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Yi HB, Lee S, Seo K, Kim H, Kim M, Lee HS. Cellular and Biophysical Applications of Genetic Code Expansion. Chem Rev 2024; 124:7465-7530. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [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: 05/18/2024]
Abstract
Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.
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Affiliation(s)
- Han Bin Yi
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Seungeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Kyungdeok Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyeongjo Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Minah Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
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2
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Berksoz M, Atilgan C. Allosteric modulation of fluorescence revealed by hydrogen bond dynamics in a genetically encoded maltose biosensor. Proteins 2024. [PMID: 38572606 DOI: 10.1002/prot.26688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/02/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Genetically encoded fluorescent biosensors (GEFBs) proved to be reliable tracers for many metabolites and cellular processes. In the simplest case, a fluorescent protein (FP) is genetically fused to a sensing protein which undergoes a conformational change upon ligand binding. This drives a rearrangement in the chromophore environment and changes the spectral properties of the FP. Structural determinants of successful biosensors are revealed only in hindsight when the crystal structures of both ligand-bound and ligand-free forms are available. This makes the development of new biosensors for desired analytes a long trial-and-error process. In the current study, we conducted μs-long all atom molecular dynamics (MD) simulations of a maltose biosensor in both the apo (dark) and holo (bright) forms. We performed detailed hydrogen bond occupancy analyses to shed light on the mechanism of ligand induced conformational change in the sensor protein and its allosteric effect on the chromophore environment. We find that two strong indicators for distinguishing bright and dark states of biosensors are due to substantial changes in hydrogen bond dynamics in the system and solvent accessibility of the chromophore.
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Affiliation(s)
- Melike Berksoz
- Faculty of Engineering and Natural Sciences, Sabanci University, Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Turkey
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3
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Han Q, Darmanin C, Rosado CJ, Veríssimo NV, Pereira JFB, Bryant G, Drummond CJ, Greaves TL. Structure, aggregation dynamics and crystallization of superfolder green fluorescent protein: Effect of long alkyl chain imidazolium ionic liquids. Int J Biol Macromol 2023; 253:127456. [PMID: 37844813 DOI: 10.1016/j.ijbiomac.2023.127456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/26/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
Green fluorescent protein (GFP) and its variants are widely used in medical and biological research, especially acting as indicators of protein structural integrity, protein-protein interactions and as biosensors. This study employs superfolder GFP (sfGFP) to investigate the impact of varying alkyl chain length of 1-Cn-3-methylimidazolium chloride ionic liquid (IL) series ([Cnmim]Cl, n = 2, 4, 6, 8, 10, 12) on the protein fluorescence, structure, hydration, aggregation dynamics and crystallization behaviour. The results revealed a concentration-dependent decrease in the sfGFP chromophore fluorescence, particularly in long alkyl chain ILs ([C10mim]Cl and [C12mim]Cl). Tryptophan (Trp) fluorescence showed the quenching rate increased with longer alkyl chains indicating a nonpolar interaction between Trp57 and the alkyl chain. Secondary structural changes were observed at the high IL concentration of 1.5 M in [C10mim]Cl and [C12mim]Cl. Small-angle X-ray scattering (SAXS) indicated relatively stable protein sizes, but with IL aggregates present in [C10mim]Cl and [C12mim]Cl solutions. Dynamic light scattering (DLS) data showed increased protein size and aggregation with longer alkyl chain ILs. Notably, ILs and salts, excluding [C2mim]Cl, promoted sfGFP crystallization. This study emphasizes the influence of the cation alkyl chain length and concentration on protein stability and aggregation, providing insights into utilizing IL solvents for protein stabilization and crystallization purposes.
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Affiliation(s)
- Qi Han
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia.
| | - Connie Darmanin
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Carlos J Rosado
- Department of Diabetes, Central Clinical School, Monash University, VIC 3004, Australia; Department of Biochemistry, Monash University, VIC 3800, Australia
| | - Nathalia Vieira Veríssimo
- School of Pharmaceutical Sciences, São Paulo University (USP), Av. Prof. Lineu Prestes, no. 580, B16, 05508-000, Cidade de Universitária, São Paulo, SP, Brazil
| | - Jorge F B Pereira
- University of Coimbra, CIEPQPF, Department of Chemical Engineering, Rua Sílvio Lima, Pólo II - Pinhal de Marrocos, 3030-790 Coimbra, Portugal
| | - Gary Bryant
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Calum J Drummond
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Tamar L Greaves
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia.
