1
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Lee D, Kim JG, Kim TW, Choi JI. Development of orthogonal aminoacyl-tRNA synthetase mutant for incorporating a non-canonical amino acid. AMB Express 2024; 14:60. [PMID: 38782816 PMCID: PMC11116331 DOI: 10.1186/s13568-024-01706-3] [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: 01/29/2024] [Accepted: 04/12/2024] [Indexed: 05/25/2024] Open
Abstract
Genetic code expansion involves introducing non-canonical amino acids (ncAAs) with unique functional groups into proteins to broaden their applications. Orthogonal aminoacyl tRNA synthetase (aaRS), essential for genetic code expansion, facilitates the charging of ncAAs to tRNA. In this study, we developed a new aaRS mutant from Methanosaeta concilii tyrosyl-tRNA synthetase (Mc TyrRS) to incorporate para-azido-L-phenylalanine (AzF). The development involved initial site-specific mutations in Mc TyrRS, followed by random mutagenesis. The new aaRS mutant with amber suppression was isolated through fluorescence-activated cell sorting. The M. concilii aaRS mutant structure was further analyzed to interpret the effect of mutations. This research provides a novel orthogonal aaRS evolution pipeline for highly efficient ncAA incorporation that will contribute to developing novel aaRS from various organisms.
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Affiliation(s)
- Dongheon Lee
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Ja Gyung Kim
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Tae Wan Kim
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju, 61186, Republic of Korea.
| | - Jong-Il Choi
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju, 61186, Republic of Korea.
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2
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Kim S, Kim S, Kim S, Kim N, Lee SW, Yi H, Lee S, Sim T, Kwon Y, Lee HS. Affinity-Directed Site-Specific Protein Labeling and Its Application to Antibody-Drug Conjugates. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306401. [PMID: 38032124 PMCID: PMC10811483 DOI: 10.1002/advs.202306401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/05/2023] [Indexed: 12/01/2023]
Abstract
Chemically modified proteins have diverse applications; however, conventional chemo-selective methods often yield heterogeneously labeled products. To address this limitation, site-specific protein labeling holds significant potential, driving extensive research in this area. Nevertheless, site-specific modification of native proteins remains challenging owing to the complexity of their functional groups. Therefore, a method for site-selective labeling of intact proteins is aimed to design. In this study, a novel approach to traceless affinity-directed intact protein labeling is established, which leverages small binding proteins and genetic code expansion technology. By applying this method, a site-specific antibody labeling with a drug, which leads to the production of highly effective antibody-drug conjugates specifically targeting breast cancer cell lines is achieved. This approach enables traceless conjugation of intact target proteins, which is a critical advantage in pharmaceutical applications. Furthermore, small helical binding proteins can be easily engineered for various target proteins, thereby expanding their potential applications in diverse fields. This innovative approach represents a significant advancement in site-specific modification of native proteins, including antibodies. It also bears immense potential for facilitating the development of therapeutic agents for various diseases.
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Affiliation(s)
- Sooin Kim
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Sanggil Kim
- New Drug Development CenterOsong Medical Innovation Foundation123 Osongsaengmyeong‐ro, Heungdeok‐guCheongjuChungbuk28160Republic of Korea
| | - Sangji Kim
- School of PharmacySungkyunkwan University2066 Seobu‐ro, Jangan‐guSuwon16419Republic of Korea
| | - Namkyoung Kim
- Department of Biomedical SciencesGraduate School of Medical ScienceBrain Korea 21 ProjectYonsei University College of Medicine50 Yonsei‐ro, Seodaemun‐guSeoul03722Republic of Korea
| | - Sang Won Lee
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Hanbin Yi
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Seungeun Lee
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Taebo Sim
- Department of Biomedical SciencesGraduate School of Medical ScienceBrain Korea 21 ProjectYonsei University College of Medicine50 Yonsei‐ro, Seodaemun‐guSeoul03722Republic of Korea
| | - Yongseok Kwon
- School of PharmacySungkyunkwan University2066 Seobu‐ro, Jangan‐guSuwon16419Republic of Korea
| | - Hyun Soo Lee
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
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3
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Perera SM, Aikawa T, Shaner SE, Moran SD, Wang L. Effects of the Intramolecular Group and Solvent on Vibrational Coupling Modes and Strengths of Fermi Resonances in Aryl Azides: A DFT Study of 4-Azidotoluene and 4-Azido- N-phenylmaleimide. J Phys Chem A 2023; 127:8911-8921. [PMID: 37819373 DOI: 10.1021/acs.jpca.3c06312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The high transition dipole strength of the azide asymmetric stretch makes aryl azides good candidates as vibrational probes (VPs). However, aryl azides have complex absorption profiles due to Fermi resonances (FRs). Understanding the origin and the vibrational modes involved in FRs of aryl azides is critically important toward developing them as VPs for studies of protein structures and structural changes in response to their surroundings. As such, we studied vibrational couplings in 4-azidotoluene and 4-azido-N-phenylmaleimide in two solvents, N,N-dimethylacetamide and tetrahydrofuran, to explore the origin and the effects of intramolecular group and solvent on the FRs of aryl azides using density functional theory (DFT) calculations with the B3LYP functional and seven basis sets, 6-31G(d,p), 6-31+G(d,p), 6-31++G(d,p), 6-311G(d,p), 6-311+G(d,p), 6-311++G(d,p), and 6-311++G(df,pd). Two combination bands consisting of the azide symmetric stretch and another mode form strong FRs with the azide asymmetric stretch for both molecules. The FR profile was altered by replacing the methyl group with maleimide. Solvents change the relative peak position and intensity more significantly for 4-azido-N-phenylmaleimide, which makes it a more sensitive VP. Furthermore, the DFT results indicate that a comparison among the results from different basis sets can be used as a means to predict more reliable vibrational spectra.
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Affiliation(s)
- Sathya M Perera
- School of Chemical and Biomolecular Sciences, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Tenyu Aikawa
- School of Chemical and Biomolecular Sciences, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Sarah E Shaner
- Department of Chemistry and Physics, Southeast Missouri State University, Cape Girardeau, Missouri 63701, United States
| | - Sean D Moran
- School of Chemical and Biomolecular Sciences, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Lichang Wang
- School of Chemical and Biomolecular Sciences, Southern Illinois University, Carbondale, Illinois 62901, United States
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4
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Liu J, Hu Y, Gu W, Lan H, Zhang Z, Jiang L, Xu X. Research progress on the application of cell-free synthesis systems for enzymatic processes. Crit Rev Biotechnol 2023; 43:938-955. [PMID: 35994247 DOI: 10.1080/07388551.2022.2090314] [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: 10/13/2021] [Revised: 02/24/2022] [Accepted: 04/09/2022] [Indexed: 11/03/2022]
Abstract
Cell-free synthesis systems can complete the transcription and translation process in vitro to produce complex proteins that are difficult to be expressed in traditional cell-based systems. Such systems also can be used for the assembly of efficient localized multienzyme cascades to synthesize products that are toxic to cells. Cell-free synthesis systems provide a simpler and faster engineering solution than living cells, allowing unprecedented design freedom. This paper reviews the latest progress on the application of cell-free synthesis systems in the field of enzymatic catalysis, including cell-free protein synthesis and cell-free metabolic engineering. In cell-free protein synthesis: complex proteins, toxic proteins, membrane proteins, and artificial proteins containing non-natural amino acids can be easily synthesized by directly controlling the reaction conditions in the cell-free system. In cell-free metabolic engineering, the synthesis of desired products can be made more specific and efficient by designing metabolic pathways and screening biocatalysts based on purified enzymes or crude extracts. Through the combination of cell-free synthesis systems and emerging technologies, such as: synthetic biology, microfluidic control, cofactor regeneration, and artificial scaffolds, we will be able to build increasingly complex biomolecule systems. In the next few years, these technologies are expected to mature and reach industrialization, providing innovative platforms for a wide range of biotechnological applications.
