51
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Ilamaran M, Sundarapandian A, Aarthy M, Shanmugam G, Ponesakki G, Ramudu KN, Niraikulam A. Growth factor-mimicking 3,4-dihydroxyphenylalanine-encoded bioartificial extracellular matrix like protein promotes wound closure and angiogenesis. Biomater Sci 2020; 8:6773-6785. [PMID: 33141121 DOI: 10.1039/d0bm01379j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The present work reports a new route to prepare a "smart biomaterial" by mimicking long-acting cellular growth factor showing enhanced cell-material interactions by promoting cell proliferation and angiogenesis. For that, reactive non-proteogenic amino acid 3,4-dihydroxyphenylalanine (DOPA) was genetically introduced into an intrinsic triple-helical hierarchical structure forming protein to initiate hierarchical self-assembly to form a macromolecular structure. The self-assembled scaffold displayed vascular endothelial growth factor mimicking the pro-angiogenic reactive group for repairing and remodeling of damaged tissue cells. We customized the recombinant collagen-like protein (CLP) with DOPA to promote rapid wound healing and cell migrations. Selective incorporation of catechol in variable and C-terminal region of CLP enhanced interaction between inter- and intra-triple-helical collagen molecules that resulted in a structure resembling higher-order native collagen fibril. Turbidity analysis indicated that the triple-helical CLP self-assembled at neutral pH via a catechol intra-crosslinking mechanism. After self-assembly, only DOPA-encoded CLP formed branched filamentous structures suggesting that catechol mediated network coordination. The catechol-encoded CLP also acted as a "smart material" by mimicking long-acting cellular growth factor showing enhanced cell-material interactions by promoting cell proliferation and angiogenesis. It eliminates release rate, stability, and shelf-life of hybrid growth factor conjugated biomaterials. The newly synthesized CLP has the potential to promote accelerated cell migration, pro-angiogenesis, and biocompatibility and could be used in the field of implantable medical devices and tissue engineering.
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Affiliation(s)
- Meganathan Ilamaran
- Division of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR) - CLRI, Chennai, India.
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52
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Galindo Casas M, Stargardt P, Mairhofer J, Wiltschi B. Decoupling Protein Production from Cell Growth Enhances the Site-Specific Incorporation of Noncanonical Amino Acids in E. coli. ACS Synth Biol 2020; 9:3052-3066. [PMID: 33150786 DOI: 10.1021/acssynbio.0c00298] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The site-specific incorporation of noncanonical amino acids (ncAAs) into proteins by amber stop codon suppression has become a routine method in academic laboratories. This approach requires an amber suppressor tRNACUA to read the amber codon and an aminoacyl-tRNA synthetase to charge the tRNACUA with the ncAA. However, a major drawback is the low yield of the mutant protein in comparison to the wild type. This effect primarily results from the competition of release factor 1 with the charged suppressor tRNACUA for the amber codon at the A-site of the ribosome. A number of laboratories have attempted to improve the incorporation efficiency of ncAAs with moderate results. We aimed at increasing the efficiency to produce high yields of ncAA-functionalized proteins in a scalable setting for industrial application. To do this, we inserted an ncAA into the enhanced green fluorescent protein and an antibody mimetic molecule using an industrial E. coli strain, which produces recombinant proteins independent of cell growth. The controlled decoupling of recombinant protein production from cell growth considerably increased the incorporation of the ncAA, producing substantially higher protein yields versus the reference E. coli strain BL21(DE3). The target proteins were expressed at high levels, and the ncAA was efficiently incorporated with excellent fidelity while the protein function was preserved.
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Affiliation(s)
- Meritxell Galindo Casas
- acib − Austrian Center of Industrial Biotechnology, 8010 Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, 8010 Graz, Austria
| | | | | | - Birgit Wiltschi
- acib − Austrian Center of Industrial Biotechnology, 8010 Graz, Austria
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53
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Abstract
Genetic code expansion is one of the most powerful technologies in protein engineering. In addition to the 20 canonical amino acids, the expanded genetic code is supplemented by unnatural amino acids, which have artificial side chains that can be introduced into target proteins in vitro and in vivo. A wide range of chemical groups have been incorporated co-translationally into proteins in single cells and multicellular organisms by using genetic code expansion. Incorporated unnatural amino acids have been used for novel structure-function relationship studies, bioorthogonal labelling of proteins in cellulo for microscopy and in vivo for tissue-specific proteomics, the introduction of post-translational modifications and optical control of protein function, to name a few examples. In this Minireview, the development of genetic code expansion technology is briefly introduced, then its applications in neurobiology are discussed, with a focus on studies using mammalian cells and mice as model organisms.
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Affiliation(s)
- Ivana Nikić‐Spiegel
- Werner Reichardt Centre for Integrative NeuroscienceUniversity of TübingenOtfried-Müller-Strasse 2572076TübingenGermany
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54
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Yang B, Kwon K, Jana S, Kim S, Avila-Crump S, Tae G, Mehl RA, Kwon I. Temporal Control of Efficient In Vivo Bioconjugation Using a Genetically Encoded Tetrazine-Mediated Inverse-Electron-Demand Diels–Alder Reaction. Bioconjug Chem 2020; 31:2456-2464. [DOI: 10.1021/acs.bioconjchem.0c00497] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Byungseop Yang
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Kiyoon Kwon
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Subhashis Jana
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Seoungkyun Kim
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Savanna Avila-Crump
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Giyoong Tae
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Ryan A. Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Inchan Kwon
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
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55
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Ancajas CF, Ricks TJ, Best MD. Metabolic labeling of glycerophospholipids via clickable analogs derivatized at the lipid headgroup. Chem Phys Lipids 2020; 232:104971. [PMID: 32898510 PMCID: PMC7606648 DOI: 10.1016/j.chemphyslip.2020.104971] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/01/2020] [Indexed: 02/09/2023]
Abstract
Metabolic labeling, in which substrate analogs containing diminutive tags can infiltrate biosynthetic pathways and generate labeled products in cells, has led to dramatic advancements in the means by which complex biomolecules can be detected and biological processes can be elucidated. Within this realm, metabolic labeling of lipid products, particularly in a manner that is headgroup-specific, brings about a number of technical challenges including the complexity of lipid metabolic pathways as well as the simplicity of biosynthetic precursors to headgroup functionality. As such, only a handful of strategies for metabolic labeling of lipids have thus far been reported. However, these approaches provide enticing examples of how strategic modifications to substrate structures, particularly by introducing clickable moieties, can enable the hijacking of lipid biosynthesis. Furthermore, early work in this field has led to an explosion in diverse applications by which these techniques have been exploited to answer key biological questions or detect and track various lipid-containing biological entities. In this article, we review these efforts and emphasize recent advancements in the development and application of lipid metabolic labeling strategies.
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Affiliation(s)
- Christelle F Ancajas
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Tanei J Ricks
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Michael D Best
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA.
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56
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Tinzl M, Hilvert D. Trapping Transient Protein Species by Genetic Code Expansion. Chembiochem 2020; 22:92-99. [PMID: 32810341 DOI: 10.1002/cbic.202000523] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/18/2020] [Indexed: 12/24/2022]
Abstract
Nature employs a limited number of genetically encoded amino acids for the construction of functional proteins. By engineering components of the cellular translation machinery, however, it is now possible to genetically encode noncanonical building blocks with tailored electronic and structural properties. The ability to incorporate unique chemical functionality into proteins provides a powerful tool to probe mechanism and create novel function. In this minireview, we highlight several recent studies that illustrate how noncanonical amino acids have been used to capture and characterize reactive intermediates, fine-tune the catalytic properties of enzymes, and stabilize short-lived protein-protein complexes.
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Affiliation(s)
- Matthias Tinzl
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
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57
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Deng J, Viel JH, Chen J, Kuipers OP. Synthesis and Characterization of Heterodimers and Fluorescent Nisin Species by Incorporation of Methionine Analogues and Subsequent Click Chemistry. ACS Synth Biol 2020; 9:2525-2536. [PMID: 32786360 PMCID: PMC7507115 DOI: 10.1021/acssynbio.0c00308] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
![]()
Noncanonical
amino acids form a highly diverse pool of building
blocks that can render unique physicochemical properties to peptides
and proteins. Here, four methionine analogues with unsaturated and
varying side chain lengths were successfully incorporated at four
different positions in nisin in Lactococcus lactis through force feeding. This approach allows for residue-specific
incorporation of methionine analogues into nisin to expand their structural
diversity and alter their activity profiles. Moreover, the insertion
of methionine analogues with biorthogonal chemical reactivity, e.g.,
azidohomoalanine and homopropargylglycine, provides the opportunity
for chemical coupling to functional moieties and fluorescent probes
as well as for intermolecular coupling of nisin variants. All resulting
nisin conjugates retained antimicrobial activity, which substantiates
the potential of this method as a tool to further study its localization
and mode of action.