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4
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Weinstein JY, Martí-Gómez C, Lipsh-Sokolik R, Hoch SY, Liebermann D, Nevo R, Weissman H, Petrovich-Kopitman E, Margulies D, Ivankov D, McCandlish DM, Fleishman SJ. Designed active-site library reveals thousands of functional GFP variants. Nat Commun 2023; 14:2890. [PMID: 37210560 DOI: 10.1038/s41467-023-38099-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 04/13/2023] [Indexed: 05/22/2023] Open
Abstract
Mutations in a protein active site can lead to dramatic and useful changes in protein activity. The active site, however, is sensitive to mutations due to a high density of molecular interactions, substantially reducing the likelihood of obtaining functional multipoint mutants. We introduce an atomistic and machine-learning-based approach, called high-throughput Functional Libraries (htFuncLib), that designs a sequence space in which mutations form low-energy combinations that mitigate the risk of incompatible interactions. We apply htFuncLib to the GFP chromophore-binding pocket, and, using fluorescence readout, recover >16,000 unique designs encoding as many as eight active-site mutations. Many designs exhibit substantial and useful diversity in functional thermostability (up to 96 °C), fluorescence lifetime, and quantum yield. By eliminating incompatible active-site mutations, htFuncLib generates a large diversity of functional sequences. We envision that htFuncLib will be used in one-shot optimization of activity in enzymes, binders, and other proteins.
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Affiliation(s)
| | - Carlos Martí-Gómez
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Rosalie Lipsh-Sokolik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shlomo Yakir Hoch
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Demian Liebermann
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Reinat Nevo
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Haim Weissman
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | | | - David Margulies
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Dmitry Ivankov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - David M McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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5
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Abstract
The genetically encoded fluorescent sensors convert chemical and physical signals into light. They are powerful tools for the visualisation of physiological processes in living cells and freely moving animals. The fluorescent protein is the reporter module of a genetically encoded biosensor. In this study, we first review the history of the fluorescent protein in full emission spectra on a structural basis. Then, we discuss the design of the genetically encoded biosensor. Finally, we briefly review several major types of genetically encoded biosensors that are currently widely used based on their design and molecular targets, which may be useful for the future design of fluorescent biosensors.
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Affiliation(s)
- Minji Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yifan Da
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
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6
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Peng W, Maydew CC, Kam H, Lynd JK, Tutol JN, Phelps SM, Abeyrathna S, Meloni G, Dodani SC. Discovery of a monomeric green fluorescent protein sensor for chloride by structure-guided bioinformatics. Chem Sci 2022; 13:12659-12672. [PMID: 36519056 PMCID: PMC9645410 DOI: 10.1039/d2sc03903f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/05/2022] [Indexed: 11/21/2022] Open
Abstract
Chloride is an essential anion for all forms of life. Beyond electrolyte balance, an increasing body of evidence points to new roles for chloride in normal physiology and disease. Over the last two decades, this understanding has been advanced by chloride-sensitive fluorescent proteins for imaging applications in living cells. To our surprise, these sensors have primarily been engineered from the green fluorescent protein (GFP) found in the jellyfish Aequorea victoria. However, the GFP family has a rich sequence space that could already encode for new sensors with desired properties, thereby minimizing protein engineering efforts and accelerating biological applications. To efficiently sample this space, we present and validate a stepwise bioinformatics strategy focused first on the chloride binding pocket and second on a monomeric oligomerization state. Using this, we identified GFPxm163 from GFPxm found in the jellyfish Aequorea macrodactyla. In vitro characterization shows that the binding of chloride as well as bromide, iodide, and nitrate rapidly tunes the ground state chromophore equilibrium from the phenolate to the phenol state generating a pH-dependent, turn-off fluorescence response. Furthermore, live-cell fluorescence microscopy reveals that GFPxm163 provides a reversible, yet indirect readout of chloride transport via iodide exchange. With this demonstration, we anticipate that the pairing of bioinformatics with protein engineering methods will provide an efficient methodology to discover and design new chloride-sensitive fluorescent proteins for cellular applications.
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Affiliation(s)
- Weicheng Peng
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson 75080 Texas USA
- Department of Biological Sciences, The University of Texas at Dallas Richardson 75080 Texas USA
| | - Caden C Maydew
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson 75080 Texas USA
| | - Hiu Kam
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson 75080 Texas USA
| | - Jacob K Lynd
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson 75080 Texas USA
| | - Jasmine N Tutol
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson 75080 Texas USA
| | - Shelby M Phelps
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson 75080 Texas USA
| | - Sameera Abeyrathna
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson 75080 Texas USA
| | - Gabriele Meloni
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson 75080 Texas USA
| | - Sheel C Dodani
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson 75080 Texas USA
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7
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Hussein RA, Ahmed M, Kuldyushev N, Schönherr R, Heinemann SH. Selenomethionine incorporation in proteins of individual mammalian cells determined with a genetically encoded fluorescent sensor. Free Radic Biol Med 2022; 192:191-199. [PMID: 36152916 DOI: 10.1016/j.freeradbiomed.2022.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/14/2022] [Accepted: 09/17/2022] [Indexed: 11/26/2022]
Abstract
Selenomethionine (SeMet) randomly replaces methionine (Met) in protein translation. Because of strongly differing redox properties of SeMet and Met, SeMet mis-incorporation may have detrimental effects on protein function, possibly compromising the use of nutritional SeMet supplementation as an anti-oxidant. Studying the functional impact of SeMet in proteins on a cellular level is hampered by the lack of accurate and efficient methods for estimating the SeMet incorporation level in individual viable cells. Here we introduce and apply a method to measure the extent of SeMet incorporation in cellular proteins by utilizing a genetically encoded fluorescent methionine oxidation probe. Supplementation of SeMet in mammalian culture medium resulted in >84% incorporation of SeMet, and SeMet labeling as low as 5% was readily measured. Kinetics and extent of SeMet incorporation on the single-cell level under live-cell imaging conditions provided direct access to protein turn-over kinetics and SeMet redox properties in a cellular context. The method is furthermore suited for experiments utilizing high-throughput fluorescence microplate readers or fluorescence-activated cell sorting (FACS) analysis.