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Affiliation(s)
- Jie Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Yongqi Hu
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wanyi Gu
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Haiquan Lan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Zhidong Zhang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Xian Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
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5
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Lecat-Guillet N, Quast RB, Liu H, Bourrier E, Møller TC, Rovira X, Soldevila S, Lamarque L, Trinquet E, Liu J, Pin JP, Rondard P, Margeat E. Concerted conformational changes control metabotropic glutamate receptor activity. SCIENCE ADVANCES 2023; 9:eadf1378. [PMID: 37267369 PMCID: PMC10413646 DOI: 10.1126/sciadv.adf1378] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 04/27/2023] [Indexed: 06/04/2023]
Abstract
Allosteric modulators bear great potential to fine-tune neurotransmitter action. Promising targets are metabotropic glutamate (mGlu) receptors, which are associated with numerous brain diseases. Orthosteric and allosteric ligands act in synergy to control the activity of these multidomain dimeric GPCRs. Here, we analyzed the effect of such molecules on the concerted conformational changes of full-length mGlu2 at the single-molecule level. We first established FRET sensors through genetic code expansion combined with click chemistry to monitor conformational changes on live cells. We then used single-molecule FRET and show that orthosteric agonist binding leads to the stabilization of most of the glutamate binding domains in their closed state, while the reorientation of the dimer into the active state remains partial. Allosteric modulators, interacting with the transmembrane domain, are required to stabilize the fully reoriented active dimer. These results illustrate how concerted conformational changes within multidomain proteins control their activity, and how these are modulated by allosteric ligands.
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Affiliation(s)
- Nathalie Lecat-Guillet
- Institut de Génomique Fonctionnelle, Univ. Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Robert B. Quast
- Centre de Biologie Structurale (CBS), Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | - Hongkang Liu
- Institut de Génomique Fonctionnelle, Univ. Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
- Key Laboratory of Molecular Biophysics of MOE, International Research Center for Sensory Biology and Technology of MOST, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China
| | | | - Thor C. Møller
- Institut de Génomique Fonctionnelle, Univ. Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Xavier Rovira
- Institut de Génomique Fonctionnelle, Univ. Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | | | | | - Eric Trinquet
- PerkinElmer Cisbio, Parc Marcel Boiteux, 30200 Codolet, France
| | - Jianfeng Liu
- Key Laboratory of Molecular Biophysics of MOE, International Research Center for Sensory Biology and Technology of MOST, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China
| | - Jean-Philippe Pin
- Institut de Génomique Fonctionnelle, Univ. Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Philippe Rondard
- Institut de Génomique Fonctionnelle, Univ. Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), Univ. Montpellier, CNRS, INSERM, Montpellier, France
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6
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Switzer HJ, Howard CA, Halonski JF, Peairs EM, Smith N, Zamecnik MP, Verma S, Young DD. Employing non-canonical amino acids towards the immobilization of a hyperthermophilic enzyme to increase protein stability. RSC Adv 2023; 13:8496-8501. [PMID: 36926306 PMCID: PMC10012417 DOI: 10.1039/d3ra00392b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 02/12/2023] [Indexed: 03/16/2023] Open
Abstract
A carboxylesterase derived from Sulfolobus solfataricus P1 was immobilized onto an epoxy-activated Sepharose resin via non-canonical amino acids. The immobilized enzyme exhibited heightened performance in organic solvents, recyclability, and stability at room temperature for over two years. The incorporation of a non-canonical amino acid afforded a high degree of control over the bioorthogonal immobilization reaction. These results indicate that the specificity conferred by genetic code expansion produces advantages in protein immobilization and broadens the utility of such proteins to non-biological settings.
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Affiliation(s)
| | | | | | - Emily M Peairs
- Department of Chemistry, William & Mary Williamsburg VA USA
| | - Nolan Smith
- Department of Chemistry, William & Mary Williamsburg VA USA
| | | | - Sanjana Verma
- Department of Chemistry, William & Mary Williamsburg VA USA
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7
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Gueta O, Amiram M. Expanding the chemical repertoire of protein-based polymers for drug-delivery applications. Adv Drug Deliv Rev 2022; 190:114460. [PMID: 36030987 DOI: 10.1016/j.addr.2022.114460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/12/2022] [Indexed: 01/24/2023]
Abstract
Expanding the chemical repertoire of natural and artificial protein-based polymers (PBPs) can enable the production of sequence-defined, yet chemically diverse, biopolymers with customized or new properties that cannot be accessed in PBPs composed of only natural amino acids. Various approaches can enable the expansion of the chemical repertoire of PBPs, including chemical and enzymatic treatments or the incorporation of unnatural amino acids. These techniques are employed to install a wide variety of chemical groups-such as bio-orthogonally reactive, cross-linkable, post-translation modifications, and environmentally responsive groups-which, in turn, can facilitate the design of customized PBP-based drug-delivery systems with modified, fine-tuned, or entirely new properties and functions. Here, we detail the existing and emerging technologies for expanding the chemical repertoire of PBPs and review several chemical groups that either demonstrate or are anticipated to show potential in the design of PBP-based drug delivery systems. Finally, we provide our perspective on the remaining challenges and future directions in this field.
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Affiliation(s)
- Osher Gueta
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel
| | - Miriam Amiram
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel.
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8
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Hadar D, Strugach DS, Amiram M. Conjugates of Recombinant Protein‐Based Polymers: Combining Precision with Chemical Diversity. ADVANCED NANOBIOMED RESEARCH 2022. [DOI: 10.1002/anbr.202100142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Dagan Hadar
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering Ben-Gurion University of the Negev P.O. Box 653 Beer-Sheva 8410501 Israel
| | - Daniela S. Strugach
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering Ben-Gurion University of the Negev P.O. Box 653 Beer-Sheva 8410501 Israel
| | - Miriam Amiram
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering Ben-Gurion University of the Negev P.O. Box 653 Beer-Sheva 8410501 Israel
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9
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Lateef OM, Akintubosun MO, Olaoba OT, Samson SO, Adamczyk M. Making Sense of "Nonsense" and More: Challenges and Opportunities in the Genetic Code Expansion, in the World of tRNA Modifications. Int J Mol Sci 2022; 23:938. [PMID: 35055121 PMCID: PMC8779196 DOI: 10.3390/ijms23020938] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 01/09/2023] Open
Abstract
The evolutional development of the RNA translation process that leads to protein synthesis based on naturally occurring amino acids has its continuation via synthetic biology, the so-called rational bioengineering. Genetic code expansion (GCE) explores beyond the natural translational processes to further enhance the structural properties and augment the functionality of a wide range of proteins. Prokaryotic and eukaryotic ribosomal machinery have been proven to accept engineered tRNAs from orthogonal organisms to efficiently incorporate noncanonical amino acids (ncAAs) with rationally designed side chains. These side chains can be reactive or functional groups, which can be extensively utilized in biochemical, biophysical, and cellular studies. Genetic code extension offers the contingency of introducing more than one ncAA into protein through frameshift suppression, multi-site-specific incorporation of ncAAs, thereby increasing the vast number of possible applications. However, different mediating factors reduce the yield and efficiency of ncAA incorporation into synthetic proteins. In this review, we comment on the recent advancements in genetic code expansion to signify the relevance of systems biology in improving ncAA incorporation efficiency. We discuss the emerging impact of tRNA modifications and metabolism in protein design. We also provide examples of the latest successful accomplishments in synthetic protein therapeutics and show how codon expansion has been employed in various scientific and biotechnological applications.
