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Grigorenko BL, Khrenova MG, Jones DD, Nemukhin AV. Histidine-assisted reduction of arylnitrenes upon photo-activation of phenyl azide chromophores in GFP-like fluorescent proteins. Org Biomol Chem 2024; 22:337-347. [PMID: 38063860 DOI: 10.1039/d3ob01450a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The photochemically active sites of the proteins sfGFP66azF and Venus66azF, members of the green fluorescent protein (GFP) family, contain a non-canonical amino acid residue p-azidophenylalanine (azF) instead of Tyr66. The light-induced decomposition of azF at these sites leads to the formation of reactive arylnitrene (nF) intermediates followed by the formation of phenylamine-containing chromophores. We report the first study of the reaction mechanism of the reduction of the arylnitrene intermediates in sfGFP66nF and Venus66nF using molecular modeling methods. The Gibbs energy profiles for the elementary steps of the chemical reaction in sfGFP66nF are computed using molecular dynamics simulations with quantum mechanics/molecular mechanics (QM/MM) potentials. Structures and energies along the reaction pathway in Venus66nF are evaluated using a QM/MM approach. According to the results of the simulations, arylnitrene reduction is coupled with oxidation of the histidine side chain on the His148 residue located near the chromophore.
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Affiliation(s)
- Bella L Grigorenko
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russian Federation.
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russian Federation
| | - Maria G Khrenova
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russian Federation.
- Bach Institute of Biochemistry, Moscow, Russian Federation
| | - D Dafydd Jones
- School of Biosciences, Molecular Biosciences Division, Cardiff University, Cardiff, UK
| | - Alexander V Nemukhin
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russian Federation.
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russian Federation
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2
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Aarthy M, George A, Ayyadurai N. Beyond protein tagging: Rewiring the genetic code of fluorescent proteins - A review. Int J Biol Macromol 2021; 191:840-851. [PMID: 34560154 DOI: 10.1016/j.ijbiomac.2021.09.108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 11/18/2022]
Abstract
Fluorescent proteins (FP) are an integral part of modern biology due to its diverse biochemical and photophysical properties. The boundaries of FP have been extended through conventional mutagenesis and directed evolution approaches. Engineering of FP based on the standard genetic code consisting of 20 amino acids with limited functional groups restrict its diversification. Degeneracy of genetic code has helped in covering this substantial gap through genetic code engineering, wherein introduction of unnatural amino acid (UAA) analogues resulted in a collection of FP with varying properties. This review features the work carried till date in the area of FP incorporated with UAAs and explores strategies employed for incorporation, impact of UAAs in chromophore and surrounding residues and changes in inherent properties of FP. The long-standing association of FP as a tool for high throughput screening of orthogonal aaRS/tRNA pairs used in site specific incorporation of UAAs is expounded. Insertion of UAAs in FP has enabled their use in contemporary fields such as biophotovoltaics, bioremediation, biosensors, biomaterials and imaging of acidic vesicles. Thus, expansion of genetic code of FP is envisaged to rejig the existing spectra of colors and future research initiative in this direction is expected to glow brighter and brighter.
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Affiliation(s)
- Mayilvahanan Aarthy
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai 600020, India
| | - Augustine George
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai 600020, India
| | - Niraikulam Ayyadurai
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai 600020, India.
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3
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Olenginski GM, Piacentini J, Harris DR, Runko NA, Papoutsis BM, Alter JR, Hess KR, Brewer SH, Phillips-Piro CM. Structural and spectrophotometric investigation of two unnatural amino-acid altered chromophores in the superfolder green fluorescent protein. Acta Crystallogr D Struct Biol 2021; 77:1010-1018. [PMID: 34342274 PMCID: PMC8329867 DOI: 10.1107/s2059798321006525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/21/2021] [Indexed: 11/10/2022] Open
Abstract
The spectrophotometric properties of the green fluorescent protein (GFP) result from the post-translationally cyclized chromophore composed of three amino acids including a tyrosine at the center of the β-barrel protein. Altering the amino acids in the chromophore or the nearby region has resulted in numerous GFP variants with differing photophysical properties. To further examine the effect of small atomic changes in the chromophore on the structure and photophysical properties of GFP, the hydroxyl group of the chromophore tyrosine was replaced with a nitro or a cyano group. The structures and spectrophotometric properties of these superfolder GFP (sfGFP) variants with the unnatural amino acids (UAAs) 4-nitro-L-phenylalanine or 4-cyano-L-phenylalanine were explored. Notably, the characteristic 487 nm absorbance band of wild-type (wt) sfGFP is absent in both unnatural amino-acid-containing protein constructs (Tyr66pNO2Phe-sfGFP and Tyr66pCNPhe-sfGFP). Consequently, neither Tyr66pNO2Phe-sfGFP nor Tyr66pCNPhe-sfGFP exhibited the characteristic emission of wt sfGFP centered at 511 nm when excited at 487 nm. Tyr66pNO2Phe-sfGFP appeared orange due to an absorbance band centered at 406 nm that was not present in wt sfGFP, while Tyr66pCNPhe-sfGFP appeared colorless with an absorbance band centered at 365 nm. Mass spectrometry and X-ray crystallography confirmed the presence of a fully formed chromophore and no significant structural changes in either of these UAA-containing protein constructs, signaling that the change in the observed photophysical properties of the proteins is the result of the presence of the UAA in the chromophore.