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Affiliation(s)
- Rama A Hussein
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Jena, Germany
| | - Marwa Ahmed
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Jena, Germany
| | - Nikita Kuldyushev
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Jena, Germany
| | - Roland Schönherr
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Jena, Germany
| | - Stefan H Heinemann
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Jena, Germany.
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8
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Cruz-Resendiz A, Acero G, Sampieri A, Gevorkian G, Salvador C, Escobar L, Rosendo-Pineda MJ, Medeiros M, Vaca L. An ambient-temperature stable nanoparticle-based vaccine for nasal application that confers long-lasting immunogenicity to carried antigens. Front Immunol 2022; 13:1057499. [DOI: 10.3389/fimmu.2022.1057499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 10/19/2022] [Indexed: 11/13/2022] Open
Abstract
Polyhedrins are viral proteins present in a large family of baculoviruses that form occlusion bodies (polyhedra). These structures protect the virus particles from the outside environment until they are ingested by susceptible insects. Occluded viruses can sustain inclement weather for long periods of time. Therefore, the polyhedra is a natural preservative that keeps the viral structure intact at ambient temperature for years. In a previous study we identified the first 110 amino acids from polyhedrin (PH(1-110)) as a good candidate to carry antigens of interest. As a proof of concept, we produced a fusion protein with PH(1-110) and the green fluorescent protein (PH(1-110)GFP). The fusion protein associates spontaneously during its synthesis resulting in the formation of nanoparticles. Nasal immunization with these nanoparticles and in the absence of any adjuvant, results in a robust immune response with the production of IgG immunoglobulins that remained elevated for months and that selectively recognize the GFP but not PH(1-110). These results indicate that PH(1-110) is poorly immunogenic but capable of enhancing the immune response to GFP.
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9
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Eliat F, Sohn R, Renner H, Kagermeier T, Volkery S, Brinkmann H, Kirschnick N, Kiefer F, Grabos M, Becker K, Bedzhov I, Schöler HR, Bruder JM. Tissue clearing may alter emission and absorption properties of common fluorophores. Sci Rep 2022; 12:5551. [PMID: 35365729 PMCID: PMC8975997 DOI: 10.1038/s41598-022-09303-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 03/15/2022] [Indexed: 11/18/2022] Open
Abstract
In recent years, 3D cell culture has been gaining a more widespread following across many fields of biology. Tissue clearing enables optical analysis of intact 3D samples and investigation of molecular and structural mechanisms by homogenizing the refractive indices of tissues to make them nearly transparent. Here, we describe and quantify that common clearing solutions including benzyl alcohol/benzyl benzoate (BABB), PEG-associated solvent system (PEGASOS), immunolabeling-enabled imaging of solvent-cleared organs (iDISCO), clear, unobstructed brain/body imaging cocktails and computational analysis (CUBIC), and ScaleS4 alter the emission spectra of Alexa Fluor fluorophores and fluorescent dyes. Clearing modifies not only the emitted light intensity but also alters the absorption and emission peaks, at times to several tens of nanometers. The resulting shifts depend on the interplay of solvent, fluorophore, and the presence of cells. For biological applications, this increases the risk for unexpected channel crosstalk, as filter sets are usually not optimized for altered fluorophore emission spectra in clearing solutions. This becomes especially problematic in high throughput/high content campaigns, which often rely on multiband excitation to increase acquisition speed. Consequently, researchers relying on clearing in quantitative multiband excitation experiments should crosscheck their fluorescent signal after clearing in order to inform the proper selection of filter sets and fluorophores for analysis.
