1
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Ding W, Yu W, Chen Y, Lao L, Fang Y, Fang C, Zhao H, Yang B, Lin S. Rare codon recoding for efficient noncanonical amino acid incorporation in mammalian cells. Science 2024; 384:1134-1142. [PMID: 38843324 DOI: 10.1126/science.adm8143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/03/2024] [Indexed: 06/16/2024]
Abstract
The ability to genetically encode noncanonical amino acids (ncAAs) has empowered proteins with improved or previously unknown properties. However, existing strategies in mammalian cells rely on the introduction of a blank codon to incorporate ncAAs, which is inefficient and limits their widespread applications. In this study, we developed a rare codon recoding strategy that takes advantage of the relative rarity of the TCG codon to achieve highly selective and efficient ncAA incorporation through systematic engineering and big data-model predictions. We highlight the broad utility of this strategy for the incorporation of dozens of ncAAs into various functional proteins at the wild-type protein expression levels, as well as the synthesis of proteins with up to six-site ncAAs or four distinct ncAAs in mammalian cells for downstream applications.
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Affiliation(s)
- Wenlong Ding
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Wei Yu
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Yulin Chen
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Lihui Lao
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Yu Fang
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Chengzhu Fang
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Hongxia Zhao
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Bo Yang
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Shixian Lin
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
- Department of Medical Oncology, State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
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2
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Ishida S, Ngo PHT, Gundlach A, Ellington A. Engineering Ribosomal Machinery for Noncanonical Amino Acid Incorporation. Chem Rev 2024. [PMID: 38829723 DOI: 10.1021/acs.chemrev.3c00912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
The introduction of noncanonical amino acids into proteins has enabled researchers to modify fundamental physicochemical and functional properties of proteins. While the alteration of the genetic code, via the introduction of orthogonal aminoacyl-tRNA synthetase:tRNA pairs, has driven many of these efforts, the various components involved in the process of translation are important for the development of new genetic codes. In this review, we will focus on recent advances in engineering ribosomal machinery for noncanonical amino acid incorporation and genetic code modification. The engineering of the ribosome itself will be considered, as well as the many factors that interact closely with the ribosome, including both tRNAs and accessory factors, such as the all-important EF-Tu. Given the success of genome re-engineering efforts, future paths for radical alterations of the genetic code will require more expansive alterations in the translation machinery.
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Affiliation(s)
- Satoshi Ishida
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Phuoc H T Ngo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Arno Gundlach
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew Ellington
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
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3
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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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4
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Rodríguez-Robles E, Müller D, Künzl T, Nemat SJ, Edelmann MP, Srivastava P, Louis D, Groaz E, Tiefenbacher K, Roberts TM, Herdewijn P, Marlière P, Panke S. Rational design of a bacterial import system for new-to-nature molecules. Metab Eng 2024:S1096-7176(24)00071-5. [PMID: 38802041 DOI: 10.1016/j.ymben.2024.05.005] [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: 01/14/2024] [Revised: 04/27/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Integration of novel compounds into biological processes holds significant potential for modifying or expanding existing cellular functions. However, the cellular uptake of these compounds is often hindered by selectively permeable membranes. We present a novel bacterial transport system that has been rationally designed to address this challenge. Our approach utilizes a highly promiscuous sulfonate membrane transporter, which allows the passage of cargo molecules attached as amides to a sulfobutanoate transport vector molecule into the cytoplasm of the cell. These cargoes can then be unloaded from the sulfobutanoyl amides using an engineered variant of the enzyme γ-glutamyl transferase, which hydrolyzes the amide bond and releases the cargo molecule within the cell. Here, we provide evidence for the broad substrate specificity of both components of the system by evaluating a panel of structurally diverse sulfobutanoyl amides. Furthermore, we successfully implement the synthetic uptake system in vivo and showcase its functionality by importing an impermeant non-canonical amino acid.
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Affiliation(s)
- Emilio Rodríguez-Robles
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - David Müller
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Tilmann Künzl
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Suren J Nemat
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Martin Peter Edelmann
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Puneet Srivastava
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Elisabetta Groaz
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Tania Michelle Roberts
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Sven Panke
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
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5
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Allen MC, Karplus PA, Mehl RA, Cooley RB. Genetic Encoding of Phosphorylated Amino Acids into Proteins. Chem Rev 2024; 124:6592-6642. [PMID: 38691379 DOI: 10.1021/acs.chemrev.4c00110] [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: 05/03/2024]
Abstract
Reversible phosphorylation is a fundamental mechanism for controlling protein function. Despite the critical roles phosphorylated proteins play in physiology and disease, our ability to study individual phospho-proteoforms has been hindered by a lack of versatile methods to efficiently generate homogeneous proteins with site-specific phosphoamino acids or with functional mimics that are resistant to phosphatases. Genetic code expansion (GCE) is emerging as a transformative approach to tackle this challenge, allowing direct incorporation of phosphoamino acids into proteins during translation in response to amber stop codons. This genetic programming of phospho-protein synthesis eliminates the reliance on kinase-based or chemical semisynthesis approaches, making it broadly applicable to diverse phospho-proteoforms. In this comprehensive review, we provide a brief introduction to GCE and trace the development of existing GCE technologies for installing phosphoserine, phosphothreonine, phosphotyrosine, and their mimics, discussing both their advantages as well as their limitations. While some of the technologies are still early in their development, others are already robust enough to greatly expand the range of biologically relevant questions that can be addressed. We highlight new discoveries enabled by these GCE approaches, provide practical considerations for the application of technologies by non-GCE experts, and also identify avenues ripe for further development.
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Affiliation(s)
- Michael C Allen
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
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6
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Awawdeh A, Radecki AA, Vargas-Rodriguez O. Suppressor tRNAs at the interface of genetic code expansion and medicine. Front Genet 2024; 15:1420331. [PMID: 38798701 PMCID: PMC11116698 DOI: 10.3389/fgene.2024.1420331] [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: 04/19/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024] Open
Abstract
Suppressor transfer RNAs (sup-tRNAs) are receiving renewed attention for their promising therapeutic properties in treating genetic diseases caused by nonsense mutations. Traditionally, sup-tRNAs have been created by replacing the anticodon sequence of native tRNAs with a suppressor sequence. However, due to their complex interactome, considering other structural and functional tRNA features for design and engineering can yield more effective sup-tRNA therapies. For over 2 decades, the field of genetic code expansion (GCE) has created a wealth of knowledge, resources, and tools to engineer sup-tRNAs. In this Mini Review, we aim to shed light on how existing knowledge and strategies to develop sup-tRNAs for GCE can be adopted to accelerate the discovery of efficient and specific sup-tRNAs for medical treatment options. We highlight methods and milestones and discuss how these approaches may enlighten the research and development of tRNA medicines.
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Affiliation(s)
| | | | - Oscar Vargas-Rodriguez
- Department of Molecular Biology and Biophysics, University of Connecticut School of Medicine, Farmington, CT, United States
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7
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Hampton JT, Liu WR. Diversification of Phage-Displayed Peptide Libraries with Noncanonical Amino Acid Mutagenesis and Chemical Modification. Chem Rev 2024; 124:6051-6077. [PMID: 38686960 PMCID: PMC11082904 DOI: 10.1021/acs.chemrev.4c00004] [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: 01/02/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Sitting on the interface between biologics and small molecules, peptides represent an emerging class of therapeutics. Numerous techniques have been developed in the past 30 years to take advantage of biological methods to generate and screen peptide libraries for the identification of therapeutic compounds, with phage display being one of the most accessible techniques. Although traditional phage display can generate billions of peptides simultaneously, it is limited to expression of canonical amino acids. Recently, several groups have successfully undergone efforts to apply genetic code expansion to introduce noncanonical amino acids (ncAAs) with novel reactivities and chemistries into phage-displayed peptide libraries. In addition to biological methods, several different chemical approaches have also been used to install noncanonical motifs into phage libraries. This review focuses on these recent advances that have taken advantage of both biological and chemical means for diversification of phage libraries with ncAAs.
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Affiliation(s)
- J. Trae Hampton
- Texas
A&M Drug Discovery Center and Department of Chemistry, College
of Arts and Sciences, Texas A&M University, College Station, Texas 77843, United States
| | - Wenshe Ray Liu
- Texas
A&M Drug Discovery Center and Department of Chemistry, College
of Arts and Sciences, Texas A&M University, College Station, Texas 77843, United States
- Institute
of Biosciences and Technology and Department of Translational Medical
Sciences, College of Medicine, Texas A&M
University, Houston, Texas 77030, United States
- Department
of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas 77843, United States
- Department
of Cell Biology and Genetics, College of Medicine, Texas A&M University, College
Station, Texas 77843, United States
- Department
of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas 77843, United States
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8
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Breunig SL, Chapman AM, LeBon J, Quijano JC, Ranasinghe M, Rawson J, Demeler B, Ku HT, Tirrell DA. 4S-fluorination of ProB29 in insulin lispro slows fibril formation. J Biol Chem 2024; 300:107332. [PMID: 38703998 PMCID: PMC11154709 DOI: 10.1016/j.jbc.2024.107332] [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: 11/21/2023] [Revised: 04/02/2024] [Accepted: 04/09/2024] [Indexed: 05/06/2024] Open
Abstract
Recombinant insulin is a life-saving therapeutic for millions of patients affected by diabetes mellitus. Standard mutagenesis has led to insulin variants with improved control of blood glucose; for instance, the fast-acting insulin lispro contains two point mutations that suppress dimer formation and expedite absorption. However, insulins undergo irreversible denaturation, a process accelerated for the insulin monomer. Here we replace ProB29 of insulin lispro with 4R-fluoroproline, 4S-fluoroproline, and 4,4-difluoroproline. All three fluorinated lispro variants reduce blood glucose in diabetic mice, exhibit similar secondary structure as measured by CD, and rapidly dissociate from the zinc- and resorcinol-bound hexamer upon dilution. Notably, however, we find that 4S-fluorination of ProB29 delays the formation of undesired insulin fibrils that can accumulate at the injection site in vivo and can complicate insulin production and storage. These results demonstrate how subtle molecular changes achieved through non-canonical amino acid mutagenesis can improve the stability of protein therapeutics.