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Affiliation(s)
- Gregory M. Olenginski
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Juliana Piacentini
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Darcy R. Harris
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Nicolette A. Runko
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Brianna M. Papoutsis
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Jordan R. Alter
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Kenneth R. Hess
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Scott H. Brewer
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
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4
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Mita M, Sugawara I, Harada K, Ito M, Takizawa M, Ishida K, Ueda H, Kitaguchi T, Tsuboi T. Development of red genetically encoded biosensor for visualization of intracellular glucose dynamics. Cell Chem Biol 2021; 29:98-108.e4. [PMID: 34197723 DOI: 10.1016/j.chembiol.2021.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 05/19/2021] [Accepted: 06/08/2021] [Indexed: 12/12/2022]
Abstract
Glucose is the main source of energy for organisms, and it is important to understand the spatiotemporal dynamics of intracellular glucose. Single fluorescent protein-based glucose indicators, named "Red Glifons" have been developed that apply to live-cell and dual-color imaging. These indicators exhibited more than 3-fold increase in fluorescence intensity in the presence of 10 mM glucose. The two Red Glifons developed have different half-maximal effective concentration (EC50) values for glucose (300 μM and 3,000 μM) and are able to monitor a wide range of glucose dynamics. Red Glifon combined with green indicators allowing visualization of the interplay between glucose and ATP, lactate, or pyruvate. Glucose influx in the pharyngeal muscle of Caenorhabditis elegans, enteroendocrine cells, and human iPS cell-derived cardiac myocytes was observed using the Red Glifons. Thus these red glucose indicators serve as a multi-color imaging toolkit for investigating complex interactions in energy metabolism.
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Affiliation(s)
- Marie Mita
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Izumi Sugawara
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Kazuki Harada
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Motoki Ito
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Mai Takizawa
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Kentaro Ishida
- Myoridge Co. Ltd., 46-29 Yoshidashimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroshi Ueda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Tetsuya Kitaguchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan.
| | - Takashi Tsuboi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan.
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5
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Auhim HS, Grigorenko BL, Harris TK, Aksakal OE, Polyakov IV, Berry C, Gomes GDP, Alabugin IV, Rizkallah PJ, Nemukhin AV, Jones DD. Stalling chromophore synthesis of the fluorescent protein Venus reveals the molecular basis of the final oxidation step. Chem Sci 2021; 12:7735-7745. [PMID: 34168826 PMCID: PMC8188506 DOI: 10.1039/d0sc06693a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/26/2021] [Indexed: 11/24/2022] Open
Abstract
Fluorescent proteins (FPs) have revolutionised the life sciences, but the mechanism of chromophore maturation is still not fully understood. Here we show that incorporation of a photo-responsive non-canonical amino acid within the chromophore stalls maturation of Venus, a yellow FP, at an intermediate stage; a crystal structure indicates the presence of O2 located above a dehydrated enolate form of the imidazolone ring, close to the strictly conserved Gly67 that occupies a twisted conformation. His148 adopts an "open" conformation so forming a channel that allows O2 access to the immature chromophore. Absorbance spectroscopy supported by QM/MM simulations suggests that the first oxidation step involves formation of a hydroperoxyl intermediate in conjunction with dehydrogenation of the methylene bridge. A fully conjugated mature chromophore is formed through release of H2O2, both in vitro and in vivo. The possibility of interrupting and photochemically restarting chromophore maturation and the mechanistic insights open up new approaches for engineering optically controlled fluorescent proteins.
