101
|
Yu Y, Hu C, Xia L, Wang J. Artificial Metalloenzyme Design with Unnatural Amino Acids and Non-Native Cofactors. ACS Catal 2018. [DOI: 10.1021/acscatal.7b03754] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yang Yu
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Cheng Hu
- Laboratory
of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Lin Xia
- Center
for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Jiangyun Wang
- Laboratory
of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| |
Collapse
|
102
|
Li JY, Qiu L, Xu XF, Pan CY, Hong CY, Zhang WJ. Photo-responsive camptothecin-based polymeric prodrug coated silver nanoparticles for drug release behaviour tracking via the nanomaterial surface energy transfer (NSET) effect. J Mater Chem B 2018; 6:1678-1687. [DOI: 10.1039/c7tb02998e] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A photo-responsive hybrid drug delivery system for drug release behaviour tracking via the nanomaterial surface energy transfer (NSET) effect.
Collapse
Affiliation(s)
- Jiao-Yang Li
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China
- Hefei 230026
- China
| | - Liang Qiu
- Institute of Biophysics, Hebei University of Technology
- Tianjin 300401
- China
| | - Xiao-Fei Xu
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China
- Hefei 230026
- China
| | - Cai-Yuan Pan
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China
- Hefei 230026
- China
| | - Chun-Yan Hong
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China
- Hefei 230026
- China
| | - Wen-Jian Zhang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China
- Hefei 230026
- China
| |
Collapse
|
103
|
Sharma V, Zeng Y, Wang WW, Qiao Y, Kurra Y, Liu WR. Evolving the N-Terminal Domain of Pyrrolysyl-tRNA Synthetase for Improved Incorporation of Noncanonical Amino Acids. Chembiochem 2017; 19:26-30. [PMID: 29096043 DOI: 10.1002/cbic.201700268] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Indexed: 11/10/2022]
Abstract
By evolving the N-terminal domain of Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) that directly interacts with tRNAPyl , a mutant clone displaying improved amber-suppression efficiency for the genetic incorporation of Nϵ -(tert-butoxycarbonyl)-l-lysine threefold more than the wild type was identified. The identified mutations were R19H/H29R/T122S. Direct transfer of these mutations to two other PylRS mutants that were previously evolved for the genetic incorporation of Nϵ -acetyl-l-lysine and Nϵ -(4-azidobenzoxycarbonyl)-l-δ,ϵ-dehydrolysine also improved the incorporation efficiency of these two noncanonical amino acids. As the three identified mutations were found in the N-terminal domain of PylRS that was separated from its catalytic domain for charging tRNAPyl with a noncanonical amino acid, they could potentially be introduced to all other PylRS mutants to improve the incorporation efficiency of their corresponding noncanonical amino acids. Therefore, it represents a general strategy to optimize the pyrrolysine incorporation system-based noncanonical amino-acid mutagenesis.
Collapse
Affiliation(s)
- Vangmayee Sharma
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Yu Zeng
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - W Wesley Wang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Yuchen Qiao
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Yadagiri Kurra
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Wenshe R Liu
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| |
Collapse
|
104
|
Zheng Y, Mukherjee R, Chin MA, Igo P, Gilgenast MJ, Chatterjee A. Expanding the Scope of Single- and Double-Noncanonical Amino Acid Mutagenesis in Mammalian Cells Using Orthogonal Polyspecific Leucyl-tRNA Synthetases. Biochemistry 2017; 57:441-445. [PMID: 29106828 DOI: 10.1021/acs.biochem.7b00952] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Engineered aminoacyl-tRNA synthetase/tRNA pairs that enable site-specific incorporation of noncanonical amino acids (ncAAs) into proteins in living cells have emerged as powerful tools in chemical biology. The Escherichia coli-derived leucyl-tRNA synthetase (EcLeuRS)/tRNA pair is a promising candidate for ncAA mutagenesis in mammalian cells, but it has been engineered to charge only a limited set of ncAAs so far. Here we show that two highly polyspecific EcLeuRS mutants can efficiently charge a large array of useful ncAAs into proteins expressed in mammalian cells, while discriminating against the 20 canonical amino acids. When combined with an opal-suppressing pyrrolysyl pair, these EcLeuRS variants further enabled site-specific incorporation of different combinations of two distinct ncAAs into proteins expressed in mammalian cells.
Collapse
Affiliation(s)
- Yunan Zheng
- Department of Chemistry, Boston College , 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Raja Mukherjee
- Department of Chemistry, Boston College , 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Melissa A Chin
- Department of Chemistry, Boston College , 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Peter Igo
- Department of Chemistry, Boston College , 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Martin J Gilgenast
- Department of Chemistry, Boston College , 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College , 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| |
Collapse
|
105
|
Brabham R, Fascione MA. Pyrrolysine Amber Stop-Codon Suppression: Development and Applications. Chembiochem 2017; 18:1973-1983. [DOI: 10.1002/cbic.201700148] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 07/28/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Robin Brabham
- York Structural Biology Laboratory; Department of Chemistry; University of York; Heslington Road York YO10 5DD UK
| | - Martin A. Fascione
- York Structural Biology Laboratory; Department of Chemistry; University of York; Heslington Road York YO10 5DD UK
| |
Collapse
|
106
|
Zheng Y, Addy PS, Mukherjee R, Chatterjee A. Defining the current scope and limitations of dual noncanonical amino acid mutagenesis in mammalian cells. Chem Sci 2017; 8:7211-7217. [PMID: 29081953 PMCID: PMC5633785 DOI: 10.1039/c7sc02560b] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/24/2017] [Indexed: 11/29/2022] Open
Abstract
We systematically evaluate potential platforms for site-specifically incorporating two distinct noncanonical amino acids into proteins expressed in mammalian cells with optimal fidelity and efficiency – a technology that will have many enabling applications.
The ability to site-specifically incorporate two distinct noncanonical amino acids (ncAAs) into the proteome of a mammalian cell with high fidelity and efficiency will have many enabling applications. It would require the use of two different engineered aminoacyl-tRNA synthetase (aaRS)/tRNA pairs, each suppressing a distinct nonsense codon, and which cross-react neither with each other, nor with their counterparts from the host cell. Three different aaRS/tRNA pairs have been developed so far to expand the genetic code of mammalian cells, which can be potentially combined in three unique ways to drive site-specific incorporation of two distinct ncAAs. To explore the suitability of using these combinations for suppressing two distinct nonsense codons with high fidelity and efficiency, here we systematically investigate: (1) how efficiently the three available aaRS/tRNA pairs suppress the three different nonsense codons, (2) preexisting cross-reactivities among these pairs that would compromise their simultaneous use, and (3) whether different nonsense-suppressor tRNAs exhibit unwanted suppression of non-cognate stop codons in mammalian cells. From these comprehensive analyses, two unique combinations of aaRS/tRNA pairs emerged as being suitable for high-fidelity dual nonsense suppression. We developed expression systems to validate the use of both combinations for the site-specific incorporation of two different ncAAs into proteins expressed in mammalian cells. Our work lays the foundation for developing powerful applications of dual-ncAA incorporation technology in mammalian cells, and highlights aspects of this nascent technology that need to be addressed to realize its full potential.
