1
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Hartman MCT. Non-canonical Amino Acid Substrates of E. coli Aminoacyl-tRNA Synthetases. Chembiochem 2022; 23:e202100299. [PMID: 34416067 PMCID: PMC9651912 DOI: 10.1002/cbic.202100299] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/03/2021] [Indexed: 01/07/2023]
Abstract
In this comprehensive review, I focus on the twenty E. coli aminoacyl-tRNA synthetases and their ability to charge non-canonical amino acids (ncAAs) onto tRNAs. The promiscuity of these enzymes has been harnessed for diverse applications including understanding and engineering of protein function, creation of organisms with an expanded genetic code, and the synthesis of diverse peptide libraries for drug discovery. The review catalogues the structures of all known ncAA substrates for each of the 20 E. coli aminoacyl-tRNA synthetases, including ncAA substrates for engineered versions of these enzymes. Drawing from the structures in the list, I highlight trends and novel opportunities for further exploitation of these ncAAs in the engineering of protein function, synthetic biology, and in drug discovery.
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Affiliation(s)
- Matthew C T Hartman
- Department of Chemistry and Massey Cancer Center, Virginia Commonwealth University, 1001 W Main St., Richmond, VA 23220, USA
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2
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Amiram M, Haimovich AD, Fan C, Wang YS, Aerni HR, Ntai I, Moonan DW, Ma NJ, Rovner AJ, Hong SH, Kelleher NL, Goodman AL, Jewett MC, Söll D, Rinehart J, Isaacs FJ. Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids. Nat Biotechnol 2015; 33:1272-1279. [PMID: 26571098 DOI: 10.1038/nbt.3372] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 09/11/2015] [Indexed: 01/24/2023]
Abstract
Expansion of the genetic code with nonstandard amino acids (nsAAs) has enabled biosynthesis of proteins with diverse new chemistries. However, this technology has been largely restricted to proteins containing a single or few nsAA instances. Here we describe an in vivo evolution approach in a genomically recoded Escherichia coli strain for the selection of orthogonal translation systems capable of multi-site nsAA incorporation. We evolved chromosomal aminoacyl-tRNA synthetases (aaRSs) with up to 25-fold increased protein production for p-acetyl-L-phenylalanine and p-azido-L-phenylalanine (pAzF). We also evolved aaRSs with tunable specificities for 14 nsAAs, including an enzyme that efficiently charges pAzF while excluding 237 other nsAAs. These variants enabled production of elastin-like-polypeptides with 30 nsAA residues at high yields (∼50 mg/L) and high accuracy of incorporation (>95%). This approach to aaRS evolution should accelerate and expand our ability to produce functionalized proteins and sequence-defined polymers with diverse chemistries.
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Affiliation(s)
- Miriam Amiram
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA.,Systems Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Adrian D Haimovich
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA.,Systems Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Chenguang Fan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Yane-Shih Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Hans-Rudolf Aerni
- Systems Biology Institute, Yale University, West Haven, Connecticut, USA.,Department of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut, USA
| | - Ioanna Ntai
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Daniel W Moonan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA.,Systems Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Natalie J Ma
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA.,Systems Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Alexis J Rovner
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA.,Systems Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Seok Hoon Hong
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.,Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Jesse Rinehart
- Systems Biology Institute, Yale University, West Haven, Connecticut, USA.,Department of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut, USA
| | - Farren J Isaacs
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA.,Systems Biology Institute, Yale University, West Haven, Connecticut, USA
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3
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Amit M, Ashkenasy N. Electronic Properties of Amyloid β-Based Peptide Filaments with Different Non-Natural Heterocyclic Side Chains. Isr J Chem 2014. [DOI: 10.1002/ijch.201400025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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4
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Wu IL, Patterson MA, Carpenter Desai HE, Mehl RA, Giorgi G, Conticello VP. Multiple Site-Selective Insertions of Noncanonical Amino Acids into Sequence-Repetitive Polypeptides. Chembiochem 2013; 14:968-78. [DOI: 10.1002/cbic.201300069] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Indexed: 11/11/2022]
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5
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Hamley IW, Brown GD, Castelletto V, Cheng G, Venanzi M, Caruso M, Placidi E, Aleman C, Revilla-López G, Zanuy D. Self-Assembly of a Designed Amyloid Peptide Containing the Functional Thienylalanine Unit. J Phys Chem B 2010; 114:10674-83. [DOI: 10.1021/jp105508g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- I. W. Hamley
- School of Chemistry, Food and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K., Department of Chemical Sciences and Technologies, CNR, Department of Physics, University of Rome Tor Vergata, Via Ricerca Scientifica 1, Rome, Italy, Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain, and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici
| | - G. D. Brown