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Affiliation(s)
- Husam Sabah Auhim
- School of Biosciences, Molecular Biosciences Division, Cardiff University Sir Martin Evans Building Cardiff CF10 3AX UK +44 (0)29 2087 4290
- Department of Biology, College of Science, University of Baghdad Baghdad Iraq
| | - Bella L Grigorenko
- Chemistry Department, Lomonosov Moscow State University Leninskie Gory, 1-3 Moscow Russian Federation +7 495 939 1096
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences Moscow Russian Federation
| | - Tessa K Harris
- School of Biosciences, Molecular Biosciences Division, Cardiff University Sir Martin Evans Building Cardiff CF10 3AX UK +44 (0)29 2087 4290
| | - Ozan E Aksakal
- School of Biosciences, Molecular Biosciences Division, Cardiff University Sir Martin Evans Building Cardiff CF10 3AX UK +44 (0)29 2087 4290
| | - Igor V Polyakov
- Chemistry Department, Lomonosov Moscow State University Leninskie Gory, 1-3 Moscow Russian Federation +7 495 939 1096
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences Moscow Russian Federation
| | - Colin Berry
- School of Biosciences, Molecular Biosciences Division, Cardiff University Sir Martin Evans Building Cardiff CF10 3AX UK +44 (0)29 2087 4290
| | - Gabriel Dos Passos Gomes
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada
- Department of Computer Science, University of Toronto 214 College St. Toronto Ontario M5T 3A1 Canada
| | - Igor V Alabugin
- Department of Chemistry and Biochemistry, Florida State University Tallahassee Fl 32306 USA +1 850 644 5795
| | | | - Alexander V Nemukhin
- Chemistry Department, Lomonosov Moscow State University Leninskie Gory, 1-3 Moscow Russian Federation +7 495 939 1096
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences Moscow Russian Federation
| | - D Dafydd Jones
- School of Biosciences, Molecular Biosciences Division, Cardiff University Sir Martin Evans Building Cardiff CF10 3AX UK +44 (0)29 2087 4290
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6
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Better together: building protein oligomers naturally and by design. Biochem Soc Trans 2020; 47:1773-1780. [PMID: 31803901 PMCID: PMC6925524 DOI: 10.1042/bst20190283] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 12/17/2022]
Abstract
Protein oligomers are more common in nature than monomers, with dimers being the most prevalent final structural state observed in known structures. From a biological perspective, this makes sense as it conserves vital molecular resources that may be wasted simply by generating larger single polypeptide units, and allows new features such as cooperativity to emerge. Taking inspiration from nature, protein designers and engineers are now building artificial oligomeric complexes using a variety of approaches to generate new and useful supramolecular protein structures. Oligomerisation is thus offering a new approach to sample structure and function space not accessible through simply tinkering with monomeric proteins.
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7
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Thomas SK, Jamieson WD, Gwyther REA, Bowen BJ, Beachey A, Worthy HL, Macdonald JE, Elliott M, Castell OK, Jones DD. Site-Specific Protein Photochemical Covalent Attachment to Carbon Nanotube Side Walls and Its Electronic Impact on Single Molecule Function. Bioconjug Chem 2020; 31:584-594. [PMID: 31743647 DOI: 10.1021/acs.bioconjchem.9b00719] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Functional integration of proteins with carbon-based nanomaterials such as nanotubes holds great promise in emerging electronic and optoelectronic applications. Control over protein attachment poses a major challenge for consistent and useful device fabrication, especially when utilizing single/few molecule properties. Here, we exploit genetically encoded phenyl azide photochemistry to define the direct covalent attachment of four different proteins, including the fluorescent protein GFP and a β-lactamase binding protein (BBP), to carbon nanotube side walls. AFM showed that on attachment BBP could still recognize and bind additional protein components. Single molecule fluorescence revealed that on attachment to SWCNTs function was retained and there was feedback to GFP in terms of fluorescence intensity and improved resistance to photobleaching; GFP is fluorescent for much longer on attachment. The site of attachment proved important in terms of electronic impact on GFP function, with the attachment site furthest from the chromophore having the larger effect on fluorescence. Our approach provides a versatile and general method for generating intimate protein-CNT hybrid bioconjugates. It can be potentially applied to any protein of choice; the attachment position and thus interface characteristics with the CNT can easily be changed by simply placing the phenyl azide chemistry at different residues by gene mutagenesis. Thus, our approach will allow consistent construction and modulate functional coupling through changing the protein attachment position.