Collapse
Affiliation(s)
- Yunan Zheng
- Department of Chemistry , Boston College , 2609 Beacon Street, Chestnut Hill , MA 02467 , USA .
| | - Partha Sarathi Addy
- Department of Chemistry , Boston College , 2609 Beacon Street, Chestnut Hill , MA 02467 , USA .
| | - Raja Mukherjee
- Department of Chemistry , Boston College , 2609 Beacon Street, Chestnut Hill , MA 02467 , USA .
| | - Abhishek Chatterjee
- Department of Chemistry , Boston College , 2609 Beacon Street, Chestnut Hill , MA 02467 , USA .
| |
Collapse
|
107
|
Villa JK, Tran HA, Vipani M, Gianturco S, Bhasin K, Russell BL, Harbron EJ, Young DD. Fluorescence Modulation of Green Fluorescent Protein Using Fluorinated Unnatural Amino Acids. Molecules 2017; 22:molecules22071194. [PMID: 28714902 PMCID: PMC5806519 DOI: 10.3390/molecules22071194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 11/28/2022] Open
Abstract
The ability to modulate protein function through minimal perturbations to amino acid structure represents an ideal mechanism to engineer optimized proteins. Due to the novel spectroscopic properties of green fluorescent protein, it has found widespread application as a reporter protein throughout the fields of biology and chemistry. Using site-specific amino acid mutagenesis, we have incorporated various fluorotyrosine residues directly into the fluorophore of the protein, altering the fluorescence and shifting the pKa of the phenolic proton associated with the fluorophore. Relative to wild type GFP, the fluorescence spectrum of the protein is altered with each additional fluorine atom, and the mutant GFPs have the potential to be employed as pH sensors due to the altered electronic properties of the fluorine atoms.
Collapse
Affiliation(s)
- Jordan K Villa
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Hong-Anh Tran
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Megha Vipani
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Stephanie Gianturco
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Konark Bhasin
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Brent L Russell
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Elizabeth J Harbron
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Douglas D Young
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| |
Collapse
|
108
|
Reynolds NM, Vargas-Rodriguez O, Söll D, Crnković A. The central role of tRNA in genetic code expansion. Biochim Biophys Acta Gen Subj 2017; 1861:3001-3008. [PMID: 28323071 DOI: 10.1016/j.bbagen.2017.03.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/14/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND The development of orthogonal translation systems (OTSs) for genetic code expansion (GCE) has allowed for the incorporation of a diverse array of non-canonical amino acids (ncAA) into proteins. Transfer RNA, the central molecule in the translation of the genetic message into proteins, plays a significant role in the efficiency of ncAA incorporation. SCOPE OF REVIEW Here we review the biochemical basis of OTSs for genetic code expansion. We focus on the role of tRNA and discuss strategies used to engineer tRNA for the improvement of ncAA incorporation into proteins. MAJOR CONCLUSIONS The engineering of orthogonal tRNAs for GCE has significantly improved the incorporation of ncAAs. However, there are numerous unintended consequences of orthogonal tRNA engineering that cannot be predicted ab initio. GENERAL SIGNIFICANCE Genetic code expansion has allowed for the incorporation of a great diversity of ncAAs and novel chemistries into proteins, making significant contributions to our understanding of biological molecules and interactions. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
Collapse
Affiliation(s)
- Noah M Reynolds
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
| |
Collapse
|
109
|
Erickson SB, Mukherjee R, Kelemen RE, Wrobel CJJ, Cao X, Chatterjee A. Precise Photoremovable Perturbation of a Virus-Host Interaction. Angew Chem Int Ed Engl 2017; 56:4234-4237. [DOI: 10.1002/anie.201700683] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Sarah B. Erickson
- Department of Chemistry; Boston College; 2609 Beacon Street Chestnut Hill MA 02467 USA
| | - Raja Mukherjee
- Department of Chemistry; Boston College; 2609 Beacon Street Chestnut Hill MA 02467 USA
| | - Rachel E. Kelemen
- Department of Chemistry; Boston College; 2609 Beacon Street Chestnut Hill MA 02467 USA
| | - Chester J. J. Wrobel
- Department of Chemistry; Boston College; 2609 Beacon Street Chestnut Hill MA 02467 USA
| | - Xiaofu Cao
- Department of Chemistry; Boston College; 2609 Beacon Street Chestnut Hill MA 02467 USA
| | - Abhishek Chatterjee
- Department of Chemistry; Boston College; 2609 Beacon Street Chestnut Hill MA 02467 USA
| |
Collapse
|
110
|
|
111
|
Gan R, Perez JG, Carlson ED, Ntai I, Isaacs FJ, Kelleher NL, Jewett MC. Translation system engineering in Escherichia coli enhances non-canonical amino acid incorporation into proteins. Biotechnol Bioeng 2017; 114:1074-1086. [PMID: 27987323 DOI: 10.1002/bit.26239] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/28/2016] [Accepted: 12/13/2016] [Indexed: 01/15/2023]
Abstract
The ability to site-specifically incorporate non-canonical amino acids (ncAAs) into proteins has made possible the study of protein structure and function in fundamentally new ways, as well as the bio synthesis of unnatural polymers. However, the task of site-specifically incorporating multiple ncAAs into proteins with high purity and yield continues to present a challenge. At the heart of this challenge lies the lower efficiency of engineered orthogonal translation system components compared to their natural counterparts (e.g., translation elements that specifically use a ncAA and do not interact with the cell's natural translation apparatus). Here, we show that evolving and tuning expression levels of multiple components of an engineered translation system together as a whole enhances ncAA incorporation efficiency. Specifically, we increase protein yield when incorporating multiple p-azido-phenylalanine(pAzF) residues into proteins by (i) evolving the Methanocaldococcus jannaschii p-azido-phenylalanyl-tRNA synthetase anti-codon binding domain, (ii) evolving the elongation factor Tu amino acid-binding pocket, and (iii) tuning the expression of evolved translation machinery components in a single vector. Use of the evolved translation machinery in a genomically recoded organism lacking release factor one enabled enhanced multi-site ncAA incorporation into proteins. We anticipate that our approach to orthogonal translation system development will accelerate and expand our ability to site-specifically incorporate multiple ncAAs into proteins and biopolymers, advancing new horizons for synthetic and chemical biotechnology. Biotechnol. Bioeng. 2017;114: 1074-1086. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Rui Gan
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120
| | - Jessica G Perez
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120
| | - Erik D Carlson
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120
| | - Ioanna Ntai
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208
| | - Farren J Isaacs
- Systems Biology Institute, Yale University, West Haven, Connecticut.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208.,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208.,Interdisciplinary Biological Sciences Program, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-0001.,Northwestern Institute on Complex Systems, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208.,Simpson Querry Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208
| |
Collapse
|
112
|
Abstract
Recently developed methods that can photochemically control protein activities and functions in live cells have opened up new opportunities for studying signaling networks at the cellular and subcellular levels. Our laboratory has reported a genetically encoded photoactivatable intein, which allows the direct photocontrol of primary sequences of proteins, and consequently, their activities and functions in live mammalian cells. Herein, we provide details on experimental design and the utilization of this photocaged intein to photoactivate the Src tyrosine kinase in human embryonic kidney (HEK) 293T cells. The described procedures may be adopted to photocontrol other proteins in other types of mammalian cells.