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Affiliation(s)
- Olubodun Michael Lateef
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
| | | | - Olamide Tosin Olaoba
- Laboratory of Functional and Structural Biochemistry, Federal University of Sao Carlos, Sao Carlos 13565-905, SP, Brazil;
| | - Sunday Ocholi Samson
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
| | - Malgorzata Adamczyk
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
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10
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Abstract
The maturation of chemical synthesis during the 20th century has elevated the discipline from a largely empirical into a rational science. This ability to purposefully craft matter at the molecular level has put chemists in a privileged position to contribute to progress in neighboring natural sciences. Recently, we have witnessed another major advance in the field in which chemists use chemical and biological "synthetic" methods together to alter the structures and properties of biological macromolecules in ways heretofore unimagined. This interdisciplinary approach to synthesis has even allowed us to expand upon the defining characteristics of living organisms at the molecular level. In this perspective, we present a case study for the successful addition of new chemistries to the fundamental processes of the central dogma of molecular biology, exemplified by the expansion of the genetic code.
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Affiliation(s)
- Christian S. Diercks
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- These authors contributed equally
| | - David A. Dik
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- These authors contributed equally
| | - Peter G. Schultz
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Lead contact
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11
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Dickey RM, Forti AM, Kunjapur AM. Advances in engineering microbial biosynthesis of aromatic compounds and related compounds. BIORESOUR BIOPROCESS 2021; 8:91. [PMID: 38650203 PMCID: PMC10992092 DOI: 10.1186/s40643-021-00434-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/18/2021] [Indexed: 01/14/2023] Open
Abstract
Aromatic compounds have broad applications and have been the target of biosynthetic processes for several decades. New biomolecular engineering strategies have been applied to improve production of aromatic compounds in recent years, some of which are expected to set the stage for the next wave of innovations. Here, we will briefly complement existing reviews on microbial production of aromatic compounds by focusing on a few recent trends where considerable work has been performed in the last 5 years. The trends we highlight are pathway modularization and compartmentalization, microbial co-culturing, non-traditional host engineering, aromatic polymer feedstock utilization, engineered ring cleavage, aldehyde stabilization, and biosynthesis of non-standard amino acids. Throughout this review article, we will also touch on unmet opportunities that future research could address.
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Affiliation(s)
- Roman M Dickey
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, USA
| | - Amanda M Forti
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, USA
| | - Aditya M Kunjapur
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, USA.
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12
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Chen X, Liu Y, Hou J, Lu Y. A linear DNA template-based framework for site-specific unnatural amino acid incorporation. Synth Syst Biotechnol 2021; 6:192-199. [PMID: 34401545 PMCID: PMC8347695 DOI: 10.1016/j.synbio.2021.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/16/2021] [Accepted: 07/27/2021] [Indexed: 11/28/2022] Open
Abstract
Site-specific incorporation of unnatural amino acids (UNAAs) into proteins using an orthogonal translation system (OTS) has expanded the scope of protein-coding chemistry. The key factor affecting UNAA embedding efficiency is the orthogonality of the OTS. Compared to traditional cell systems, cell-free systems are more convenient to control the reaction process and improve the utilization rate of UNAA. In this study, a linear DNA template-based cell-free unnatural protein synthesis system for rapid high-throughput screening and evolution was proposed. A total of 14 cell extracts were selected for screening out cell extract with high expression level. The result showed that EcAR7 ΔA ΔSer cell extract was optimal for the cell-free system. In addition, the screening results of four UNAAs, p-propargyloxy-l-phenylalanine (pPaF), p-azyl-phenylalanine (pAzF), p-acetyl-l-phenylalanine (pAcF), and p-benzoyl-l-phenylalanine (pBpF), showed that o-aaRS and o-tRNA of pPaF had good orthogonality. A new pair of corresponding o-aaRS and o-tRNA for pBpF was screened out. These results proved that this method could speed up the screening of optimal OTS components for UNAAs with versatile functions.
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Affiliation(s)
- Xinjie Chen
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yingying Liu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Jiaqi Hou
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
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13
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Baraniak D, Boryski J. Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry. Biomedicines 2021; 9:628. [PMID: 34073038 PMCID: PMC8229351 DOI: 10.3390/biomedicines9060628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.
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Affiliation(s)
- Dagmara Baraniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland;
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14
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Hadar D, Gelkop S, Vaserman L, Amiram M. Efficient Incorporation of Clickable Unnatural Amino Acids Enables Rapid and Biocompatible Labeling of Proteins in Vitro and in Bacteria. Chembiochem 2021; 22:1379-1384. [PMID: 33350556 DOI: 10.1002/cbic.202000663] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/22/2020] [Indexed: 11/09/2022]
Abstract
Site-specific incorporation of unnatural amino acids (uAAs) bearing a bioorthogonal group has enabled the attachment - typically at a single site or at a few sites per protein - of chemical groups at precise locations for protein and biomaterial labeling, conjugation, and functionalization. Herein, we report the evolution of chromosomal Methanocaldococcus jannaschii tyrosyl-tRNA synthetase (aaRS) for the alkyne-bearing uAA, 4-propargyloxy-l-phenylalanine (pPR), with ∼30-fold increased production of green fluorescent protein containing three instances of pPR compared with a previously described M. jannaschii-derived aaRS for pPR, when expressed from a single chromosomal copy. We show that when expressed from multicopy plasmids, the evolved aaRSs enable the production - using a genomically recoded Escherichia coli and the non-recoded BL21 E. coli strain - of elastin-like polypeptides (ELPs) containing multiple pPR residues in high yields. We further show that the multisite incorporation of pPR in ELPs facilitates the rapid, robust, and nontoxic fluorescent labeling of these proteins in bacteria. The evolved variants described in this work can be used to produce a variety of protein and biomaterial conjugates and to create efficient minimal tags for protein labeling.
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Affiliation(s)
- Dagan Hadar
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
| | - Sigal Gelkop
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
| | - Livne Vaserman
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
| | - Miriam Amiram
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
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15
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Covalent peptides and proteins for therapeutics. Bioorg Med Chem 2021; 29:115896. [DOI: 10.1016/j.bmc.2020.115896] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/19/2020] [Accepted: 11/21/2020] [Indexed: 12/11/2022]
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16
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Tamshen K, Wang Y, Jamieson SMF, Perry JK, Maynard HD. Genetic Code Expansion Enables Site-Specific PEGylation of a Human Growth Hormone Receptor Antagonist through Click Chemistry. Bioconjug Chem 2020; 31:2179-2190. [PMID: 32786367 DOI: 10.1021/acs.bioconjchem.0c00365] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Regulation of human growth hormone (GH) signaling has important applications in the remediation of several diseases including acromegaly and cancer. Growth hormone receptor (GHR) antagonists currently provide the most effective means for suppression of GH signaling. However, these small 22 kDa recombinantly engineered GH analogues exhibit short plasma circulation times. To improve clinical viability, between four and six molecules of 5 kDa poly(ethylene glycol) (PEG) are nonspecifically conjugated to the nine amines of the GHR antagonist designated as B2036 in the FDA-approved therapeutic pegvisomant. PEGylation increases the molecular weight of B2036 and considerably extends its circulation time, but also dramatically reduces its bioactivity, contributing to high dosing requirements and increased cost. As an alternative to nonspecific PEGylation, we report the use of genetic code expansion technology to site-specifically incorporate the unnatural amino acid propargyl tyrosine (pglY) into B2036 with the goal of producing site-specific protein-polymer conjugates. Substitution of tyrosine 35 with pglY yielded a B2036 variant containing an alkyne functional group without compromising bioactivity, as verified by a cellular assay. Subsequent conjugation of 5, 10, and 20 kDa azide-containing PEGs via the copper-catalyzed click reaction yielded high purity, site-specific conjugates with >89% conjugation efficiencies. Site-specific attachment of PEG to B2036 is associated with substantially improved in vitro bioactivity values compared to pegvisomant, with an inverse relationship between polymer size and activity observed. Notably, the B2036-20 kDa PEG conjugate has a molecular weight comparable to pegvisomant, while exhibiting a 12.5 fold improvement in half-maximal inhibitory concentration in GHR-expressing Ba/F3 cells (103.3 nM vs 1289 nM). We expect that this straightforward route to achieve site-specific GHR antagonists will be useful for GH signal regulation.
