascular Research Institute, and Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lei Wang
- Department of Pharmaceutical Chemistry, the Cardiovascular Research Institute, and Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Lead contact
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4
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Yi HB, Lee S, Seo K, Kim H, Kim M, Lee HS. Cellular and Biophysical Applications of Genetic Code Expansion. Chem Rev 2024; 124:7465-7530. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.
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Affiliation(s)
- Han Bin Yi
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Seungeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Kyungdeok Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyeongjo Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Minah Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
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5
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Cheng L, Wang Y, Guo Y, Zhang SS, Xiao H. Advancing protein therapeutics through proximity-induced chemistry. Cell Chem Biol 2024; 31:428-445. [PMID: 37802076 PMCID: PMC10960704 DOI: 10.1016/j.chembiol.2023.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/21/2023] [Accepted: 09/15/2023] [Indexed: 10/08/2023]
Abstract
Recent years have seen a remarkable growth in the field of protein-based medical treatments. Nevertheless, concerns have arisen regarding the cytotoxicity limitations, low affinity, potential immunogenicity, low stability, and challenges to modify these proteins. To overcome these obstacles, proximity-induced chemistry has emerged as a next-generation strategy for advancing protein therapeutics. This method allows site-specific modification of proteins with therapeutic agents, improving their effectiveness without extensive engineering. In addition, this innovative approach enables spatial control of the reaction based on proximity, facilitating the formation of irreversible covalent bonds between therapeutic proteins and their targets. This capability becomes particularly valuable in addressing challenges such as the low affinity frequently encountered between therapeutic proteins and their targets, as well as the limited availability of small molecules for specific protein targets. As a result, proximity-induced chemistry is reshaping the field of protein drug preparation and propelling the revolution in novel protein therapeutics.
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Affiliation(s)
- Linqi Cheng
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Yixian Wang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Yiming Guo
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Sophie S Zhang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Han Xiao
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77005, USA; Department of Biosciences, Rice University, 6100 Main Street, Houston, TX 77005, USA; Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX 77005, USA.
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6
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Lugtenburg T, Gran-Scheuch A, Drienovská I. Non-canonical amino acids as a tool for the thermal stabilization of enzymes. Protein Eng Des Sel 2023; 36:gzad003. [PMID: 36897290 PMCID: PMC10064326 DOI: 10.1093/protein/gzad003] [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: 08/04/2022] [Revised: 01/31/2023] [Accepted: 02/20/2023] [Indexed: 03/11/2023] Open
Abstract
Biocatalysis has become a powerful alternative for green chemistry. Expanding the range of amino acids used in protein biosynthesis can improve industrially appealing properties such as enantioselectivity, activity and stability. This review will specifically delve into the thermal stability improvements that non-canonical amino acids (ncAAs) can confer to enzymes. Methods to achieve this end, such as the use of halogenated ncAAs, selective immobilization and rational design, will be discussed. Additionally, specific enzyme design considerations using ncAAs are discussed along with the benefits and limitations of the various approaches available to enhance the thermal stability of enzymes.
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Affiliation(s)
- Tim Lugtenburg
- Department of Chemistry & Pharmaceutical Sciences, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Alejandro Gran-Scheuch
- Department of Chemistry & Pharmaceutical Sciences, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Ivana Drienovská
- Department of Chemistry & Pharmaceutical Sciences, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
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7
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Koch NG, Budisa N. Focused Engineering of Pyrrolysyl-tRNA Synthetase-Based Orthogonal Translation Systems for the Incorporation of Various Noncanonical Amino Acids. Methods Mol Biol 2023; 2676:3-19. [PMID: 37277621 DOI: 10.1007/978-1-0716-3251-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The expansion of the genetic code has become a valuable tool for molecular biology, biochemistry, and biotechnology. The pyrrolysyl-tRNA synthetase (PylRS) variants with their cognate tRNAPyl derived from methanogenic archaea of the genus Methanosarcina are the most popular tools for ribosomally mediated site-specific and proteome-wide statistical incorporation of noncanonical amino acids (ncAAs) into proteins. The incorporation of ncAAs can be used for numerous biotechnological and even therapeutically relevant applications. Here we present a protocol of engineering PylRS for novel substrates with unique chemical functionalities. These functional groups can act as intrinsic probes, especially in complex biological environments such as mammalian cells, tissues, and even whole animals.
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Affiliation(s)
- Nikolaj G Koch
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Nediljko Budisa
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany.
- Chemical Synthetic Biology, Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada.