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Affiliation(s)
- Jingjing Deng
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jakob H. Viel
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jingqi Chen
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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58
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Chen Y, Tang J, Wang L, Tian Z, Cardenas A, Fang X, Chatterjee A, Xiao H. Creation of Bacterial cells with 5-Hydroxytryptophan as a 21 st Amino Acid Building Block. Chem 2020; 6:2717-2727. [PMID: 33102928 DOI: 10.1016/j.chempr.2020.07.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
While most organisms utilize 20 canonical amino acid building blocks for protein synthesis, adding additional candidates to the amino acid repertoire can greatly facilitate the investigation and manipulation of protein structures and functions. In this study, we report the generation of completely autonomous organisms with a 21st ncAA, 5-hydroxytryptophan (5HTP). Like 20 canonical amino acids, 5-hydroxytryptophan can be biosynthesized in vivo from simple carbon sources and is subsequently incorporated into proteins in response to the amber stop codon. Using this unnatural organism, we have prepared a single-chain immunoglobulin variable fragment conjugated with a fluorophore and demonstrated the utility of these autonomous cells to monitor oxidative stress. Creation of this and other cells containing the 21st amino acid will provide an opportunity to generate proteins and organisms with novel activities, as well as to determine the evolutionary consequences of using additional amino acid buildings.
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Affiliation(s)
- Yuda Chen
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A
| | - Juan Tang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A
| | - Lushun Wang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A
| | - Zeru Tian
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A
| | - Adam Cardenas
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A
| | - Xinlei Fang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA, 02467, U.S.A
| | - Han Xiao
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A.,Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A.,Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A.,Lead Contact
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59
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Tharp JM, Krahn N, Varshney U, Söll D. Hijacking Translation Initiation for Synthetic Biology. Chembiochem 2020; 21:1387-1396. [PMID: 32023356 PMCID: PMC7237318 DOI: 10.1002/cbic.202000017] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Indexed: 12/17/2022]
Abstract
Genetic code expansion (GCE) has revolutionized the field of protein chemistry. Over the past several decades more than 150 different noncanonical amino acids (ncAAs) have been co-translationally installed into proteins within various host organisms. The vast majority of these ncAAs have been incorporated between the start and stop codons within an open reading frame. This requires that the ncAA be able to form a peptide bond at the α-amine, limiting the types of molecules that can be genetically encoded. In contrast, the α-amine of the initiating amino acid is not required for peptide bond formation. Therefore, including the initiator position in GCE allows for co-translational insertion of more diverse molecules that are modified, or completely lacking an α-amine. This review explores various methods which have been used to initiate protein synthesis with diverse molecules both in vitro and in vivo.
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Affiliation(s)
- Jeffery M Tharp
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
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60
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Rayamajhi S, Aryal S. Surface functionalization strategies of extracellular vesicles. J Mater Chem B 2020; 8:4552-4569. [PMID: 32377649 DOI: 10.1039/d0tb00744g] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Extracellular vesicles (EVs) are lipid-protein bilayer vesicular constructs secreted to the extracellular spaces by cells. All cells secrete EVs as a regular biological process that appears to be conserved throughout the evolution. Owing to the rich molecular cargo of EVs with specific lipid and protein content and documented role in cellular communication, EVs have been exploited as a versatile agent in the biomedical arena, including as diagnostic, drug delivery, immunomodulatory, and therapeutic agents. With these multifaceted applications in the biomedical field, the functionalization of EVs to add diverse functionality has garnered rapid attention. EVs can be functionalized with an exogenous imaging and targeting moiety that allows for the target specificity and the real-time tracking of EVs for diagnostic and therapeutic applications. Importantly, such added functionalities can be used to explore EVs' biogenesis pathway and their role in cellular communication, which can lead to a better understanding of EVs' cellular mechanisms and processes. In this report, we have reviewed the existing surface functionalization strategies of EVs and broadly classified them into three major approaches: physical, biological, and chemical approaches. The physical approach of EV functionalization includes methods like sonication, extrusion, and freeze-thaw that can change the surface properties of EVs via membrane rearrangements. The biological approach includes genetically and metabolically engineering cells to express protein or cargo molecules of interest in secreted EVs. The chemical approach includes different facile click type chemistries that can be used to covalently conjugate the EV lipid or protein construct with different linker groups for diverse functionality. Different chemistries like thiol-maleimide, EDC/NHS, azide-alkyne cycloaddition, and amidation chemistry have been discussed to functionalize EVs. Finally, a comparative discussion of all approaches has been done focusing on the significance of each approach. The collective knowledge of the major approach of surface functionalization can be used to improve the limitation of one technique by combining it with another. An optimized surface functionalization approach developed accordingly can efficiently add required functionality to EVs while maintaining their natural integrity.
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Affiliation(s)
- Sagar Rayamajhi
- Department of Chemistry, Nanotechnology Innovation Center of Kansas State (NICKS), Kansas State University, Manhattan, KS 66506, USA.
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61
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Jeong YS, Yang B, Yang B, Shin M, Seong J, Cha HJ, Kwon I. Enhanced production of Dopa-incorporated mussel adhesive protein using engineered translational machineries. Biotechnol Bioeng 2020; 117:1961-1969. [PMID: 32196642 DOI: 10.1002/bit.27339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 11/05/2022]
Abstract
Mussel adhesive proteins (MAPs) have great potential as bioglues, particularly in wet conditions. Although in vivo residue-specific incorporation of 3,4-dihydroxyphenylalanine (Dopa) in tyrosine-auxotrophic Escherichia coli cells allows for production of Dopa-incorporated bioengineered MAPs (dMAPs), the low production yield hinders the practical application of dMAPs. This low production yield of dMAPs is due to low translational activity of a noncanonical amino acid, Dopa, in E. coli cells. Herein, to enhance the production yield of dMAPs, we investigated the coexpression of Dopa-recognizing tyrosyl-tRNA synthetases (TyrRSs). To use the Dopa-specific Methanococcus jannaschii TyrRS (MjTyrRS-Dopa), we altered the anticodon of tyrosyl-tRNA amber suppressor into AUA (MjtRNATyr AUA ) to recognize a tyrosine codon (AUA). Co-overexpression of MjTyrRS-Dopa and MjtRNATyr AUA increased the production yield of Dopa-incorporated MAP foot protein type 3 (dfp-3) by 57%. Similarly, overexpression of E. coli TyrRS (EcTyrRS) led to a 72% higher production yield of dfp-3. Even with coexpression of Dopa-recognizing TyrRSs, dfp-3 has a high Dopa incorporation yield (over 90%) compared to ones prepared without TyrRS coexpression.
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Affiliation(s)
- Ye Seul Jeong
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Byeongseon Yang
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Byungseop Yang
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Mincheol Shin
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Jihyoun Seong
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Hyung Joon Cha
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Inchan Kwon
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
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62
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Seifried BM, Qi W, Yang YJ, Mai DJ, Puryear WB, Runstadler JA, Chen G, Olsen BD. Glycoprotein Mimics with Tunable Functionalization through Global Amino Acid Substitution and Copper Click Chemistry. Bioconjug Chem 2020; 31:554-566. [PMID: 32078297 DOI: 10.1021/acs.bioconjchem.9b00601] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Glycoproteins and their mimics are challenging to produce because of their large number of polysaccharide side chains that form a densely grafted protein-polysaccharide brush architecture. Herein a new approach to protein bioconjugate synthesis is demonstrated that can approach the functionalization densities of natural glycoproteins through oligosaccharide grafting. Global amino acid substitution is used to replace the methionine residues in a methionine-enriched elastin-like polypeptide with homopropargylglycine (HPG); the substitution was found to replace 93% of the 41 methionines in the protein sequence as well as broaden and increase the thermoresponsive transition. A series of saccharides were conjugated to the recombinant protein backbones through copper(I)-catalyzed alkyne-azide cycloaddition to determine reactivity trends, with 83-100% glycosylation of HPGs. Only an acetyl-protected sialyllactose moiety showed a lower level of 42% HPG glycosylation that is attributed to steric hindrance. The recombinant glycoproteins reproduced the key biofunctional properties of their natural counterparts such as viral inhibition and lectin binding.