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Affiliation(s)
- Kyle Tamshen
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Yue Wang
- Liggins Institute, University of Auckland, Auckland 1203, New Zealand
| | - Stephen M F Jamieson
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1023, New Zealand.,Auckland Cancer Society Research Centre, School of Medical Sciences, University of Auckland, Auckland 1023, New Zealand
| | - Jo K Perry
- Liggins Institute, University of Auckland, Auckland 1203, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1023, New Zealand
| | - Heather D Maynard
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States.,California NanoSystems Institute, University of California, Los Angeles, California 90095-1569, United States.,Department of Bioengineering, University of California, Los Angeles, California 90095-1569, United States
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17
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Dehling E, Rüschenbaum J, Diecker J, Dörner W, Mootz HD. Photo-crosslink analysis in nonribosomal peptide synthetases reveals aberrant gel migration of branched crosslink isomers and spatial proximity between non-neighboring domains. Chem Sci 2020; 11:8945-8954. [PMID: 34123148 PMCID: PMC8163358 DOI: 10.1039/d0sc01969k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are large, multi-modular enzyme templates for the biosynthesis of important peptide natural products. Modules are composed of a set of semi-autonomous domains that facilitate the individual reaction steps. Only little is known about the existence and relevance of a higher-order architecture in these mega-enzymes, for which contacts between non-neighboring domains in three-dimensional space would be characteristic. Similarly poorly understood is the structure of communication-mediating (COM) domains that facilitate NRPS subunit docking at the boundaries between epimerization and condensation domains. We investigated a COM domain pair in a minimal two module NRPS using genetically encoded photo-crosslinking moieties in the N-terminal acceptor COM domain. Crosslinks into the C-terminal donor COM domain of the partner module resulted in protein products with the expected migration behavior on SDS-PAGE gels corresponding to the added molecular weight of the proteins. Additionally, an unexpected apparent high-molecular weight crosslink product was revealed by mass spectrometric analysis to represent a T-form isomer with branched connectivity of the two polypeptide chains. Synthesis of the linear L-form and branched T-form isomers by click chemistry confirmed this designation. Our data revealed a surprising spatial proximity between the acceptor COM domain and the functionally unrelated small subdomain of the preceding adenylation domain. These findings provide an insight into three-dimensional domain arrangements in NRPSs in solution and suggest the described photo-crosslinking approach as a promising tool for the systematic investigation of their higher-order architecture. Photo-crosslink analysis reveals unexpected insights into the higher-order architecture of NRPS and the nature of crosslink isomers.![]()
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Affiliation(s)
- Eva Dehling
- Institute of Biochemistry, Department of Chemistry and Pharmacy, University of Muenster D-48149 Münster Germany
| | - Jennifer Rüschenbaum
- Institute of Biochemistry, Department of Chemistry and Pharmacy, University of Muenster D-48149 Münster Germany
| | - Julia Diecker
- Institute of Biochemistry, Department of Chemistry and Pharmacy, University of Muenster D-48149 Münster Germany
| | - Wolfgang Dörner
- Institute of Biochemistry, Department of Chemistry and Pharmacy, University of Muenster D-48149 Münster Germany
| | - Henning D Mootz
- Institute of Biochemistry, Department of Chemistry and Pharmacy, University of Muenster D-48149 Münster Germany
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18
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Iannuzzelli JA, Fasan R. Expanded toolbox for directing the biosynthesis of macrocyclic peptides in bacterial cells. Chem Sci 2020; 11:6202-6208. [PMID: 32953014 PMCID: PMC7480269 DOI: 10.1039/d0sc01699c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/27/2020] [Indexed: 12/26/2022] Open
Abstract
A new suite of unnatural amino acids is reported for directing the biosynthesis of genetically encoded macrocyclic peptides in live bacteria.
The macrocyclization of recombinant polypeptides by means of genetically encodable non-canonical amino acids has recently provided an attractive strategy for the screening and discovery of macrocyclic peptide inhibitors of protein–protein interactions. Here, we report the development of an expanded suite of electrophilic unnatural amino acids (eUAAs) useful for directing the biosynthesis of genetically encoded thioether-bridged macrocyclic peptides in bacterial cells (E. coli). These reagents are shown to provide efficient access to a broad range of macrocyclic peptide scaffolds spanning from 2 to 20 amino acid residues, with the different eUAAs offering complementary reactivity profiles toward mediating short- vs. long-range macrocyclizations. Swapping of the eUAA cyclization module in a cyclopeptide inhibitor of streptavidin and Keap1 led to compounds with markedly distinct binding affinity toward the respective target proteins, highlighting the effectiveness of this strategy toward tuning the structural and functional properties of bioactive macrocyclic peptides. The peptide cyclization strategies reported here expand opportunities for the combinatorial biosynthesis of natural product-like peptide macrocycles in bacterial cells or in combination with display platforms toward the discovery of selective agents capable of targeting proteins and protein-mediated interactions.
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Affiliation(s)
- Jacob A Iannuzzelli
- Department of Chemistry , University of Rochester , Rochester , New York 14627 , USA .
| | - Rudi Fasan
- Department of Chemistry , University of Rochester , Rochester , New York 14627 , USA .
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19
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Oller‐Salvia B, Chin JW. Efficient Phage Display with Multiple Distinct Non‐Canonical Amino Acids Using Orthogonal Ribosome‐Mediated Genetic Code Expansion. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Benjamí Oller‐Salvia
- Medical Research Council Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
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20
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Oller-Salvia B, Chin JW. Efficient Phage Display with Multiple Distinct Non-Canonical Amino Acids Using Orthogonal Ribosome-Mediated Genetic Code Expansion. Angew Chem Int Ed Engl 2019; 58:10844-10848. [PMID: 31157495 PMCID: PMC6771915 DOI: 10.1002/anie.201902658] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/30/2019] [Indexed: 11/10/2022]
Abstract
Phage display is a powerful approach for evolving proteins and peptides with new functions, but the properties of the molecules that can be evolved are limited by the chemical diversity encoded. Herein, we report a system for incorporating non-canonical amino acids (ncAAs) into proteins displayed on phage using the pyrrolysyl-tRNA synthetase/tRNA pair. We improve the efficiency of ncAA incorporation using an evolved orthogonal ribosome (riboQ1), and encode a cyclopropene-containing ncAA (CypK) at diverse sites on a displayed single-chain antibody variable fragment (ScFv), in response to amber and quadruplet codons. CypK and an alkyne-containing ncAA are incorporated at distinct sites, enabling the double labeling of ScFv with distinct probes, through mutually orthogonal reactions, in a one-pot procedure. These advances expand the number of functionalities that can be encoded on phage-displayed proteins and provide a foundation to further expand the scope of phage display applications.
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Affiliation(s)
- Benjamí Oller-Salvia
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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21
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Li JC, Nastertorabi F, Xuan W, Han GW, Stevens RC, Schultz PG. A Single Reactive Noncanonical Amino Acid Is Able to Dramatically Stabilize Protein Structure. ACS Chem Biol 2019; 14:1150-1153. [PMID: 31181898 DOI: 10.1021/acschembio.9b00002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A p-isothiocyanate phenylalanine mutant of the homodimeric protein homoserine o-succinyltransferase (MetA) was isolated in a temperature dependent selection from a library of metA mutants containing noncanonical amino acids. This mutant protein has a dramatic increase of 24 °C in thermal stability compared to the wild type protein. Peptide mapping experiments revealed that the isothiocyanate group forms a thiourea cross-link to the N terminal proline of the other monomer, despite the two positions being >30 Å apart in the X-ray crystal structure of the wild type protein. These results show that an expanded set of building blocks beyond the canonical 20 amino acids can lead to significant changes in the properties of proteins.