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Affiliation(s)
- Farsam Eliat
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany.,University of Münster, Schlossplatz 2, 48143, Münster, Germany
| | - Rebecca Sohn
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany
| | - Henrik Renner
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany
| | - Theresa Kagermeier
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany.,University of Münster, Schlossplatz 2, 48143, Münster, Germany
| | - Stefan Volkery
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany
| | - Heike Brinkmann
- Embryonic Self-Organization research group, Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany
| | - Nils Kirschnick
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany.,University of Münster, European Institute for Molecular Imaging, Waldeyerstraße 15, 48149, Münster, Germany
| | - Friedemann Kiefer
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany.,University of Münster, European Institute for Molecular Imaging, Waldeyerstraße 15, 48149, Münster, Germany
| | - Martha Grabos
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany
| | - Katharina Becker
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany.,University of Münster, Schlossplatz 2, 48143, Münster, Germany
| | - Ivan Bedzhov
- Embryonic Self-Organization research group, Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany
| | - Hans R Schöler
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany
| | - Jan M Bruder
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany.
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10
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List NH, Jones CM, Martínez TJ. Internal conversion of the anionic GFP chromophore: in and out of the I-twisted S 1/S 0 conical intersection seam. Chem Sci 2022; 13:373-385. [PMID: 35126970 PMCID: PMC8729814 DOI: 10.1039/d1sc05849e] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 11/11/2021] [Indexed: 11/21/2022] Open
Abstract
The functional diversity of the green fluorescent protein (GFP) family is intimately connected to the interplay between competing photo-induced transformations of the chromophore motif, anionic p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI-). Its ability to undergo Z/E-isomerization is of particular importance for super-resolution microscopy and emerging opportunities in optogenetics. Yet, key dynamical features of the underlying internal conversion process in the native HBDI- chromophore remain largely elusive. We investigate the intrinsic excited-state behavior of isolated HBDI- to resolve competing decay pathways and map out the factors governing efficiency and the stereochemical outcome of photoisomerization. Based on non-adiabatic dynamics simulations, we demonstrate that non-selective progress along the two bridge-torsional (i.e., phenolate, P, or imidazolinone, I) pathways accounts for the three decay constants reported experimentally, leading to competing ultrafast relaxation primarily along the I-twisted pathway and S1 trapping along the P-torsion. The majority of the population (∼70%) is transferred to S0 in the vicinity of two approximately enantiomeric minima on the I-twisted intersection seam (MECI-Is). Despite their sloped, reactant-biased topographies (suggesting low photoproduct yields), we find that decay through these intersections leads to products with a surprisingly high quantum yield of ∼30%. This demonstrates that E-isomer generation results at least in part from direct isomerization on the excited state. A photoisomerization committor analysis reveals a difference in intrinsic photoreactivity of the two MECI-Is and that the observed photoisomerization is the combined result of two effects: early, non-statistical dynamics around the less reactive intersection followed by later, near-statistical behavior around the more reactive MECI-I. Our work offers new insight into internal conversion of HBDI- that both establishes the intrinsic properties of the chromophore and enlightens principles for the design of chromophore derivatives and protein variants with improved photoswitching properties.
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Affiliation(s)
- Nanna H List
- Department of Chemistry and the PULSE Institute, Stanford University Stanford CA 94305 USA .,SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA
| | - Chey M Jones
- Department of Chemistry and the PULSE Institute, Stanford University Stanford CA 94305 USA .,SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA
| | - Todd J Martínez
- Department of Chemistry and the PULSE Institute, Stanford University Stanford CA 94305 USA .,SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA
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11
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E/ Z Molecular Photoswitches Activated by Two-Photon Absorption: Comparison between Different Families. Molecules 2021; 26:molecules26237379. [PMID: 34885961 PMCID: PMC8659108 DOI: 10.3390/molecules26237379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/25/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022] Open
Abstract
Nonlinear optical techniques as two-photon absorption (TPA) have raised relevant interest within the last years due to the capability to excite chromophores with photons of wavelength equal to only half of the corresponding one-photon absorption energy. At the same time, its probability being proportional to the square of the light source intensity, it allows a better spatial control of the light-induced phenomenon. Although a consistent number of experimental studies focus on increasing the TPA cross section, very few of them are devoted to the study of photochemical phenomena induced by TPA. Here, we show a design strategy to find suitable E/Z photoswitches that can be activated by TPA. A theoretical approach is followed to predict the TPA cross sections related to different excited states of various photoswitches’ families, finally concluding that protonated Schiff-bases (retinal)-like photoswitches outperform compared to the others. The donor-acceptor substitution effect is therefore rationalized for the successful TPA activatable photoswitch, in order to maximize its properties, finally also forecasting a possible application in optogenetics. Some experimental measurements are also carried out to support our conclusions.