- School of Chemistry, Food and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K., Department of Chemical Sciences and Technologies, CNR, Department of Physics, University of Rome Tor Vergata, Via Ricerca Scientifica 1, Rome, Italy, Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain, and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici
| | - V. Castelletto
- School of Chemistry, Food and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K., Department of Chemical Sciences and Technologies, CNR, Department of Physics, University of Rome Tor Vergata, Via Ricerca Scientifica 1, Rome, Italy, Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain, and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici
| | - G. Cheng
- School of Chemistry, Food and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K., Department of Chemical Sciences and Technologies, CNR, Department of Physics, University of Rome Tor Vergata, Via Ricerca Scientifica 1, Rome, Italy, Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain, and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici
| | - M. Venanzi
- School of Chemistry, Food and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K., Department of Chemical Sciences and Technologies, CNR, Department of Physics, University of Rome Tor Vergata, Via Ricerca Scientifica 1, Rome, Italy, Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain, and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici
| | - M. Caruso
- School of Chemistry, Food and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K., Department of Chemical Sciences and Technologies, CNR, Department of Physics, University of Rome Tor Vergata, Via Ricerca Scientifica 1, Rome, Italy, Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain, and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici
| | - E. Placidi
- School of Chemistry, Food and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K., Department of Chemical Sciences and Technologies, CNR, Department of Physics, University of Rome Tor Vergata, Via Ricerca Scientifica 1, Rome, Italy, Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain, and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici
| | - C. Aleman
- School of Chemistry, Food and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K., Department of Chemical Sciences and Technologies, CNR, Department of Physics, University of Rome Tor Vergata, Via Ricerca Scientifica 1, Rome, Italy, Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain, and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici
| | - G. Revilla-López
- School of Chemistry, Food and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K., Department of Chemical Sciences and Technologies, CNR, Department of Physics, University of Rome Tor Vergata, Via Ricerca Scientifica 1, Rome, Italy, Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain, and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici
| | - D. Zanuy
- School of Chemistry, Food and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K., Department of Chemical Sciences and Technologies, CNR, Department of Physics, University of Rome Tor Vergata, Via Ricerca Scientifica 1, Rome, Italy, Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain, and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici
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6
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Viswanathan K, Li G, Gross RA. Protease Catalyzed In Situ C-Terminal Modification of Oligoglutamate. Macromolecules 2010. [DOI: 10.1021/ma100562j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kodandaraman Viswanathan
- Department of Chemical and Biological Sciences, NSF I/UCRC for Biocatalysis and Bioprocessing of Macromolecules, Polytechnic Institute of New York University, Six Metrotech Center, Brooklyn, New York 11201
| | - Geng Li
- Department of Chemical and Biological Sciences, NSF I/UCRC for Biocatalysis and Bioprocessing of Macromolecules, Polytechnic Institute of New York University, Six Metrotech Center, Brooklyn, New York 11201
| | - Richard A. Gross
- Department of Chemical and Biological Sciences, NSF I/UCRC for Biocatalysis and Bioprocessing of Macromolecules, Polytechnic Institute of New York University, Six Metrotech Center, Brooklyn, New York 11201
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7
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Sletten E, Bertozzi C. Bioorthogonale Chemie - oder: in einem Meer aus Funktionalität nach Selektivität fischen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900942] [Citation(s) in RCA: 522] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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8
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A new and general route to 2-pyrrolylglycine, 2-pyrrolylalanine and homo-2-pyrrolylalanine derivatives. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.tetasy.2009.06.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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9
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Sletten EM, Bertozzi CR. Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew Chem Int Ed Engl 2009; 48:6974-98. [PMID: 19714693 PMCID: PMC2864149 DOI: 10.1002/anie.200900942] [Citation(s) in RCA: 2305] [Impact Index Per Article: 153.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The study of biomolecules in their native environments is a challenging task because of the vast complexity of cellular systems. Technologies developed in the last few years for the selective modification of biological species in living systems have yielded new insights into cellular processes. Key to these new techniques are bioorthogonal chemical reactions, whose components must react rapidly and selectively with each other under physiological conditions in the presence of the plethora of functionality necessary to sustain life. Herein we describe the bioorthogonal chemical reactions developed to date and how they can be used to study biomolecules.