Collapse
|
113
|
Padilla MS, Farley CA, Chatkewitz LE, Young DD. Synthesis and incorporation of a caged tyrosine amino acid possessing a bioorthogonal handle. Tetrahedron Lett 2016; 57:4709-4712. [PMID: 28533567 PMCID: PMC5438197 DOI: 10.1016/j.tetlet.2016.09.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Reversing a bioconjugation in a spatial and temporal fashion has widespread applications, especially toward targeted drug delivery. We report the synthesis and incorporation of an unnatural amino acid with an alkyne modified dimethoxy-ortho-nitrobenzyl caging group. This unnatural amino acid can be utilized in a Glaser-Hay conjugation to generate a bioconjugate, but also is able to disrupt the bioconjugate when irradiated with light. These combined features allow for the preparation of bioconjugates with a high degree of site-specificity and allow for the separation of the two components if necessary.
Collapse
Affiliation(s)
- Marshall S Padilla
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA
| | - Christopher A Farley
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA
| | - Lindsay E Chatkewitz
- 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
| |
Collapse
|
114
|
Fan X, Ge Y, Lin F, Yang Y, Zhang G, Ngai WSC, Lin Z, Zheng S, Wang J, Zhao J, Li J, Chen PR. Optimized Tetrazine Derivatives for Rapid Bioorthogonal Decaging in Living Cells. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Xinyuan Fan
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
| | - Yun Ge
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Feng Lin
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Yi Yang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Gong Zhang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
| | - William Shu Ching Ngai
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Zhi Lin
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Siqi Zheng
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Jie Wang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
| | - Jingyi Zhao
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
| | - Jie Li
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Peng R. Chen
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
| |
Collapse
|
115
|
Fan X, Ge Y, Lin F, Yang Y, Zhang G, Ngai WSC, Lin Z, Zheng S, Wang J, Zhao J, Li J, Chen PR. Optimized Tetrazine Derivatives for Rapid Bioorthogonal Decaging in Living Cells. Angew Chem Int Ed Engl 2016; 55:14046-14050. [DOI: 10.1002/anie.201608009] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Xinyuan Fan
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
| | - Yun Ge
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Feng Lin
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Yi Yang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Gong Zhang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
| | - William Shu Ching Ngai
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Zhi Lin
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Siqi Zheng
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Jie Wang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
| | - Jingyi Zhao
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
| | - Jie Li
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Peng R. Chen
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
| |
Collapse
|
116
|
Hu P, Feng T, Yeung CC, Koo CK, Lau KC, Lam MHW. A Photo-Triggered Traceless Staudinger-Bertozzi Ligation Reaction. Chemistry 2016; 22:11537-42. [DOI: 10.1002/chem.201601807] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Peng Hu
- Department of Chemistry and Biology; City University of Hong Kong; 83 Tat Chee Avenue Hong Kong SAR China
| | - Tianshi Feng
- Department of Chemistry and Biology; City University of Hong Kong; 83 Tat Chee Avenue Hong Kong SAR China
- Advanced Laboratory for Environmental Research & Technology; USTC-CityU Suzhou China
- CAS Key Laboratory of Soft Matter Chemistry; Department of Polymer Science and Engineering; University of Science and Technology of China, Hefei; Anhui 230026 China
| | - Chi-Chung Yeung
- Department of Chemistry and Biology; City University of Hong Kong; 83 Tat Chee Avenue Hong Kong SAR China
| | - Chi-Kin Koo
- Department of Chemistry and Biology; City University of Hong Kong; 83 Tat Chee Avenue Hong Kong SAR China
| | - Kai-Chung Lau
- Department of Chemistry and Biology; City University of Hong Kong; 83 Tat Chee Avenue Hong Kong SAR China
| | - Michael H. W. Lam
- Department of Chemistry and Biology; City University of Hong Kong; 83 Tat Chee Avenue Hong Kong SAR China
| |
Collapse
|
117
|
Abstract
The site-specific incorporation of unnatural amino acids (Uaas) via genetic code expansion provides a powerful method to introduce synthetic moieties into specific positions of a protein directly in the live cell. The technique, first developed in bacteria, is nowadays widely applicable in mammalian cells. In general, different Uaas are incorporated with different efficiency. By comparing the incorporation efficiency of several Uaas recently designed for bioorthogonal chemistry, we present here a facile dual-fluorescence assay to evaluate relative yields of Uaa incorporation. Several biological questions can be addressed using Uaas tools. In recent years, photo-cross-linking Uaas have been extensively applied to map ligand-binding sites on G protein-coupled receptors (GPCRs). We describe a simple and efficient two-plasmid system to incorporate a photoactivatable Uaa into a class B GPCR, and demonstrate cross-linking to its nonmodified natural ligand.
Collapse
|
118
|
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]
|
119
|
Walker OS, Elsässer SJ, Mahesh M, Bachman M, Balasubramanian S, Chin JW. Photoactivation of Mutant Isocitrate Dehydrogenase 2 Reveals Rapid Cancer-Associated Metabolic and Epigenetic Changes. J Am Chem Soc 2016; 138:718-21. [PMID: 26761588 PMCID: PMC4821487 DOI: 10.1021/jacs.5b07627] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Isocitrate dehydrogenase is mutated
at a key active site arginine
residue (Arg172 in IDH2) in many cancers, leading to the synthesis
of the oncometabolite (R)-2-hydroxyglutarate (2HG).