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8
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Zhang C, Bai X, Chen S, Dedkova LM, Hecht SM. Local Conformational Constraint of Firefly Luciferase Can Affect the Energy of Bioluminescence and Enzyme Stability. CCS CHEMISTRY 2022; 4:1695-1707. [PMID: 36939446 PMCID: PMC10022883 DOI: 10.31635/ccschem.022.202101733] [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] [Indexed: 11/19/2022] Open
Abstract
Conformational dynamics contribute importantly to enzyme catalysis, such that targeted conformational constraint may affect catalysis. Firefly luciferases undergo extensive structural change during catalysis; key residues form a hydrophobic pocket, excluding water and enabling maximally energetic light production. Point mutants almost always luminesce at longer wavelengths (lower energy) than the wild type. Conformational constraint, using dipeptide analogue 3 at a position critical for optimized excited state structure, produced luciferase emission at a shorter wavelength by ~10 nm. In comparison, introduction of conformationally constrained analogues 4, 5, or 7 afforded luciferases emitting at longer wavelengths, while a related unconstrained luciferase (analogue 6) exhibited wild-type emission. The constrained luciferases tested were more stable than the wild type. Protein modeling demonstrated that the "inside" or "outside" orientation of the conformationally constrained dipeptide led to the shorter or longer emission wavelength, respectively. More broadly, these results suggest that local conformational constraint can control specific elements of enzyme behavior, both in vitro and in vivo. This represents the first example of studying enzyme function by introducing conformationally constrained dipeptides at a specific protein position. The principles discovered here in luciferase modification will enable studies to control the wavelength emission and photophysical properties of modified luciferases.
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Affiliation(s)
- Chao Zhang
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287
| | - Xiaoguang Bai
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287
| | - Shengxi Chen
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287
| | - Larisa M. Dedkova
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287
- Corresponding authors: ;
| | - Sidney M. Hecht
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287
- Corresponding authors: ;
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9
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Koch NG, Baumann T, Budisa N. Efficient Unnatural Protein Production by Pyrrolysyl-tRNA Synthetase With Genetically Fused Solubility Tags. Front Bioeng Biotechnol 2022; 9:807438. [PMID: 35284428 PMCID: PMC8905625 DOI: 10.3389/fbioe.2021.807438] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/17/2021] [Indexed: 11/27/2022] Open
Abstract
Introducing non-canonical amino acids (ncAAs) by engineered orthogonal pairs of aminoacyl-tRNA synthetases and tRNAs has proven to be a highly useful tool for the expansion of the genetic code. Pyrrolysyl-tRNA synthetase (PylRS) from methanogenic archaeal and bacterial species is particularly attractive due to its natural orthogonal reactivity in bacterial and eukaryotic cells. However, the scope of such a reprogrammed translation is often limited, due to low yields of chemically modified target protein. This can be the result of substrate specificity engineering, which decreases the aminoacyl-tRNA synthetase stability and reduces the abundance of active enzyme. We show that the solubility and folding of these engineered enzymes can become a bottleneck for the production of ncAA-containing proteins in vivo. Solubility tags derived from various species provide a strategy to remedy this issue. We find the N-terminal fusion of the small metal binding protein from Nitrosomonas europaea to the PylRS sequence to improve enzyme solubility and to boost orthogonal translation efficiency. Our strategy enhances the production of site-specifically labelled proteins with a variety of engineered PylRS variants by 200–540%, and further allows triple labeling. Even the wild-type enzyme gains up to 245% efficiency for established ncAA substrates.
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Affiliation(s)
- Nikolaj G Koch
- Biokatalyse, Institut für Chemie, Technische Universität Berlin, Berlin, Germany.,Bioanalytik, Institut für Biotechnologie, Technische Universität Berlin, Berlin, Germany
| | - Tobias Baumann
- Biokatalyse, Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Nediljko Budisa
- Biokatalyse, Institut für Chemie, Technische Universität Berlin, Berlin, Germany.,Chemical Synthetic Biology, Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
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10
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Genetically encoding latent bioreactive amino acids and the development of covalent protein drugs. Curr Opin Chem Biol 2021; 66:102106. [PMID: 34968810 DOI: 10.1016/j.cbpa.2021.102106] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/07/2021] [Accepted: 11/25/2021] [Indexed: 12/11/2022]
Abstract
As natural proteins generally do not bind targets in a covalent mode, the therapeutic potential of covalent protein drugs remains largely unexplored. Recently, latent bioreactive amino acids have been incorporated into proteins through genetic code expansion, which selectively react with nearby natural residues via proximity-enabled reactivity, generating diverse covalent linkages for proteins in vitro and in cells. These new covalent linkages provide novel avenues for protein research and engineering. In addition, a general platform technology, proximity-enabled reactive therapeutics (PERx), has been established for the development of covalent protein drugs. The first covalent protein drug demonstrates advantageous features in cancer immunotherapy in mice. Selective introduction of covalent bonds into proteins will advance biological studies, synthetic biology, and biotherapeutics with the power of biocompatible covalent chemistries.