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Affiliation(s)
- Ellen M. Sletten
- Department of Chemistry, University of California, Berkeley, CA 94720 (USA)
| | - Carolyn R. Bertozzi
- Departments of Chemistry and Molecular and Cell Biology and Howard Hughes Medical Institute, University of California and The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (USA), Fax: (+1)510-643-2628
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10
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11
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Krejchi MT, Atkins EDT, Fournier MJ, Mason TL, Tirrell DA. Observation of a Silk-Like Crystal Structure in a Genetically Engineered Periodic Polypeptide. JOURNAL OF MACROMOLECULAR SCIENCE PART A-PURE AND APPLIED CHEMISTRY 2006. [DOI: 10.1080/10601329608014915] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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13
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Datta D, Vaidehi N, Zhang D, Goddard WA. Selectivity and specificity of substrate binding in methionyl-tRNA synthetase. Protein Sci 2005; 13:2693-705. [PMID: 15388861 PMCID: PMC2286561 DOI: 10.1110/ps.04792204] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The accuracy of in vivo incorporation of amino acids during protein biosynthesis is controlled to a significant extent by aminoacyl-tRNA synthetases (aaRS). This paper describes the application of the HierDock computational method to study the molecular basis of amino acid binding to the Escherichia coli methionyl tRNA synthetase (MetRS). Starting with the protein structure from the MetRS cocrystal, the HierDock calculations predict the binding site of methionine in MetRS to a root mean square deviation in coordinates (CRMS) of 0.55 A for all the atoms, compared with the crystal structure. The MetRS conformation in the cocrystal structure shows good discrimination between cognate and the 19 noncognate amino acids. In addition, the calculated binding energies of a set of five methionine analogs show a good correlation (R(2) = 0.86) to the relative free energies of binding derived from the measured in vitro kinetic parameters, K(m) and k(cat). Starting with the crystal structure of MetRS without the methionine (apo-MetRS), the putative binding site of methionine was predicted. We demonstrate that even the apo-MetRS structure shows a preference for binding methionine compared with the 19 other natural amino acids. On comparing the calculated binding energies of the 20 natural amino acids for apo-MetRS with those for the cocrystal structure, we observe that the discrimination against the noncognate substrate increases dramatically in the second step of the physical binding process associated with the conformation change in the protein.
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Affiliation(s)
- Deepshikha Datta
- Materials and Process Simulation Center (MC 139-74), Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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14
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15
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Abstract
Although chemists can synthesize virtually any small organic molecule, our ability to rationally manipulate the structures of proteins is quite limited, despite their involvement in virtually every life process. For most proteins, modifications are largely restricted to substitutions among the common 20 amino acids. Herein we describe recent advances that make it possible to add new building blocks to the genetic codes of both prokaryotic and eukaryotic organisms. Over 30 novel amino acids have been genetically encoded in response to unique triplet and quadruplet codons including fluorescent, photoreactive, and redox-active amino acids, glycosylated amino acids, and amino acids with keto, azido, acetylenic, and heavy-atom-containing side chains. By removing the limitations imposed by the existing 20 amino acid code, it should be possible to generate proteins and perhaps entire organisms with new or enhanced properties.