To investigate the early events following acquisition of this mutation
in mammalian cells we created a photoactivatable version of IDH2(R172K),
in which K172 is replaced with a photocaged lysine (PCK), via genetic
code expansion. Illumination of cells expressing this mutant protein
led to a rapid increase in the levels of 2HG, with 2HG levels reaching
those measured in patient tumor samples, within 8 h. 2HG accumulation
is closely followed by a global decrease in 5-hydroxymethylcytosine
(5-hmC) in DNA, demonstrating that perturbations in epigenetic DNA
base modifications are an early consequence of mutant IDH2 in cells.
Our results provide a paradigm for rapidly and synchronously uncloaking
diverse oncogenic mutations in live cells to reveal the sequence of
events through which they may ultimately cause transformation.
Collapse
Affiliation(s)
- Olivia S Walker
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.,Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Simon J Elsässer
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.,Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Mohan Mahesh
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Martin Bachman
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom.,Cancer Research U.K. Cambridge Institute , Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom.,Cancer Research U.K. Cambridge Institute , Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.,Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| |
Collapse
|
120
|
|
121
|
Abstract
S-Sulfenylation is a post-translational modification with a crucial role in regulating protein function. However, its analysis has remained challenging due to the lack of facile sulfenic acid models. We report the first photocaged cysteine sulfenic acid with efficient photodeprotection and demonstrate its utility by generating sulfenic acid in a thiol peroxidase after illumination in vitro. These caged sulfoxides should be promising for site-specific incorporation of Cys sulfenic acid in living cells via genetic code expansion.
Collapse
Affiliation(s)
- Jia Pan
- The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458
| | - Kate S. Carroll
- The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458
| |
Collapse
|
122
|
Ren W, Truong TM, Ai HW. Study of the Binding Energies between Unnatural Amino Acids and Engineered Orthogonal Tyrosyl-tRNA Synthetases. Sci Rep 2015; 5:12632. [PMID: 26220470 PMCID: PMC4518261 DOI: 10.1038/srep12632] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/03/2015] [Indexed: 11/08/2022] Open
Abstract
We utilized several computational approaches to evaluate the binding energies of tyrosine (Tyr) and several unnatural Tyr analogs, to several orthogonal aaRSes derived from Methanocaldococcus jannaschii and Escherichia coli tyrosyl-tRNA synthetases. The present study reveals the following: (1) AutoDock Vina and ROSETTA were able to distinguish binding energy differences for individual pairs of favorable and unfavorable aaRS-amino acid complexes, but were unable to cluster together all experimentally verified favorable complexes from unfavorable aaRS-Tyr complexes; (2) MD-MM/PBSA provided the best prediction accuracy in terms of clustering favorable and unfavorable enzyme-substrate complexes, but also required the highest computational cost; and (3) MM/PBSA based on single energy-minimized structures has a significantly lower computational cost compared to MD-MM/PBSA, but still produced sufficiently accurate predictions to cluster aaRS-amino acid interactions. Although amino acid-aaRS binding is just the first step in a complex series of processes to acylate a tRNA with its corresponding amino acid, the difference in binding energy, as shown by MD-MM/PBSA, is important for a mutant orthogonal aaRS to distinguish between a favorable unnatural amino acid (unAA) substrate from unfavorable natural amino acid substrates. Our computational study should assist further designing and engineering of orthogonal aaRSes for the genetic encoding of novel unAAs.
Collapse
Affiliation(s)
- Wei Ren
- Department of Chemistry, University of California-Riverside, 501 Big Springs Road, Riverside, California 92521, United States
| | - Tan M. Truong
- Cell, Molecular, and Developmental Biology Graduate Program, University of California-Riverside, Riverside, California 92521, United States
| | - Hui-wang Ai
- Department of Chemistry, University of California-Riverside, 501 Big Springs Road, Riverside, California 92521, United States
- Cell, Molecular, and Developmental Biology Graduate Program, University of California-Riverside, Riverside, California 92521, United States
| |
Collapse
|
123
|
Ravikumar Y, Nadarajan SP, Yoo TH, Lee CS, Yun H. Unnatural amino acid mutagenesis-based enzyme engineering. Trends Biotechnol 2015; 33:462-70. [PMID: 26088007 DOI: 10.1016/j.tibtech.2015.05.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/07/2015] [Accepted: 05/13/2015] [Indexed: 02/09/2023]
Abstract
Traditional enzyme engineering relies on substituting one amino acid by one of the other 19 natural amino acids to change the functional properties of an enzyme. However, incorporation of unnatural amino acids (UAAs) has been harnessed to engineer efficient enzymes for biocatalysis. Residue-specific and site-specific in vivo incorporation methods are becoming the preferred approach for producing enzymes with altered or improved functions. We describe the contribution of in vivo UAA incorporation methodologies to enzyme engineering as well as the future prospects for the field, including the integration of UAAs with other new advances in enzyme engineering.
Collapse
Affiliation(s)
- Yuvaraj Ravikumar
- School of Biotechnology, Department of Biochemistry, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea
| | | | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea
| | - Chong-soon Lee
- School of Biotechnology, Department of Biochemistry, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea
| | - Hyungdon Yun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Korea.
| |
Collapse
|
124
|
Hartley AM, Zaki AJ, McGarrity AR, Robert-Ansart C, Moskalenko AV, Jones GF, Craciun MF, Russo S, Elliott M, Macdonald JE, Jones DD. Functional modulation and directed assembly of an enzyme through designed non-natural post-translation modification. Chem Sci 2015; 6:3712-3717. [PMID: 28706718 PMCID: PMC5496188 DOI: 10.1039/c4sc03900a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/31/2015] [Indexed: 11/21/2022] Open
Abstract
Designed phenyl azide incorporation combined with bioorthogonal Click chemistry to regulate enzyme activity, or promote its stable assembly on graphene.
Post-translational modification (PTM) modulates and supplements protein functionality. In nature this high precision event requires specific motifs and/or associated modification machinery. To overcome the inherent complexity that hinders PTM's wider use, we have utilized a non-native biocompatible Click chemistry approach to site-specifically modify TEM β-lactamase that adds new functionality. In silico modelling was used to design TEM β-lactamase variants with the non-natural amino acid p-azido-l-phenylalanine (azF) placed at functionally strategic positions permitting residue-specific modification with alkyne adducts by exploiting strain-promoted azide–alkyne cycloaddition. Three designs were implemented so that the modification would: (i) inhibit TEM activity (Y105azF); (ii) restore activity compromised by the initial mutation (P174azF); (iii) facilitate assembly on pristine graphene (W165azF). A dibenzylcyclooctyne (DBCO) with amine functionality was enough to modulate enzymatic activity. Modification of TEMW165azF with a DBCO–pyrene adduct had little effect on activity despite the modification site being close to a key catalytic residue but allowed directed assembly of the enzyme on graphene, potentially facilitating the construction of protein-gated carbon transistor systems.