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Affiliation(s)
- Jack C. Li
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Fariborz Nastertorabi
- Department of Biological Sciences, Bridge Institute, Michaelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, United States
| | - Weimin Xuan
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Gye Won Han
- Department of Biological Sciences, Bridge Institute, Michaelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, United States
| | - Raymond C. Stevens
- Department of Biological Sciences, Bridge Institute, Michaelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, United States
| | - Peter G. Schultz
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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22
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Abstract
![]()
The manipulation
and modulation of biomolecules has the potential
to herald new modes of Biology and Medicine through chemical “editing”.
Key to the success of such processes will be the selectivities, reactivities
and efficiencies that may be brought to bear in bond-formation and
bond-cleavage in a benign manner. In this Perspective, we use select
examples, primarily from our own research, to examine the current
opportunities, limitations and the particular potential of metal-mediated
processes as exemplars of possible alternative catalytic modes and
manifolds to those already found in nature.
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Affiliation(s)
- Patrick G Isenegger
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Benjamin G Davis
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , Mansfield Road , Oxford OX1 3TA , United Kingdom
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23
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Efficient Incorporation of Unnatural Amino Acids into Proteins with a Robust Cell-Free System. Methods Protoc 2019; 2:mps2010016. [PMID: 31164598 PMCID: PMC6481062 DOI: 10.3390/mps2010016] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/07/2019] [Accepted: 02/07/2019] [Indexed: 01/25/2023] Open
Abstract
Unnatural proteins are crucial biomacromolecules and have been widely applied in fundamental science, novel biopolymer materials, enzymes, and therapeutics. Cell-free protein synthesis (CFPS) system can serve as a robust platform to synthesize unnatural proteins by highly effective site-specific incorporation of unnatural amino acids (UNAAs), without the limitations of cell membrane permeability and the toxicity of unnatural components. Here, we describe a quick and simple method to synthesize unnatural proteins in CFPS system based on Escherichia coli crude extract, with unnatural orthogonal aminoacyl-tRNA synthetase and suppressor tRNA evolved from Methanocaldococcus jannaschii. The superfolder green fluorescent protein (sfGFP) and p-propargyloxyphenylalanine (pPaF) were used as the model protein and UNAA. The synthesis of unnatural sfGFPs was characterized by microplate spectrophotometer, affinity chromatography, and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). This protocol provides a detailed procedure guiding how to use the powerful CFPS system to synthesize unnatural proteins on demand.
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24
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Quast RB, Fatemi F, Kranendonk M, Margeat E, Truan G. Accurate Determination of Human CPR Conformational Equilibrium by smFRET Using Dual Orthogonal Noncanonical Amino Acid Labeling. Chembiochem 2019; 20:659-666. [DOI: 10.1002/cbic.201800607] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Robert B. Quast
- LISBP; Université de Toulouse; CNRS; INRA; INSA; 135 Avenue de Rangueil 31077 Toulouse France
| | - Fataneh Fatemi
- Protein Research Center; Shahid Beheshti University, G.C.; Evin 1983969411 Tehran Iran
| | - Michel Kranendonk
- Center for Toxicogenomics and Human Health (ToxOmics); Genetics, Oncology and Human Toxicology; NOVA Medical School; Faculdade de Ciências Médicas; Universidade Nova de Lisboa; Rua Câmara Pestana, no. 6 1150-082 Lisboa Portugal
| | - Emmanuel Margeat
- BS; CNRS; CINSERM; Université de Montpellier; Montpellier France
| | - Gilles Truan
- LISBP; Université de Toulouse; CNRS; INRA; INSA; 135 Avenue de Rangueil 31077 Toulouse France
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25
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Tran TV, Couture G, Do LH. Evaluation of dicopper azacryptand complexes in aqueous CuAAC reactions and their tolerance toward biological thiols. Dalton Trans 2019; 48:9751-9758. [DOI: 10.1039/c9dt00724e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The catalytic activity of dicopper azacryptands was evaluated in water and in the presence of biological thiols.
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Affiliation(s)
- Thi V. Tran
- Department of Chemistry
- University of Houston
- Houston
- USA
| | | | - Loi H. Do
- Department of Chemistry
- University of Houston
- Houston
- USA
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26
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Site-Specific Labelling of Multidomain Proteins by Amber Codon Suppression. Sci Rep 2018; 8:14864. [PMID: 30291265 PMCID: PMC6173736 DOI: 10.1038/s41598-018-33115-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 09/18/2018] [Indexed: 01/30/2023] Open
Abstract
The access to information on the dynamic behaviour of large proteins is usually hindered as spectroscopic methods require the site-specific attachment of biophysical probes. A powerful emerging tool to tackle this issue is amber codon suppression. Till date, its application on large and complex multidomain proteins of MDa size has not been reported. Herein, we systematically investigate the feasibility to introduce different non-canonical amino acids into a 540 kDa homodimeric fatty acid synthase type I by genetic code expansion with subsequent fluorescent labelling. Our approach relies on a microplate-based reporter assay of low complexity using a GFP fusion protein to quickly screen for sufficient suppression conditions. Once identified, these findings were successfully utilized to upscale both the expression scale and the protein size to full-length constructs. These fluorescently labelled samples of fatty acid synthase were subjected to initial biophysical experiments, including HPLC analysis, activity assays and fluorescence spectroscopy. Successful introduction of such probes into a molecular machine such as fatty acid synthases may pave the way to understand the conformational variability, which is a primary intrinsic property required for efficient interplay of all catalytic functionalities, and to engineer them.
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27
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Cell-Free Expression of Unnatural Amino Acid Incorporated Aquaporin SS9 with Improved Separation Performance in Biomimetic Membranes. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3560894. [PMID: 30363687 PMCID: PMC6181008 DOI: 10.1155/2018/3560894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/29/2018] [Accepted: 09/06/2018] [Indexed: 11/17/2022]
Abstract
Aquaporins (AQPs) are widely applied in biomimetic membranes for water recycling and desalination. In this study, a novel aquaporin was isolated from Photobacterium profundum SS9 (AQP SS9), which showed high water permeability and potential for practical water purification applications. To improve the stability of the AQP SS9 embedded biomimetic membranes, a modified AQP SS9 was obtained by incorporation of an unnatural amino acid (p-propargyloxyphenylalanine, pPpa) (P-AQP SS9) in vitro using a mutated Methanocaldococcus jannaschii tyrosyl-tRNA synthetase (TyrRS) and the cell-free expression system. The modified AQP SS9 can covalently link with phospholipids and hence significantly improve the stability of biomimetic membranes. The concentration of Mg2+ and fusion expression with signal peptides were evaluated to enhance the expression level of P-AQP SS9, resulting in a highest yield of 49 mg/L. The modified AQP SS9 was then reconstituted into DOPC liposomes and analyzed by a stopped-flow spectrophotometer. The obtained water permeability coefficient (Pf) of 7.46×10−4 m/s was 5.7 times higher than that of proteoliposomes with the wild-type AQP SS9 (Pf=1.31×10−4 m/s) and 12.1 times higher than that of the DOPC liposomes (Pf=6.15×10−5m/s). This study demonstrates the development of a cell-free system for the expression of membrane proteins with much higher stability and the potential application of the modified aquaporins for water filtration.