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Affiliation(s)
- Lei Wang
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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16
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Budisa N. Prolegomena zum experimentellen Engineering des genetischen Codes durch Erweiterung seines Aminosäurerepertoires. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200300646] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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17
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Budisa N. Prolegomena to Future Experimental Efforts on Genetic Code Engineering by Expanding Its Amino Acid Repertoire. Angew Chem Int Ed Engl 2004; 43:6426-63. [PMID: 15578784 DOI: 10.1002/anie.200300646] [Citation(s) in RCA: 208] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Protein synthesis and its relation to the genetic code was for a long time a central issue in biology. Rapid experimental progress throughout the past decade, crowned with the recently elucidated ribosomal structures, provided an almost complete description of this process. In addition important experiments provided solid evidence that the natural protein translation machinery can be reprogrammed to encode genetically a vast number of non-coded (i.e. noncanonical) amino acids. Indeed, in the set of 20 canonical amino acids as prescribed by the universal genetic code, many desirable functionalities, such as halogeno, keto, cyano, azido, nitroso, nitro, and silyl groups, as well as C=C or C[triple bond]C bonds, are absent. The ability to encode genetically such chemical diversity will enable us to reprogram living cells, such as bacteria, to express tailor-made proteins exhibiting functional diversity. Accordingly, genetic code engineering has developed into an exciting emerging research field at the interface of biology, chemistry, and physics.
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Affiliation(s)
- Nediljko Budisa
- Max-Planck-Institut für Biochemie, Junior Research Group "Moleculare Biotechnologie", Am Klopferspitz 18a, 82152 Martinsried bei München, Germany.
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Abstract
Two fluorinated derivatives of isoleucine: d,l-2-amino-3-trifluoromethyl pentanoic acid (3TFI, 2) and d,l-2-amino-5,5,5-trifluoro-3-methyl pentanoic acid (5TFI, 3) were prepared. 5TFI was incorporated into a model target protein, murine dihydrofolate reductase (mDHFR), in an isoleucine auxotrophic Escherichia coli host strain suspended in 5TFI-supplemented minimal medium depleted of isoleucine. Incorporation of 5TFI was confirmed by tryptic peptide analysis and matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) of the protein product. Amino acid analysis showed that more than 93% of the encoded isoleucine residues were replaced by 5TFI. Measurement of the rate of activation of 5TFI by the E. coli isoleucyl-tRNA synthetase (IleRS) yielded a specificity constant (k(cat)/K(m)) 134-fold lower than that for isoleucine. 5TFI was successfully introduced into the cytokine murine interleukin-2 (mIL-2) at the encoded isoleucine positions. The concentration of fluorinated protein that elicits 50% of the maximal proliferative response is 3.87 ng/mL, about 30% higher than that of wild-type mIL-2 (EC(50) = 2.70 ng/mL). The maximal responses are equivalent for the fluorinated and wild-type cytokines, indicating that fluorinated proteins can fold into stable and functional structures. 3TFI yielded no evidence for in vivo incorporation into recombinant proteins, and no evidence for activation by IleRS in vitro.
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Affiliation(s)
- Pin Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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Wang P, Vaidehi N, Tirrell DA, Goddard WA. Virtual screening for binding of phenylalanine analogues to phenylalanyl-tRNA synthetase. J Am Chem Soc 2002; 124:14442-9. [PMID: 12452720 DOI: 10.1021/ja0175441] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although incorporation of nonnatural amino acids provides a powerful means of controlling protein structure and function, experimental investigations of amino acid analogues for utilization by the protein biosynthetic machinery can be costly and time-consuming. In this paper, we describe a computational protocol (HierDock) for predicting the relative energies of binding of phenylalanine analogues to phenylalanyl-tRNA synthetase (PheRS). Starting with the crystal structure of Thermus thermophilus PheRS without bound ligand, HierDock predicts the binding site of phenylalanine (Phe) within 1.1 A of that revealed by the crystal structure of PheRS cocrystallized with Phe. The calculated binding energies of Phe analogues in PheRS, using HierDock, correlate well with the translational activities of the same analogues in Escherichia coli. HierDock identifies p-fluorophenylalanine and 3-thienylalanine as especially good substrates for PheRS, in agreement with experiment. These results suggest that the HierDock protocol may be useful for virtual screening of amino acid analogues prior to experiment.