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Affiliation(s)
- Stephanie L Breunig
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Alex M Chapman
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Jeanne LeBon
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute City of Hope, Duarte, California, USA
| | - Janine C Quijano
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute City of Hope, Duarte, California, USA
| | - Maduni Ranasinghe
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Jeffrey Rawson
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute City of Hope, Duarte, California, USA
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada; Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana, USA
| | - Hsun Teresa Ku
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute City of Hope, Duarte, California, USA; Irell & Manella Graduate School of Biological Science, City of Hope, Duarte, California, USA
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA.
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9
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Fröhlich M, Söllner J, Derler I. Insights into the dynamics of the Ca2+ release-activated Ca2+ channel pore-forming complex Orai1. Biochem Soc Trans 2024; 52:747-760. [PMID: 38526208 DOI: 10.1042/bst20230815] [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: 12/20/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/26/2024]
Abstract
An important calcium (Ca2+) entry pathway into the cell is the Ca2+ release-activated Ca2+ (CRAC) channel, which controls a series of downstream signaling events such as gene transcription, secretion and proliferation. It is composed of a Ca2+ sensor in the endoplasmic reticulum (ER), the stromal interaction molecule (STIM), and the Ca2+ ion channel Orai in the plasma membrane (PM). Their activation is initiated by receptor-ligand binding at the PM, which triggers a signaling cascade within the cell that ultimately causes store depletion. The decrease in ER-luminal Ca2+ is sensed by STIM1, which undergoes structural rearrangements that lead to coupling with Orai1 and its activation. In this review, we highlight the current understanding of the Orai1 pore opening mechanism. In this context, we also point out the questions that remain unanswered and how these can be addressed by the currently emerging genetic code expansion (GCE) technology. GCE enables the incorporation of non-canonical amino acids with novel properties, such as light-sensitivity, and has the potential to provide novel insights into the structure/function relationship of CRAC channels at a single amino acid level in the living cell.
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Affiliation(s)
- Maximilian Fröhlich
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020 Linz, Austria
| | - Julia Söllner
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020 Linz, Austria
| | - Isabella Derler
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020 Linz, Austria
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10
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Jansen S, Mayer C. A Robust Growth-Based Selection Platform to Evolve an Enzyme via Dependency on Noncanonical Tyrosine Analogues. JACS AU 2024; 4:1583-1590. [PMID: 38665651 PMCID: PMC11040555 DOI: 10.1021/jacsau.4c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 04/28/2024]
Abstract
Growth-based selections evaluate the fitness of individual organisms at a population level. In enzyme engineering, such growth selections allow for the rapid and straightforward identification of highly efficient biocatalysts from extensive libraries. However, selection-based improvement of (synthetically useful) biocatalysts is challenging, as they require highly dependable strategies that artificially link their activities to host survival. Here, we showcase a robust and scalable growth-based selection platform centered around the complementation of noncanonical amino acid-dependent bacteria. Specifically, we demonstrate how serial passaging of populations featuring millions of carbamoylase variants autonomously selects biocatalysts with up to 90,000-fold higher initial rates. Notably, selection of replicate populations enriched diverse biocatalysts, which feature distinct amino acid motifs that drastically boost carbamoylase activity. As beneficial substitutions also originated from unintended copying errors during library preparation or cell division, we anticipate that our growth-based selection platform will be applicable to the continuous, autonomous evolution of diverse biocatalysts in the future.
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Affiliation(s)
- Suzanne
C. Jansen
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
| | - Clemens Mayer
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
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11
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Wang JH, Gessler DJ, Zhan W, Gallagher TL, Gao G. Adeno-associated virus as a delivery vector for gene therapy of human diseases. Signal Transduct Target Ther 2024; 9:78. [PMID: 38565561 PMCID: PMC10987683 DOI: 10.1038/s41392-024-01780-w] [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: 07/05/2023] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 04/04/2024] Open
Abstract
Adeno-associated virus (AAV) has emerged as a pivotal delivery tool in clinical gene therapy owing to its minimal pathogenicity and ability to establish long-term gene expression in different tissues. Recombinant AAV (rAAV) has been engineered for enhanced specificity and developed as a tool for treating various diseases. However, as rAAV is being more widely used as a therapy, the increased demand has created challenges for the existing manufacturing methods. Seven rAAV-based gene therapy products have received regulatory approval, but there continue to be concerns about safely using high-dose viral therapies in humans, including immune responses and adverse effects such as genotoxicity, hepatotoxicity, thrombotic microangiopathy, and neurotoxicity. In this review, we explore AAV biology with an emphasis on current vector engineering strategies and manufacturing technologies. We discuss how rAAVs are being employed in ongoing clinical trials for ocular, neurological, metabolic, hematological, neuromuscular, and cardiovascular diseases as well as cancers. We outline immune responses triggered by rAAV, address associated side effects, and discuss strategies to mitigate these reactions. We hope that discussing recent advancements and current challenges in the field will be a helpful guide for researchers and clinicians navigating the ever-evolving landscape of rAAV-based gene therapy.
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Affiliation(s)
- Jiang-Hui Wang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, 3002, Australia
| | - Dominic J Gessler
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Neurological Surgery, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Wei Zhan
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Thomas L Gallagher
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
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12
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Nagasawa Y, Nakayama M, Kato Y, Ogawa Y, Aribam SD, Tsugami Y, Iwata T, Mikami O, Sugiyama A, Onishi M, Hayashi T, Eguchi M. A novel vaccine strategy using quick and easy conversion of bacterial pathogens to unnatural amino acid-auxotrophic suicide derivatives. Microbiol Spectr 2024; 12:e0355723. [PMID: 38385737 PMCID: PMC10986568 DOI: 10.1128/spectrum.03557-23] [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: 10/04/2023] [Accepted: 01/24/2024] [Indexed: 02/23/2024] Open
Abstract
We propose a novel strategy for quick and easy preparation of suicide live vaccine candidates against bacterial pathogens. This method requires only the transformation of one or more plasmids carrying genes encoding for two types of biological devices, an unnatural amino acid (uAA) incorporation system and toxin-antitoxin systems in which translation of the antitoxins requires the uAA incorporation. Escherichia coli BL21-AI laboratory strains carrying the plasmids were viable in the presence of the uAA, whereas the free toxins killed these strains after the removal of the uAA. The survival time after uAA removal could be controlled by the choice of the uAA incorporation system and toxin-antitoxin systems. Multilayered toxin-antitoxin systems suppressed escape frequency to less than 1 escape per 109 generations in the best case. This conditional suicide system also worked in Salmonella enterica and E. coli clinical isolates. The S. enterica vaccine strains were attenuated with a >105 fold lethal dose. Serum IgG response and protection against the parental pathogenic strain were confirmed. In addition, the live E. coli vaccine strain was significantly more immunogenic and provided greater protection than a formalin-inactivated vaccine. The live E. coli vaccine was not detected after inoculation, presumably because the uAA is not present in the host animals or the natural environment. These results suggest that this strategy provides a novel way to rapidly produce safe and highly immunogenic live bacterial vaccine candidates. IMPORTANCE Live vaccines are the oldest vaccines with a history of more than 200 years. Due to their strong immunogenicity, live vaccines are still an important category of vaccines today. However, the development of live vaccines has been challenging due to the difficulties in achieving a balance between safety and immunogenicity. In recent decades, the frequent emergence of various new and old pathogens at risk of causing pandemics has highlighted the need for rapid vaccine development processes. We have pioneered the use of uAAs to control gene expression and to conditionally kill host bacteria as a biological containment system. This report proposes a quick and easy conversion of bacterial pathogens into live vaccine candidates using this containment system. The balance between safety and immunogenicity can be modulated by the selection of the genetic devices used. Moreover, the uAA-auxotrophy can prevent the vaccine from infecting other individuals or establishing the environment.
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Affiliation(s)
- Yuya Nagasawa
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Momoko Nakayama
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Yusuke Kato
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Yohsuke Ogawa
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Swarmistha Devi Aribam
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Yusaku Tsugami
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Taketoshi Iwata
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Osamu Mikami
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Aoi Sugiyama
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Megumi Onishi
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Tomohito Hayashi
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Masahiro Eguchi
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
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13
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Munoz-Robles BG, DeForest CA. Irreversible light-activated SpyLigation mediates split-protein assembly in 4D. Nat Protoc 2024; 19:1015-1052. [PMID: 38253657 DOI: 10.1038/s41596-023-00938-0] [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: 04/18/2023] [Accepted: 10/23/2023] [Indexed: 01/24/2024]
Abstract
The conditional assembly of split-protein pairs to modulate biological activity is commonly achieved by fusing split-protein fragments to dimerizing components that bring inactive pairs into close proximity in response to an exogenous trigger. However, current methods lack full spatial and temporal control over reconstitution, require sustained activation and lack specificity. Here light-activated SpyLigation (LASL), based on the photoregulation of the covalent SpyTag (ST)/SpyCatcher (SC) peptide-protein reaction, assembles nonfunctional split fragment pairs rapidly and irreversibly in solution, in engineered biomaterials and intracellularly. LASL introduces an ortho-nitrobenzyl(oNB)-caged lysine into SC's reactive site to generate a photoactivatable SC (pSC). Split-protein pairs of interest fused to pSC and ST are conditionally assembled via near-ultraviolet or pulsed near-infrared irradiation, as the uncaged SC can react with ST to ligate appended fragments. We describe procedures for the efficient synthesis of the photocaged amino acid that is incorporated within pSC (<5 days) as well as the design and cloning of LASL plasmids (1-4 days) for recombinant protein expression in either Escherichia coli (5-6 days) or mammalian cells (4-6 days), which require some prior expertise in protein engineering. We provide a chemoenzymatic scheme for appending bioorthogonal reactive handles onto E. coli-purified pSC protein (<4 days) that permits LASL component incorporation and patterned protein activation within many common biomaterial platforms. Given that LASL is irreversible, the photolithographic patterning procedures are fast and do not require sustained light exposure. Overall, LASL can be used to interrogate and modulate cell signaling in various settings.
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Affiliation(s)
- Brizzia G Munoz-Robles
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Cole A DeForest
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, USA.