Collapse
Affiliation(s)
| | - Athraa J Zaki
- School of Physics and Astronomy , Cardiff University , Cardiff , Wales , UK
| | | | | | | | - Gareth F Jones
- Centre for Graphene Science , University of Exeter , Exeter , Devon , UK
| | - Monica F Craciun
- Centre for Graphene Science , University of Exeter , Exeter , Devon , UK
| | - Saverio Russo
- Centre for Graphene Science , University of Exeter , Exeter , Devon , UK
| | - Martin Elliott
- School of Physics and Astronomy , Cardiff University , Cardiff , Wales , UK
| | - J Emyr Macdonald
- School of Physics and Astronomy , Cardiff University , Cardiff , Wales , UK
| | - D Dafydd Jones
- School of Biosciences , Cardiff University , Cardiff , UK .
| |
Collapse
|
125
|
Ren W, Ji A, Ai HW. Light Activation of Protein Splicing with a Photocaged Fast Intein. J Am Chem Soc 2015; 137:2155-8. [DOI: 10.1021/ja508597d] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Wei Ren
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, California 92521, United States
| | - Ao Ji
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, California 92521, United States
| | - Hui-wang Ai
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, California 92521, United States
| |
Collapse
|
126
|
Dumas A, Lercher L, Spicer CD, Davis BG. Designing logical codon reassignment - Expanding the chemistry in biology. Chem Sci 2015; 6:50-69. [PMID: 28553457 PMCID: PMC5424465 DOI: 10.1039/c4sc01534g] [Citation(s) in RCA: 327] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 07/14/2014] [Indexed: 12/18/2022] Open
Abstract
Over the last decade, the ability to genetically encode unnatural amino acids (UAAs) has evolved rapidly. The programmed incorporation of UAAs into recombinant proteins relies on the reassignment or suppression of canonical codons with an amino-acyl tRNA synthetase/tRNA (aaRS/tRNA) pair, selective for the UAA of choice. In order to achieve selective incorporation, the aaRS should be selective for the designed tRNA and UAA over the endogenous amino acids and tRNAs. Enhanced selectivity has been achieved by transferring an aaRS/tRNA pair from another kingdom to the organism of interest, and subsequent aaRS evolution to acquire enhanced selectivity for the desired UAA. Today, over 150 non-canonical amino acids have been incorporated using such methods. This enables the introduction of a large variety of structures into proteins, in organisms ranging from prokaryote, yeast and mammalian cells lines to whole animals, enabling the study of protein function at a level that could not previously be achieved. While most research to date has focused on the suppression of 'non-sense' codons, recent developments are beginning to open up the possibility of quadruplet codon decoding and the more selective reassignment of sense codons, offering a potentially powerful tool for incorporating multiple amino acids. Here, we aim to provide a focused review of methods for UAA incorporation with an emphasis in particular on the different tRNA synthetase/tRNA pairs exploited or developed, focusing upon the different UAA structures that have been incorporated and the logic behind the design and future creation of such systems. Our hope is that this will help rationalize the design of systems for incorporation of unexplored unnatural amino acids, as well as novel applications for those already known.
Collapse
Affiliation(s)
- Anaëlle Dumas
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
| | - Lukas Lercher
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
| | - Christopher D Spicer
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
| | - Benjamin G Davis
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
| |
Collapse
|
127
|
Schiller SM. Protein Tectons in Synthetic Biology. Synth Biol (Oxf) 2015. [DOI: 10.1007/978-3-319-02783-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
|
128
|
Leisle L, Valiyaveetil F, Mehl RA, Ahern CA. Incorporation of Non-Canonical Amino Acids. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 869:119-51. [PMID: 26381943 DOI: 10.1007/978-1-4939-2845-3_7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In this chapter we discuss the strengths, caveats and technical considerations of three approaches for reprogramming the chemical composition of selected amino acids within a membrane protein. In vivo nonsense suppression in the Xenopus laevis oocyte, evolved orthogonal tRNA and aminoacyl-tRNA synthetase pairs and protein ligation for biochemical production of semisynthetic proteins have been used successfully for ion channel and receptor studies. The level of difficulty for the application of each approach ranges from trivial to technically demanding, yet all have untapped potential in their application to membrane proteins.
Collapse
Affiliation(s)
- Lilia Leisle
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Road, 52246, Iowa City, IA, USA
| | - Francis Valiyaveetil
- Department of Physiology and Pharmacology, Oregon Health and Sciences University, 97239, Portland, OR, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University Corvallis, 97331, Corvallis, OR, USA
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Road, 52246, Iowa City, IA, USA.
| |
Collapse
|
129
|
Sun F, Zhang L, Yan J, Xu L, Fang D, Luo SZ. The synthesis and photolysis mechanisms of 8-nitroquinoline-based photolabile caging groups for carboxylic acid. J PHYS ORG CHEM 2014. [DOI: 10.1002/poc.3385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Fude Sun
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology; Beijing University of Chemical Technology; Beijing 100029 China
| | - Lei Zhang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry; Beijing Normal University; Beijing 100875 China
| | - Jianhua Yan
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology; Beijing University of Chemical Technology; Beijing 100029 China
| | - Lida Xu
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology; Beijing University of Chemical Technology; Beijing 100029 China
| | - Decai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry; Beijing Normal University; Beijing 100875 China
| | - Shi-Zhong Luo
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology; Beijing University of Chemical Technology; Beijing 100029 China
| |
Collapse
|
130
|
Luo J, Uprety R, Naro Y, Chou C, Nguyen DP, Chin JW, Deiters A. Genetically encoded optochemical probes for simultaneous fluorescence reporting and light activation of protein function with two-photon excitation. J Am Chem Soc 2014; 136:15551-8. [PMID: 25341086 PMCID: PMC4333581 DOI: 10.1021/ja5055862] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
![]()
The site-specific
incorporation of three new coumarin lysine analogues
into proteins was achieved in bacterial and mammalian cells using
an engineered pyrrolysyl-tRNA synthetase system. The genetically encoded
coumarin lysines were successfully applied as fluorescent cellular
probes for protein localization and for the optical activation of
protein function. As a proof-of-principle, photoregulation of firefly
luciferase was achieved in live cells by caging a key lysine residue,
and excellent OFF to ON light-switching ratios were observed. Furthermore,
two-photon and single-photon optochemical control of EGFP maturation
was demonstrated, enabling the use of different, potentially orthogonal
excitation wavelengths (365, 405, and 760 nm) for the sequential activation
of protein function in live cells. These results demonstrate that
coumarin lysines are a new and valuable class of optical probes that
can be used for the investigation and regulation of protein structure,
dynamics, function, and localization in live cells. The small size
of coumarin, the site-specific incorporation, the application as both
a light-activated caging group and as a fluorescent probe, and the
broad range of excitation wavelengths are advantageous over other
genetically encoded photocontrol systems and provide a precise and
multifunctional tool for cellular biology.