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12
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Kovács E, Cseri L, Jancsó A, Terényi F, Fülöp A, Rózsa B, Galbács G, Mucsi Z. Synthesis and Fluorescence Mechanism of the Aminoimidazolone Analogues of the Green Fluorescent Protein: Towards Advanced Dyes with Enhanced Stokes Shift, Quantum Yield and Two‐Photon Absorption. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Ervin Kovács
- Department of Chemistry Femtonics Inc. Tűzoltó u. 58 1094 Budapest Hungary
- Institute of Materials and Environmental Chemistry Research Centre for Natural Sciences Magyar tudósok körútja 2 1117 Budapest Hungary
| | - Levente Cseri
- Department of Chemistry Femtonics Inc. Tűzoltó u. 58 1094 Budapest Hungary
- Department of Chemical Engineering & Analytical Science The University of Manchester The Mill, Sackville Street Manchester M1 3BB United Kingdom
| | - Attila Jancsó
- Department of Inorganic and Analytical Chemistry University of Szeged Dóm tér 8 Szeged 6720 Hungary
| | - Ferenc Terényi
- Department of Inorganic and Analytical Chemistry University of Szeged Dóm tér 8 Szeged 6720 Hungary
| | - Anna Fülöp
- Department of Chemistry Femtonics Inc. Tűzoltó u. 58 1094 Budapest Hungary
| | - Balázs Rózsa
- Two-Photon Measurement Technology Research Group The Faculty of Information Technology Pázmány Péter Catholic University Práter u. 50/A Budapest 1083 Hungary
- Laboratory of 3D Functional Imaging of Neuronal Networks and Dendritic Integration Institute of Experimental Medicine Szigony utca 43 Budapest 1083 Hungary
| | - Gábor Galbács
- Department of Inorganic and Analytical Chemistry University of Szeged Dóm tér 8 Szeged 6720 Hungary
| | - Zoltán Mucsi
- Department of Chemistry Femtonics Inc. Tűzoltó u. 58 1094 Budapest Hungary
- Institute of Chemistry Faculty of Materials Science and Engineering University of Miskolc Egyetem út 1 Miskolc 3515 Hungary
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13
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Sulatskaya AI, Kosolapova AO, Bobylev AG, Belousov MV, Antonets KS, Sulatsky MI, Kuznetsova IM, Turoverov KK, Stepanenko OV, Nizhnikov AA. β-Barrels and Amyloids: Structural Transitions, Biological Functions, and Pathogenesis. Int J Mol Sci 2021; 22:11316. [PMID: 34768745 PMCID: PMC8582884 DOI: 10.3390/ijms222111316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 01/17/2023] Open
Abstract
Insoluble protein aggregates with fibrillar morphology called amyloids and β-barrel proteins both share a β-sheet-rich structure. Correctly folded β-barrel proteins can not only function in monomeric (dimeric) form, but also tend to interact with one another-followed, in several cases, by formation of higher order oligomers or even aggregates. In recent years, findings proving that β-barrel proteins can adopt cross-β amyloid folds have emerged. Different β-barrel proteins were shown to form amyloid fibrils in vitro. The formation of functional amyloids in vivo by β-barrel proteins for which the amyloid state is native was also discovered. In particular, several prokaryotic and eukaryotic proteins with β-barrel domains were demonstrated to form amyloids in vivo, where they participate in interspecies interactions and nutrient storage, respectively. According to recent observations, despite the variety of primary structures of amyloid-forming proteins, most of them can adopt a conformational state with the β-barrel topology. This state can be intermediate on the pathway of fibrillogenesis ("on-pathway state"), or can be formed as a result of an alternative assembly of partially unfolded monomers ("off-pathway state"). The β-barrel oligomers formed by amyloid proteins possess toxicity, and are likely to be involved in the development of amyloidoses, thus representing promising targets for potential therapy of these incurable diseases. Considering rapidly growing discoveries of the amyloid-forming β-barrels, we may suggest that their real number and diversity of functions are significantly higher than identified to date, and represent only "the tip of the iceberg". Here, we summarize the data on the amyloid-forming β-barrel proteins, their physicochemical properties, and their biological functions, and discuss probable means and consequences of the amyloidogenesis of these proteins, along with structural relationships between these two widespread types of β-folds.
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Affiliation(s)
- Anna I. Sulatskaya
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Anastasiia O. Kosolapova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Alexander G. Bobylev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 3 Institutskaya St., 142290 Moscow, Russia;
| | - Mikhail V. Belousov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Maksim I. Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia;
| | - Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Olesya V. Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
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14
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Nottoli M, Nifosì R, Mennucci B, Lipparini F. Energy, Structures, and Response Properties with a Fully Coupled QM/AMOEBA/ddCOSMO Implementation. J Chem Theory Comput 2021; 17:5661-5672. [PMID: 34476941 PMCID: PMC8444335 DOI: 10.1021/acs.jctc.1c00555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
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We present the implementation
of a fully coupled polarizable QM/MM/continuum
model based on the AMOEBA polarizable force field and the domain decomposition
implementation of the conductor-like screening model. Energies, response
properties, and analytical gradients with respect to both QM and MM
nuclear positions are available, and a generic, atomistic cavity can
be employed. The model is linear scaling in memory requirements and
computational cost with respect to the number of classical atoms and
is therefore suited to model large, complex systems. Using three variants
of the green-fluorescent protein, we investigate the overall computational
cost of such calculations and the effect of the continuum model on
the convergence of the computed properties with respect to the size
of the embedding. We also demonstrate the fundamental role of polarization
effects by comparing polarizable and nonpolarizable embeddings to
fully QM ones.