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA.
- Department of Chemistry, University of Washington, Seattle, WA, USA.
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
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14
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Haney AK, Cropp TA. Blocking and rescuing tryptophan interactions. Nat Chem 2024; 16:485-486. [PMID: 38528104 DOI: 10.1038/s41557-024-01478-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Affiliation(s)
- Aidan K Haney
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, USA
| | - T Ashton Cropp
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, USA.
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15
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Charalampidou A, Nehls T, Meyners C, Gandhesiri S, Pomplun S, Pentelute BL, Lermyte F, Hausch F. Automated Flow Peptide Synthesis Enables Engineering of Proteins with Stabilized Transient Binding Pockets. ACS CENTRAL SCIENCE 2024; 10:649-657. [PMID: 38559286 PMCID: PMC10979424 DOI: 10.1021/acscentsci.3c01283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 04/04/2024]
Abstract
Engineering at the amino acid level is key to enhancing the properties of existing proteins in a desired manner. So far, protein engineering has been dominated by genetic approaches, which have been extremely powerful but only allow for minimal variations beyond the canonical amino acids. Chemical peptide synthesis allows the unrestricted incorporation of a vast set of unnatural amino acids with much broader functionalities, including the incorporation of post-translational modifications or labels. Here we demonstrate the potential of chemical synthesis to generate proteins in a specific conformation, which would have been unattainable by recombinant protein expression. We use recently established rapid automated flow peptide synthesis combined with solid-phase late-stage modifications to rapidly generate a set of FK506-binding protein 51 constructs bearing defined intramolecular lactam bridges. This trapped an otherwise rarely populated transient pocket-as confirmed by crystal structures-which led to an up to 39-fold improved binding affinity for conformation-selective ligands and represents a unique system for the development of ligands for this rare conformation. Overall, our results show how rapid automated flow peptide synthesis can be applied to precision protein engineering.
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Affiliation(s)
- Anna Charalampidou
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
| | - Thomas Nehls
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
| | - Christian Meyners
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
| | - Satish Gandhesiri
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Sebastian Pomplun
- Leiden
Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg
55, 2333 CC Leiden, The Netherlands
| | - Bradley L. Pentelute
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Frederik Lermyte
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
- Department
of Synthetic Biology, Technical University
of Darmstadt, 64287 Darmstadt, Germany
| | - Felix Hausch
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
- Department
of Synthetic Biology, Technical University
of Darmstadt, 64287 Darmstadt, Germany
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16
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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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17
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Bell EL, Hutton AE, Burke AJ, O'Connell A, Barry A, O'Reilly E, Green AP. Strategies for designing biocatalysts with new functions. Chem Soc Rev 2024; 53:2851-2862. [PMID: 38353665 PMCID: PMC10946311 DOI: 10.1039/d3cs00972f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Indexed: 03/19/2024]
Abstract
The engineering of natural enzymes has led to the availability of a broad range of biocatalysts that can be used for the sustainable manufacturing of a variety of chemicals and pharmaceuticals. However, for many important chemical transformations there are no known enzymes that can serve as starting templates for biocatalyst development. These limitations have fuelled efforts to build entirely new catalytic sites into proteins in order to generate enzymes with functions beyond those found in Nature. This bottom-up approach to enzyme development can also reveal new fundamental insights into the molecular origins of efficient protein catalysis. In this tutorial review, we will survey the different strategies that have been explored for designing new protein catalysts. These methods will be illustrated through key selected examples, which demonstrate how highly proficient and selective biocatalysts can be developed through experimental protein engineering and/or computational design. Given the rapid pace of development in the field, we are optimistic that designer enzymes will begin to play an increasingly prominent role as industrial biocatalysts in the coming years.
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Affiliation(s)
- Elizabeth L Bell
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Amy E Hutton
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Ashleigh J Burke
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Adam O'Connell
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Amber Barry
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Elaine O'Reilly
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Anthony P Green
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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18
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Loynd C, Singha Roy SJ, Ovalle VJ, Canarelli SE, Mondal A, Jewel D, Ficaretta ED, Weerapana E, Chatterjee A. Electrochemical labelling of hydroxyindoles with chemoselectivity for site-specific protein bioconjugation. Nat Chem 2024; 16:389-397. [PMID: 38082177 PMCID: PMC10932882 DOI: 10.1038/s41557-023-01375-y] [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: 05/23/2022] [Accepted: 10/18/2023] [Indexed: 02/06/2024]
Abstract
Electrochemistry has recently emerged as a powerful approach in small-molecule synthesis owing to its numerous attractive features, including precise control over the fundamental reaction parameters, mild reaction conditions and innate scalability. Even though these advantages also make it an attractive strategy for chemoselective modification of complex biomolecules such as proteins, such applications remain poorly developed. Here we report an electrochemically promoted coupling reaction between 5-hydroxytryptophan (5HTP) and simple aromatic amines-electrochemical labelling of hydroxyindoles with chemoselectivity (eCLIC)-that enables site-specific labelling of full-length proteins under mild conditions. Using genetic code expansion technology, the 5HTP residue can be incorporated into predefined sites of a recombinant protein expressed in either prokaryotic or eukaryotic hosts for subsequent eCLIC labelling. We used the eCLIC reaction to site-specifically label various recombinant proteins, including a full-length human antibody. Furthermore, we show that eCLIC is compatible with strain-promoted alkyne-azide and alkene-tetrazine click reactions, enabling site-specific modification of proteins at two different sites with distinct labels.
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Affiliation(s)
- Conor Loynd
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | | | - Vincent J Ovalle
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Sarah E Canarelli
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Atanu Mondal
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Delilah Jewel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Elise D Ficaretta
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA.
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19
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Jewel D, Kelemen RE, Huang RL, Zhu Z, Sundaresh B, Malley K, Pham Q, Loynd C, Huang Z, van Opijnen T, Chatterjee A. Enhanced Directed Evolution in Mammalian Cells Yields a Hyperefficient Pyrrolysyl tRNA for Noncanonical Amino Acid Mutagenesis. Angew Chem Int Ed Engl 2024; 63:e202316428. [PMID: 38279536 PMCID: PMC10922736 DOI: 10.1002/anie.202316428] [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: 11/01/2023] [Indexed: 01/28/2024]
Abstract
Heterologous tRNAs used for noncanonical amino acid (ncAA) mutagenesis in mammalian cells typically show poor activity. We recently introduced a virus-assisted directed evolution strategy (VADER) that can enrich improved tRNA mutants from naïve libraries in mammalian cells. However, VADER was limited to processing only a few thousand mutants; the inability to screen a larger sequence space precluded the identification of highly active variants with distal synergistic mutations. Here, we report VADER2.0, which can process significantly larger mutant libraries. It also employs a novel library design, which maintains base-pairing between distant residues in the stem regions, allowing us to pack a higher density of functional mutants within a fixed sequence space. VADER2.0 enabled simultaneous engineering of the entire acceptor stem of M. mazei pyrrolysyl tRNA (tRNAPyl ), leading to a remarkably improved variant, which facilitates more efficient incorporation of a wider range of ncAAs, and enables facile development of viral vectors and stable cell-lines for ncAA mutagenesis.
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Affiliation(s)
- Delilah Jewel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Rachel E Kelemen
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Rachel L Huang
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Zeyu Zhu
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
| | | | - Kaitlin Malley
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Quan Pham
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Conor Loynd
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Zeyi Huang
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Tim van Opijnen
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
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20
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Kozma E, Kele P. Bioorthogonal Reactions in Bioimaging. Top Curr Chem (Cham) 2024; 382:7. [PMID: 38400853 PMCID: PMC10894152 DOI: 10.1007/s41061-024-00452-1] [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: 10/27/2023] [Accepted: 01/22/2024] [Indexed: 02/26/2024]
Abstract
Visualization of biomolecules in their native environment or imaging-aided understanding of more complex biomolecular processes are one of the focus areas of chemical biology research, which requires selective, often site-specific labeling of targets. This challenging task is effectively addressed by bioorthogonal chemistry tools in combination with advanced synthetic biology methods. Today, the smart combination of the elements of the bioorthogonal toolbox allows selective installation of multiple markers to selected targets, enabling multicolor or multimodal imaging of biomolecules. Furthermore, recent developments in bioorthogonally applicable probe design that meet the growing demands of superresolution microscopy enable more complex questions to be addressed. These novel, advanced probes enable highly sensitive, low-background, single- or multiphoton imaging of biological species and events in live organisms at resolutions comparable to the size of the biomolecule of interest. Herein, the latest developments in bioorthogonal fluorescent probe design and labeling schemes will be discussed in the context of in cellulo/in vivo (multicolor and/or superresolved) imaging schemes. The second part focuses on the importance of genetically engineered minimal bioorthogonal tags, with a particular interest in site-specific protein tagging applications to answer biological questions.
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Affiliation(s)
- Eszter Kozma
- Chemical Biology Research Group, Institute of Organic Chemistry, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, Budapest, 1117, Hungary
| | - Péter Kele
- Chemical Biology Research Group, Institute of Organic Chemistry, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, Budapest, 1117, Hungary.
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21
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Weinzapfel EN, Fedder-Semmes KN, Sun ZW, Keogh MC. Beyond the tail: the consequence of context in histone post-translational modification and chromatin research. Biochem J 2024; 481:219-244. [PMID: 38353483 PMCID: PMC10903488 DOI: 10.1042/bcj20230342] [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: 12/30/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
The role of histone post-translational modifications (PTMs) in chromatin structure and genome function has been the subject of intense debate for more than 60 years. Though complex, the discourse can be summarized in two distinct - and deceptively simple - questions: What is the function of histone PTMs? And how should they be studied? Decades of research show these queries are intricately linked and far from straightforward. Here we provide a historical perspective, highlighting how the arrival of new technologies shaped discovery and insight. Despite their limitations, the tools available at each period had a profound impact on chromatin research, and provided essential clues that advanced our understanding of histone PTM function. Finally, we discuss recent advances in the application of defined nucleosome substrates, the study of multivalent chromatin interactions, and new technologies driving the next era of histone PTM research.