Collapse
Affiliation(s)
- Ji Luo
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | | | | | | | | | | | | |
Collapse
|
131
|
Baker AS, Deiters A. Optical control of protein function through unnatural amino acid mutagenesis and other optogenetic approaches. ACS Chem Biol 2014; 9:1398-407. [PMID: 24819585 DOI: 10.1021/cb500176x] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Biological processes are naturally regulated with high spatial and temporal resolution at the molecular, cellular, and systems level. To control and study processes with the same resolution, light-sensitive groups and domains have been employed to optically activate and deactivate protein function. Optical control is a noninvasive technique in which the amplitude, wavelength, spatial location, and timing of the light illumination can be easily controlled. This review focuses on applications of genetically encoded unnatural amino acids containing light-removable protecting groups to optically trigger protein function, while also discussing select optogenetic approaches using natural light-sensitive domains to engineer optical control of biological processes.
Collapse
Affiliation(s)
- Austin S. Baker
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
132
|
Zeng Y, Wang W, Liu WR. Towards reassigning the rare AGG codon in Escherichia coli. Chembiochem 2014; 15:1750-4. [PMID: 25044341 DOI: 10.1002/cbic.201400075] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Indexed: 11/09/2022]
Abstract
The rare AGG codon in Escherichia coli has been reassigned to code non-canonical amino acids (ncAAs) by using the PylRS-tRNA(Pyl)(CCU) pair. When N(ε) -alloc-lysine was used as a PylRS substrate, almost quantitative occupancy of N(ε) -alloc-lysine at an AGG codon site was achieved in minimal medium. ncAAs can be potentially incorporated at the AGG codon with varying efficiencies, depending on their activities towards corresponding enzymes. As AGG is a sense codon, the approach reported here resolves the typical low ncAA incorporation issue that has been associated with ncAA mutagenesis and therefore allows bulk preparation of proteins with site-selectively incorporated ncAAs for applications such as therapeutic protein production.
Collapse
Affiliation(s)
- Yu Zeng
- Department of Chemistry, Texas A&M University, College Station, TX 77843 (USA)
| | | | | |
Collapse
|
133
|
Uprety R, Luo J, Liu J, Naro Y, Samanta S, Deiters A. Genetic Encoding of Caged Cysteine and Caged Homocysteine in Bacterial and Mammalian Cells. Chembiochem 2014; 15:1793-9. [DOI: 10.1002/cbic.201400073] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Indexed: 12/19/2022]
|
134
|
Tharp JM, Wang YS, Lee YJ, Yang Y, Liu WR. Genetic incorporation of seven ortho-substituted phenylalanine derivatives. ACS Chem Biol 2014; 9:884-90. [PMID: 24451054 PMCID: PMC3997995 DOI: 10.1021/cb400917a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
![]()
Seven
phenylalanine derivatives with small ortho substitutions
were genetically encoded in Escherichia coli and
mammalian cells at an amber codon using a previously reported,
rationally designed pyrrolysyl-tRNA synthetase mutant (PylRS(N346A/C348A))
coupled with tRNACUAPyl. Ortho substitutions of the phenylalanine
derivatives reported herein include three halides, methyl, methoxy,
nitro, and nitrile. These compounds have the potential for use in
multiple biochemical and biophysical applications. Specifically, we
demonstrated that o-cyano-phenylalanine could be
used as a selective sensor to probe the local environment of proteins
and applied this to study protein folding/unfolding. For six of these
compounds this constitutes the first report of their genetic incorporation
in living cells. With these compounds the total number of substrates
available for PylRS(N346A/C348A) is increased to nearly 40, which
demonstrates that PylRS(N346A/C348A) is able to recognize phenylalanine
with a substitution at any side-chain aromatic position as a substrate.
To our knowledge, PylRS(N346A/C348A) is the only aminoacyl-tRNA synthetase
with such a high substrate promiscuity.
Collapse
Affiliation(s)
- Jeffery M. Tharp
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yane-Shih Wang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yan-Jiun Lee
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yanyan Yang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Wenshe R. Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
135
|
Kolev JN, Zaengle JM, Ravikumar R, Fasan R. Enhancing the efficiency and regioselectivity of P450 oxidation catalysts by unnatural amino acid mutagenesis. Chembiochem 2014; 15:1001-10. [PMID: 24692265 DOI: 10.1002/cbic.201400060] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Indexed: 01/28/2023]
Abstract
The development of effective strategies for modulating the reactivity and selectivity of cytochrome P450 enzymes represents a key step toward expediting the use of these biocatalysts for synthetic applications. We have investigated the potential of unnatural amino acid mutagenesis to aid efforts in this direction. Four unnatural amino acids with diverse aromatic side chains were incorporated at 11 active-site positions of a substrate-promiscuous CYP102A1 variant. The resulting "uP450s" were then tested for their catalytic activity and regioselectivity in the oxidation of two representative substrates: a small-molecule drug and a natural product. Large shifts in regioselectivity resulted from these single mutations, and in particular, for para-acetyl-Phe substitutions at positions close to the heme cofactor. Screening this mini library of uP450s enabled us to identify P450 catalysts for the selective hydroxylation of four aliphatic positions in the target substrates, including a C(sp(3))-H site not oxidized by the parent enzyme. Furthermore, we discovered a general activity-enhancing effect of active-site substitutions involving the unnatural amino acid para-amino-Phe, which resulted in P450 catalysts capable of supporting the highest total turnover number reported to date on a complex molecule (34,650). The functional changes induced by the unnatural amino acids could not be reproduced by any of the 20 natural amino acids. This study thus demonstrates that unnatural amino acid mutagenesis constitutes a promising new strategy for improving the catalytic activity and regioselectivity of P450 oxidation catalysts.
Collapse
Affiliation(s)
- Joshua N Kolev
- Department of Chemistry, University of Rochester, Hutchison Hall, Rochester, NY 14620 (USA)
| | | | | | | |
Collapse
|
136
|
Lang K, Chin JW. Cellular incorporation of unnatural amino acids and bioorthogonal labeling of proteins. Chem Rev 2014; 114:4764-806. [PMID: 24655057 DOI: 10.1021/cr400355w] [Citation(s) in RCA: 791] [Impact Index Per Article: 79.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kathrin Lang
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | | |
Collapse
|
137
|
Abstract
Genetic code expansion and reprogramming enable the site-specific incorporation of diverse designer amino acids into proteins produced in cells and animals. Recent advances are enhancing the efficiency of unnatural amino acid incorporation by creating and evolving orthogonal ribosomes and manipulating the genome. Increasing the number of distinct amino acids that can be site-specifically encoded has been facilitated by the evolution of orthogonal quadruplet decoding ribosomes and the discovery of mutually orthogonal synthetase/tRNA pairs. Rapid progress in moving genetic code expansion from bacteria to eukaryotic cells and animals (C. elegans and D. melanogaster) and the incorporation of useful unnatural amino acids has been aided by the development and application of the pyrrolysyl-transfer RNA (tRNA) synthetase/tRNA pair for unnatural amino acid incorporation. Combining chemoselective reactions with encoded amino acids has facilitated the installation of posttranslational modifications, as well as rapid derivatization with diverse fluorophores for imaging.
