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Aarthy M, George A, Ayyadurai N. Beyond protein tagging: Rewiring the genetic code of fluorescent proteins - A review. Int J Biol Macromol 2021; 191:840-851. [PMID: 34560154 DOI: 10.1016/j.ijbiomac.2021.09.108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 11/18/2022]
Abstract
Fluorescent proteins (FP) are an integral part of modern biology due to its diverse biochemical and photophysical properties. The boundaries of FP have been extended through conventional mutagenesis and directed evolution approaches. Engineering of FP based on the standard genetic code consisting of 20 amino acids with limited functional groups restrict its diversification. Degeneracy of genetic code has helped in covering this substantial gap through genetic code engineering, wherein introduction of unnatural amino acid (UAA) analogues resulted in a collection of FP with varying properties. This review features the work carried till date in the area of FP incorporated with UAAs and explores strategies employed for incorporation, impact of UAAs in chromophore and surrounding residues and changes in inherent properties of FP. The long-standing association of FP as a tool for high throughput screening of orthogonal aaRS/tRNA pairs used in site specific incorporation of UAAs is expounded. Insertion of UAAs in FP has enabled their use in contemporary fields such as biophotovoltaics, bioremediation, biosensors, biomaterials and imaging of acidic vesicles. Thus, expansion of genetic code of FP is envisaged to rejig the existing spectra of colors and future research initiative in this direction is expected to glow brighter and brighter.
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Affiliation(s)
- Mayilvahanan Aarthy
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai 600020, India
| | - Augustine George
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai 600020, India
| | - Niraikulam Ayyadurai
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai 600020, India.
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2
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Navaratna T, Atangcho L, Mahajan M, Subramanian V, Case M, Min A, Tresnak D, Thurber GM. Directed Evolution Using Stabilized Bacterial Peptide Display. J Am Chem Soc 2020; 142:1882-1894. [PMID: 31880439 DOI: 10.1021/jacs.9b10716] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chemically stabilized peptides have attracted intense interest by academics and pharmaceutical companies due to their potential to hit currently "undruggable" targets. However, engineering an optimal sequence, stabilizing linker location, and physicochemical properties is a slow and arduous process. By pairing non-natural amino acid incorporation and cell surface click chemistry in bacteria with high-throughput sorting, we developed a method to quantitatively select high affinity ligands and applied the Stabilized Peptide Evolution by E. coli Display technique to develop disrupters of the therapeutically relevant MDM2-p53 interface. Through in situ stabilization on the bacterial surface, we demonstrate rapid isolation of stabilized peptides with improved affinity and novel structures. Several peptides evolved a second loop including one sequence (Kd = 1.8 nM) containing an i, i+4 disulfide bond. NMR structural determination indicated a bent helix in solution and bound to MDM2. The bicyclic peptide had improved protease stability, and we demonstrated that protease resistance could be measured both on the bacterial surface and in solution, enabling the method to test and/or screen for additional drug-like properties critical for biologically active compounds.
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Affiliation(s)
- Tejas Navaratna
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Lydia Atangcho
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Mukesh Mahajan
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | | | - Marshall Case
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Andrew Min
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Daniel Tresnak
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Greg M Thurber
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Biomedical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
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Ui M, Miyauchi Y, Inoue M, Murakami M, Araki Y, Wada T, Kinbara K. Development of an Engineered Photoactive Yellow Protein as a Cross‐Linking Junction for Construction of Photoresponsive Protein‐Polymer Conjugates. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mihoko Ui
- Institute of Multidisciplinary Research for Advanced MaterialsTohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Yusuke Miyauchi
- Institute of Multidisciplinary Research for Advanced MaterialsTohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Masataka Inoue