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22
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Brown W, Davidson LA, Deiters A. Expanding the Genetic Code of Xenopus laevis Embryos. ACS Chem Biol 2024; 19:516-525. [PMID: 38277773 PMCID: PMC10877573 DOI: 10.1021/acschembio.3c00686] [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: 11/10/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/28/2024]
Abstract
The incorporation of unnatural amino acids into proteins through genetic code expansion has been successfully adapted to African claw-toed frog embryos. Six unique unnatural amino acids are incorporated site-specifically into proteins and demonstrate robust and reliable protein expression. Of these amino acids, several are caged analogues that can be used to establish conditional control over enzymatic activity. Using light or small molecule triggers, we exhibit activation and tunability of protein functions in live embryos. This approach was then applied to optical control over the activity of a RASopathy mutant of NRAS, taking advantage of generating explant cultures from Xenopus. Taken together, genetic code expansion is a robust approach in the Xenopus model to incorporate novel chemical functionalities into proteins of interest to study their function and role in a complex biological setting.
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Affiliation(s)
- Wes Brown
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Lance A. Davidson
- Departments
of Bioengineering, Developmental Biology, and Computational and Systems
Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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23
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Blake LA, De La Cruz A, Wu B. Imaging spatiotemporal translation regulation in vivo. Semin Cell Dev Biol 2024; 154:155-164. [PMID: 36963991 PMCID: PMC10514244 DOI: 10.1016/j.semcdb.2023.03.006] [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: 03/23/2022] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/26/2023]
Abstract
Translation is regulated spatiotemporally to direct protein synthesis when and where it is needed. RNA localization and local translation have been observed in various subcellular compartments, allowing cells to rapidly and finely adjust their proteome post-transcriptionally. Local translation on membrane-bound organelles is important to efficiently synthesize proteins targeted to the organelles. Protein-RNA phase condensates restrict RNA spatially in membraneless organelles and play essential roles in translation regulation and RNA metabolism. In addition, the temporal translation kinetics not only determine the amount of protein produced, but also serve as an important checkpoint for the quality of ribosomes, mRNAs, and nascent proteins. Translation imaging provides a unique capability to study these fundamental processes in the native environment. Recent breakthroughs in imaging enabled real-time visualization of translation of single mRNAs, making it possible to determine the spatial distribution and key biochemical parameters of in vivo translation dynamics. Here we reviewed the recent advances in translation imaging methods and their applications to study spatiotemporal translation regulation in vivo.
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Affiliation(s)
- Lauren A Blake
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ana De La Cruz
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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24
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Giltrap A, Yuan Y, Davis BG. Late-Stage Functionalization of Living Organisms: Rethinking Selectivity in Biology. Chem Rev 2024; 124:889-928. [PMID: 38231473 PMCID: PMC10870719 DOI: 10.1021/acs.chemrev.3c00579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 01/18/2024]
Abstract
With unlimited selectivity, full post-translational chemical control of biology would circumvent the dogma of genetic control. The resulting direct manipulation of organisms would enable atomic-level precision in "editing" of function. We argue that a key aspect that is still missing in our ability to do this (at least with a high degree of control) is the selectivity of a given chemical reaction in a living organism. In this Review, we systematize existing illustrative examples of chemical selectivity, as well as identify needed chemical selectivities set in a hierarchy of anatomical complexity: organismo- (selectivity for a given organism over another), tissuo- (selectivity for a given tissue type in a living organism), cellulo- (selectivity for a given cell type in an organism or tissue), and organelloselectivity (selectivity for a given organelle or discrete body within a cell). Finally, we analyze more traditional concepts such as regio-, chemo-, and stereoselective reactions where additionally appropriate. This survey of late-stage biomolecule methods emphasizes, where possible, functional consequences (i.e., biological function). In this way, we explore a concept of late-stage functionalization of living organisms (where "late" is taken to mean at a given state of an organism in time) in which programmed and selective chemical reactions take place in life. By building on precisely analyzed notions (e.g., mechanism and selectivity) we believe that the logic of chemical methodology might ultimately be applied to increasingly complex molecular constructs in biology. This could allow principles developed at the simple, small-molecule level to progress hierarchically even to manipulation of physiology.
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Affiliation(s)
- Andrew
M. Giltrap
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Yizhi Yuan
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Benjamin G. Davis
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
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25
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Zhang XD, Wang YS, Xiang H, Bai LW, Cheng P, Li K, Huang R, Wang X, Lei X. Nucleoside modification-based flexizymes with versatile activity for tRNA aminoacylation. Chem Commun (Camb) 2024; 60:1607-1610. [PMID: 38230513 DOI: 10.1039/d3cc05673b] [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: 01/18/2024]
Abstract
Extensive research has focused on genetic code reprogramming using flexizymes (Fxs), ribozymes enabling diverse tRNA acylation. Here we describe a nucleoside-modification strategy for the preparation of flexizyme variants derived from 2'-OMe, 2'-F, and 2'-MOE modifications with unique and versatile activities, enabling the charging of tRNAs with a broad range of substrates. This innovative strategy holds promise for synthetic biology applications, offering a robust pathway to expand the genetic code for diverse substrate incorporation.
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Affiliation(s)
- Xin-Dan Zhang
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China.
| | - Yi-Shen Wang
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China.
| | - Hua Xiang
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China.
| | - Li-Wen Bai
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China.
| | - Peng Cheng
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China.
| | - Kai Li
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Rong Huang
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China.
| | - Xiaolei Wang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Xinxiang Lei
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China.
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
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26
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Galano‐Frutos JJ, Sancho J. Energy, water, and protein folding: A molecular dynamics-based quantitative inventory of molecular interactions and forces that make proteins stable. Protein Sci 2024; 33:e4905. [PMID: 38284492 PMCID: PMC10804899 DOI: 10.1002/pro.4905] [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: 06/21/2023] [Revised: 12/12/2023] [Accepted: 01/05/2024] [Indexed: 01/30/2024]
Abstract
Protein folding energetics can be determined experimentally on a case-by-case basis but it is not understood in sufficient detail to provide deep control in protein design. The fundamentals of protein stability have been outlined by calorimetry, protein engineering, and biophysical modeling, but these approaches still face great difficulty in elucidating the specific contributions of the intervening molecules and physical interactions. Recently, we have shown that the enthalpy and heat capacity changes associated to the protein folding reaction can be calculated within experimental error using molecular dynamics simulations of native protein structures and their corresponding unfolded ensembles. Analyzing in depth molecular dynamics simulations of four model proteins (CI2, barnase, SNase, and apoflavodoxin), we dissect here the energy contributions to ΔH (a key component of protein stability) made by the molecular players (polypeptide and solvent molecules) and physical interactions (electrostatic, van der Waals, and bonded) involved. Although the proteins analyzed differ in length, isoelectric point and fold class, their folding energetics is governed by the same quantitative pattern. Relative to the unfolded ensemble, the native conformations are enthalpically stabilized by comparable contributions from protein-protein and solvent-solvent interactions, and almost equally destabilized by interactions between protein and solvent molecules. The native protein surface seems to interact better with water than the unfolded one, but this is outweighed by the unfolded surface being larger. From the perspective of physical interactions, the native conformations are stabilized by van de Waals and Coulomb interactions and destabilized by conformational strain arising from bonded interactions. Also common to the four proteins, the sign of the heat capacity change is set by interactions between protein and solvent molecules or, from the alternative perspective, by Coulomb interactions.
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Affiliation(s)
- Juan José Galano‐Frutos
- Biocomputation and Complex Systems Physics Institute (BIFI)‐Joint Unit GBsC‐CSICUniversity of ZaragozaZaragozaSpain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de CienciasUniversity of ZaragozaZaragozaSpain
| | - Javier Sancho
- Biocomputation and Complex Systems Physics Institute (BIFI)‐Joint Unit GBsC‐CSICUniversity of ZaragozaZaragozaSpain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de CienciasUniversity of ZaragozaZaragozaSpain
- Aragon Health Research Institute (IIS Aragón)ZaragozaSpain
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27
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Wang Y, Ji Y, Sun L, Huang Z, Ye S, Xuan W. A Sirtuin-Dependent T7 RNA Polymerase Variant. ACS Synth Biol 2024; 13:54-60. [PMID: 38117980 DOI: 10.1021/acssynbio.3c00607] [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: 12/22/2023]
Abstract
Transcriptional regulation is of great significance for cells to maintain homeostasis and, meanwhile, represents an innovative but less explored means to control biological processes in synthetic biology and bioengineering. Herein we devised a T7 RNA polymerase (T7RNAP) variant through replacing an essential lysine located in the catalytic core (K631) with Nε-acetyl-l-lysine (AcK) via genetic code expansion. This T7RNAP variant requires the deacetylase activity of NAD-dependent sirtuins to recover its enzymatic activities and thereby sustains sirtuin-dependent transcription of the gene of interest in live cells including bacteria and mammalian cells as well as in in vitro systems. This T7RNAP variant could link gene transcription to sirtuin expression and NAD availability, thus holding promise to support some relevant research.
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Affiliation(s)
- Yongan Wang
- Frontiers Science Center for Synthetic Biology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Yanli Ji
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Lin Sun
- Frontiers Science Center for Synthetic Biology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Zhifen Huang
- Frontiers Science Center for Synthetic Biology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Sheng Ye
- Frontiers Science Center for Synthetic Biology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Weimin Xuan
- Frontiers Science Center for Synthetic Biology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
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28
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Erickson SB, Pham Q, Cao X, Glicksman J, Kelemen RE, Shahraeini SS, Bodkin S, Kiyam Z, Chatterjee A. Precise Manipulation of the Site and Stoichiometry of Capsid Modification Enables Optimization of Functional Adeno-Associated Virus Conjugates. Bioconjug Chem 2024; 35:64-71. [PMID: 38103182 PMCID: PMC10924286 DOI: 10.1021/acs.bioconjchem.3c00411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
The ability to engineer adeno-associated virus (AAV) vectors for targeted transduction of specific cell types is critically important to fully harness their potential for human gene therapy. A promising approach to achieve this objective involves chemically attaching retargeting ligands onto the virus capsid. Site-specific incorporation of a bioorthogonal noncanonical amino acid (ncAA) into the AAV capsid proteins provides a particularly attractive strategy to introduce such modifications with exquisite precision. In this study, we show that using ncAA mutagenesis, it is possible to systematically alter the attachment site of a retargeting ligand (cyclic-RGD) on the AAV capsid to create diverse conjugate architectures and that the site of attachment heavily impacts the retargeting efficiency. We further demonstrate that the performance of these AAV conjugates is highly sensitive to the stoichiometry of capsid labeling (labels per capsid), with an intermediate labeling density providing optimal activity for cRGD-mediated retargeting. Finally, we developed a technology to more precisely control the number of attachment sites per AAV capsid by selectively incorporating an ncAA into the minor capsid proteins with high fidelity and efficiency, such that AAV conjugates with varying stoichiometry can be synthesized. Together, this platform provides unparalleled control over the site and stoichiometry of capsid modification, which will enable the development of next-generation AAV vectors tailored with desirable attributes.