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Affiliation(s)
- Brian M Seifried
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wenjing Qi
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200000, China
| | - Yun Jung Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Danielle J Mai
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wendy B Puryear
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts 01536, United States
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts 01536, United States
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200000, China
| | - Bradley D Olsen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Macromolecular Science, Fudan University, Shanghai 200000, China
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63
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Tharp JM, Ad O, Amikura K, Ward FR, Garcia EM, Cate JHD, Schepartz A, Söll D. Initiation of Protein Synthesis with Non‐Canonical Amino Acids In Vivo. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914671] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jeffery M. Tharp
- Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA
| | - Omer Ad
- Department of Chemistry Yale University New Haven CT 06520 USA
| | - Kazuaki Amikura
- Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA
| | - Fred R. Ward
- Department of Molecular and Cell Biology University of California Berkeley CA 94720 USA
| | - Emma M. Garcia
- Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA
| | - Jamie H. D. Cate
- Department of Molecular and Cell Biology University of California Berkeley CA 94720 USA
- Department of Chemistry University of California Berkeley CA 94720 USA
| | - Alanna Schepartz
- Department of Chemistry Yale University New Haven CT 06520 USA
- Department of Molecular and Cell Biology University of California Berkeley CA 94720 USA
- Department of Chemistry University of California Berkeley CA 94720 USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA
- Department of Chemistry Yale University New Haven CT 06520 USA
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64
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Wang F, Pan H, Yao X, He H, Liu L, Luo Y, Zhou H, Zheng M, Zhang R, Ma Y, Cai L. Bioorthogonal Metabolic Labeling Utilizing Protein Biosynthesis for Dynamic Visualization of Nonenveloped Enterovirus 71 Infection. ACS APPLIED MATERIALS & INTERFACES 2020; 12:3363-3370. [PMID: 31845579 DOI: 10.1021/acsami.9b17412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bioorthogonal metabolic labeling through the endogenous cellular metabolic pathways (e.g., phospholipid and sugar) is a promising approach for effectively labeling live viruses. However, it remains a big challenge to label nonenveloped viruses due to lack of host-derived envelopes. Herein, a novel bioorthogonal labeling strategy is developed utilizing protein synthesis pathway to label and trace nonenveloped viruses. The results show that l-azidohomoalanine (Aha), an azido derivative of methionine, is more effective than azido sugars to introduce azido motifs into viral capsid proteins by substituting methionine residues during viral protein biosynthesis and assembly. The azide-modified EV71 (N3-EV71) particles are then effectively labeled with dibenzocyclooctyl (DBCO)-functionalized fluorescence probes through an in situ bioorthogonal reaction with well-preserved viral infectivity. Dual-labeled imaging clearly clarifies that EV71 virions primarily bind to scavenger receptors and are internalized through clathrin-mediated endocytosis. The viral particles are then transported into early and late endosomes where viral RNA is released in a low-pH dependent manner at about 70 min postinfection. These results first reveal viral trafficking and uncoating mechanisms, which may shed light on the pathogenesis of EV71 infection and contribute to antiviral drug discovery.
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Affiliation(s)
- Fangfang Wang
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Lab for Health Informatics, Shenzhen Engineering Laboratory of Nanomedicine and Nanoformulations , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P.R. China
| | - Hong Pan
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Lab for Health Informatics, Shenzhen Engineering Laboratory of Nanomedicine and Nanoformulations , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P.R. China
| | - Xiangjie Yao
- Shenzhen Centre for Disease Control and Prevention , Shenzhen 518100 , P. R. China
| | - Huamei He
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Lab for Health Informatics, Shenzhen Engineering Laboratory of Nanomedicine and Nanoformulations , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055 , P. R. China
| | - Lanlan Liu
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Lab for Health Informatics, Shenzhen Engineering Laboratory of Nanomedicine and Nanoformulations , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P.R. China
| | - Yingmei Luo
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Lab for Health Informatics, Shenzhen Engineering Laboratory of Nanomedicine and Nanoformulations , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055 , P. R. China
| | - Haimei Zhou
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Lab for Health Informatics, Shenzhen Engineering Laboratory of Nanomedicine and Nanoformulations , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055 , P. R. China
| | - Mingbin Zheng
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Lab for Health Informatics, Shenzhen Engineering Laboratory of Nanomedicine and Nanoformulations , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055 , P. R. China
| | - Renli Zhang
- Shenzhen Centre for Disease Control and Prevention , Shenzhen 518100 , P. R. China
| | - Yifan Ma
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Lab for Health Informatics, Shenzhen Engineering Laboratory of Nanomedicine and Nanoformulations , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055 , P. R. China
- HRYZ Biotech Co. , Shenzhen 518057 , P. R. China
| | - Lintao Cai
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Lab for Health Informatics, Shenzhen Engineering Laboratory of Nanomedicine and Nanoformulations , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055 , P. R. China
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65
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Tharp JM, Ad O, Amikura K, Ward FR, Garcia EM, Cate JHD, Schepartz A, Söll D. Initiation of Protein Synthesis with Non-Canonical Amino Acids In Vivo. Angew Chem Int Ed Engl 2020; 59:3122-3126. [PMID: 31828898 DOI: 10.1002/anie.201914671] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Indexed: 12/21/2022]
Abstract
By transplanting identity elements into E. coli tRNAfMet , we have engineered an orthogonal initiator tRNA (itRNATy2 ) that is a substrate for Methanocaldococcus jannaschii TyrRS. We demonstrate that itRNATy2 can initiate translation in vivo with aromatic non-canonical amino acids (ncAAs) bearing diverse sidechains. Although the initial system suffered from low yields, deleting redundant copies of tRNAfMet from the genome afforded an E. coli strain in which the efficiency of non-canonical initiation equals elongation. With this improved system we produced a protein containing two distinct ncAAs at the first and second positions, an initial step towards producing completely unnatural polypeptides in vivo. This work provides a valuable tool to synthetic biology and demonstrates remarkable versatility of the E. coli translational machinery for initiation with ncAAs in vivo.
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Affiliation(s)
- Jeffery M Tharp
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Omer Ad
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Kazuaki Amikura
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Fred R Ward
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Emma M Garcia
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jamie H D Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.,Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Alanna Schepartz
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.,Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.,Department of Chemistry, Yale University, New Haven, CT, 06520, USA
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66
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Segal I, Nachmias D, Konig A, Alon A, Arbely E, Elia N. A straightforward approach for bioorthogonal labeling of proteins and organelles in live mammalian cells, using a short peptide tag. BMC Biol 2020; 18:5. [PMID: 31937312 PMCID: PMC6961407 DOI: 10.1186/s12915-019-0708-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 10/15/2019] [Indexed: 11/29/2022] Open
Abstract
Background In the high-resolution microscopy era, genetic code expansion (GCE)-based bioorthogonal labeling offers an elegant way for direct labeling of proteins in live cells with fluorescent dyes. This labeling approach is currently not broadly used in live-cell applications, partly because it needs to be adjusted to the specific protein under study. Results We present a generic, 14-residue long, N-terminal tag for GCE-based labeling of proteins in live mammalian cells. Using this tag, we generated a library of GCE-based organelle markers, demonstrating the applicability of the tag for labeling a plethora of proteins and organelles. Finally, we show that the HA epitope, used as a backbone in our tag, may be substituted with other epitopes and, in some cases, can be completely removed, reducing the tag length to 5 residues. Conclusions The GCE-tag presented here offers a powerful, easy-to-implement tool for live-cell labeling of cellular proteins with small and bright probes.
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Affiliation(s)
- Inbar Segal
- Department of Life Sciences, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.,National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Dikla Nachmias
- Department of Life Sciences, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.,National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Andres Konig
- Department of Life Sciences, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.,National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Ariel Alon
- Department of Life Sciences, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.,National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Eyal Arbely
- National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.,Department of Chemistry, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Natalie Elia
- Department of Life Sciences, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel. .,National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.
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67
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Drienovská I, Roelfes G. Expanding the enzyme universe with genetically encoded unnatural amino acids. Nat Catal 2020. [DOI: 10.1038/s41929-019-0410-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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68
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Hou Z, Wang D, Li Y, Zhao R, Wan C, Ma Y, Lian C, Yin F, Li Z. A Sulfonium Triggered Thiol-yne Reaction for Cysteine Modification. J Org Chem 2020; 85:1698-1705. [DOI: 10.1021/acs.joc.9b02505] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Zhanfeng Hou
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Dongyuan Wang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430043, Wuhan, China
| | - Yang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Rongtong Zhao
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Chuan Wan
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Yue Ma
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Chenshan Lian
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Feng Yin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, China
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69
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Liu J, Hao C, Wu L, Madej D, Chan W, Lam H. Proteomic analysis of thioproline misincorporation in Escherichia coli. J Proteomics 2020; 210:103541. [DOI: 10.1016/j.jprot.2019.103541] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/27/2019] [Accepted: 10/07/2019] [Indexed: 01/01/2023]
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70
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Jivan F, Alge DL. Bio-orthogonal, Site-Selective Conjugation of Recombinant Proteins to Microporous Annealed Particle Hydrogels for Tissue Engineering. ADVANCED THERAPEUTICS 2020; 3:1900148. [PMID: 38882245 PMCID: PMC11178337 DOI: 10.1002/adtp.201900148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Indexed: 06/18/2024]
Abstract
Protein conjugation to biomaterial scaffolds is a powerful approach for tissue engineering. However, typical chemical conjugation methods lack site-selectivity and can negatively impact protein bioactivity. To overcome this problem, a site-selective strategy is reported here for installing tetrazine groups on terminal poly-histidines (His-tags) of recombinant proteins. These tetrazine groups are then leveraged for bio-orthogonal conjugation to poly(ethylene glycol) (PEG) hydrogel microparticles, which are subsequently assembled into microporous annealed particle (MAP) hydrogels. Efficacy of the strategy is demonstrated using recombinant, green fluorescent protein with a His tag (His-GFP), which enhanced fluorescence of the MAP hydrogels compared to control protein lacking tetrazine groups. Subsequently, to demonstrate efficacy with a therapeutic protein, recombinant human bone morphogenetic protein-2 (His-BMP2) was conjugated. Human mesenchymal stem cells growing in the MAP hydrogels responded to the conjugated BMP2 and significantly increased mineralization after 21 days compared to controls. Thus, this site-selective protein modification strategy coupled with bio-orthogonal click chemistry is expected to be useful for bone defect repair and regeneration therapies. Broader application to the integration of protein therapeutics with biomaterials is also envisioned.