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Affiliation(s)
- Suzanne K Thomas
- School of Physics and Astronomy, Cardiff University, Cardiff, CF24 3AA, United Kingdom
| | - W David Jamieson
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, United Kingdom
| | - Rebecca E A Gwyther
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, United Kingdom
| | - Benjamin J Bowen
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, United Kingdom
| | - Adam Beachey
- School of Physics and Astronomy, Cardiff University, Cardiff, CF24 3AA, United Kingdom
| | - Harley L Worthy
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, United Kingdom
| | - J Emyr Macdonald
- School of Physics and Astronomy, Cardiff University, Cardiff, CF24 3AA, United Kingdom
| | - Martin Elliott
- School of Physics and Astronomy, Cardiff University, Cardiff, CF24 3AA, United Kingdom
| | - Oliver K Castell
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, United Kingdom
| | - D Dafydd Jones
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, United Kingdom
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8
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Worthy HL, Auhim HS, Jamieson WD, Pope JR, Wall A, Batchelor R, Johnson RL, Watkins DW, Rizkallah P, Castell OK, Jones DD. Positive functional synergy of structurally integrated artificial protein dimers assembled by Click chemistry. Commun Chem 2019. [DOI: 10.1038/s42004-019-0185-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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9
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Richardson MB, Brown DB, Vasquez CA, Ziller JW, Johnston KM, Weiss GA. Synthesis and Explosion Hazards of 4-Azido-l-phenylalanine. J Org Chem 2018; 83:4525-4536. [PMID: 29577718 PMCID: PMC6008159 DOI: 10.1021/acs.joc.8b00270] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A reliable, scalable, cost-effective, and chromatography-free synthesis of 4-azido-l-phenylalanine beginning from l-phenylalanine is described. Investigations into the safety of the synthesis reveal that the Ullman-like Cu(I)-catalyzed azidation step does not represent a significant risk. The isolated 4-azido-l-phenylalanine product, however, exhibits previously undocumented explosive characteristics.
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Affiliation(s)
- Mark B. Richardson
- Department of Chemistry, 1102 Natural Sciences 2, University of California, Irvine, Irvine CA 92697-2025 USA
| | - Derek B. Brown
- Amgen Inc. One Amgen Center Drive, Thousand Oaks CA 91320 USA
| | - Carlos A. Vasquez
- Department of Chemistry, 1102 Natural Sciences 2, University of California, Irvine, Irvine CA 92697-2025 USA
| | - Joseph W. Ziller
- Department of Chemistry, 1102 Natural Sciences 2, University of California, Irvine, Irvine CA 92697-2025 USA
| | - Kevin M. Johnston
- Department of Chemistry, 1102 Natural Sciences 2, University of California, Irvine, Irvine CA 92697-2025 USA
| | - Gregory A. Weiss
- Department of Chemistry, 1102 Natural Sciences 2, University of California, Irvine, Irvine CA 92697-2025 USA
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Marth G, Hartley AM, Reddington SC, Sargisson LL, Parcollet M, Dunn KE, Jones DD, Stulz E. Precision Templated Bottom-Up Multiprotein Nanoassembly through Defined Click Chemistry Linkage to DNA. ACS NANO 2017; 11:5003-5010. [PMID: 28414900 DOI: 10.1021/acsnano.7b01711] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We demonstrate an approach that allows attachment of single-stranded DNA (ssDNA) to a defined residue in a protein of interest (POI) so as to provide optimal and well-defined multicomponent assemblies. Using an expanded genetic code system, azido-phenylalanine (azF) was incorporated at defined residue positions in each POI; copper-free click chemistry was used to attach exactly one ssDNA at precisely defined residues. By choosing an appropriate residue, ssDNA conjugation had minimal impact on protein function, even when attached close to active sites. The protein-ssDNA conjugates were used to (i) assemble double-stranded DNA systems with optimal communication (energy transfer) between normally separate groups and (ii) generate multicomponent systems on DNA origami tiles, including those with enhanced enzyme activity when bound to the tile. Our approach allows any potential protein to be simply engineered to attach ssDNA or related biomolecules, creating conjugates for designed and highly precise multiprotein nanoscale assembly with tailored functionality.