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28
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Ngo AH, Bose S, Do LH. Intracellular Chemistry: Integrating Molecular Inorganic Catalysts with Living Systems. Chemistry 2018; 24:10584-10594. [DOI: 10.1002/chem.201800504] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/16/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Anh H. Ngo
- Department of Chemistry; University of Houston; 4800 Calhoun Road Houston TX 77004 USA
| | - Sohini Bose
- Department of Chemistry; University of Houston; 4800 Calhoun Road Houston TX 77004 USA
| | - Loi H. Do
- Department of Chemistry; University of Houston; 4800 Calhoun Road Houston TX 77004 USA
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29
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Abstract
Our understanding of the complex molecular processes of living organisms at the molecular level is growing exponentially. This knowledge, together with a powerful arsenal of tools for manipulating the structures of macromolecules, is allowing chemists to to harness and reprogram the cellular machinery in ways previously unimaged. Here we review one example in which the genetic code itself has been expanded with new building blocks that allow us to probe and manipulate the structures and functions of proteins with unprecedented precision.
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Affiliation(s)
- Douglas D. Young
- Department of Chemistry, College of William & Mary,
P.O. Box 8795, Williamsburg, VA 23187 (USA)
| | - Peter G. Schultz
- Department of Chemistry, The Scripps Research Institute,
La Jolla, CA 92037 (USA),
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30
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Nimmo ZM, Halonski JF, Chatkewitz LE, Young DD. Development of optimized conditions for Glaser-Hay bioconjugations. Bioorg Chem 2018; 76:326-331. [PMID: 29227916 PMCID: PMC5818283 DOI: 10.1016/j.bioorg.2017.11.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 11/27/2017] [Accepted: 11/29/2017] [Indexed: 02/02/2023]
Abstract
The efficient preparation of protein bioconjugates represents a route to novel materials, diagnostics, and therapeutics. We previously reported a novel bioorthogonal Glaser-Hay reaction for the preparation of covalent linkages between proteins and a reaction partner; however, deleterious protein degradation was observed under extended reaction conditions. Herein, we describe the systematic optimization of the reaction to increase coupling efficiency and decrease protein degradation. Two optimized conditions were identified varying either the pH of the reaction or the bidentate ligand employed, allowing for more rapid conjugations and/or less protein oxidation.
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Affiliation(s)
- Zachary M Nimmo
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 23187, USA
| | - John F Halonski
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 23187, USA
| | - Lindsay E Chatkewitz
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 23187, USA
| | - Douglas D Young
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 23187, USA.
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31
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Haney CM, Petersson EJ. Fluorescence spectroscopy reveals N-terminal order in fibrillar forms of α-synuclein. Chem Commun (Camb) 2018; 54:833-836. [PMID: 29313531 PMCID: PMC5961496 DOI: 10.1039/c7cc08601f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The neuronal protein α-synuclein (αS) plays a key role in Parkinson's disease, forming inclusions termed Lewy bodies and Lewy neurites. Recent improvements in cryo-electron diffraction and solid state NMR (ssNMR) have led to the elucidation of the structures of peptides derived from the αS fibril core and full-length human αS in fibrils. Despite the valuable insight offered by these methods, there are still several questions about the structures' relevance to pathological aggregates. Herein, we present fluorescence data collected in vitro under the conditions which fibrils are typically assembled. Our data suggest that, in solution, fibrils are largely structured as observed by ssNMR. However, we observe significant disparities in the αS N-terminus as compared to ssNMR data, which provide insight on its important role in αS aggregation and fibril structure.
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Affiliation(s)
- Conor M. Haney
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA. ; Tel: +1-215-746-2221
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA. ; Tel: +1-215-746-2221
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32
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Chatkewitz LE, Halonski JF, Padilla MS, Young DD. Investigation of copper-free alkyne/azide 1,3-dipolar cycloadditions using microwave irradiation. Bioorg Med Chem Lett 2018; 28:81-84. [PMID: 29248298 PMCID: PMC5761740 DOI: 10.1016/j.bmcl.2017.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 11/29/2017] [Accepted: 12/04/2017] [Indexed: 11/18/2022]
Abstract
The prevalence of 1,3-dipolar cycloadditions of azides and alkynes within both biology and chemistry highlights the utility of these reactions. However, the use of a copper catalyst can be prohibitive to some applications. Consequently, we have optimized a copper-free microwave-assisted reaction to alleviate the necessity for the copper catalyst. A small array of triazoles was prepared to examine the scope of this approach, and the methodology was translated to a protein context through the use of unnatural amino acids to demonstrate one of the first microwave-mediated bioconjugations involving a full length protein.
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Affiliation(s)
- Lindsay E Chatkewitz
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187 USA
| | - John F Halonski
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187 USA
| | - Marshall S Padilla
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187 USA
| | - Douglas D Young
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187 USA.
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33
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Abstract
Thermostabilization represents a critical and often obligatory step toward enhancing the robustness of enzymes for organic synthesis and other applications. While directed evolution methods have provided valuable tools for this purpose, these protocols are laborious and time-consuming and typically require the accumulation of several mutations, potentially at the expense of catalytic function. Here, we report a minimally invasive strategy for enzyme stabilization that relies on the installation of genetically encoded, nonreducible covalent staples in a target protein scaffold using computational design. This methodology enables the rapid development of myoglobin-based cyclopropanation biocatalysts featuring dramatically enhanced thermostability (ΔTm = +18.0 °C and ΔT50 = +16.0 °C) as well as increased stability against chemical denaturation [ΔCm (GndHCl) = 0.53 M], without altering their catalytic efficiency and stereoselectivity properties. In addition, the stabilized variants offer superior performance and selectivity compared with the parent enzyme in the presence of a high concentration of organic cosolvents, enabling the more efficient cyclopropanation of a water-insoluble substrate. This work introduces and validates an approach for protein stabilization which should be applicable to a variety of other proteins and enzymes.
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Thompson JW, Griffin ME, Hsieh-Wilson LC. Methods for the Detection, Study, and Dynamic Profiling of O-GlcNAc Glycosylation. Methods Enzymol 2017; 598:101-135. [PMID: 29306432 PMCID: PMC5886303 DOI: 10.1016/bs.mie.2017.06.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The addition of O-linked β-N-acetylglucosamine (O-GlcNAc) to serine/threonine residues of proteins is a ubiquitous posttranslational modification found in all multicellular organisms. Like phosphorylation, O-GlcNAc glycosylation (O-GlcNAcylation) is inducible and regulates a myriad of physiological and pathological processes. However, understanding the diverse functions of O-GlcNAcylation is often challenging due to the difficulty of detecting and quantifying the modification. Thus, robust methods to study O-GlcNAcylation are essential to elucidate its key roles in the regulation of individual proteins, complex cellular processes, and disease. In this chapter, we describe a set of chemoenzymatic labeling methods to (1) detect O-GlcNAcylation on proteins of interest, (2) monitor changes in both the total levels of O-GlcNAcylation and its stoichiometry on proteins of interest, and (3) enable mapping of O-GlcNAc to specific serine/threonine residues within proteins to facilitate functional studies. First, we outline a procedure for the expression and purification of a multiuse mutant galactosyltransferase enzyme (Y289L GalT). We then describe the use of Y289L GalT to modify O-GlcNAc residues with a functional handle, N-azidoacetylgalactosamine (GalNAz). Finally, we discuss several applications of the copper-catalyzed azide-alkyne cycloaddition "click" reaction to attach various alkyne-containing chemical probes to GalNAz and demonstrate how this functionalization of O-GlcNAc-modified proteins can be used to realize (1)-(3) above. Overall, these methods, which utilize commercially available reagents and standard protein analytical tools, will serve to advance our understanding of the diverse and important functions of O-GlcNAcylation.