Collapse
Affiliation(s)
- Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 OQH, United Kingdom;
| |
Collapse
|
138
|
Nguyen DP, Mahesh M, Elsässer SJ, Hancock SM, Uttamapinant C, Chin JW. Genetic encoding of photocaged cysteine allows photoactivation of TEV protease in live mammalian cells. J Am Chem Soc 2014; 136:2240-3. [PMID: 24479649 PMCID: PMC4333589 DOI: 10.1021/ja412191m] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
We demonstrate the evolution of the
PylRS/tRNACUA pair
for genetically encoding photocaged cysteine. By characterizing the
incorporation in Escherichia coli and
mammalian cells, and the photodeprotection process in vitro and in mammalian cells, we establish conditions for rapid efficient
photodeprotection to reveal native proteins in live cells. We demonstrate
the utility of this approach by rapidly activating TEV protease following
illumination of single cells.
Collapse
Affiliation(s)
- Duy P Nguyen
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | | | | | | | | | | |
Collapse
|
139
|
Zimmerman ES, Heibeck TH, Gill A, Li X, Murray CJ, Madlansacay MR, Tran C, Uter NT, Yin G, Rivers PJ, Yam AY, Wang WD, Steiner AR, Bajad SU, Penta K, Yang W, Hallam TJ, Thanos CD, Sato AK. Production of site-specific antibody-drug conjugates using optimized non-natural amino acids in a cell-free expression system. Bioconjug Chem 2014; 25:351-61. [PMID: 24437342 DOI: 10.1021/bc400490z] [Citation(s) in RCA: 260] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Antibody-drug conjugates (ADCs) are a targeted chemotherapeutic currently at the cutting edge of oncology medicine. These hybrid molecules consist of a tumor antigen-specific antibody coupled to a chemotherapeutic small molecule. Through targeted delivery of potent cytotoxins, ADCs exhibit improved therapeutic index and enhanced efficacy relative to traditional chemotherapies and monoclonal antibody therapies. The currently FDA-approved ADCs, Kadcyla (Immunogen/Roche) and Adcetris (Seattle Genetics), are produced by conjugation to surface-exposed lysines, or partial disulfide reduction and conjugation to free cysteines, respectively. These stochastic modes of conjugation lead to heterogeneous drug products with varied numbers of drugs conjugated across several possible sites. As a consequence, the field has limited understanding of the relationships between the site and extent of drug loading and ADC attributes such as efficacy, safety, pharmacokinetics, and immunogenicity. A robust platform for rapid production of ADCs with defined and uniform sites of drug conjugation would enable such studies. We have established a cell-free protein expression system for production of antibody drug conjugates through site-specific incorporation of the optimized non-natural amino acid, para-azidomethyl-l-phenylalanine (pAMF). By using our cell-free protein synthesis platform to directly screen a library of aaRS variants, we have discovered a novel variant of the Methanococcus jannaschii tyrosyl tRNA synthetase (TyrRS), with a high activity and specificity toward pAMF. We demonstrate that site-specific incorporation of pAMF facilitates near complete conjugation of a DBCO-PEG-monomethyl auristatin (DBCO-PEG-MMAF) drug to the tumor-specific, Her2-binding IgG Trastuzumab using strain-promoted azide-alkyne cycloaddition (SPAAC) copper-free click chemistry. The resultant ADCs proved highly potent in in vitro cell cytotoxicity assays.
Collapse
Affiliation(s)
- Erik S Zimmerman
- Sutro Biopharma, Inc. 310 Utah Ave Suite 150 South San Francisco, California 94080, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
140
|
Krishnakumar R, Ling J. Experimental challenges of sense codon reassignment: an innovative approach to genetic code expansion. FEBS Lett 2013; 588:383-8. [PMID: 24333334 DOI: 10.1016/j.febslet.2013.11.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 11/19/2013] [Accepted: 11/27/2013] [Indexed: 10/25/2022]
Abstract
The addition of new and versatile chemical and biological properties to proteins pursued through incorporation of non-canonical amino acids is at present primarily achieved by stop codon suppression. However, it is critical to find new "blank" codons to increase the variety and efficiency of such insertions, thereby taking 'sense codon recoding' to center stage in the field of genetic code expansion. Current thought optimistically suggests the use of the pyrrolysine system coupled with re-synthesis of genomic information towards achieving sense codon reassignment. Upon review of the serious experimental challenges reported in recent studies, we propose that success in this area will depend on the re-synthesis of genomes, but also on 'rewiring' the mechanism of protein synthesis and of its quality control.
Collapse
Affiliation(s)
- Radha Krishnakumar
- Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD 20850, USA.
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| |
Collapse
|
141
|
Mittelstaet J, Konevega AL, Rodnina MV. A kinetic safety gate controlling the delivery of unnatural amino acids to the ribosome. J Am Chem Soc 2013; 135:17031-8. [PMID: 24079513 DOI: 10.1021/ja407511q] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Improving the yield of unnatural amino acid incorporation is an important challenge in producing novel designer proteins with unique chemical properties. Here we examine the mechanisms that restrict the incorporation of the fluorescent unnatural amino acid εNH2-Bodipy576/589-lysine (BOP-Lys) into a model protein. While the delivery of BOP-Lys-tRNA(Lys) to the ribosome is limited by its poor binding to elongation factor Tu (EF-Tu), the yield of incorporation into peptide is additionally controlled at the step of BOP-Lys-tRNA release from EF-Tu into the ribosome. The unnatural amino acid appears to disrupt the interactions that balance the strength of tRNA binding to EF-Tu-GTP with the velocity of tRNA dissociation from EF-Tu-GDP on the ribosome, which ensure uniform incorporation of standard amino acids. Circumventing this potential quality control checkpoint that specifically prevents incorporation of unnatural amino acids into proteins may provide a new strategy to increase yields of unnatural polymers.