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Affiliation(s)
| | | | - Xiaofu Cao
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Jake Glicksman
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Rachel E. Kelemen
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Seyed S. Shahraeini
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Sebastian Bodkin
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Zainab Kiyam
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
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29
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Icking LS, Riedlberger AM, Krause F, Widder J, Frederiksen A, Stockert F, Spädt M, Edel N, Armbruster D, Forlani G, Franchini S, Kaas P, Kırpat Konak BM, Krier F, Lefebvre M, Mazraeh D, Ranniger J, Gerstenecker J, Gescher P, Voigt K, Salavei P, Gensch N, Di Ventura B, Öztürk MA. iNClusive: a database collecting useful information on non-canonical amino acids and their incorporation into proteins for easier genetic code expansion implementation. Nucleic Acids Res 2024; 52:D476-D482. [PMID: 37986218 PMCID: PMC10767842 DOI: 10.1093/nar/gkad1090] [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: 08/14/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
The incorporation of non-canonical amino acids (ncAAs) into proteins is a powerful technique used in various research fields. Genetic code expansion (GCE) is the most common way to achieve this: a specific codon is selected to be decoded by a dedicated tRNA orthogonal to the endogenous ones. In the past 30 years, great progress has been made to obtain novel tRNA synthetases (aaRSs) accepting a variety of ncAAs with distinct physicochemical properties, to develop robust in vitro assays or approaches for codon reassignment. This sparked the use of the technique, leading to the accumulation of publications, from which gathering all relevant information can appear daunting. Here we present iNClusive (https://non-canonical-aas.biologie.uni-freiburg.de/), a manually curated, extensive repository using standardized nomenclature that provides organized information on ncAAs successfully incorporated into target proteins as verified by mass spectrometry. Since we focused on tRNA synthetase-based tRNA loading, we provide the sequence of the tRNA and aaRS used for the incorporation. Derived from more than 687 peer-reviewed publications, it currently contains 2432 entries about 466 ncAAs, 569 protein targets, 500 aaRSs and 144 tRNAs. We foresee iNClusive will encourage more researchers to experiment with ncAA incorporation thus contributing to the further development of this exciting technique.
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Affiliation(s)
- Leon-Samuel Icking
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Andreas Martin Riedlberger
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Fabian Krause
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Jonas Widder
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Anne Smedegaard Frederiksen
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Fabian Stockert
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Michael Spädt
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Nikita Edel
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Daniel Armbruster
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Giada Forlani
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstr. 19A, 79104, Freiburg, Germany
| | - Selene Franchini
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Paulina Kaas
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Büşra Merve Kırpat Konak
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Fabrice Krier
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Maïwenn Lefebvre
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Daniel Mazraeh
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Jeremy Ranniger
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Johanna Gerstenecker
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Pia Gescher
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Karsten Voigt
- Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Pavel Salavei
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Nicole Gensch
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Barbara Di Ventura
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Mehmet Ali Öztürk
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
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30
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Lee CH, Park S, Kim S, Hyun JY, Lee HS, Shin I. Engineering of cell-surface receptors for analysis of receptor internalization and detection of receptor-specific glycosylation. Chem Sci 2024; 15:555-565. [PMID: 38179521 PMCID: PMC10762726 DOI: 10.1039/d3sc05054h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
The epidermal growth factor receptor (EGFR) is a cell-surface glycoprotein that is involved mainly in cell proliferation. Overexpression of this receptor is intimately related to the development of a broad spectrum of tumors. In addition, glycans linked to the EGFR are known to affect its EGF-induced activation. Because of the pathophysiological significance of the EGFR, we prepared a fluorescently labeled EGFR (EGFR128-AZDye 488) on the cell surface by employing the genetic code expansion technique and bioorthogonal chemistry. EGFR128-AZDye 488 was initially utilized to investigate time-dependent endocytosis of the EGFR in live cells. The results showed that an EGFR inhibitor and antibody suppress endocytosis of the EGFR promoted by the EGF, and that lectins recognizing glycans of the EGFR do not enhance EGFR internalization into cells. Observations made in studies of the effects of appended glycans on the entry of the EGFR into cells indicate that a de-sialylated or de-fucosylated EGFR is internalized into cells more efficiently than a wild-type EGFR. Furthermore, by using the FRET-based imaging method of cells which contain an EGFR linked to AZDye 488 (a FRET donor) and cellular glycans labeled with rhodamine (a FRET acceptor), sialic acid residues attached to the EGFR were specifically detected on the live cell surface. Taken together, the results suggest that a fluorescently labeled EGFR will be a valuable tool in studies aimed at gaining an understanding of cellular functions of the EGFR.
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Affiliation(s)
- Chang-Hee Lee
- Department of Chemistry, Yonsei University Seoul 03722 Republic of Korea
| | - Sookil Park
- Department of Chemistry, Yonsei University Seoul 03722 Republic of Korea
| | - Sanggil Kim
- Department of Chemistry, Sogang University Seoul 04107 Republic of Korea
| | - Ji Young Hyun
- Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology Daejeon 34114 Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University Seoul 04107 Republic of Korea
| | - Injae Shin
- Department of Chemistry, Yonsei University Seoul 03722 Republic of Korea
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31
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Dunkelmann DL, Piedrafita C, Dickson A, Liu KC, Elliott TS, Fiedler M, Bellini D, Zhou A, Cervettini D, Chin JW. Adding α,α-disubstituted and β-linked monomers to the genetic code of an organism. Nature 2024; 625:603-610. [PMID: 38200312 PMCID: PMC10794150 DOI: 10.1038/s41586-023-06897-6] [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: 04/29/2023] [Accepted: 11/23/2023] [Indexed: 01/12/2024]
Abstract
The genetic code of living cells has been reprogrammed to enable the site-specific incorporation of hundreds of non-canonical amino acids into proteins, and the encoded synthesis of non-canonical polymers and macrocyclic peptides and depsipeptides1-3. Current methods for engineering orthogonal aminoacyl-tRNA synthetases to acylate new monomers, as required for the expansion and reprogramming of the genetic code, rely on translational readouts and therefore require the monomers to be ribosomal substrates4-6. Orthogonal synthetases cannot be evolved to acylate orthogonal tRNAs with non-canonical monomers (ncMs) that are poor ribosomal substrates, and ribosomes cannot be evolved to polymerize ncMs that cannot be acylated onto orthogonal tRNAs-this co-dependence creates an evolutionary deadlock that has essentially restricted the scope of translation in living cells to α-L-amino acids and closely related hydroxy acids. Here we break this deadlock by developing tRNA display, which enables direct, rapid and scalable selection for orthogonal synthetases that selectively acylate their cognate orthogonal tRNAs with ncMs in Escherichia coli, independent of whether the ncMs are ribosomal substrates. Using tRNA display, we directly select orthogonal synthetases that specifically acylate their cognate orthogonal tRNA with eight non-canonical amino acids and eight ncMs, including several β-amino acids, α,α-disubstituted-amino acids and β-hydroxy acids. We build on these advances to demonstrate the genetically encoded, site-specific cellular incorporation of β-amino acids and α,α-disubstituted amino acids into a protein, and thereby expand the chemical scope of the genetic code to new classes of monomers.
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Affiliation(s)
| | - Carlos Piedrafita
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Alexandre Dickson
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kim C Liu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Thomas S Elliott
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Marc Fiedler
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Dom Bellini
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Andrew Zhou
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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32
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Reddi R, Chatterjee S, Matulef K, Gustafson A, Gao L, Valiyaveetil FI. A facile approach for incorporating tyrosine esters to probe ion-binding sites and backbone hydrogen bonds. J Biol Chem 2024; 300:105517. [PMID: 38042487 PMCID: PMC10790091 DOI: 10.1016/j.jbc.2023.105517] [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: 07/20/2023] [Revised: 11/06/2023] [Accepted: 11/22/2023] [Indexed: 12/04/2023] Open
Abstract
Amide-to-ester substitutions are used to study the role of the amide bonds of the protein backbone in protein structure, function, and folding. An amber suppressor tRNA/synthetase pair has been reported for incorporation of p-hydroxy-phenyl-L-lactic acid (HPLA), thereby introducing ester substitution at tyrosine residues. However, the application of this approach was limited due to the low yields of the modified proteins and the high cost of HPLA. Here we report the in vivo generation of HPLA from the significantly cheaper phenyl-L-lactic acid. We also construct an optimized plasmid with the HPLA suppressor tRNA/synthetase pair that provides higher yields of the modified proteins. The combination of the new plasmid and the in-situ generation of HPLA provides a facile and economical approach for introducing tyrosine ester substitutions. We demonstrate the utility of this approach by introducing tyrosine ester substitutions into the K+ channel KcsA and the integral membrane enzyme GlpG. We introduce the tyrosine ester in the selectivity filter of the M96V mutant of the KcsA to probe the role of the second ion binding site in the conformation of the selectivity filter and the process of inactivation. We use tyrosine ester substitutions in GlpG to perturb backbone H-bonds to investigate the contribution of these H-bonds to membrane protein stability. We anticipate that the approach developed in this study will facilitate further investigations using tyrosine ester substitutions.