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Affiliation(s)
- Faraz Jivan
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Daniel L Alge
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA
- Department of Materials Science and Engineering, Texas A&M University, College Station, TX, 77843, USA
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71
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Hossain MS, Liu X, Maynard TI, Mozhdehi D. Genetically Encoded Inverse Bolaamphiphiles. Biomacromolecules 2019; 21:660-669. [DOI: 10.1021/acs.biomac.9b01380] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Md Shahadat Hossain
- Department of Chemistry, 1-014 Center for Science and Technology, 111 College Place, Syracuse University, Syracuse, New York 13244, United States
| | - Xin Liu
- Department of Chemistry, 1-014 Center for Science and Technology, 111 College Place, Syracuse University, Syracuse, New York 13244, United States
| | - Timothy I. Maynard
- Department of Chemistry, 1-014 Center for Science and Technology, 111 College Place, Syracuse University, Syracuse, New York 13244, United States
| | - Davoud Mozhdehi
- Department of Chemistry, 1-014 Center for Science and Technology, 111 College Place, Syracuse University, Syracuse, New York 13244, United States
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72
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Nigro G, Bourcier S, Lazennec-Schurdevin C, Schmitt E, Marlière P, Mechulam Y. Use of β 3-methionine as an amino acid substrate of Escherichia coli methionyl-tRNA synthetase. J Struct Biol 2019; 209:107435. [PMID: 31862305 DOI: 10.1016/j.jsb.2019.107435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/15/2019] [Accepted: 12/13/2019] [Indexed: 11/17/2022]
Abstract
Polypeptides containing β-amino acids are attractive tools for the design of novel proteins having unique properties of medical or industrial interest. Incorporation of β-amino acids in vivo requires the development of efficient aminoacyl-tRNA synthetases specific of these non-canonical amino acids. Here, we have performed a detailed structural and biochemical study of the recognition and use of β3-Met by Escherichia coli methionyl-tRNA synthetase (MetRS). We show that MetRS binds β3-Met with a 24-fold lower affinity but catalyzes the esterification of the non-canonical amino acid onto tRNA with a rate lowered by three orders of magnitude. Accurate measurements of the catalytic parameters required careful consideration of the presence of contaminating α-Met in β3-Met commercial samples. The 1.45 Å crystal structure of the MetRS: β3-Met complex shows that β3-Met binds the enzyme essentially like α-Met, but the carboxylate moiety is mobile and not adequately positioned to react with ATP for aminoacyl adenylate formation. This study provides structural and biochemical bases for engineering MetRS with improved β3-Met aminoacylation capabilities.
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Affiliation(s)
- Giuliano Nigro
- Laboratoire de Biochimie, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Sophie Bourcier
- Laboratoire de Chimie Moléculaire, LCM, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Christine Lazennec-Schurdevin
- Laboratoire de Biochimie, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biochimie, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France.
| | - Philippe Marlière
- Xenome Research Group, Institute of Systems and Synthetic Biology, CNRS, UMR8030, UEVE, CEA, GENOPOLE, 5 rue Henri Desbruères, 91030 Evry Cedex, France
| | - Yves Mechulam
- Laboratoire de Biochimie, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France.
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73
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Rosselin M, Xiao Y, Belhomme L, Lecommandoux S, Garanger E. Expanding the Toolbox of Chemoselective Modifications of Protein-Like Polymers at Methionine Residues. ACS Macro Lett 2019; 8:1648-1653. [PMID: 35619386 DOI: 10.1021/acsmacrolett.9b00862] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Selective modifications at methionyl residues in proteins have attracted particular attention in recent years. Previously described methods to chemoselectively modify the methionine side chain in elastin-like polypeptides (ELPs) involved nucleophilic addition using alkyl halides or epoxides yielding a sulfonium group with a positive charge strongly affecting ELPs' physicochemical properties, in particular their thermal responsiveness. We herein explored the recently reported ReACT method (Redox-Activated Chemical Tagging) based on the use of oxaziridine derivatives, yielding an uncharged sulfimide as an alternative route for chemoselective modifications of methionine-containing ELPs in aqueous medium. The different synthetic strategies are herein compared in order to provide a furnished toolbox for further biorthogonal postmodifications of any protein polymers.
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Affiliation(s)
- Marie Rosselin
- Universite Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
| | - Ye Xiao
- Universite Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
| | - Ludovic Belhomme
- Universite Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
| | | | - Elisabeth Garanger
- Universite Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
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74
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Gupta K, Toombes GE, Swartz KJ. Exploring structural dynamics of a membrane protein by combining bioorthogonal chemistry and cysteine mutagenesis. eLife 2019; 8:50776. [PMID: 31714877 PMCID: PMC6850778 DOI: 10.7554/elife.50776] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/11/2019] [Indexed: 12/12/2022] Open
Abstract
The functional mechanisms of membrane proteins are extensively investigated with cysteine mutagenesis. To complement cysteine-based approaches, we engineered a membrane protein with thiol-independent crosslinkable groups using azidohomoalanine (AHA), a non-canonical methionine analogue containing an azide group that can selectively react with cycloalkynes through a strain-promoted azide-alkyne cycloaddition (SPAAC) reaction. We demonstrate that AHA can be readily incorporated into the Shaker Kv channel in place of methionine residues and modified with azide-reactive alkyne probes in Xenopus oocytes. Using voltage-clamp fluorometry, we show that AHA incorporation permits site-specific fluorescent labeling to track voltage-dependent conformational changes similar to cysteine-based methods. By combining AHA incorporation and cysteine mutagenesis in an orthogonal manner, we were able to site-specifically label the Shaker Kv channel with two different fluorophores simultaneously. Our results identify a facile and straightforward approach for chemical modification of membrane proteins with bioorthogonal chemistry to explore their structure-function relationships in live cells. Living cells can sense cues from their environment via molecules located at the interface between the inside and the outside of the cell. These molecules are mostly proteins and are made up of building blocks known as amino acids. To understand how these proteins work, fluorescent probes can be attached to amino acids within them – which can then tell when different parts of proteins move in response to a signal. Scientists often target fluorescent probes at the amino acid cysteine, because it has a chemically reactive side group and is rare enough so that unique positions can be labeled in the protein of interest. However, being able to target other amino acids would allow scientists to ask, and potentially solve, more precise questions about these proteins. Methionine is another amino acid that has a low abundance in most proteins. Previous research has shown that the cell’s normal protein-building machinery can incorporate synthetic versions of methionine into proteins. This suggested that the introduction of chemically reactive alternatives to methionine could offer a way to label membrane proteins with fluorescent probes and free up the cysteines to be targeted with other approaches. Gupta et al. set out to develop a straightforward method to achieve this and started with a well-studied membrane protein, called Shaker, and cells from female African clawed frogs, which are widely used to study membrane proteins. Gupta et al. found that the cells could readily take up a chemically reactive methionine alternative called azidohomoalanine (AHA) from their surrounding solution and incorporate it within the Shaker protein. The AHA took the place of the methionines that are normally found in Shaker, and just like in cysteine-based methods, fluorescent probes could be easily attached to the AHAs in this membrane protein. Shaker is a protein that allows potassium ions to flow across the cell membrane by changing shape in response to the membrane voltage. The fluorescence from those probes also changed with the membrane voltage in a way that was comparable to cysteine-mediated approaches. This indicated that the AHA modification could also be used to track structural changes in the Shaker protein. Finally, Gupta et al. showed that AHA- and cysteine-mediated labeling approaches could be combined to attach two different fluorescent probes onto the Shaker protein. This method will expand the toolbox for researchers studying the relationship between the structure and function of membrane proteins in live cells. In future, it could be applied more widely once the properties of the fluorescent probes for AHA-mediated labeling can be optimized.