- School of Life Science and TechnologyTokyo Institute of Technology 4259 B58, Nagatsuta-cho, Midori-ku Yokohama 226-8501 Japan
| | - Makoto Murakami
- Institute of Multidisciplinary Research for Advanced MaterialsTohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Yasuyuki Araki
- Institute of Multidisciplinary Research for Advanced MaterialsTohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced MaterialsTohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Kazushi Kinbara
- School of Life Science and TechnologyTokyo Institute of Technology 4259 B58, Nagatsuta-cho, Midori-ku Yokohama 226-8501 Japan
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Ravikumar S, David Y, Park SJ, Choi JI. A Chimeric Two-Component Regulatory System-Based Escherichia coli Biosensor Engineered to Detect Glutamate. Appl Biochem Biotechnol 2018; 186:335-349. [DOI: 10.1007/s12010-018-2746-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/21/2018] [Indexed: 12/13/2022]
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Lama S, Seol E, Park S. Metabolic engineering of Klebsiella pneumoniae J2B for the production of 1,3-propanediol from glucose. BIORESOURCE TECHNOLOGY 2017; 245:1542-1550. [PMID: 28549809 DOI: 10.1016/j.biortech.2017.05.052] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/09/2017] [Accepted: 05/11/2017] [Indexed: 06/07/2023]
Abstract
The production of 1,3-propanediol (1,3-PDO) from glucose was investigated using Klebsiella pneumoniae J2B, which converts glycerol to 1,3-PDO and synthesize an essential coenzyme B12. In order to connect the glycolytic pathway with the pathway of 1,3-PDO synthesis from glycerol, i.e., to directly produce diol from glucose, glycerol-3-phosphate dehydrogenase and glycerol-3-phosphate phosphatase from Saccharomyces cerevisiae were overexpressed. Additionally, the effect of expression levels and the use of isoforms of these two enzymes on glycerol and 1,3-PDO production were studied. Furthermore, to prevent loss of produced glycerol, the glycerol oxidation pathways were disrupted. Finally, the conversion rate of glycerol to 1,3-PDO was increased via homologous overexpression of glycerol dehydratase and 1,3-PDO oxidoreductase. The resultant strain successfully produced 1,3-PDO from glucose at a yield of 0.27mol/mol along with glycerol at 0.52mol/mol. Improvement of the engineered K. pneumoniae J2B to further increase conversion of glycerol to 1,3-PDO is discussed.
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Affiliation(s)
- Suman Lama
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan, Republic of Korea
| | - Eunhee Seol
- School of Energy and Chemical Engineering, UNIST, Ulsan, Republic of Korea
| | - Sunghoon Park
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan, Republic of Korea; School of Energy and Chemical Engineering, UNIST, Ulsan, Republic of Korea.
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Sankaranarayanan M, Somasundar A, Seol E, Chauhan AS, Kwon S, Jung GY, Park S. Production of 3-hydroxypropionic acid by balancing the pathway enzymes using synthetic cassette architecture. J Biotechnol 2017; 259:140-147. [DOI: 10.1016/j.jbiotec.2017.07.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 07/18/2017] [Accepted: 07/23/2017] [Indexed: 10/19/2022]
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Seo KH, Chu HS, Yoo TH, Lee SG, Won JI. Separation efficiency of free-solution conjugated electrophoresis with drag-tags incorporating a synthetic amino acid. Electrophoresis 2016; 37:818-25. [PMID: 26757485 DOI: 10.1002/elps.201500506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/22/2015] [Accepted: 12/29/2015] [Indexed: 11/10/2022]
Abstract
DNA sequencing or separation by conventional capillary electrophoresis with a polymer matrix has some inherent drawbacks, such as the expense of polymer matrix and limitations in sequencing read length. As DNA fragments have a linear charge-to-friction ratio in free solution, DNA fragments cannot be separated by size. However, size-based separation of DNA is possible in free-solution conjugate electrophoresis (FSCE) if a "drag-tag" is attached to DNA fragments because the tag breaks the linear charge-to-friction scaling. Although several previous studies have demonstrated the feasibility of DNA separation by free-solution conjugated electrophoresis, generation of a monodisperse drag-tag and identification of a strong, site-specific conjugation method between a DNA fragment and a drag-tag are challenges that still remain. In this study, we demonstrate an efficient FSCE method by conjugating a biologically synthesized elastin-like polypeptide (ELP) and green fluorescent protein (GFP) to DNA fragments. In addition, to produce strong and site-specific conjugation, a methionine residue in drag-tags is replaced with homopropargylglycine (Hpg), which can be conjugated specifically to a DNA fragment with an azide site.