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Affiliation(s)
- Gabriella Marth
- School of Chemistry and Institute for Life Sciences, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom
| | - Andrew M Hartley
- School of Biosciences, Cardiff University , Cardiff CF10 3AT, United Kingdom
| | - Samuel C Reddington
- School of Biosciences, Cardiff University , Cardiff CF10 3AT, United Kingdom
| | - Lauren L Sargisson
- School of Chemistry and Institute for Life Sciences, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom
| | - Marlène Parcollet
- School of Chemistry and Institute for Life Sciences, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom
| | - Katherine E Dunn
- Department of Electronics, University of York , Heslington, York YO10 5DD, United Kingdom
| | - D Dafydd Jones
- School of Biosciences, Cardiff University , Cardiff CF10 3AT, United Kingdom
| | - Eugen Stulz
- School of Chemistry and Institute for Life Sciences, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom
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11
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Hartley AM, Worthy HL, Reddington SC, Rizkallah PJ, Jones DD. Molecular basis for functional switching of GFP by two disparate non-native post-translational modifications of a phenyl azide reaction handle. Chem Sci 2016; 7:6484-6491. [PMID: 28451106 PMCID: PMC5355941 DOI: 10.1039/c6sc00944a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/28/2016] [Indexed: 01/15/2023] Open
Abstract
Through the genetic incorporation of a single phenyl azide group into superfolder GFP (sfGFP) at residue 148 we provide a molecular description of how this highly versatile chemical handle can be used to positively switch protein function in vitro and in vivo via either photochemistry or bioconjugation.
Through the genetic incorporation of a single phenyl azide group into superfolder GFP (sfGFP) at residue 148 we provide a molecular description of how this highly versatile chemical handle can be used to positively switch protein function in vitro and in vivo via either photochemistry or bioconjugation. Replacement of H148 with p-azido-l-phenylalanine (azF) blue shifts the major excitation peak ∼90 nm by disrupting the H-bond and proton transfer network that defines the chromophore charged state. Bioorthogonal click modification with a simple dibenzylcyclooctyne or UV irradiation shifts the neutral-anionic chromophore equilibrium, switching fluorescence to the optimal ∼490 nm excitation. Click modification also improved quantum yield over both the unmodified and original protein. Crystal structures of both the click modified and photochemically converted forms show that functional switching is due to local conformational changes that optimise the interaction networks surrounding the chromophore. Crystal structure and mass spectrometry studies of the irradiated protein suggest that the phenyl azide converts to a dehydroazepine and/or an azepinone. Thus, protein embedded phenyl azides can be used beyond simple photocrosslinkers and passive conjugation handles, and mimic many natural post-translational modifications: modulation though changes in interaction networks.
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Affiliation(s)
| | | | | | | | - D Dafydd Jones
- School of Biosciences , Cardiff University , Cardiff , UK .
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12
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Dippel AB, Olenginski GM, Maurici N, Liskov MT, Brewer SH, Phillips-Piro CM. Probing the effectiveness of spectroscopic reporter unnatural amino acids: a structural study. Acta Crystallogr D Struct Biol 2016; 72:121-30. [PMID: 26894540 PMCID: PMC4756619 DOI: 10.1107/s2059798315022858] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/29/2015] [Indexed: 11/10/2022] Open
Abstract
The X-ray crystal structures of superfolder green fluorescent protein (sfGFP) containing the spectroscopic reporter unnatural amino acids (UAAs) 4-cyano-L-phenylalanine (pCNF) or 4-ethynyl-L-phenylalanine (pCCF) at two unique sites in the protein have been determined. These UAAs were genetically incorporated into sfGFP in a solvent-exposed loop region and/or a partially buried site on the β-barrel of the protein. The crystal structures containing the UAAs at these two sites permit the structural implications of UAA incorporation for the native protein structure to be assessed with high resolution and permit a direct correlation between the structure and spectroscopic data to be made. The structural implications were quantified by comparing the root-mean-square deviation (r.m.s.d.) between the crystal structure of wild-type sfGFP and the protein constructs containing either pCNF or pCCF in the local environment around the UAAs and in the overall protein structure. The results suggest that the selective placement of these spectroscopic reporter UAAs permits local protein environments to be studied in a relatively nonperturbative fashion with site-specificity.
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Affiliation(s)
- Andrew B. Dippel
- Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Gregory M. Olenginski
- Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Nicole Maurici
- Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Melanie T. Liskov
- Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Scott H. Brewer
- Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
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