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Affiliation(s)
- Ravikumar Reddi
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Multnomah County, Portland, Oregon, USA
| | - Satyaki Chatterjee
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Multnomah County, Portland, Oregon, USA
| | - Kimberly Matulef
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Multnomah County, Portland, Oregon, USA
| | - Andrew Gustafson
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Multnomah County, Portland, Oregon, USA
| | - Lujia Gao
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Multnomah County, Portland, Oregon, USA
| | - Francis I Valiyaveetil
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Multnomah County, Portland, Oregon, USA.
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33
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Liu Y, Lu X, Chen M, Wei Z, Peng G, Yang J, Tang C, Yu P. Advances in screening, synthesis, modification, and biomedical applications of peptides and peptide aptamers. Biofactors 2024; 50:33-57. [PMID: 37646383 DOI: 10.1002/biof.2001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
Peptides and peptide aptamers have emerged as promising molecules for a wide range of biomedical applications due to their unique properties and versatile functionalities. The screening strategies for identifying peptides and peptide aptamers with desired properties are discussed, including high-throughput screening, display screening technology, and in silico design approaches. The synthesis methods for the efficient production of peptides and peptide aptamers, such as solid-phase peptide synthesis and biosynthesis technology, are described, along with their advantages and limitations. Moreover, various modification techniques are explored to enhance the stability, specificity, and pharmacokinetic properties of peptides and peptide aptamers. This includes chemical modifications, enzymatic modifications, biomodifications, genetic engineering modifications, and physical modifications. Furthermore, the review highlights the diverse biomedical applications of peptides and peptide aptamers, including targeted drug delivery, diagnostics, and therapeutic. This review provides valuable insights into the advancements in screening, synthesis, modification, and biomedical applications of peptides and peptide aptamers. A comprehensive understanding of these aspects will aid researchers in the development of novel peptide-based therapeutics and diagnostic tools for various biomedical challenges.
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Affiliation(s)
- Yijie Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Xiaoling Lu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Meilun Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Zheng Wei
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Guangnan Peng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Jie Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Chunhua Tang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Peng Yu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
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34
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Šlachtová V, Chovanec M, Rahm M, Vrabel M. Bioorthogonal Chemistry in Cellular Organelles. Top Curr Chem (Cham) 2023; 382:2. [PMID: 38103067 PMCID: PMC10725395 DOI: 10.1007/s41061-023-00446-5] [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: 10/06/2023] [Accepted: 11/12/2023] [Indexed: 12/17/2023]
Abstract
While bioorthogonal reactions are routinely employed in living cells and organisms, their application within individual organelles remains limited. In this review, we highlight diverse examples of bioorthogonal reactions used to investigate the roles of biomolecules and biological processes as well as advanced imaging techniques within cellular organelles. These innovations hold great promise for therapeutic interventions in personalized medicine and precision therapies. We also address existing challenges related to the selectivity and trafficking of subcellular dynamics. Organelle-targeted bioorthogonal reactions have the potential to significantly advance our understanding of cellular organization and function, provide new pathways for basic research and clinical applications, and shape the direction of cell biology and medical research.
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Affiliation(s)
- Veronika Šlachtová
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic
| | - Marek Chovanec
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic
- University of Chemistry and Technology, Technická 5, 166 28, Prague 6, Czech Republic
| | - Michal Rahm
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic
- University of Chemistry and Technology, Technická 5, 166 28, Prague 6, Czech Republic
| | - Milan Vrabel
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic.
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35
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Chang H, Du A, Jiang J, Ren L, Liu N, Zhou X, Liang J, Gao G, Wang D. Non-canonical amino acid incorporation into AAV5 capsid enhances lung transduction in mice. Mol Ther Methods Clin Dev 2023; 31:101129. [PMID: 37886602 PMCID: PMC10597788 DOI: 10.1016/j.omtm.2023.101129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023]
Abstract
Gene therapy using recombinant adeno-associated virus (rAAV) relies on safe, efficient, and precise in vivo gene delivery that is largely dependent on the AAV capsid. The proteinaceous capsid is highly amenable to engineering using a variety of approaches, and most resulting capsids carry substitutions or insertions comprised of natural amino acids. Here, we incorporated a non-canonical amino acid (ncAA), Nε-2-azideoethyloxycarbonyl-L-lysine (also known as NAEK), into the AAV5 capsid using genetic code expansion, and serendipitously found that several NAEK-AAV5 vectors transduced various cell lines more efficiently than the parental rAAV5. Furthermore, one NAEK-AAV5 vector showed lung-specific transduction enhancement following systemic or intranasal delivery in mice. Structural modeling suggests that the long side chain of NAEK may impact on the 3-fold protrusion on the capsid surface that plays a key role in tropism, thereby modulating vector transduction. Recent advances in genetic code expansion have generated synthetic proteins carrying an increasing number of ncAAs that possess diverse biological properties. Our study suggests that ncAA incorporation into the AAV capsid may confer novel vector properties, opening a new and complementary avenue to gene therapy vector discovery.
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Affiliation(s)
- Hao Chang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Ailing Du
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jun Jiang
- GeneLeap Bio, Luye Life Sciences, Woburn, MA 01801, USA
| | - Lingzhi Ren
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nan Liu
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Xuntao Zhou
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jialing Liang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Dan Wang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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36
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Wang TY, Meng FD, Sang GJ, Zhang HL, Tian ZJ, Zheng H, Cai XH, Tang YD. A novel viral vaccine platform based on engineered transfer RNA. Emerg Microbes Infect 2023; 12:2157339. [PMID: 36482724 PMCID: PMC9769134 DOI: 10.1080/22221751.2022.2157339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In recent years, an increasing number of emerging and remerging virus outbreaks have occurred and the rapid development of vaccines against these viruses has been crucial. Controlling the replication of premature termination codon (PTC)-containing viruses is a promising approach to generate live but replication-defective viruses that can be used for potent vaccines. Here, we used anticodon-engineered transfer RNAs (ACE-tRNAs) as powerful precision switches to control the replication of PTC-containing viruses. We showed that ACE-tRNAs display higher potency of reading through PTCs than genetic code expansion (GCE) technology. Interestingly, ACE-tRNA has a site preference that may influence its read-through efficacy. We further attempted to use ACE-tRNAs as a novel viral vaccine platform. Using a human immunodeficiency virus type 1 (HIV-1) pseudotyped virus as an RNA virus model, we found that ACE-tRNAs display high potency for read-through viral PTCs and precisely control their production. Pseudorabies virus (PRV), a herpesvirus, was used as a DNA virus model. We found that ACE-tRNAs display high potency for reading through viral PTCs and precisely controlling PTC-containing virus replication. In addition, PTC-engineered PRV completely attenuated and lost virulence in mice in vivo, and immunization with PRV containing a PTC elicited a robust immune response and provided complete protection against wild-type PRV challenge. Overall, replication-controllable PTC-containing viruses based on ACE-tRNAs provide a new strategy to rapidly attenuate virus infection and prime robust immune responses. This technology can be used as a platform for rapidly developing viral vaccines in the future.
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Affiliation(s)
- Tong-Yun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China,Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, People's Republic of China
| | - Fan-Dan Meng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China,Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, People's Republic of China
| | - Guo-Ju Sang
- Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, People's Republic of China
| | - Hong-Liang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Zhi-Jun Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Hao Zheng
- Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China,Hao Zheng Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai150001, People’s Republic of China
| | - Xue-Hui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China,Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, People's Republic of China,Heilongjiang Provincial Research Center for Veterinary Biomedicine, Harbin, People's Republic of China,Xue-Hui Cai State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, People’s Republic of China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin150001, People’s Republic of China
| | - Yan-Dong Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China,Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, People's Republic of China, Yan-Dong Tang
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Ornelas MY, Cournoyer JE, Bram S, Mehta AP. Evolution and synthetic biology. Curr Opin Microbiol 2023; 76:102394. [PMID: 37801925 PMCID: PMC10842511 DOI: 10.1016/j.mib.2023.102394] [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: 02/19/2023] [Revised: 08/29/2023] [Accepted: 09/08/2023] [Indexed: 10/08/2023]
Abstract
Evolutionary observations have often served as an inspiration for biological design. Decoding of the central dogma of life at a molecular level and understanding of the cellular biochemistry have been elegantly used to engineer various synthetic biology applications, including building genetic circuits in vitro and in cells, building synthetic translational systems, and metabolic engineering in cells to biosynthesize and even bioproduce complex high-value molecules. Here, we review three broad areas of synthetic biology that are inspired by evolutionary observations: (i) combinatorial approaches toward cell-based biomolecular evolution, (ii) engineering interdependencies to establish microbial consortia, and (iii) synthetic immunology. In each of the areas, we will highlight the evolutionary premise that was central toward designing these platforms. These are only a subset of the examples where evolution and natural phenomena directly or indirectly serve as a powerful source of inspiration in shaping synthetic biology and biotechnology.
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Affiliation(s)
- Marya Y Ornelas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, IL 61801, United States
| | - Jason E Cournoyer
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, IL 61801, United States
| | - Stanley Bram
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, IL 61801, United States
| | - Angad P Mehta
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, IL 61801, United States; Institute for Genomic Biology, University of Illinois at Urbana, Champaign, United States; Cancer Center at Illinois, University of Illinois at Urbana, Champaign, United States.
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Hanaee-Ahvaz H, Cserjan-Puschmann M, Mayer F, Tauer C, Albrecht B, Furtmüller PG, Wiltschi B, Hahn R, Striedner G. Antibody fragments functionalized with non-canonical amino acids preserving structure and functionality - A door opener for new biological and therapeutic applications. Heliyon 2023; 9:e22463. [PMID: 38046162 PMCID: PMC10686840 DOI: 10.1016/j.heliyon.2023.e22463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 12/05/2023] Open
Abstract
Functionalization of proteins by incorporating reactive non-canonical amino acids (ncAAs) has been widely applied for numerous biological and therapeutic applications. The requirement not to lose the intrinsic properties of these proteins is often underestimated and not considered. Main purpose of this study was to answer the question whether functionalization via residue-specific incorporation of the ncAA N6-[(2-Azidoethoxy) carbonyl]-l-lysine (Azk) influences the properties of the anti-tumor-necrosis-factor-α-Fab (FTN2). Therefore, FTN2Azk variants with different Azk incorporation sites were designed and amber codon suppression was used for production. The functionalized FTN2Azk variants were efficiently produced in fed-batch like μ-bioreactor cultivations in the periplasm of E. coli displaying correct structure and antigen binding affinities comparable to those of wild-type FTN2. Our FTN2Azk variants with reactive handles for diverse conjugates enable tracking of recombinant protein in the production cell, pharmacological studies and translation into new pharmaceutical applications.