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Affiliation(s)
- John W Thompson
- California Institute of Technology, Pasadena, CA, United States
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35
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Shang X, Wang N, Cerny R, Niu W, Guo J. Fluorescent Protein-Based Turn-On Probe through a General Protection-Deprotection Design Strategy. ACS Sens 2017; 2:961-966. [PMID: 28750537 DOI: 10.1021/acssensors.7b00223] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrated a general protection-deprotection strategy for the design of fluorescent protein biosensors through the construction of a turn-on Hg2+ sensor. A combination of fluorescent protein engineering and unnatural amino acid mutagenesis was used. Unlike previously reported fluorescent protein-based Hg2+ sensors that relied on the binding of Hg2+ to the sulfhydryl group of cysteine residues, a well-established chemical reaction, oxymercuration, was transformed into biological format and incorporated into our sensor design. This novel Hg2+ sensor displayed good sensitivity and selectivity both in vitro and in live bacterial cells. Over 60-fold change in fluorescence signal output was observed in the presence of 10 μM Hg2+, while such a change was undetectable when nine other metal ions were tested. This new design strategy could expand the repertoire of fluorescent protein-based biosensors for the detection of small-molecule analytes.
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Affiliation(s)
- Xin Shang
- Department of Chemistry and ‡Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Nanxi Wang
- Department of Chemistry and ‡Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Ronald Cerny
- Department of Chemistry and ‡Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Wei Niu
- Department of Chemistry and ‡Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Jiantao Guo
- Department of Chemistry and ‡Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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36
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Heravi MM, Hosseinnejad T, Nazari N. Computational investigations on structural and electronic properties of CuI nanoparticles immobilized on modified poly(styrene-co-maleic anhydride), leading to an unexpected but efficient catalyzed synthesis of 1,4-dihydropyridine via Hantzsch pyridine synthesis. CAN J CHEM 2017. [DOI: 10.1139/cjc-2016-0507] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A quantitative description for the interaction of Cu(I) with poly(styrene-co-maleic anhydride) modified with 4-aminopyridine (denoted as CuI/SMI complex) is presented using density functional theory (DFT) and quantum theory of atoms in molecules (QTAIM) approaches. Topological analysis of electron density revealed the existence of effective interactions between Cu(I) ions and the nitrogen in the pyridine ring. Interestingly, the results also showed that there is considerable interaction between Cu(I) and the oxygen of the carbonyl motif in the SMI ligand. Thus, CuI/SMI was examined as a heterogeneous and recyclable catalyst in Hantzsch pyridine synthesis under solvent-free conditions, affording diverse 1,4-dihydropyridines (1,4-DHPs) in excellent yields with relatively short reaction times.
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Affiliation(s)
- Majid M. Heravi
- Department of Chemistry, Alzahra University, Vanak, Tehran, Iran
- Department of Chemistry, Alzahra University, Vanak, Tehran, Iran
| | - Tayebeh Hosseinnejad
- Department of Chemistry, Alzahra University, Vanak, Tehran, Iran
- Department of Chemistry, Alzahra University, Vanak, Tehran, Iran
| | - Niousha Nazari
- Department of Chemistry, Alzahra University, Vanak, Tehran, Iran
- Department of Chemistry, Alzahra University, Vanak, Tehran, Iran
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37
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Zemskov I, Altaner S, Dietrich DR, Wittmann V. Total Synthesis of Microcystin-LF and Derivatives Thereof. J Org Chem 2017; 82:3680-3691. [PMID: 28294610 DOI: 10.1021/acs.joc.7b00175] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microcystins (MCs) are highly toxic natural products which are produced by cyanobacteria. They can be released to the water during harmful algal blooms and are a serious threat to animals and humans. Described is the total synthesis of the cyanotoxin microcystin-LF (MC-LF, 1a) and two derivatives thereof. Deuterated derivative 1b is of interest as an internal standard during MC quantification in biological samples by mass spectrometry and alkyne-labeled 1c can be employed for toxin derivatization by click chemistry with an azide-containing reporter molecule or as an activity-based probe to identify interaction partners. Application of tert-butyl ester protecting groups for erythro-β-d-methylaspartic acid and γ-d-glutamic acid were key for an isomerization-free synthesis. The analytical data of synthetic MC-LF were identical to those of an authentic sample of the natural product. All derivatives 1a-c were determined to be potent inhibitors of protein phosphatase-1 with similar activity.
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Affiliation(s)
- Ivan Zemskov
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz , 78457 Konstanz, Germany
| | - Stefan Altaner
- Department of Biology and Graduate School Biological Sciences (GBS), University of Konstanz , 78457 Konstanz, Germany
| | - Daniel R Dietrich
- Department of Biology and Graduate School Biological Sciences (GBS), University of Konstanz , 78457 Konstanz, Germany
| | - Valentin Wittmann
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz , 78457 Konstanz, Germany
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38
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Adhikary R, Zimmermann J, Romesberg FE. Transparent Window Vibrational Probes for the Characterization of Proteins With High Structural and Temporal Resolution. Chem Rev 2017; 117:1927-1969. [DOI: 10.1021/acs.chemrev.6b00625] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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39
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Kim S, Ko W, Park H, Lee HS. Efficient and Site-specific Antibody Labeling by Strain-promoted Azide-alkyne Cycloaddition. J Vis Exp 2016:54922. [PMID: 28060353 PMCID: PMC5226445 DOI: 10.3791/54922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
There are currently many chemical tools available to introduce chemical probes into proteins to study their structure and function. A useful method is protein conjugation by genetically introducing an unnatural amino acid containing a bioorthogonal functional group. This report describes a detailed protocol for site-specific antibody conjugation. The protocol includes experimental details for the genetic incorporation of an azide-containing amino acid, and the conjugation reaction by strain-promoted azide-alkyne cycloaddition (SPAAC). This strain-promoted reaction proceeds by simple mixing of the reacting molecules at physiological pH and temperature, and does not require additional reagents such as copper(I) ions and copper-chelating ligands. Therefore, this method would be useful for general protein conjugation and development of antibody drug conjugates (ADCs).
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Affiliation(s)
| | - Wooseok Ko
- Department of Chemistry, Sogang University
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40
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Maza JC, Howard CA, Vipani MA, Travis CR, Young DD. Utilization of alkyne bioconjugations to modulate protein function. Bioorg Med Chem Lett 2016; 27:30-33. [PMID: 27894869 DOI: 10.1016/j.bmcl.2016.11.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 10/20/2022]
Abstract
The ability to introduce or modify protein function has widespread application to multiple scientific disciplines. The introduction of unique unnatural amino acids represents an excellent mechanism to incorporate new functionality; however, this approach is limited by ability of the translational machinery to recognize and incorporate the chemical moiety. To overcome this potential limitation, we aimed to exploit the functionality of existing unnatural amino acids to perform bioorthogonal reactions to introduce the desired protein modification, altering its function. Specifically, via the introduction of a terminal alkyne containing unnatural amino acid, we demonstrated chemically programmable protein modification through the Glaser-Hay coupling to other terminal alkynes, altering the function of a protein. In a proof-of-concept experiment, this approach has been utilized to modify the fluorescence spectrum of green fluorescent protein.
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Affiliation(s)
- Johnathan C Maza
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA
| | - Christina A Howard
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA
| | - Megha A Vipani
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA
| | - Christopher R Travis
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA
| | - Douglas D Young
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA.
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41
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Maza JC, Nimmo ZM, Young DD. Expanding the scope of alkyne-mediated bioconjugations utilizing unnatural amino acids. Chem Commun (Camb) 2016; 52:88-91. [PMID: 26499242 DOI: 10.1039/c5cc08287k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The importance of bioconjugates within the field of chemistry drives the need for novel methodologies for their preparation. Well-defined and stable bioconjugates are easily accessible via the utilization of unnatural amino acids (UAAs). As such, we have synthesized and incorporated two new UAAs into green fluorescent protein, and optimized a novel Cadiot-Chodkiewicz bioconjugation, effectively expanding the toolbox of chemical reactions that can be employed in the preparation of bioconjugates.