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11
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Koch NG, Goettig P, Rappsilber J, Budisa N. Engineering Pyrrolysyl-tRNA Synthetase for the Incorporation of Non-Canonical Amino Acids with Smaller Side Chains. Int J Mol Sci 2021; 22:11194. [PMID: 34681855 PMCID: PMC8538471 DOI: 10.3390/ijms222011194] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 01/11/2023] Open
Abstract
Site-specific incorporation of non-canonical amino acids (ncAAs) into proteins has emerged as a universal tool for systems bioengineering at the interface of chemistry, biology, and technology. The diversification of the repertoire of the genetic code has been achieved for amino acids with long and/or bulky side chains equipped with various bioorthogonal tags and useful spectral probes. Although ncAAs with relatively small side chains and similar properties are of great interest to biophysics, cell biology, and biomaterial science, they can rarely be incorporated into proteins. To address this gap, we report the engineering of PylRS variants capable of incorporating an entire library of aliphatic "small-tag" ncAAs. In particular, we performed mutational studies of a specific PylRS, designed to incorporate the shortest non-bulky ncAA (S-allyl-l-cysteine) possible to date and based on this knowledge incorporated aliphatic ncAA derivatives. In this way, we have not only increased the number of translationally active "small-tag" ncAAs, but also determined key residues responsible for maintaining orthogonality, while engineering the PylRS for these interesting substrates. Based on the known plasticity of PylRS toward different substrates, our approach further expands the reassignment capacities of this enzyme toward aliphatic amino acids with smaller side chains endowed with valuable functionalities.
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Affiliation(s)
- Nikolaj G. Koch
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany;
- Institut für Biotechnologie-Bioanalytik, Technische Universität Berlin, 10623 Berlin, Germany;
| | - Peter Goettig
- Structural Biology Group, Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria;
| | - Juri Rappsilber
- Institut für Biotechnologie-Bioanalytik, Technische Universität Berlin, 10623 Berlin, Germany;
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Nediljko Budisa
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany;
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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12
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Xiong W, Liu B, Shen Y, Jing K, Savage TR. Protein engineering design from directed evolution to de novo synthesis. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108096] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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13
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Genetically encoded selective cross-linkers and emerging applications. Biochem Soc Trans 2021; 48:1807-1817. [PMID: 32657352 DOI: 10.1042/bst20200508] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/05/2020] [Accepted: 06/11/2020] [Indexed: 02/08/2023]
Abstract
There has been a large amount of interest in the development of genetically encoded cross-linkers that target functional groups naturally present in cells. Recently, a new class of unnatural amino acids that specifically react with target residues were developed and genetically incorporated. The selective reaction shows higher cross-linking efficiency, lower background and predictable cross-linking sites. It has been applied to enhance protein/peptide stability, pinpoint protein-protein interactions, stabilize protein complexes, engineer covalent protein inhibitors, identify phosphatases in living cells, etc. These new covalent linkages provide excellent new tools for protein engineering and biological studies. Their applications in biotherapy will provide considerable opportunities for innovating and improving biomolecular medicines.
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14
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Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H. Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet. Chem Rev 2021; 121:6173-6245. [PMID: 33886302 DOI: 10.1021/acs.chemrev.0c01201] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.