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Affiliation(s)
- Hana Hanaee-Ahvaz
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Florian Mayer
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Christopher Tauer
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Bernd Albrecht
- Biopharma Austria, Process Science, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, A-1121, Vienna, Austria
| | - Paul G. Furtmüller
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, 1190, Vienna, Austria
| | - Birgit Wiltschi
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Rainer Hahn
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
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Xu SY, Zhou L, Xu Y, Hong HY, Dai C, Wang YJ, Zheng YG. Recent advances in structure-based enzyme engineering for functional reconstruction. Biotechnol Bioeng 2023; 120:3427-3445. [PMID: 37638646 DOI: 10.1002/bit.28540] [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: 05/04/2023] [Revised: 07/27/2023] [Accepted: 08/15/2023] [Indexed: 08/29/2023]
Abstract
Structural information can help engineer enzymes. Usually, specific amino acids in particular regions are targeted for functional reconstruction to enhance the catalytic performance, including activity, stereoselectivity, and thermostability. Appropriate selection of target sites is the key to structure-based design, which requires elucidation of the structure-function relationships. Here, we summarize the mutations of residues in different specific regions, including active center, access tunnels, and flexible loops, on fine-tuning the catalytic performance of enzymes, and discuss the effects of altering the local structural environment on the functions. In addition, we keep up with the recent progress of structure-based approaches for enzyme engineering, aiming to provide some guidance on how to take advantage of the structural information.
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Affiliation(s)
- Shen-Yuan Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Lei Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Ying Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Han-Yue Hong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Chen Dai
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
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40
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Núñez-Villanueva D, Hunter CA. Replication of synthetic recognition-encoded oligomers by ligation of trimer building blocks. Org Chem Front 2023; 10:5950-5957. [PMID: 38022796 PMCID: PMC10661083 DOI: 10.1039/d3qo01717f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023]
Abstract
The development of methods for replication of synthetic information oligomers will underpin the use of directed evolution to search new chemical space. Template-directed replication of triazole oligomers has been achieved using a covalent primer in conjunction with non-covalent binding of complementary building blocks. A phenol primer equipped with an alkyne was first attached to a benzoic recognition unit on a mixed sequence template via selective covalent ester base-pair formation. The remaining phenol recognition units on the template were then used for non-covalent binding of phosphine oxide oligomers equipped with an azide. The efficiency of the templated CuAAC reaction between the primer and phosphine oxide building blocks was investigated as a function of the number of H-bonds formed with the template. Increasing the strength of the non-covalent interaction between the template and the azide lead to a significant acceleration of the templated reaction. For shorter phosphine oxide oligomers intermolecular reactions compete with the templated process, but quantitative templated primer elongation was achieved with a phosphine oxide 3-mer building block that was able to form three H-bonds with the template. NMR spectroscopy and molecular models suggest that the template can fold, but addition of the phosphine oxide 3-mer leads to a complex with three H-bonds between phosphine oxide and phenol groups, aligning the azide and alkyne groups in a favourable geometry for the CuAAC reaction. In the product duplex, 1H and 31P NMR data confirm the presence of the three H-bonded base-pairs, demonstrating that the covalent and non-covalent base-pairs are geometrically compatible. A complete replication cycle was carried out starting from the oligotriazole template by covalent attachment of the primer, followed by template-directed elongation, and hydrolysis of the the ester base-pair in the resulting duplex to regenerate the template and liberate the copy strand. We have previously demonstrated sequence-selective oligomer replication using covalent base-pairing, but the trimer building block approach described here is suitable for replication of sequence information using non-covalent binding of the monomer building blocks to a template.
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Affiliation(s)
- Diego Núñez-Villanueva
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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41
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Song CH, Jeong M, In H, Kim JH, Lin CW, Han KH. Trends in the Development of Antibody-Drug Conjugates for Cancer Therapy. Antibodies (Basel) 2023; 12:72. [PMID: 37987250 PMCID: PMC10660735 DOI: 10.3390/antib12040072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023] Open
Abstract
In cancer treatment, the first-generation, cytotoxic drugs, though effective against cancer cells, also harmed healthy ones. The second-generation targeted cancer cells precisely to inhibit their growth. Enter the third-generation, consisting of immuno-oncology drugs, designed to combat drug resistance and bolster the immune system's defenses. These advanced therapies operate by obstructing the uncontrolled growth and spread of cancer cells through the body, ultimately eliminating them effectively. Within the arsenal of cancer treatment, monoclonal antibodies offer several advantages, including inducing cancer cell apoptosis, precise targeting, prolonged presence in the body, and minimal side effects. A recent development in cancer therapy is Antibody-Drug Conjugates (ADCs), initially developed in the mid-20th century. The second generation of ADCs addressed this issue through innovative antibody modification techniques, such as DAR regulation, amino acid substitutions, incorporation of non-natural amino acids, and enzymatic drug attachment. Currently, a third generation of ADCs is in development. This study presents an overview of 12 available ADCs, reviews 71 recent research papers, and analyzes 128 clinical trial reports. The overarching objective is to gain insights into the prevailing trends in ADC research and development, with a particular focus on emerging frontiers like potential targets, linkers, and drug payloads within the realm of cancer treatment.
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Affiliation(s)
- Chi Hun Song
- Department of Biological Sciences and Biotechnology, Hannam University, Daejeon 34054, Republic of Korea; (C.H.S.); (M.J.); (H.I.); (J.H.K.)
| | - Minchan Jeong
- Department of Biological Sciences and Biotechnology, Hannam University, Daejeon 34054, Republic of Korea; (C.H.S.); (M.J.); (H.I.); (J.H.K.)
| | - Hyukmin In
- Department of Biological Sciences and Biotechnology, Hannam University, Daejeon 34054, Republic of Korea; (C.H.S.); (M.J.); (H.I.); (J.H.K.)
| | - Ji Hoe Kim
- Department of Biological Sciences and Biotechnology, Hannam University, Daejeon 34054, Republic of Korea; (C.H.S.); (M.J.); (H.I.); (J.H.K.)
| | - Chih-Wei Lin
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung 406, Taiwan;
| | - Kyung Ho Han
- Department of Biological Sciences and Biotechnology, Hannam University, Daejeon 34054, Republic of Korea; (C.H.S.); (M.J.); (H.I.); (J.H.K.)
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Sushkin ME, Koehler C, Lemke EA. Remodeling the cellular stress response for enhanced genetic code expansion in mammalian cells. Nat Commun 2023; 14:6931. [PMID: 37903771 PMCID: PMC10616097 DOI: 10.1038/s41467-023-42689-2] [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: 09/30/2022] [Accepted: 10/18/2023] [Indexed: 11/01/2023] Open
Abstract
Genetic code expansion (GCE) reprograms the translational machinery to site-specifically incorporate noncanonical amino acids (ncAAs) into a selected protein. The efficiency of GCE in mammalian cells might be compromised by cellular stress responses, among which, the protein kinase R(PKR)-dependent eIF2α phosphorylation pathway can reduce translation rates. Here we test several strategies to engineer the eIF2α pathway and boost the rate of translation and show that such interventions increase GCE efficiency in mammalian cells. In particular, addition of the N-terminal PKR fragment (1-174) provides a substantial enhancement in cytoplasmic GCE and also in GCE realized by OTOs (orthogonally translating designer organelles), which built on the principle of 2D phase separation to enable mRNA-selective ncAA incorporation. Our study demonstrates an approach for improving the efficiency of GCE and provides a means by which the power of designer organelles can be further optimized to tune protein translation.
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Affiliation(s)
- Mikhail E Sushkin
- Biocenter, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
- International PhD Programme of the Institute of Molecular Biology, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Christine Koehler
- Biocenter, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
- VERAXA Biotech GmbH, Carl-Friedrich-Gauß-Ring 5, 69124, Heidelberg, Germany
| | - Edward A Lemke
- Biocenter, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany.
- Institute of Molecular Biology gGmbH, Ackermannweg 4, 55128, Mainz, Germany.
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Furuhashi T, Sakamoto K, Wada A. Genetic Code Expansion and a Photo-Cross-Linking Reaction Facilitate Ribosome Display Selections for Identifying a Wide Range of Affinity Peptides. Int J Mol Sci 2023; 24:15661. [PMID: 37958644 PMCID: PMC10650079 DOI: 10.3390/ijms242115661] [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: 09/03/2023] [Revised: 10/12/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Cell-free molecular display techniques have been utilized to select various affinity peptides from peptide libraries. However, conventional techniques have difficulties associated with the translational termination through in-frame UAG stop codons and the amplification of non-specific peptides, which hinders the desirable selection of low-affinity peptides. To overcome these problems, we established a scheme for ribosome display selection of peptide epitopes bound to monoclonal antibodies and then applied genetic code expansion with synthetic X-tRNAUAG reprogramming of the UAG codons (X = Tyr, Trp, or p-benzoyl-l-phenylalanine (pBzo-Phe)) to the scheme. Based on the assessment of the efficiency of in vitro translation with X-tRNAUAG, we carried out ribosome display selection with genetic code expansion using Trp-tRNAUAG, and we verified that affinity peptides could be identified efficiently regardless of the presence of UAG codons in the peptide coding sequences. Additionally, after evaluating the photo-cross-linking reactions of pBzo-Phe-incorporated peptides, we performed ribosome display selection of low-affinity peptides in combination with genetic code expansion using pBzo-Phe-tRNAUAG and photo-irradiation. The results demonstrated that sub-micromolar low-affinity peptide epitopes could be identified through the formation of photo-induced covalent bonds with monoclonal antibodies. Thus, the developed ribosome display techniques could contribute to the promotion of diverse peptide-based research.