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Affiliation(s)
- Pin Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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20
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Zhang D, Vaidehi N, Goddard WA, Danzer JF, Debe D. Structure-based design of mutant Methanococcus jannaschii tyrosyl-tRNA synthetase for incorporation of O-methyl-L-tyrosine. Proc Natl Acad Sci U S A 2002; 99:6579-84. [PMID: 12011422 PMCID: PMC124445 DOI: 10.1073/pnas.052150499] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2002] [Indexed: 11/18/2022] Open
Abstract
Although incorporation of amino acid analogs provides a powerful means of producing new protein structures with interesting functions, many amino acid analogs cannot be incorporated easily by using the wild-type aminoacyl-tRNA synthetase (aaRS). To be able to incorporate specific amino acid analogs site-specifically, it is useful to build a mutant aaRS that preferentially activates the analog compared with the natural amino acids. Experimental combinatorial studies to find such mutant aaRSs have been successful but can easily become costly and time-consuming. In this article, we describe the clash opportunity progressive (COP) computational method for designing a mutant aaRS to preferentially take up the analog compared with the natural amino acids. To illustrate this COP procedure, we apply it to the design of mutant Methanococcus jannaschii tyrosyl-tRNA synthetase (M.jann-TyrRS). Because the three-dimensional structure for M.jann-TyrRS was not available, we used the STRUCTFAST homology modeling procedure plus molecular dynamics with continuum solvent forces to predict the structure of wild-type M.jann-TyrRS. We validate this structure by predicting the binding site for tyrosine and calculating the binding energies of the 20 natural amino acids, which shows that tyrosine binds the strongest. With the COP design algorithm we then designed a mutant tyrosyl tRNA synthetase to activate O-methyl-l-tyrosine preferentially compared with l-tyrosine. This mutant [Y32Q, D158A] is similar to the mutant designed with combinatorial experiments, [Y32Q, D158A, E107T, L162P], by Wang et al. [Wang, L., Brock, A., Herberich, B. & Schultz, P. G. (2001) Science 292, 498-500]. We predict that the new one will have much greater activity while retaining significant discrimination between O-methyl-l-tyrosine and tyrosine.
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Affiliation(s)
- Deqiang Zhang
- Materials and Process Simulation Center, Beckman Institute, California Institute of Technology, Pasadena, CA 91125; and BionomiX, Pasadena, CA 91106, USA
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Ferrocene-modified oligopeptide as model compound for charge-transfer interactions with organic electron acceptors. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2001. [DOI: 10.1016/s0928-4931(01)00379-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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A novel polynuclear donor complex based on helical peptides with aligned electroactive moieties. Chem Phys Lett 2001. [DOI: 10.1016/s0009-2614(01)01325-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Budisa N, Alefelder S, Bae JH, Golbik R, Minks C, Huber R, Moroder L. Proteins with beta-(thienopyrrolyl)alanines as alternative chromophores and pharmaceutically active amino acids. Protein Sci 2001; 10:1281-92. [PMID: 11420430 PMCID: PMC2374119 DOI: 10.1110/ps.51601] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
L-beta-(Thieno[3,2-b]pyrrolyl)alanine and L-beta-(thieno[2,3-b]pyrrolyl)alanine are mutually isosteric and pharmaceutically active amino acids that mimic tryptophan with the benzene ring in the indole moiety replaced by thiophene. Sulfur as a heteroatom causes physicochemical changes in these tryptophan surrogates that bring about completely new properties not found in the indole moiety. These synthetic amino acids were incorporated into recombinant proteins in response to the Trp UGG codons by fermentation in a Trp-auxotrophic Escherichia coli host strain using the selective pressure incorporation method. Related protein mutants expectedly retain the secondary structure of the native proteins but show significantly changed optical and thermodynamic properties. In this way, new spectral windows, fluorescence, polarity, thermodynamics, or pharmacological properties are inserted into proteins. Such an engineering approach by translational integration of synthetic amino acids with a priori defined properties, as shown in this study, proved to be a novel and useful tool for protein rational design.
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Affiliation(s)
- N Budisa
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, D-82152 Martinsried, Germany.