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Affiliation(s)
- Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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15
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Singh T, Yadav SK, Vainstein A, Kumar V. Genome recoding strategies to improve cellular properties: mechanisms and advances. ABIOTECH 2021; 2:79-95. [PMID: 34377578 PMCID: PMC7675020 DOI: 10.1007/s42994-020-00030-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 10/07/2020] [Indexed: 11/10/2022]
Abstract
The genetic code, once believed to be universal and immutable, is now known to contain many variations and is not quite universal. The basis for genome recoding strategy is genetic code variation that can be harnessed to improve cellular properties. Thus, genome recoding is a promising strategy for the enhancement of genome flexibility, allowing for novel functions that are not commonly documented in the organism in its natural environment. Here, the basic concept of genetic code and associated mechanisms for the generation of genetic codon variants, including biased codon usage, codon reassignment, and ambiguous decoding, are extensively discussed. Knowledge of the concept of natural genetic code expansion is also detailed. The generation of recoded organisms and associated mechanisms with basic targeting components, including aminoacyl-tRNA synthetase-tRNA pairs, elongation factor EF-Tu and ribosomes, are highlighted for a comprehensive understanding of this concept. The research associated with the generation of diverse recoded organisms is also discussed. The success of genome recoding in diverse multicellular organisms offers a platform for expanding protein chemistry at the biochemical level with non-canonical amino acids, genetically isolating the synthetic organisms from the natural ones, and fighting viruses, including SARS-CoV2, through the creation of attenuated viruses. In conclusion, genome recoding can offer diverse applications for improving cellular properties in the genome-recoded organisms.
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Affiliation(s)
- Tanya Singh
- Department of Botany, School of Basic Sciences, Central University of Punjab, Bathinda, 151001 India
| | | | - Alexander Vainstein
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Vinay Kumar
- Department of Botany, School of Basic Sciences, Central University of Punjab, Bathinda, 151001 India
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16
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Krauskopf K, Lang K. Increasing the chemical space of proteins in living cells via genetic code expansion. Curr Opin Chem Biol 2020; 58:112-120. [PMID: 32911429 DOI: 10.1016/j.cbpa.2020.07.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/20/2020] [Accepted: 07/27/2020] [Indexed: 01/30/2023]
Abstract
In recent years it has become possible to genetically encode an expanded set of designer amino acids with tailored chemical and physical properties (dubbed unnatural amino acids, UAAs) into proteins in living cells by expanding the genetic code. Together with developments in chemistries that are amenable to and selective within physiological settings, these strategies have started to have a big impact on biological studies, as they enable exciting in cellulo applications. Here we highlight recent advances to covalently stabilize transient protein-protein interactions and capture enzyme substrate-complexes in living cells using proximity-triggered and residue-selective photo-induced crosslinking approaches. Furthermore, we describe recent efforts in controlling enzyme activity with photocaged UAAs and in extending their application to a variety of enzymatic scaffolds. In addition, we discuss the site-specific incorporation of UAAs mimicking post-translational modifications (PTMs) and approaches to generate natively-linked ubiquitin-protein conjugates to probe the role of PTMs in modulating complex cellular networks.
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Affiliation(s)
- Kristina Krauskopf
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany.
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Yi D, Xing J, Gao Y, Pan X, Xie P, Yang J, Wang Q, Gao X. Enhancement of keratin-degradation ability of the keratinase KerBL from Bacillus licheniformis WHU by proximity-triggered chemical crosslinking. Int J Biol Macromol 2020; 163:1458-1470. [PMID: 32771518 DOI: 10.1016/j.ijbiomac.2020.08.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 02/06/2023]
Abstract
Keratinases are valuable enzymes, given their application in keratin-rich waste recycling. Considering that keratinases usually require reducing agents to efficiently degrade keratin, improving the stability of keratinases under reducing conditions is highly desirable for practical applications. Here, we show that the introduction of several tyrosine derivatives containing para-substituted long-chain haloalkanes into the keratinase KerBL, which enabled proximity-triggered covalent crosslinking by rational design, could improve both the thermostability and autolytic resistance of the enzyme. After screening a series of noncanonical amino acid (ncAA)-based variants generated by rational design, two variants, N159C/Y260BprY and N159C/Y260BbtY, with enhanced keratinolytic activity were obtained. Both variants increased the Tm of the enzyme by approximately 10 °C. The potential mechanism underlying these improvements was investigated by molecular dynamics (MD) analysis. The results indicated that BprY-Cys and BbtY-Cys covalent bonds in the N159C/Y260TAG variant could significantly decrease the flexibility and fluctuations of the long loop (residues 151-162).
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Affiliation(s)
- Dong Yi
- School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Juan Xing
- Department of Pathophysiology, College of Basic Medical Science, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Yanping Gao
- School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Xianchao Pan
- School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Peijuan Xie
- School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Jian Yang
- School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Qin Wang
- School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China.
| | - Xiaowei Gao
- School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China; Key Laboratory of Medical Electrophysiology, Ministry of Education, Institute of Cardiovascular Research of Southwest Medical University, Luzhou 646000, China.
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