Collapse
Affiliation(s)
- Joerg Mittelstaet
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry , 37077 Göttingen, Germany
| | | | | |
Collapse
|
142
|
Genetically encoding phenyl azide chemistry: new uses and ideas for classical biochemistry. Biochem Soc Trans 2013; 41:1177-82. [DOI: 10.1042/bst20130094] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Introducing new physicochemical properties into proteins through genetically encoded Uaa (unnatural amino acid) incorporation can lead to the generation of proteins with novel properties not normally accessible with the 20 natural amino acids. Phenyl azide chemistry represents one such useful addition to the protein repertoire. Classically used in biochemistry as a non-specific photochemical protein cross-linker, genetically encoding phenyl azide chemistry at selected residues provides more powerful routes to post-translationally modify protein function in situ. The two main routes are modulation by light (optogenetics) and site-specific bio-orthogonal modification (bioconjugation) via Click chemistry. In the present article, we discuss both approaches and their influence on protein function.
Collapse
|
143
|
Hemphill J, Chou C, Chin JW, Deiters A. Genetically encoded light-activated transcription for spatiotemporal control of gene expression and gene silencing in mammalian cells. J Am Chem Soc 2013; 135:13433-9. [PMID: 23931657 DOI: 10.1021/ja4051026] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photocaging provides a method to spatially and temporally control biological function and gene expression with high resolution. Proteins can be photochemically controlled through the site-specific installation of caging groups on amino acid side chains that are essential for protein function. The photocaging of a synthetic gene network using unnatural amino acid mutagenesis in mammalian cells was demonstrated with an engineered bacteriophage RNA polymerase. A caged T7 RNA polymerase was expressed in cells with an expanded genetic code and used in the photochemical activation of genes under control of an orthogonal T7 promoter, demonstrating tight spatial and temporal control. The synthetic gene expression system was validated with two reporter genes (luciferase and EGFP) and applied to the light-triggered transcription of short hairpin RNA constructs for the induction of RNA interference.
Collapse
Affiliation(s)
- James Hemphill
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
| | | | | | | |
Collapse
|
144
|
Hu X, Tian J, Liu T, Zhang G, Liu S. Photo-Triggered Release of Caged Camptothecin Prodrugs from Dually Responsive Shell Cross-Linked Micelles. Macromolecules 2013. [DOI: 10.1021/ma400691j] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xianglong Hu
- CAS Key Laboratory of Soft Matter
Chemistry, Department of Polymer Science and Engineering, Hefei National
Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026,
China
| | - Jie Tian
- Engineering and Materials
Science Experiment Center, University of Science and Technology of China, Hefei 230027, China
| | - Tao Liu
- CAS Key Laboratory of Soft Matter
Chemistry, Department of Polymer Science and Engineering, Hefei National
Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026,
China
| | - Guoying Zhang
- CAS Key Laboratory of Soft Matter
Chemistry, Department of Polymer Science and Engineering, Hefei National
Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026,
China
| | - Shiyong Liu
- CAS Key Laboratory of Soft Matter
Chemistry, Department of Polymer Science and Engineering, Hefei National
Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026,
China
| |
Collapse
|
145
|
Kim CH, Axup JY, Schultz PG. Protein conjugation with genetically encoded unnatural amino acids. Curr Opin Chem Biol 2013; 17:412-9. [PMID: 23664497 DOI: 10.1016/j.cbpa.2013.04.017] [Citation(s) in RCA: 202] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 03/27/2013] [Accepted: 04/15/2013] [Indexed: 10/26/2022]
Abstract
The site-specific incorporation of unnatural amino acids with orthogonal chemical reactivity into proteins enables the synthesis of structurally defined protein conjugates. Amino acids containing ketone, azide, alkyne, alkene, and tetrazine side chains can be genetically encoded in response to nonsense and frameshift codons. These bio-orthogonal chemical handles allow precise control over the site and stoichiometry of conjugation, and have enabled medicinal chemistry-like optimization of the physical and biological properties of protein conjugates, especially the next-generation protein therapeutics.
Collapse
Affiliation(s)
- Chan Hyuk Kim
- California Institute for Biomedical Research, 11119 N. Torrey Pines Road, La Jolla, CA 92037, United States
| | | | | |
Collapse
|
146
|
Wang YS, Fang X, Chen HY, Wu B, Wang ZU, Hilty C, Liu WR. Genetic incorporation of twelve meta-substituted phenylalanine derivatives using a single pyrrolysyl-tRNA synthetase mutant. ACS Chem Biol 2013; 8:405-15. [PMID: 23138887 DOI: 10.1021/cb300512r] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
When coexpressed with its cognate amber suppressing tRNACUAPyl(CUA), a pyrrolysyltRNA synthetase mutant N346A/C348A is able to genetically incorporate 12 meta-substituted phenylalanine derivatives into proteins site-specifically at amber mutation sites in Escherichia coli. These genetically encoded noncanonical amino acids resemble phenylalanine in size and contain diverse bioorthogonal functional groups such as halide, trifluoromethyl, nitrile, nitro,ketone, alkyne, and azide moieties. The genetic installation of these functional groups in proteins provides multiple ways to site-selectively label proteins with biophysical and biochemical probes for their functional investigations. We demonstrate that a genetically incorporated trifluoromethyl group can be used as a sensitive 19F NMR probe to study protein folding/unfolding, and that genetically incorporated reactive functional groups such as ketone,alkyne, and azide moieties can be applied to site-specifically label proteins with fluorescent probes. This critical discovery allows the synthesis of proteins with diverse bioorthogonal functional groups for a variety of basic studies and biotechnology development using a single recombinant expression system.
Collapse
Affiliation(s)
- Yane-Shih Wang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Xinqiang Fang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hsueh-Ying Chen
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Bo Wu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Zhiyong U. Wang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Christian Hilty
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Wenshe R. Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
147
|
Labòria N, Wieneke R, Tampé R. Control of Nanomolar Interaction and In Situ Assembly of Proteins in Four Dimensions by Light. Angew Chem Int Ed Engl 2013; 52:848-53. [DOI: 10.1002/anie.201206698] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Revised: 10/10/2012] [Indexed: 11/12/2022]
|
148
|
Labòria N, Wieneke R, Tampé R. Steuerung von nanomolaren Wechselwirkungen und In-situ-Immobilisierung von Proteinen in vier Dimensionen durch Licht. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201206698] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
149
|
Matsuo K, Kioi Y, Yasui R, Takaoka Y, Miki T, Fujishima SH, Hamachi I. One-step construction of caged carbonic anhydrase I using a ligand-directed acyl imidazole-based protein labeling method. Chem Sci 2013. [DOI: 10.1039/c3sc50560j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
150
|
Ahmed I, Fruk L. The power of light: photosensitive tools for chemical biology. ACTA ACUST UNITED AC 2013; 9:565-70. [DOI: 10.1039/c2mb25407g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|