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Affiliation(s)
- Kanchan Gupta
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, United States
| | - Gilman Es Toombes
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, United States
| | - Kenton J Swartz
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, United States
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75
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Abstract
Subtiligase-catalyzed peptide ligation is a powerful approach for site-specific protein bioconjugation, synthesis and semisynthesis of proteins and peptides, and chemoproteomic analysis of cellular N termini. Here, we provide a comprehensive review of the subtiligase technology, including its development, applications, and impacts on protein science. We highlight key advantages and limitations of the tool and compare it to other peptide ligase enzymes. Finally, we provide a perspective on future applications and challenges and how they may be addressed.
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Affiliation(s)
- Amy M Weeks
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California 94143, United States
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76
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Israeli B, Vaserman L, Amiram M. Multi‐Site Incorporation of Nonstandard Amino Acids into Protein‐Based Biomaterials. Isr J Chem 2019. [DOI: 10.1002/ijch.201900043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Bar Israeli
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering Ben-Gurion University of the Negev Beer-Sheva Israel
| | - Livne Vaserman
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering Ben-Gurion University of the Negev Beer-Sheva Israel
| | - Miriam Amiram
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering Ben-Gurion University of the Negev Beer-Sheva Israel
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77
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Budisa N, Schneider T. Expanding the DOPA Universe with Genetically Encoded, Mussel-Inspired Bioadhesives for Material Sciences and Medicine. Chembiochem 2019; 20:2163-2190. [PMID: 30830997 DOI: 10.1002/cbic.201900030] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Indexed: 12/21/2022]
Abstract
Catechols are a biologically relevant group of aromatic diols that have attracted much attention as mediators of adhesion of "bio-glue" proteins in mussels of the genus Mytilus. These organisms use catechols in the form of the noncanonical amino acid l-3,4-dihydroxyphenylalanine (DOPA) as a building block for adhesion proteins. The DOPA is generated post-translationally from tyrosine. Herein, we review the properties, natural occurrence, and reactivity of catechols in the design of bioinspired materials. We also provide a basic description of the mussel's attachment apparatus, the interplay between its different molecules that play a crucial role in adhesion, and the role of post-translational modifications (PTMs) of these proteins. Our focus is on the microbial production of mussel foot proteins with the aid of orthogonal translation systems (OTSs) and the use of genetic code engineering to solve some fundamental problems in the bioproduction of these bioadhesives and to expand their chemical space. The major limitation of bacterial expression systems is their intrinsic inability to introduce PTMs. OTSs have the potential to overcome these challenges by replacing canonical amino acids with noncanonical ones. In this way, PTM steps are circumvented while the genetically programmed precision of protein sequences is preserved. In addition, OTSs should enable spatiotemporal control over the complex adhesion process, because the catechol function can be masked by suitable chemical protection. Such caged residues can then be noninvasively unmasked by, for example, UV irradiation or thermal treatment. All of these features make OTSs based on genetic code engineering in reprogrammed microbial strains new and promising tools in bioinspired materials science.
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Affiliation(s)
- Nediljko Budisa
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin, 10623, Germany.,Chair of Chemical Synthetic Biology, Department of Chemistry, University of Manitoba, 144 Dysart Road, R3T 2N2, Winnipeg, MB, Canada
| | - Tobias Schneider
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin, 10623, Germany
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78
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Ratnatilaka Na Bhuket P, Luckanagul JA, Rojsitthisak P, Wang Q. Chemical modification of enveloped viruses for biomedical applications. Integr Biol (Camb) 2019; 10:666-679. [PMID: 30295307 DOI: 10.1039/c8ib00118a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The unique characteristics of enveloped viruses including nanometer size, consistent morphology, narrow size distribution, versatile functionality and biocompatibility have attracted attention from scientists to develop enveloped viruses for biomedical applications. The biomedical applications of the viral-based nanoparticles include vaccine development, imaging and targeted drug delivery. The modification of the structural elements of enveloped viruses is necessary for the desired functions. Here, we review the chemical approaches that have been utilized to develop bionanomaterials based on enveloped viruses for biomedical applications. We first provide an overview of the structures of enveloped viruses which are composed of nucleic acids, structural and functional proteins, glycan residues and lipid envelope. The methods for modification, including direct conjugation, metabolic incorporation of functional groups and peptide tag insertion, are described based on the biomolecular types of viral components. Layer-by-layer technology is also included in this review to illustrate the non-covalent modification of enveloped viruses. Then, we further elaborate the applications of chemically-modified enveloped viruses, virus-like particles and viral subcomponents in biomedical research.
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Affiliation(s)
- Pahweenvaj Ratnatilaka Na Bhuket
- Biomedicinal Chemistry Program, Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
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79
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Sheldon RA, Brady D. Broadening the Scope of Biocatalysis in Sustainable Organic Synthesis. CHEMSUSCHEM 2019; 12:2859-2881. [PMID: 30938093 DOI: 10.1002/cssc.201900351] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 02/05/2019] [Accepted: 03/04/2019] [Indexed: 05/21/2023]
Abstract
This Review is aimed at synthetic organic chemists who may be familiar with organometallic catalysis but have no experience with biocatalysis, and seeks to provide an answer to the perennial question: if it is so attractive, why wasn't it extensively used in the past? The development of biocatalysis in industrial organic synthesis is traced from the middle of the last century. Advances in molecular biology in the last two decades, in particular genome sequencing, gene synthesis and directed evolution of proteins, have enabled remarkable improvements in scope and substantially reduced biocatalyst development times and cost contributions. Additionally, improvements in biocatalyst recovery and reuse have been facilitated by developments in enzyme immobilization technologies. Biocatalysis has become eminently competitive with chemocatalysis and the biocatalytic production of important pharmaceutical intermediates, such as enantiopure alcohols and amines, has become mainstream organic synthesis. The synthetic space of biocatalysis has significantly expanded and is currently being extended even further to include new-to-nature biocatalytic reactions.
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Affiliation(s)
- Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
- Department of Biotechnology, Delft University of Technology, Section BOC, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Dean Brady
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
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80
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Wang Y, Katyal P, Montclare JK. Protein-Engineered Functional Materials. Adv Healthc Mater 2019; 8:e1801374. [PMID: 30938924 PMCID: PMC6703858 DOI: 10.1002/adhm.201801374] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 02/25/2019] [Indexed: 12/13/2022]
Abstract
Proteins are versatile macromolecules that can perform a variety of functions. In the past three decades, they have been commonly used as building blocks to generate a range of biomaterials. Owing to their flexibility, proteins can either be used alone or in combination with other functional molecules. Advances in synthetic and chemical biology have enabled new protein fusions as well as the integration of new functional groups leading to biomaterials with emergent properties. This review discusses protein-engineered materials from the perspectives of domain-based designs as well as physical and chemical approaches for crosslinked materials, with special emphasis on the creation of hydrogels. Engineered proteins that organize or template metal ions, bear noncanonical amino acids (NCAAs), and their potential applications, are also reviewed.
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Affiliation(s)
- Yao Wang
- Department of Chemical and Biomolecular Engineering, New
York University, Tandon School of Engineering, Brooklyn, NY 11201, United
States
| | - Priya Katyal
- Department of Chemical and Biomolecular Engineering, New
York University, Tandon School of Engineering, Brooklyn, NY 11201, United
States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New
York University, Tandon School of Engineering, Brooklyn, NY 11201, United
States
- Department of Chemistry, New York University, New York, NY
10003, United States
- Department of Biomaterials, New York University College of
Dentistry, New York, NY 10010, United States
- Department of Radiology, New York University School of
Medicine, New York, New York, 10016, United States
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81
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Sandanaraj BS, Reddy MM, Rao KJ, Bhandari PJ. Rational Design of Semi‐Synthetic Protein Complexes with the Defined Oligomeric State. ChemistrySelect 2019. [DOI: 10.1002/slct.201901317] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Britto S Sandanaraj
- Department of ChemistryIndian Institute of Science Education and Research (IISER), Pune 411 008 India
| | - Mullapudi Mohan Reddy
- Department of ChemistryIndian Institute of Science Education and Research (IISER), Pune 411 008 India
| | - Kasuladevu Jagannadha Rao
- Department of ChemistryIndian Institute of Science Education and Research (IISER), Pune 411 008 India
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82
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St Amant AH, Huang F, Lin J, Rickert K, Oganesyan V, Lemen D, Mao S, Harper J, Marelli M, Wu H, Gao C, Read de Alaniz J, Christie RJ. A Diene-Containing Noncanonical Amino Acid Enables Dual Functionality in Proteins: Rapid Diels-Alder Reaction with Maleimide or Proximity-Based Dimerization. Angew Chem Int Ed Engl 2019; 58:8489-8493. [PMID: 31018033 DOI: 10.1002/anie.201903494] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Indexed: 12/19/2022]
Abstract
Here, we describe a diene-containing noncanonical amino acid (ncAA) capable of undergoing fast and selective normal electron-demand Diels-Alder (DA) reactions following its incorporation into antibodies. A cyclopentadiene derivative of lysine (CpHK) served as the reactive handle for DA transformations and the substrate for genetic incorporation. CpHK incorporated into antibodies with high efficiency and was available for maleimide conjugation or self-reaction depending on position in the amino acid sequence. CpHK at position K274 reacted with the maleimide drug-linker AZ1508 at a rate of ≈79 m-1 s-1 to produce functional antibody-drug conjugates (ADCs) in a one-step process. Incorporation of CpHK at position S239 resulted in dimerization, which covalently linked antibody heavy chains together. The diene ncAA described here is capable of producing therapeutic protein conjugates with clinically validated and widely available maleimide compounds, while also enabling proximity-based stapling through a DA dimerization reaction.