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Affiliation(s)
- Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Riccardo Nifosì
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro 12, I-56127 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
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15
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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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16
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Luo T, Deng L, Li A, Zhou C, Shao S, Sun Q, Gong H, Yang X, Li X. Scalable Resin Embedding Method for Large-Volume Brain Tissues with High Fluorescence Preservation Capacity. iScience 2020; 23:101717. [PMID: 33196032 PMCID: PMC7645060 DOI: 10.1016/j.isci.2020.101717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/06/2020] [Accepted: 10/16/2020] [Indexed: 01/15/2023] Open
Abstract
Resin embedding is widely used to dissect the fine structure of bio-tissue with electron and optical microscopy. However, it is difficult to embed large-volume tissues with resin. Here, we modified the formula of LR-White resin to prevent the sample cracking during polymerization process and applied this method to the intact brains of mouse, ferret, and macaque. Meanwhile, we increased the fluorescence preservation rate for green fluorescent protein (GFP) from 73 ± 4.0% to 126 ± 3.0% and tdTomato from 60 ± 3.3% to 117 ± 2.8%. Combined with the whole-brain imaging system, we acquired the cytoarchitectonic information and the circuit information such as individual axon and boutons which were labeled with multiple fluorescent proteins. This method shows great potential in the study of continuous fine microstructure information in large-volume tissues from different species, which can facilitate the neuroscience research and help the understanding of the structure-function relationship in complex bio-tissues. Modified LR-White resin embedding was proposed to embed large-volume tissues Retarder α-methyl-styrene was added to prevent cracking during polymerization Resin formula was modified to preserve multiple fluorescent proteins Microstructure information was acquired from the brains of different species
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Affiliation(s)
- Ting Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Lei Deng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Anan Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,HUST-Suzhou Institute for Brainsmatics, Suzhou 215125, China
| | - Can Zhou
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shuai Shao
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Qingtao Sun
- HUST-Suzhou Institute for Brainsmatics, Suzhou 215125, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,HUST-Suzhou Institute for Brainsmatics, Suzhou 215125, China
| | - Xiaoquan Yang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,HUST-Suzhou Institute for Brainsmatics, Suzhou 215125, China
| | - Xiangning Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,HUST-Suzhou Institute for Brainsmatics, Suzhou 215125, China
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17
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Rossano-Tapia M, Olsen JMH, Brown A. Two-Photon Absorption Cross-Sections in Fluorescent Proteins Containing Non-canonical Chromophores Using Polarizable QM/MM. Front Mol Biosci 2020; 7:111. [PMID: 32596253 PMCID: PMC7303285 DOI: 10.3389/fmolb.2020.00111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 11/13/2022] Open
Abstract
Multi-photon absorption properties, particularly two-photon absorption (2PA), of fluorescent proteins (FPs) have made them attractive tools in deep-tissue clinical imaging. Although the diversity of photophysical properties for FPs is wide, there are some caveats predominant among the existing FP variants that need to be overcome, such as low quantum yields and small 2PA cross-sections. From a computational perspective, Salem et al. (2016) suggested the inclusion of non-canonical amino acids in the chromophore of the red fluorescent protein DsRed, through the replacement of the tyrosine amino acid. The 2PA properties of these new non-canonical chromophores (nCCs) were determined in vacuum, i.e., without taking into account the protein environment. However, in the computation of response properties, such as 2PA cross-sections, the environment plays an important role. To account for environment and protein-chromophore coupling effects, quantum mechanical/molecular mechanical (QM/MM) schemes can be useful. In this work, the polarizable embedding (PE) model is employed along with time-dependent density functional theory to describe the 2PA properties of a selected set of chromophores made from non-canonical amino acids as they are embedded in the DsRed protein matrix. The objective is to provide insights to determine whether or not the nCCs could be developed and, thus, generate a new class of FPs. Results from this investigation show that within the DsRed environment, the nCC 2PA cross-sections are diminished relative to their values in vacuum. However, further studies toward understanding the 2PA limit of these nCCs using different protein environments are needed.