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Affiliation(s)
- Johnathan C Maza
- Department of Chemistry, College of William & Mary, Williamsburg, Virginia 23187, USA.
| | - Zachary M Nimmo
- Department of Chemistry, College of William & Mary, Williamsburg, Virginia 23187, USA.
| | - Douglas D Young
- Department of Chemistry, College of William & Mary, Williamsburg, Virginia 23187, USA.
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42
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Kim S, Ko W, Sung BH, Kim SC, Lee HS. Direct protein-protein conjugation by genetically introducing bioorthogonal functional groups into proteins. Bioorg Med Chem 2016; 24:5816-5822. [PMID: 27670101 DOI: 10.1016/j.bmc.2016.09.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/13/2016] [Accepted: 09/14/2016] [Indexed: 01/21/2023]
Abstract
Proteins often function as complex structures in conjunction with other proteins. Because these complex structures are essential for sophisticated functions, developing protein-protein conjugates has gained research interest. In this study, site-specific protein-protein conjugation was performed by genetically incorporating an azide-containing amino acid into one protein and a bicyclononyne (BCN)-containing amino acid into the other. Three to four sites in each of the proteins were tested for conjugation efficiency, and three combinations showed excellent conjugation efficiency. The genetic incorporation of unnatural amino acids (UAAs) is technically simple and produces the mutant protein in high yield. In addition, the conjugation reaction can be conducted by simple mixing, and does not require additional reagents or linker molecules. Therefore, this method may prove very useful for generating protein-protein conjugates and protein complexes of biochemical significance.
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Affiliation(s)
- Sanggil Kim
- Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea
| | - Wooseok Ko
- Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea
| | - Bong Hyun Sung
- Bioenergy and Biochemical Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea.
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43
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Xuan W, Li J, Luo X, Schultz PG. Genetic Incorporation of a Reactive Isothiocyanate Group into Proteins. Angew Chem Int Ed Engl 2016; 55:10065-8. [DOI: 10.1002/anie.201604891] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/17/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Weimin Xuan
- Department of Chemistry The Scripps Research Institute 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Jack Li
- Department of Chemistry The Scripps Research Institute 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Xiaozhou Luo
- Department of Chemistry The Scripps Research Institute 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Peter G. Schultz
- Department of Chemistry The Scripps Research Institute 10550 N. Torrey Pines Road La Jolla CA 92037 USA
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44
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Xuan W, Li J, Luo X, Schultz PG. Genetic Incorporation of a Reactive Isothiocyanate Group into Proteins. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604891] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Weimin Xuan
- Department of Chemistry The Scripps Research Institute 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Jack Li
- Department of Chemistry The Scripps Research Institute 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Xiaozhou Luo
- Department of Chemistry The Scripps Research Institute 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Peter G. Schultz
- Department of Chemistry The Scripps Research Institute 10550 N. Torrey Pines Road La Jolla CA 92037 USA
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45
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Frost JR, Wu Z, Lam YC, Owens AE, Fasan R. Side-chain-to-tail cyclization of ribosomally derived peptides promoted by aryl and alkyl amino-functionalized unnatural amino acids. Org Biomol Chem 2016; 14:5803-12. [PMID: 27064594 PMCID: PMC4909536 DOI: 10.1039/c6ob00192k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A strategy for the production of side-chain-to-tail cyclic peptides from ribosomally derived polypeptide precursors is reported. Two genetically encodable unnatural amino acids, bearing either an aryl or alkyl amino group, were investigated for their efficiency toward promoting the formation of medium to large-sized peptide macrocycles via intein-mediated side-chain-to-C-terminus cyclization. While only partial cyclization was observed with precursor proteins containing para-amino-phenylalanine, efficient peptide macrocyclization could be achieved using O-2-aminoethyl-tyrosine as the reactive moiety. Conveniently, the latter was generated upon quantitative, post-translational reduction of the azido-containing counterpart, O-2-azidoethyl-tyrosine, directly in E. coli cells. This methodology could be successfully applied for the production of a 12 mer cyclic peptide with enhanced binding affinity for the model target protein streptavidin as compared to the acyclic counterpart (KD: 5.1 μM vs. 22.4 μM), thus demonstrating its utility toward the creation and investigation of novel, functional macrocyclic peptides.
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Affiliation(s)
- John R Frost
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA.
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46
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Incorporation of non-canonical amino acids into proteins in yeast. Fungal Genet Biol 2016; 89:137-156. [DOI: 10.1016/j.fgb.2016.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 12/22/2022]
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47
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Machida T, Winssinger N. One-Step Derivatization of Reducing Oligosaccharides for Rapid and Live-Cell-Compatible Chelation-Assisted CuAAC Conjugation. Chembiochem 2016; 17:811-5. [DOI: 10.1002/cbic.201600003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Takuya Machida
- Department of Organic Chemistry; NCCR Chemical Biology; University of Geneva; 30 quai Ernest Ansermet 1211 Geneva Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry; NCCR Chemical Biology; University of Geneva; 30 quai Ernest Ansermet 1211 Geneva Switzerland
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48
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Forbes CR, Pandey AK, Ganguly HK, Yap GPA, Zondlo NJ. 4R- and 4S-iodophenyl hydroxyproline, 4R-pentynoyl hydroxyproline, and S-propargyl-4-thiolphenylalanine: conformationally biased and tunable amino acids for bioorthogonal reactions. Org Biomol Chem 2016; 14:2327-46. [PMID: 26806113 PMCID: PMC5824642 DOI: 10.1039/c5ob02473k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bioorthogonal reactions allow the introduction of new functionalities into peptides, proteins, and other biological molecules. The most readily accessible amino acids for bioorthogonal reactions have modest conformational preferences or bases for molecular interactions. Herein we describe the synthesis of 4 novel amino acids containing functional groups for bioorthogonal reactions. (2S,4R)- and (2S,4S)-iodophenyl ethers of hydroxyproline are capable of modification via rapid, specific Suzuki and Sonogashira reactions in water. The synthesis of these amino acids, as Boc-, Fmoc- and free amino acids, was achieved through succinct sequences. These amino acids exhibit well-defined conformational preferences, with the 4S-iodophenyl hydroxyproline crystallographically exhibiting β-turn (ϕ, ψ∼-80°, 0°) or relatively extended (ϕ, ψ∼-80°, +170°) conformations, while the 4R-diastereomer prefers a more compact conformation (ϕ∼-60°). The aryloxyproline diastereomers present the aryl groups in a highly divergent manner, suggesting their stereospecific use in molecular design, medicinal chemistry, and catalysis. Thus, the 4R- and 4S-iodophenyl hydroxyprolines can be differentially applied in distinct structural contexts. The pentynoate ester of 4R-hydroxyproline introduces an alkyne functional group within an amino acid that prefers compact conformations. The propargyl thioether of 4-thiolphenylalanine was synthesized via copper-mediated cross-coupling reaction of thioacetic acid with protected 4-iodophenylalanine, followed by thiolysis and alkylation. This amino acid combines an alkyne functional group with an aromatic amino acid and the ability to tune aromatic and side chain properties via sulfur oxidation. These amino acids provide novel loci for peptide functionalization, with greater control of conformation possible than with other amino acids containing these functional groups.
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Affiliation(s)
- Christina R. Forbes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Anil K. Pandey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Himal K. Ganguly
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Glenn P. A. Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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49
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Jung S, Kwon I. Expansion of bioorthogonal chemistries towards site-specific polymer–protein conjugation. Polym Chem 2016. [DOI: 10.1039/c6py00856a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bioorthogonal chemistries have been used to achieve polymer-protein conjugation with the retained critical properties.
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Affiliation(s)
- Secheon Jung
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology (GIST)
- Gwangju 61005
- Republic of Korea
| | - Inchan Kwon
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology (GIST)
- Gwangju 61005
- Republic of Korea
- Department of Chemical Engineering
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50
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