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Affiliation(s)
- Andre H St Amant
- Department of Chemistry and Biochemistry, University of California - Santa Barbara, Santa Barbara, California, 93106, USA
| | - Fengying Huang
- Antibody Discovery and Protein Engineering Department, AstraZeneca Biopharmaceuticals R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Jia Lin
- Antibody Discovery and Protein Engineering Department, AstraZeneca Biopharmaceuticals R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Keith Rickert
- Antibody Discovery and Protein Engineering Department, AstraZeneca Biopharmaceuticals R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Vaheh Oganesyan
- Antibody Discovery and Protein Engineering Department, AstraZeneca Biopharmaceuticals R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Daniel Lemen
- Antibody Discovery and Protein Engineering Department, AstraZeneca Biopharmaceuticals R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Shenlan Mao
- AstraZeneca Oncology R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Jay Harper
- AstraZeneca Oncology R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Marcello Marelli
- Antibody Discovery and Protein Engineering Department, AstraZeneca Biopharmaceuticals R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Herren Wu
- Antibody Discovery and Protein Engineering Department, AstraZeneca Biopharmaceuticals R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Changshou Gao
- Antibody Discovery and Protein Engineering Department, AstraZeneca Biopharmaceuticals R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Javier Read de Alaniz
- Department of Chemistry and Biochemistry, University of California - Santa Barbara, Santa Barbara, California, 93106, USA
| | - R James Christie
- Antibody Discovery and Protein Engineering Department, AstraZeneca Biopharmaceuticals R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
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83
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St. Amant AH, Huang F, Lin J, Rickert K, Oganesyan V, Lemen D, Mao S, Harper J, Marelli M, Wu H, Gao C, Read de Alaniz J, Christie RJ. A Diene‐Containing Noncanonical Amino Acid Enables Dual Functionality in Proteins: Rapid Diels–Alder Reaction with Maleimide or Proximity‐Based Dimerization. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Andre H. St. Amant
- Department of Chemistry and BiochemistryUniversity of California – Santa Barbara Santa Barbara California 93106 USA
| | - Fengying Huang
- Antibody Discovery and Protein Engineering DepartmentAstraZeneca Biopharmaceuticals R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Jia Lin
- Antibody Discovery and Protein Engineering DepartmentAstraZeneca Biopharmaceuticals R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Keith Rickert
- Antibody Discovery and Protein Engineering DepartmentAstraZeneca Biopharmaceuticals R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Vaheh Oganesyan
- Antibody Discovery and Protein Engineering DepartmentAstraZeneca Biopharmaceuticals R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Daniel Lemen
- Antibody Discovery and Protein Engineering DepartmentAstraZeneca Biopharmaceuticals R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Shenlan Mao
- AstraZeneca Oncology R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Jay Harper
- AstraZeneca Oncology R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Marcello Marelli
- Antibody Discovery and Protein Engineering DepartmentAstraZeneca Biopharmaceuticals R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Herren Wu
- Antibody Discovery and Protein Engineering DepartmentAstraZeneca Biopharmaceuticals R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Changshou Gao
- Antibody Discovery and Protein Engineering DepartmentAstraZeneca Biopharmaceuticals R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Javier Read de Alaniz
- Department of Chemistry and BiochemistryUniversity of California – Santa Barbara Santa Barbara California 93106 USA
| | - R. James Christie
- Antibody Discovery and Protein Engineering DepartmentAstraZeneca Biopharmaceuticals R&D One MedImmune Way Gaithersburg MD 20878 USA
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84
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Iqbal ES, Dods KK, Hartman MCT. Ribosomal incorporation of backbone modified amino acids via an editing-deficient aminoacyl-tRNA synthetase. Org Biomol Chem 2019; 16:1073-1078. [PMID: 29367962 DOI: 10.1039/c7ob02931d] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ability to incorporate non-canonical amino acids (ncAA) using translation offers researchers the ability to extend the functionality of proteins and peptides for many applications including synthetic biology, biophysical and structural studies, and discovery of novel ligands. Here we describe the high promiscuity of an editing-deficient valine-tRNA synthetase (ValRS T222P). Using this enzyme, we demonstrate ribosomal translation of 11 ncAAs including those with novel side chains, α,α-disubstitutions, and cyclic β-amino acids.
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Affiliation(s)
- Emil S Iqbal
- Department of Chemistry, Virginia Commonwealth University (VCU), 1001 West Main Street, P.O. Box 842006, Richmond, Virginia 23284, USA.
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85
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Kofoed C, Riesenberg S, Šmolíková J, Meldal M, Schoffelen S. Semisynthesis of an Active Enzyme by Quantitative Click Ligation. Bioconjug Chem 2019; 30:1169-1174. [PMID: 30883092 DOI: 10.1021/acs.bioconjchem.9b00110] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The incorporation of clickable noncanonical amino acids (ncAAs) has proven to an invaluable tool in chemical biology and protein science research. Nevertheless, the number of examples in which the method is used for preparative purposes is extremely limited. We report the synthesis of an active enzyme by quantitative, Cu(I)-catalyzed ligation of two inactive protein halves, expressed and equipped with an azide and alkyne moiety, respectively, through ncAA incorporation. The reported quantitative conversion is exceptional given the large size of the protein fragments and the fact that no linker or excess of either of the polypeptides was used. The triazole bridge formed between the ncAA side chains was shown to effectively mimic a natural protein loop, providing an enzyme with the same activity as its natural counterpart. We envision that this strategy, termed split-click protein chemistry, can be used for the production of proteins that are difficult to express as full-length entities. It also paves the way for the design of new proteins with tailor-made functionalities.
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Affiliation(s)
- Christian Kofoed
- Center for Evolutionary Chemical Biology, Department of Chemistry , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen , Denmark
| | - Stephan Riesenberg
- Center for Evolutionary Chemical Biology, Department of Chemistry , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen , Denmark
| | - Jaroslava Šmolíková
- Center for Evolutionary Chemical Biology, Department of Chemistry , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen , Denmark
| | - Morten Meldal
- Center for Evolutionary Chemical Biology, Department of Chemistry , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen , Denmark
| | - Sanne Schoffelen
- Center for Evolutionary Chemical Biology, Department of Chemistry , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen , Denmark
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86
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Pena-Francesch A, Demirel MC. Squid-Inspired Tandem Repeat Proteins: Functional Fibers and Films. Front Chem 2019; 7:69. [PMID: 30847338 PMCID: PMC6393770 DOI: 10.3389/fchem.2019.00069] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 01/25/2019] [Indexed: 02/05/2023] Open
Abstract
Production of repetitive polypeptides that comprise one or more tandem copies of a single unit with distinct amorphous and ordered regions have been an interest for the last couple of decades. Their molecular structure provides a rich architecture that can micro-phase-separate to form periodic nanostructures (e.g., lamellar and cylindrical repeating phases) with enhanced physicochemical properties via directed or natural evolution that often exceed those of conventional synthetic polymers. Here, we review programmable design, structure, and properties of functional fibers and films from squid-inspired tandem repeat proteins, with applications in soft photonics and advanced textiles among others.
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Affiliation(s)
- Abdon Pena-Francesch
- Center for Research on Advanced Fiber Technologies, Materials Research Institute, Pennsylvania State University, University Park, PA, United States
- Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA, United States
| | - Melik C. Demirel
- Center for Research on Advanced Fiber Technologies, Materials Research Institute, Pennsylvania State University, University Park, PA, United States
- Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA, United States
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87
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Efficient Incorporation of Unnatural Amino Acids into Proteins with a Robust Cell-Free System. Methods Protoc 2019; 2:mps2010016. [PMID: 31164598 PMCID: PMC6481062 DOI: 10.3390/mps2010016] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/07/2019] [Accepted: 02/07/2019] [Indexed: 01/25/2023] Open
Abstract
Unnatural proteins are crucial biomacromolecules and have been widely applied in fundamental science, novel biopolymer materials, enzymes, and therapeutics. Cell-free protein synthesis (CFPS) system can serve as a robust platform to synthesize unnatural proteins by highly effective site-specific incorporation of unnatural amino acids (UNAAs), without the limitations of cell membrane permeability and the toxicity of unnatural components. Here, we describe a quick and simple method to synthesize unnatural proteins in CFPS system based on Escherichia coli crude extract, with unnatural orthogonal aminoacyl-tRNA synthetase and suppressor tRNA evolved from Methanocaldococcus jannaschii. The superfolder green fluorescent protein (sfGFP) and p-propargyloxyphenylalanine (pPaF) were used as the model protein and UNAA. The synthesis of unnatural sfGFPs was characterized by microplate spectrophotometer, affinity chromatography, and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). This protocol provides a detailed procedure guiding how to use the powerful CFPS system to synthesize unnatural proteins on demand.