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Affiliation(s)
| | - Jógvan Magnus Haugaard Olsen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, Tromsø, Norway
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
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18
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Palanisamy N, Öztürk MA, Akmeriç EB, Di Ventura B. C-terminal eYFP fusion impairs Escherichia coli MinE function. Open Biol 2020; 10:200010. [PMID: 32456552 PMCID: PMC7276532 DOI: 10.1098/rsob.200010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The Escherichia coli Min system plays an important role in the proper placement of the septum ring at mid-cell during cell division. MinE forms a pole-to-pole spatial oscillator with the membrane-bound ATPase MinD, resulting in MinD concentration being the lowest at mid-cell. MinC, the direct inhibitor of the septum initiator protein FtsZ, forms a complex with MinD at the membrane, mirroring its polar gradients. Therefore, MinC-mediated FtsZ inhibition occurs away from mid-cell. Min oscillations are often studied in living cells by time-lapse microscopy using fluorescently labelled Min proteins. Here, we show that, despite permitting oscillations to occur in a range of protein concentrations, the enhanced yellow fluorescent protein (eYFP) C-terminally fused to MinE impairs its function. Combining in vivo, in vitro and in silico approaches, we demonstrate that eYFP compromises the ability of MinE to displace MinC from MinD, to stimulate MinD ATPase activity and to directly bind to the membrane. Moreover, we reveal that MinE-eYFP is prone to aggregation. In silico analyses predict that other fluorescent proteins are also likely to compromise several functionalities of MinE, suggesting that the results presented here are not specific to eYFP.
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Affiliation(s)
- Navaneethan Palanisamy
- Faculty of Biology, Institute of Biology II, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.,Centers for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.,Heidelberg Biosciences International Graduate School (HBIGS), University of Heidelberg, 69120 Heidelberg, Germany
| | - Mehmet Ali Öztürk
- Faculty of Biology, Institute of Biology II, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.,Centers for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Emir Bora Akmeriç
- Faculty of Biology, Institute of Biology II, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.,Centers for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Barbara Di Ventura
- Faculty of Biology, Institute of Biology II, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.,Centers for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
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19
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Steinmetzger C, Bessi I, Lenz AK, Höbartner C. Structure-fluorescence activation relationships of a large Stokes shift fluorogenic RNA aptamer. Nucleic Acids Res 2020; 47:11538-11550. [PMID: 31740962 PMCID: PMC7145527 DOI: 10.1093/nar/gkz1084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/13/2019] [Accepted: 11/01/2019] [Indexed: 12/21/2022] Open
Abstract
The Chili RNA aptamer is a 52 nt long fluorogen-activating RNA aptamer (FLAP) that confers fluorescence to structurally diverse derivatives of fluorescent protein chromophores. A key feature of Chili is the formation of highly stable complexes with different ligands, which exhibit bright, highly Stokes-shifted fluorescence emission. In this work, we have analyzed the interactions between the Chili RNA and a family of conditionally fluorescent ligands using a variety of spectroscopic, calorimetric and biochemical techniques to reveal key structure–fluorescence activation relationships (SFARs). The ligands under investigation form two categories with emission maxima of ∼540 or ∼590 nm, respectively, and bind with affinities in the nanomolar to low-micromolar range. Isothermal titration calorimetry was used to elucidate the enthalpic and entropic contributions to binding affinity for a cationic ligand that is unique to the Chili aptamer. In addition to fluorescence activation, ligand binding was also observed by NMR spectroscopy, revealing characteristic signals for the formation of a G-quadruplex only upon ligand binding. These data shed light on the molecular features required and responsible for the large Stokes shift and the strong fluorescence enhancement of red and green emitting RNA–chromophore complexes.
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Affiliation(s)
- Christian Steinmetzger
- Institute of Organic Chemistry, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Irene Bessi
- Institute of Organic Chemistry, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Ann-Kathrin Lenz
- Institute of Organic Chemistry, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany
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20
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Marathe P, H S MS, Nair D, Bhattacharyya D. mEosBrite Are Bright Variants of mEos3.2 Developed by Semirational Protein Engineering. J Fluoresc 2020; 30:703-715. [PMID: 32385659 DOI: 10.1007/s10895-020-02537-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 04/13/2020] [Indexed: 10/24/2022]
Abstract
mEos3.2 is a photoconvertible fluorescence protein with comparatively low brightness, which limits its application in live Super resolution microscopy. To address this issue, we have used semi-rational protein engineering to develop mEosBrite, a new class of improved brightness variants. The improvement in the brightness was confirmed by expression in E.coli as well as mammalian cell lines. Furthermore, biophysical characterization suggests that all the three mEosBrite variant proteins display higher quantum yield, truly monomeric form, less cytotoxicity and lower protein aggregation as compared to the wild type mEos3.2 protein. Most importantly, because of their high photoconversion efficiency mEosBrite variants could be an excellent tool for single-molecule and intensity fluctuation based super-resolution microscopy.