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Tang Y, Ghirlanda G, Petka WA, Nakajima T, DeGrado WF, Tirrell DA. Fluorinated Coiled-Coil Proteins Prepared In Vivo Display Enhanced Thermal and Chemical Stability. Angew Chem Int Ed Engl 2001; 40:1494-1496. [DOI: 10.1002/1521-3773(20010417)40:8<1494::aid-anie1494>3.0.co;2-x] [Citation(s) in RCA: 161] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2001] [Indexed: 11/10/2022]
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25
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Tang Y, Ghirlanda G, Petka WA, Nakajima T, DeGrado WF, Tirrell DA. Fluorinated Coiled-Coil Proteins Prepared In Vivo Display Enhanced Thermal and Chemical Stability. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010417)113:8<1542::aid-ange1542>3.0.co;2-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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26
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Kiick KL, Tirrell DA. Protein Engineering by In Vivo Incorporation of Non-Natural Amino Acids: Control of Incorporation of Methionine Analogues by Methionyl-tRNA Synthetase. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00833-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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Kiick K, van Hest J, Tirrell D. Expanding the Scope of Protein Biosynthesis by Altering the Methionyl-tRNA Synthetase Activity of a Bacterial Expression Host. Angew Chem Int Ed Engl 2000. [DOI: 10.1002/1521-3757(20000616)112:12<2232::aid-ange2232>3.0.co;2-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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Abstract
[reaction: see text] Furanomycin is a Streptomyces metabolite that substitutes for isoleucine in protein translation. We report a concise and modular synthesis starting from the Garner aldehyde and proceeding in seven steps to furanomycin. The key steps include a stereoselective acetylide addition and the Ag+-mediated cyclization of an alpha-allenic alcohol to construct the trans-2,5-dihydrofuran. The efficiency (12% overall yield) and flexibility of the route will provide ample quantities of furanomycin and analogues for protein engineering.
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Affiliation(s)
- M P VanBrunt
- Texas A&M University, Department of Chemistry, College Station 77842-3012, USA
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29
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Sharma N, Furter R, Kast P, Tirrell DA. Efficient introduction of aryl bromide functionality into proteins in vivo. FEBS Lett 2000; 467:37-40. [PMID: 10664452 DOI: 10.1016/s0014-5793(00)01120-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Artificial proteins can be engineered to exhibit interesting solid state, liquid crystal or interfacial properties and may ultimately serve as important alternatives to conventional polymeric materials. The utility of protein-based materials is limited, however, by the availability of just the 20 amino acids that are normally recognized and utilized by biological systems; many desirable functional groups cannot be incorporated directly into proteins by biosynthetic means. In this study, we incorporate para-bromophenylalanine (p-Br-phe) into a model target protein, mouse dihydrofolate reductase (DHFR), by using a bacterial phenylalanyl-tRNA synthetase (PheRS) variant with relaxed substrate specificity. Coexpression of the mutant PheRS and DHFR in a phenylalanine auxotrophic Escherichia coli host strain grown in p-Br-phe-supplemented minimal medium resulted in 88% replacement of phenylalanine residues by p-Br-phe; variation in the relative amounts of phe and p-Br-phe in the medium allows control of the degree of substitution by the analog. Protein expression yields of 20-25 mg/l were obtained from cultures supplemented with p-Br-phe; this corresponds to about two-thirds of the expression levels characteristic of cultures supplemented with phe. The aryl bromide function is stable under the conditions used to purify DHFR and creates new opportunities for post-translational derivatization of brominated proteins via metal-catalyzed coupling reactions. In addition, bromination may be useful in X-ray studies of proteins via the multiwavelength anomalous diffraction (MAD) technique.
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Affiliation(s)
- N Sharma
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003, USA
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30
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van Hest JCM, Kiick KL, Tirrell DA. Efficient Incorporation of Unsaturated Methionine Analogues into Proteins in Vivo. J Am Chem Soc 2000. [DOI: 10.1021/ja992749j] [Citation(s) in RCA: 215] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Sisido M, Hohsaka T. Extension of Protein Functions by the Incorporation of Nonnatural Amino Acids. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1999. [DOI: 10.1246/bcsj.72.1409] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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32
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Budisa N, Minks C, Alefelder S, Wenger W, Dong F, Moroder L, Huber R. Toward the experimental codon reassignment in vivo: protein building with an expanded amino acid repertoire. FASEB J 1999; 13:41-51. [PMID: 9872928 DOI: 10.1096/fasebj.13.1.41] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The high precision and fidelity of the genetic message transmission are ensured by numerous proofreading steps, from DNA replication and transcription to protein translation. The key event for translational fidelity is the proper codon assignment for 20 canonical amino acids. An experimental codon reassignment is possible for noncanonical amino acids in vivo using artificially constructed expression hosts under efficient selective pressure. However, such amino acids may interfere with the cellular metabolism and thus do not belong to the 'first' or 'restricted' part of the universal code, but rather to a second or 'relaxed' part, which is limited mainly by the downstream proofreading in the natural translational machinery. Correspondingly, not all possible alpha-amino acids can be introduced into proteins. The aim of this study is to discuss biological and evolutionary constraints on possible candidates for this second coding level of the universal code. Engineering of such a 'second' code is expected to have great academic as well as practical impact, ranging from protein folding studies to biomedicine.