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88
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Mozhdehi D, Luginbuhl KM, Dzuricky M, Costa SA, Xiong S, Huang FC, Lewis MM, Zelenetz SR, Colby CD, Chilkoti A. Genetically Encoded Cholesterol-Modified Polypeptides. J Am Chem Soc 2019; 141:945-951. [PMID: 30608674 DOI: 10.1021/jacs.8b10687] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Biological systems use post-translational modifications (PTMs) to control the structure, location, and function of proteins after expression. Despite the ubiquity of PTMs in biology, their use to create genetically encoded recombinant biomaterials is limited. We have utilized a natural lipidation PTM (hedgehog-mediated cholesterol modification of proteins) to create a class of hybrid biomaterials called cholesterol-modified polypeptides (CHaMPs) that exhibit programmable self-assembly at the nanoscale. To demonstrate the biomedical utility of CHaMPs, we used this approach to append cholesterol to biologically active peptide exendin-4 that is an approved drug for the treatment of type II diabetes. The exendin-cholesterol conjugate self-assembled into micelles, and these micelles activate the glucagon-like peptide-1 receptor with a potency comparable to that of current gold standard treatments.
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Affiliation(s)
- Davoud Mozhdehi
- Department of Biomedical Engineering , Duke University , 1427 FCIEMAS , Box 90281, Durham , North Carolina 27708-0281 , United States
| | - Kelli M Luginbuhl
- Department of Biomedical Engineering , Duke University , 1427 FCIEMAS , Box 90281, Durham , North Carolina 27708-0281 , United States
| | - Michael Dzuricky
- Department of Biomedical Engineering , Duke University , 1427 FCIEMAS , Box 90281, Durham , North Carolina 27708-0281 , United States
| | - Simone A Costa
- Department of Biomedical Engineering , Duke University , 1427 FCIEMAS , Box 90281, Durham , North Carolina 27708-0281 , United States
| | - Sinan Xiong
- Department of Biomedical Engineering , Duke University , 1427 FCIEMAS , Box 90281, Durham , North Carolina 27708-0281 , United States
| | - Fred C Huang
- Department of Biomedical Engineering , Duke University , 1427 FCIEMAS , Box 90281, Durham , North Carolina 27708-0281 , United States
| | - Mae M Lewis
- Department of Biomedical Engineering , Duke University , 1427 FCIEMAS , Box 90281, Durham , North Carolina 27708-0281 , United States
| | - Stephanie R Zelenetz
- Department of Biomedical Engineering , Duke University , 1427 FCIEMAS , Box 90281, Durham , North Carolina 27708-0281 , United States
| | - Christian D Colby
- Department of Biomedical Engineering , Duke University , 1427 FCIEMAS , Box 90281, Durham , North Carolina 27708-0281 , United States
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering , Duke University , 1427 FCIEMAS , Box 90281, Durham , North Carolina 27708-0281 , United States
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89
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Nandy T, Mondal S, Singh PC. Solvent organization around the noncanonical part of tyrosine modulates its fluorescence properties. Phys Chem Chem Phys 2019; 21:6042-6050. [DOI: 10.1039/c8cp06410e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Solvent interactions with the fluorocarbon group of noncanonical amino acids are the cause of their diverse fluorescence behaviors, which implies their usefulness as solvent-sensitive environmental sensors in many biological processes.
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Affiliation(s)
- Tonima Nandy
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Saptarsi Mondal
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata
- India
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90
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Won Y, Jeon H, Pagar AD, Patil MD, Nadarajan SP, Flood DT, Dawson PE, Yun H. In vivo biosynthesis of tyrosine analogs and their concurrent incorporation into a residue-specific manner for enzyme engineering. Chem Commun (Camb) 2019; 55:15133-15136. [DOI: 10.1039/c9cc08503c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A cellular system for the in vivo biosynthesis of Tyr-analogs and their concurrent incorporation into target proteins is reported.
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Affiliation(s)
- Yumi Won
- Department of Systems Biotechnology
- Konkuk University
- Gwangjin-gu
- Korea
| | - Hyunwoo Jeon
- Department of Systems Biotechnology
- Konkuk University
- Gwangjin-gu
- Korea
| | - Amol D. Pagar
- Department of Systems Biotechnology
- Konkuk University
- Gwangjin-gu
- Korea
| | - Mahesh D. Patil
- Department of Systems Biotechnology
- Konkuk University
- Gwangjin-gu
- Korea
| | | | - Dillon T. Flood
- Department of Chemistry
- The Scripps Research Institute
- La Jolla
- USA
| | - Philip E. Dawson
- Department of Chemistry
- The Scripps Research Institute
- La Jolla
- USA
| | - Hyungdon Yun
- Department of Systems Biotechnology
- Konkuk University
- Gwangjin-gu
- Korea
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91
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Structure and Synthesis of Antifungal Disulfide β-Strand Proteins from Filamentous Fungi. Microorganisms 2018; 7:microorganisms7010005. [PMID: 30591636 PMCID: PMC6352176 DOI: 10.3390/microorganisms7010005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/24/2018] [Accepted: 12/24/2018] [Indexed: 02/03/2023] Open
Abstract
The discovery and understanding of the mode of action of new antimicrobial agents is extremely urgent, since fungal infections cause 1.5 million deaths annually. Antifungal peptides and proteins represent a significant group of compounds that are able to kill pathogenic fungi. Based on phylogenetic analyses the ascomycetous, cysteine-rich antifungal proteins can be divided into three different groups: Penicillium chrysogenum antifungal protein (PAF), Neosartorya fischeri antifungal protein 2 (NFAP2) and “bubble-proteins” (BP) produced, for example, by P. brevicompactum. They all dominantly have β-strand secondary structures that are stabilized by several disulfide bonds. The PAF group (AFP antifungal protein from Aspergillus giganteus, PAF and PAFB from P. chrysogenum,Neosartorya fischeri antifungal protein (NFAP)) is the best characterized with their common β-barrel tertiary structure. These proteins and variants can efficiently be obtained either from fungi production or by recombinant expression. However, chemical synthesis may be a complementary aid for preparing unusual modifications, e.g., the incorporation of non-coded amino acids, fluorophores, or even unnatural disulfide bonds. Synthetic variants up to ca. 6–7 kDa can also be put to good use for corroborating structure determination. A short overview of the structural peculiarities of antifungal β-strand disulfide bridged proteins will be given. Here, we describe the structural propensities of some known antifungal proteins from filamentous fungi which can also be prepared with modern synthetic chemistry methods.
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92
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Ilamaran M, Sriram Raghavan S, Karthik S, Sanjay Nalawade K, Samvedna S, Routray W, Kamini NR, Saravanan P, Ayyadurai N. A facile method for high level dual expression of recombinant and congener protein in a single expression system. Protein Expr Purif 2018; 156:1-7. [PMID: 30562573 DOI: 10.1016/j.pep.2018.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 12/12/2018] [Accepted: 12/12/2018] [Indexed: 10/27/2022]
Abstract
Protein engineering is an emerging field for developing novel therapeutic proteins and commercial enzymes, along with a major impact on the global market. In recent decades, advanced methods employing protein modification through expansion of the genetic code have led to the development of proteins with new biochemical and physical properties. These techniques have produced engineered proteins with improved attribute comprising substrate relaxation, protein drug conjugation and high stability under extreme conditions of high temperatures, pH and organic solvents. Furthermore, residue specific incorporation is the simplest method for the global incorporation of non-canonical amino acid (NCAA) for protein modification; however it has the major drawbacks of high production cost and manpower requirement. In the present study, we developed a method for the incorporation of single NCAA in two different proteins by using Escherichia coli (E. coli) expression system. For that, the dual protein expressing Escherichia coli JW2581 strain was constructed by transforming pQE80L and pD881-PpiBT vectors with different promoters, selectable markers and AnnexinV, GFPHS gene. To modify the protein, the 3,4 dihydroxy phenyl alanine (DOPA) was globally incorporated into the GFPHS and Annexin V protein using dual protein expression system. The incorporation efficiency during the dual protein expression was achieved through optimized concentrations of amino acids, carbohydrate and inducers in minimal medium. This method for the incorporation of single NCAA into two different proteins using a single expression host system saves the production cost, manpower and time substantially.