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Affiliation(s)
- Kyung-Ho Seo
- Department of Chemical Engineering, Hongik University, Seoul, Korea
| | - Hun-Su Chu
- Department of Chemical Engineering, Hongik University, Seoul, Korea.,Material Research Center, SAMSUNG ELECTRONICS Co, Suwon, Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, Korea
| | - Sun-Gu Lee
- Department of Chemical Engineering, Pusan National University, Pusan, Korea
| | - Jong-In Won
- Department of Chemical Engineering, Hongik University, Seoul, Korea
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Engineering Escherichia coli to sense acidic amino acids by introduction of a chimeric two-component system. KOREAN J CHEM ENG 2015. [DOI: 10.1007/s11814-015-0024-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Ganesh I, Ravikumar S, Yoo IK, Hong SH. Construction of malate-sensing Escherichia coli by introduction of a novel chimeric two-component system. Bioprocess Biosyst Eng 2014; 38:797-804. [DOI: 10.1007/s00449-014-1321-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 10/30/2014] [Indexed: 11/29/2022]
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Ganesh I, Ravikumar S, Lee SH, Park SJ, Hong SH. Engineered fumarate sensing Escherichia coli based on novel chimeric two-component system. J Biotechnol 2013; 168:560-6. [DOI: 10.1016/j.jbiotec.2013.09.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 09/11/2013] [Indexed: 11/29/2022]
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A comparative study on the stability and structure of two different green fluorescent proteins in organic co-solvent systems. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-012-0579-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Raghunathan G, Soundrarajan N, Sokalingam S, Yun H, Lee SG. Deletional protein engineering based on stable fold. PLoS One 2012; 7:e51510. [PMID: 23240034 PMCID: PMC3519881 DOI: 10.1371/journal.pone.0051510] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 11/01/2012] [Indexed: 12/14/2022] Open
Abstract
Diversification of protein sequence-structure space is a major concern in protein engineering. Deletion mutagenesis can generate a protein sequence-structure space different from substitution mutagenesis mediated space, but it has not been widely used in protein engineering compared to substitution mutagenesis, because it causes a relatively huge range of structural perturbations of target proteins which often inactivates the proteins. In this study, we demonstrate that, using green fluorescent protein (GFP) as a model system, the drawback of the deletional protein engineering can be overcome by employing the protein structure with high stability. The systematic dissection of N-terminal, C-terminal and internal sequences of GFPs with two different stabilities showed that GFP with high stability (s-GFP), was more tolerant to the elimination of amino acids compared to a GFP with normal stability (n-GFP). The deletion studies of s-GFP enabled us to achieve three interesting variants viz. s-DL4, s-N14, and s-C225, which could not been obtained from n-GFP. The deletion of 191–196 loop sequences led to the variant s-DL4 that was expressed predominantly as insoluble form but mostly active. The s-N14 and s-C225 are the variants without the amino acid residues involving secondary structures around N- and C-terminals of GFP fold respectively, exhibiting comparable biophysical properties of the n-GFP. Structural analysis of the variants through computational modeling study gave a few structural insights that can explain the spectral properties of the variants. Our study suggests that the protein sequence-structure space of deletion mutants can be more efficiently explored by employing the protein structure with higher stability.
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Affiliation(s)
- Govindan Raghunathan
- Department of Chemical Engineering, Pusan National University, Busan, South Korea
| | | | - Sriram Sokalingam
- Department of Chemical Engineering, Pusan National University, Busan, South Korea
| | - Hyungdon Yun
- School of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Sun-Gu Lee
- Department of Chemical Engineering, Pusan National University, Busan, South Korea
- * E-mail:
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Abstract
Techniques to manipulate cellular gene expression such that amino acid analogs not encoded by the genetic code are incorporated into a polypeptide chain have recently gained increasing interest. The so-called noncanonical amino acids often have unusual properties that can be translated into target proteins by reprogrammed ribosomal protein synthesis. Residue-specific substitution of a specific canonical amino acid by its analogs provokes global effects in the resulting protein congeners that include improved stability or catalytic activity, reduced redox sensitivity, as well as altered spectral properties. Thus, the approach holds great promise for the engineering of synthetic proteins.This contribution describes a protocol for the incorporation of a noncanonical amino acid into a target protein expressed in an appropriate amino acid auxotrophic E. coli strain.
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Edwardraja S, Sriram S, Govindan R, Budisa N, Lee SG. Enhancing the thermal stability of a single-chain Fv fragment by in vivo global fluorination of the proline residues. ACTA ACUST UNITED AC 2011; 7:258-65. [DOI: 10.1039/c0mb00154f] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Selvakumar E, Rameshkumar N, Lee SG, Lee SJ, Park HS. In vivo Production of Functional Single-Chain Fv Fragment with an N-Terminal-Specific Bio-orthogonal Reactive Group. Chembiochem 2010; 11:498-501. [DOI: 10.1002/cbic.200900685] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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