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Affiliation(s)
- Takuto Furuhashi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
- Laboratory for Advanced Biomolecular Engineering, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
| | - Kensaku Sakamoto
- Laboratory for Nonnatural Amino Acid Technology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan;
- Department of Drug Target Protein Research, School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto 390-8621, Nagano, Japan
| | - Akira Wada
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
- Laboratory for Advanced Biomolecular Engineering, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
- Laboratory for Nonnatural Amino Acid Technology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan;
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Zhao S, Liu D. Applications of genetic code expansion and photosensitive UAAs in studying membrane proteins. Open Life Sci 2023; 18:20220752. [PMID: 37828978 PMCID: PMC10566474 DOI: 10.1515/biol-2022-0752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 10/14/2023] Open
Abstract
Membrane proteins are the targets for most drugs and play essential roles in many life activities in organisms. In recent years, unnatural amino acids (UAAs) encoded by genetic code expansion (GCE) technology have been widely used, which endow proteins with different biochemical properties. A class of photosensitive UAAs has been widely used to study protein structure and function. Combined with photochemical control with high temporal and spatial resolution, these UAAs have shown broad applicability to solve the problems of natural ion channels and receptor biology. This review will focus on several application examples of light-controlled methods to integrate GCE technology to study membrane protein function in recent years. We will summarize the typical research methods utilizing some photosensitive UAAs to provide common strategies and further new ideas for studying protein function and advancing biological processes.
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Affiliation(s)
- Shu Zhao
- School of Life Sciences, Nantong Laboratory of Development and Diseases, Nantong University, Nantong, 226019, China
| | - Dong Liu
- School of Life Sciences, Nantong Laboratory of Development and Diseases, Nantong University, Nantong, 226019, China
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45
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Zhou W, Ryan A, Janosko CP, Shoger KE, Haugh JM, Gottschalk RA, Deiters A. Isoform-specific optical activation of kinase function reveals p38-ERK signaling crosstalk. RSC Chem Biol 2023; 4:765-773. [PMID: 37799579 PMCID: PMC10549237 DOI: 10.1039/d2cb00157h] [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: 06/28/2022] [Accepted: 08/08/2023] [Indexed: 10/07/2023] Open
Abstract
Evolution has diversified the mammalian proteome by the generation of protein isoforms that originate from identical genes, e.g., through alternative gene splicing or post-translational modifications, or very similar genes found in gene families. Protein isoforms can have either overlapping or unique functions and traditional chemical, biochemical, and genetic techniques are often limited in their ability to differentiate between isoforms due to their high similarity. This is particularly true in the context of highly dynamic cell signaling cascades, which often require acute spatiotemporal perturbation to assess mechanistic details. To that end, we describe a method for the selective perturbation of the individual protein isoforms of the mitogen-activated protein kinase (MAPK) p38. The genetic installation of a photocaging group at a conserved active site lysine enables the precise light-controlled initiation of kinase signaling, followed by investigation of downstream events. Through optical control, we have identified a novel point of crosstalk between two major signaling cascades: the p38/MAPK pathway and the extracellular signal-regulated kinase (ERK)/MAPK pathway. Specifically, using the photoactivated p38 isoforms, we have found the p38γ and p38δ variants to be positive regulators of the ERK signaling cascade, while confirming the p38α and p38β variants as negative regulators.
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Affiliation(s)
- Wenyuan Zhou
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
| | - Amy Ryan
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
| | - Chasity P Janosko
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
| | - Karsen E Shoger
- Department of Immunology, University of Pittsburgh School of Medicine Pittsburgh PA 15260 USA
- Center for Systems Immunology, University of Pittsburgh Pittsburgh PA 15261 USA
| | - Jason M Haugh
- Department of Chemical and Biomolecular Engineering, North Carolina State University Raleigh NC 27606 USA
| | - Rachel A Gottschalk
- Department of Immunology, University of Pittsburgh School of Medicine Pittsburgh PA 15260 USA
- Center for Systems Immunology, University of Pittsburgh Pittsburgh PA 15261 USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
- Center for Systems Immunology, University of Pittsburgh Pittsburgh PA 15261 USA
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Yang X, Zhao L, Wang Y, Ji Y, Su XC, Ma JA, Xuan W. Constructing Photoactivatable Protein with Genetically Encoded Photocaged Glutamic Acid. Angew Chem Int Ed Engl 2023; 62:e202308472. [PMID: 37587083 DOI: 10.1002/anie.202308472] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/28/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023]
Abstract
Genetically replacing an essential residue with the corresponding photocaged analogues via genetic code expansion (GCE) constitutes a useful and unique strategy to directly and effectively generate photoactivatable proteins. However, the application of this strategy is severely hampered by the limited number of encoded photocaged proteinogenic amino acids. Herein, we report the genetic incorporation of photocaged glutamic acid analogues in E. coli and mammalian cells and demonstrate their use in constructing photoactivatable variants of various fluorescent proteins and SpyCatcher. We believe genetically encoded photocaged Glu would significantly promote the design and application of photoactivatable proteins in many areas.
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Affiliation(s)
- Xiaochen Yang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Lei Zhao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Ying Wang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Yanli Ji
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xun-Cheng Su
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Jun-An Ma
- Department of Chemistry, Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
| | - Weimin Xuan
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
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47
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Royer CA, Tyers M, Tollis S. Absolute quantification of protein number and dynamics in single cells. Curr Opin Struct Biol 2023; 82:102673. [PMID: 37595512 DOI: 10.1016/j.sbi.2023.102673] [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: 04/07/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 08/20/2023]
Abstract
Quantitative characterization of protein abundance and interactions in live cells is necessary to understand and predict cellular behavior. The accurate determination of copy number for individual proteins and heterologous complexes in individual cells is critical because small changes in protein dosage, often less than two-fold, can have strong phenotypic consequences. Here, we review the merits and pitfalls of different quantitative fluorescence imaging methods for single-cell determination of protein abundance, localization, interactions, and dynamics. In particular, we discuss how scanning number and brightness (sN&B) and its variation, Raster scanning image correlation spectroscopy (RICS), exploit stochastic noise in small measurement volumes to quantify protein abundance, stoichiometry, and dynamics with high accuracy.
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Affiliation(s)
- Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy NY 12180, USA.
| | - Mike Tyers
- Program in Molecular Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sylvain Tollis
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210 Finland
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Obeng EM, Steer DL, Fulcher A, Wagstaff KM. Steric-Deficient Oligoglycine Surrogates Facilitate Multivalent and Bifunctional Nanobody Synthesis via Combined Sortase A Transpeptidation and Click Chemistry. Bioconjug Chem 2023; 34:1667-1678. [PMID: 37534819 DOI: 10.1021/acs.bioconjchem.3c00319] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
Conferring multifunctional properties to proteins via enzymatic approaches has greatly facilitated recent progress in protein nanotechnology. In this regard, sortase (Srt) A transpeptidation has facilitated many of these developments due to its exceptional specificity, mild reaction conditions, and complementation with other bioorthogonal techniques, such as click chemistry. In most of these developments, Srt A is used to seamlessly tether oligoglycine-containing molecules to a protein of interest that is equipped with the enzyme's recognition sequence, LPXTG. However, the dependence on oligoglycine attacking nucleophiles and the associated cost of certain derivatives (e.g., cyclooctyne) limit the utility of this approach to lab-scale applications only. Thus, the quest to identify appropriate alternatives and understand their effectiveness remains an important area of research. This study identifies that steric and nucleophilicity-associated effects influence Srt A transpeptidation when two oligoglycine surrogates were examined. The approach was further used in complementation with click chemistry to synthesize bivalent and bifunctional nanobody conjugates for application in epithelial growth factor receptor targeting. The overall technique and tools developed here may facilitate the advancement of future nanotechnologies.
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Affiliation(s)
- Eugene M Obeng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - David L Steer
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton 3800, Victoria, Australia
| | - Alex Fulcher
- Monash Micro Imaging, Monash University, Clayton 3800, Victoria, Australia
| | - Kylie M Wagstaff
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
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49
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Fu J, Li S, Deng L, Zhao X, Yu Z. A genetically encodable and fluorogenic photo-crosslinker via photo-induced defluorination acyl fluoride exchange. Chem Commun (Camb) 2023; 59:11073-11076. [PMID: 37624030 DOI: 10.1039/d3cc02771f] [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: 08/26/2023]
Abstract
We report a genetically encodable m-trifluoromethylaniline modified L-lysine (m-TFMAK) which defluorinates upon light activation and covalently conjugates to native residues via acyl fluoride exchange. The encoded m-TFMAK photo-crosslinks with temporal controllability, residue selectivity, and fluorogenic tracking features, making it suitable for identifying protein interactions in living systems.
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Affiliation(s)
- Jielin Fu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
| | - Sitong Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
| | - Lijun Deng
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
| | - Xiaohu Zhao
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
| | - Zhipeng Yu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
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50
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Zhang X, Huang H, Liu Y, Wu Z, Wang F, Fan X, Chen PR, Wang J. Optical Control of Protein Functions via Genetically Encoded Photocaged Aspartic Acids. J Am Chem Soc 2023; 145:19218-19224. [PMID: 37632461 DOI: 10.1021/jacs.3c03701] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2023]
Abstract
Site-specific protein decaging by light has become an effective approach for in situ manipulation of protein activities in a gain-of-function fashion. Although successful decaging of amino acid side chains of Lys, Tyr, Cys, and Glu has been demonstrated, this strategy has not been extended to aspartic acid (Asp), an essential amino acid residue with a range of protein functions and protein-protein interactions. We herein reported a genetically encoded photocaged Asp and applied it to the photocontrolled manipulation of a panel of proteins including firefly luciferase, kinases (e.g., BRAF), and GTPase (e.g., KRAS) as well as mimicking the in situ phosphorylation event on kinases. As a new member of the increasingly expanded amino acid-decaging toolbox, photocaged Asp may find broad applications for gain-of-function study of diverse proteins as well as biological processes in living cells.
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Affiliation(s)
- Xianrui Zhang
- Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Haoran Huang
- Department of Chemistry, Research Center for Chemical Biology and Omics Analysis, College of Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuan Liu
- Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhigang Wu
- Department of Chemistry, Research Center for Chemical Biology and Omics Analysis, College of Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Fengzhang Wang
- Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xinyuan Fan
- Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Peng R Chen
- Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jie Wang
- Department of Chemistry, Research Center for Chemical Biology and Omics Analysis, College of Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
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