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Affiliation(s)
- M Ilamaran
- Department of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR), Central Leather Research Institute (CLRI), Chennai, India
| | - S Sriram Raghavan
- Department of Crystallography and Biophysics, Madras University, Chennai, India
| | - S Karthik
- Department of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR), Central Leather Research Institute (CLRI), Chennai, India
| | | | - S Samvedna
- Department of Biotechnology, Rajalakshmi Engineering Collage, Chennai, India
| | - W Routray
- Department of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR), Central Leather Research Institute (CLRI), Chennai, India
| | - N R Kamini
- Department of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR), Central Leather Research Institute (CLRI), Chennai, India
| | - P Saravanan
- Department of Biotechnology, Rajalakshmi Engineering Collage, Chennai, India
| | - N Ayyadurai
- Department of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR), Central Leather Research Institute (CLRI), Chennai, India.
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93
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Barkley DA, Han SU, Koga T, Rudick JG. Peptide-Dendron Hybrids that Adopt Sequence-Encoded β-Sheet Conformations. Polym Chem 2018; 9:4994-5001. [PMID: 30923581 PMCID: PMC6433408 DOI: 10.1039/c8py00882e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Rational design rules for programming hierarchical organization and function through mutations of monomers in sequence-defined polymers can accelerate the development of novel polymeric and supramolecular materials. Our strategy for designing peptide-dendron hybrids that adopt predictable secondary and quaternary structures in bulk is based on patterning the sites at which dendrons are conjugated to short peptides. To validate this approach, we have designed and characterized a series of β-sheet-forming peptide-dendron hybrids. Spectroscopic studies of the hybrids in films reveal that the peptide portion of the hybrids adopts the intended secondary structure.
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Affiliation(s)
- Deborah A. Barkley
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Sang Uk Han
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Tadanori Koga
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Materials Science and Engineering, Stony Brook University, Stony Brook, New York 11794, United States
| | - Jonathan G. Rudick
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
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94
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Fang KY, Lieblich SA, Tirrell DA. Replacement of ProB28 by pipecolic acid protects insulin against fibrillation and slows hexamer dissociation. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/pola.29225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Katharine Y. Fang
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology Pasadena California 91125
| | - Seth A. Lieblich
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology Pasadena California 91125
| | - David A. Tirrell
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology Pasadena California 91125
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95
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De Filippis V, Pozzi N, Acquasaliente L, Artusi I, Pontarollo G, Peterle D. Protein engineering by chemical methods: Incorporation of nonnatural amino acids as a tool for studying protein folding, stability, and function. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Vincenzo De Filippis
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Nicola Pozzi
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Laura Acquasaliente
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Ilaria Artusi
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Giulia Pontarollo
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Daniele Peterle
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
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96
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Stieglitz JT, Kehoe HP, Lei M, Van Deventer JA. A Robust and Quantitative Reporter System To Evaluate Noncanonical Amino Acid Incorporation in Yeast. ACS Synth Biol 2018; 7:2256-2269. [PMID: 30139255 PMCID: PMC6214617 DOI: 10.1021/acssynbio.8b00260] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Engineering protein translation machinery to incorporate noncanonical amino acids (ncAAs) into proteins has advanced applications ranging from proteomics to single-molecule studies. As applications of ncAAs emerge, efficient ncAA incorporation is crucial to exploiting unique chemistries. We have established a quantitative reporter platform to evaluate ncAA incorporation in response to the TAG (amber) codon in yeast. This yeast display-based reporter utilizes an antibody fragment containing an amber codon at which a ncAA is incorporated when the appropriate orthogonal translation system (OTS) is present. Epitope tags at both termini allow for flow cytometry-based end point readouts of OTS efficiency and fidelity. Using this reporter, we evaluated several factors that influence amber suppression, including the amber codon position and different aminoacyl-tRNA synthetase/tRNA (aaRS/tRNA) pairs. Interestingly, previously described aaRSs that evolved from different parent enzymes to incorporate O-methyl-l-tyrosine exhibit vastly different behavior. Escherichia coli leucyl-tRNA synthetase variants demonstrated efficient incorporation of a range of ncAAs, and we discovered unreported activities of several variants. Compared to a plate reader-based reporter, our assay yields more precise bulk-level measurements while also supporting single-cell readouts compatible with cell sorting. This platform is expected to allow quantitative elucidation of principles dictating efficient stop codon suppression and evolution of next-generation stop codon suppression systems to further enhance genetic code manipulation in eukaryotes. These efforts will improve our understanding of how the genetic code can be further evolved while expanding the range of chemical diversity available in proteins for applications ranging from fundamental epigenetics studies to engineering new classes of therapeutics.
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Affiliation(s)
- Jessica T. Stieglitz
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
| | - Haixing P. Kehoe
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
| | - Ming Lei
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, MA 02155, United States
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97
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Arranz-Gibert P, Vanderschuren K, Isaacs FJ. Next-generation genetic code expansion. Curr Opin Chem Biol 2018; 46:203-211. [PMID: 30072242 DOI: 10.1016/j.cbpa.2018.07.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/07/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
Abstract
Engineering of the translation apparatus has permitted the site-specific incorporation of nonstandard amino acids (nsAAs) into proteins, thereby expanding the genetic code of organisms. Conventional approaches have focused on porting tRNAs and aminoacyl-tRNA synthetases (aaRS) from archaea into bacterial and eukaryotic systems where they have been engineered to site-specifically encode nsAAs. More recent work in genome engineering has opened up the possibilities of whole genome recoding, in which organisms with alternative genetic codes have been constructed whereby codons removed from the genetic code can be repurposed as new sense codons dedicated for incorporation of nsAAs. These advances, together with the advent of engineered ribosomes and new molecular evolution methods, enable multisite incorporation of nsAAs and nonstandard monomers (nsM) paving the way for the template-directed production of functionalized proteins, new classes of polymers, and genetically encoded materials.
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Affiliation(s)
- Pol Arranz-Gibert
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Equal contribution
| | - Koen Vanderschuren
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Equal contribution
| | - Farren J Isaacs
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA.
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98
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Wang J, Scheibel T. Recombinant Production of Mussel Byssus Inspired Proteins. Biotechnol J 2018; 13:e1800146. [DOI: 10.1002/biot.201800146] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 06/28/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Jia Wang
- Lehrstuhl BiomaterialienUniversität BayreuthUniversitätsstraße 3095440BayreuthGermany
| | - Thomas Scheibel
- Lehrstuhl BiomaterialienUniversität BayreuthUniversitätsstraße 3095440BayreuthGermany
- Forschungszentrum für Bio‐Makromoleküle (BIOmac)Universität BayreuthBayreuthGermany
- Bayreuther Zentrum für Kolloide und Grenzflächen (BZKG)Universität BayreuthBayreuthGermany
- Bayreuther Materialzentrum (BayMat)Universität BayreuthBayreuthGermany
- Bayreuther Zentrum für Molekulare Biowissenschaften (BZMB)Universität BayreuthBayreuthGermany
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99
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Chen H, Venkat S, McGuire P, Gan Q, Fan C. Recent Development of Genetic Code Expansion for Posttranslational Modification Studies. Molecules 2018; 23:E1662. [PMID: 29986538 PMCID: PMC6100177 DOI: 10.3390/molecules23071662] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/03/2018] [Accepted: 07/05/2018] [Indexed: 12/29/2022] Open
Abstract
Nowadays advanced mass spectrometry techniques make the identification of protein posttranslational modifications (PTMs) much easier than ever before. A series of proteomic studies have demonstrated that large numbers of proteins in cells are modified by phosphorylation, acetylation and many other types of PTMs. However, only limited studies have been performed to validate or characterize those identified modification targets, mostly because PTMs are very dynamic, undergoing large changes in different growth stages or conditions. To overcome this issue, the genetic code expansion strategy has been introduced into PTM studies to genetically incorporate modified amino acids directly into desired positions of target proteins. Without using modifying enzymes, the genetic code expansion strategy could generate homogeneously modified proteins, thus providing powerful tools for PTM studies. In this review, we summarized recent development of genetic code expansion in PTM studies for research groups in this field.
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Affiliation(s)
- Hao Chen
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Sumana Venkat
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Paige McGuire
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Chenguang Fan
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA.
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
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100
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K C TB, Tada S, Zhu L, Uzawa T, Minagawa N, Luo SC, Zhao H, Yu HH, Aigaki T, Ito Y. In vitro selection of electrochemical peptide probes using bioorthogonal tRNA for influenza virus detection. Chem Commun (Camb) 2018; 54:5201-5204. [PMID: 29718049 DOI: 10.1039/c8cc01775a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An electrosensitive peptide probe has been developed from an in vitro selection technique using biorthogonal tRNA prepared with an electroreactive non-natural amino acid, 3,4-ethylenedioxythiophene-conjugated aminophenylalanine. The selected probe quantitatively detected the influenza virus based on a signal "turn-on" mechanism. The developed strategy could be used to develop electrochemical biosensors toward a variety of targets.
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Affiliation(s)
- Tara Bahadur K C
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, Saitama 351-0198, Japan.
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