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Affiliation(s)
- N Budisa
- Max Planck Institut für Biochemie, D-82152 Martinsried, Germany.
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33
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34
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Deming TJ, Fournier MJ, Mason TL, Tirrell DA. Biosynthetic Incorporation and Chemical Modification of Alkene Functionality in Genetically Engineered Polymers. JOURNAL OF MACROMOLECULAR SCIENCE PART A-PURE AND APPLIED CHEMISTRY 1997. [DOI: 10.1080/10601329708010331] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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35
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Mahal LK, Bertozzi CR. Engineered cell surfaces: fertile ground for molecular landscaping. CHEMISTRY & BIOLOGY 1997; 4:415-22. [PMID: 9224572 DOI: 10.1016/s1074-5521(97)90193-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The cell surface contains a wealth of information that determines how cells interact with their environment. Methods for directing the cell surface expression of novel protein-based and oligosaccharide-based epitopes are stimulating new directions in biotechnology and biomedical research.
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Affiliation(s)
- L K Mahal
- Department of Chemistry, University of California and Center for Advanced Materials, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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36
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Abstract
The work reported herein concerns the assembly of N-stearoyl L-cysteine methyl ester [CH3(CH2)16COCysOMe, 1] on the surface of gold. This compound serves as a simple model of a related polypeptide, which has been designed to adopt a beta-sheet architecture on metallic and oxide surfaces. We describe the preparation of monolayers of 1, and characterization of these layers via ellipsometry, vibrational spectroscopy and X-ray photoelectron spectroscopy. The results are most consistent with a disordered array of the alkyl chains, in which close packing is frustrated by a mismatch in the cross-sectional areas of the cysteinyl ester head group and the stearoyl chains of the thiol. Despite the disorder, the alkyl chains form a hydrophobic surface layer, with an advancing contact angle for water comparable to that observed for octadecanethiol on gold.
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Affiliation(s)
- S L Dawson
- Polymer Science and Engineering Department, University of Massachusetts at Amherst 01003, USA
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37
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Deming TJ, Fournier MJ, Mason TL, Tirrell DA. Structural Modification of a Periodic Polypeptide through Biosynthetic Replacement of Proline with Azetidine-2-carboxylic Acid. Macromolecules 1996. [DOI: 10.1021/ma9510698] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Timothy J. Deming
- Departments of Polymer Science and Engineering, and Biochemistry and Molecular Biology, University of Massachusetts at Amherst, Amherst, Massachusetts 01003
| | - Maurille J. Fournier
- Departments of Polymer Science and Engineering, and Biochemistry and Molecular Biology, University of Massachusetts at Amherst, Amherst, Massachusetts 01003
| | - Thomas L. Mason
- Departments of Polymer Science and Engineering, and Biochemistry and Molecular Biology, University of Massachusetts at Amherst, Amherst, Massachusetts 01003
| | - David A. Tirrell
- Departments of Polymer Science and Engineering, and Biochemistry and Molecular Biology, University of Massachusetts at Amherst, Amherst, Massachusetts 01003
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38
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Wang J, Parkhe AD, Tirrell DA, Thompson LK. Crystalline Aggregates of the Repetitive Polypeptide {(AlaGly)3GluGly(GlyAla)3GluGly}10: Structure and Dynamics Probed by 13C Magic Angle Spinning Nuclear Magnetic Resonance Spectroscopy. Macromolecules 1996. [DOI: 10.1021/ma9512972] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jianxin Wang
- Departments of Chemistry and of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003
| | - Ajay D. Parkhe
- Departments of Chemistry and of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003
| | - David A. Tirrell
- Departments of Chemistry and of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003
| | - Lynmarie K. Thompson
- Departments of Chemistry and of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003
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