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Affiliation(s)
- Pravin Marathe
- Department of Cell and Tumor Biology, Advanced Centre for Treatment Research & Education in Cancer (ACTREC), Tata Memorial Centre, Sector 22, Kharghar, Navi Mumbai, MH, 410210, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, 400085, India
| | - Mahadeva Swamy H S
- Centre For Neuroscience, Indian Institute of Science, Bangalore, 560012, India
| | - Deepak Nair
- Centre For Neuroscience, Indian Institute of Science, Bangalore, 560012, India
| | - Dibyendu Bhattacharyya
- Department of Cell and Tumor Biology, Advanced Centre for Treatment Research & Education in Cancer (ACTREC), Tata Memorial Centre, Sector 22, Kharghar, Navi Mumbai, MH, 410210, India. .,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, 400085, India.
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21
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Pakhomov AA, Frolova AY, Tabakmakher VM, Chugunov AO, Efremov RG, Martynov VI. Impact of external amino acids on fluorescent protein chromophore biosynthesis revealed by molecular dynamics and mutagenesis studies. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 206:111853. [PMID: 32272363 DOI: 10.1016/j.jphotobiol.2020.111853] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/27/2020] [Accepted: 03/13/2020] [Indexed: 11/16/2022]
Abstract
The precise positioning of catalytic amino acids against the substrate in an enzyme active site is a crucial factor in biocatalysis. Biosynthesis of the chromophores of fluorescent proteins (FPs) is an autocatalytic process that must conform to these requirements. Here, we show that, in addition to the internal amino acid residues in the proximity of the chromophore, chromophore biosynthesis is influenced by the remote amino acids exposed on the outer surface of the β-barrel structure of the FP. It has been shown earlier that chromophore biosynthesis of the red FP from Zoanthus sp. (zoan2RFP) proceeds via an immature green state. At the same time, the green state is the final stage of chromophore biosynthesis of green FP (zoanGFP), which is highly homologous to zoan2RFP. It was also shown that a single N66D substitution in the chromophore-forming sequence of zoanGFP might trigger the synthesis of the red chromophore. However, in this case, the synthesis of the red chromophore is incomplete and occurs only at elevated temperatures. Here, we tried to uncover additional structural determinants that govern the biosynthesis of the red chromophore. A comparison of zoanGFP and zoan2RFP revealed intrabarrel amino acid differences at five positions. Exhaustive substitutions of these five positions in zoanGFP-N66D gave rise to zoanGFPmut with the same intrabarrel amino acid composition as zoan2RFP. zoanGFPmut showed only partial green-to-red chromophore transformation at elevated temperatures. To elucidate the extra factors that can affect red chromophore biosynthesis, we performed comparative molecular dynamics simulations of zoan2RFP and zoanGFPmut. The simulations revealed several external amino acids that might influence the arrangement and flexibility of the chromophore-surrounding amino acid residues in these proteins. Mutagenesis experiments confirmed the crucial role of these residues in red chromophore biosynthesis. The obtained zoanGFPmut2 exhibited complete green-to-red transformation, suggesting that the mutated amino acids exposed on the surface of the β-barrel contribute to red chromophore biosynthesis.
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Affiliation(s)
- Alexey A Pakhomov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; A.N. Nesmeyanov Institute of Organoelement Compounds, Moscow 119334, Russia.
| | - Anastasiya Yu Frolova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; A.N. Nesmeyanov Institute of Organoelement Compounds, Moscow 119334, Russia
| | - Valentin M Tabakmakher
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; School of Biomedicine, Far Eastern Federal University, Vladivostok 690950, Russia
| | - Anton O Chugunov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; National Research University Higher School of Economics, Moscow 101000, Russia; Moscow Institute of Physics and Technology (State University), Dolgoprudny 141701, Moscow Oblast, Russia
| | - Roman G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; National Research University Higher School of Economics, Moscow 101000, Russia; Moscow Institute of Physics and Technology (State University), Dolgoprudny 141701, Moscow Oblast, Russia
| | - Vladimir I Martynov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
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22
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Dolgopolova EA, Berseneva AA, Faillace MS, Ejegbavwo OA, Leith GA, Choi SW, Gregory HN, Rice AM, Smith MD, Chruszcz M, Garashchuk S, Mythreye K, Shustova NB. Confinement-Driven Photophysics in Cages, Covalent−Organic Frameworks, Metal–Organic Frameworks, and DNA. J Am Chem Soc 2020; 142:4769-4783. [DOI: 10.1021/jacs.9b13505] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ekaterina A. Dolgopolova
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Anna A. Berseneva
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Martín S. Faillace
- INFIQC-UNC, CONICET, Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
| | - Otega A. Ejegbavwo
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Gabrielle A. Leith
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Seok W. Choi
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Haley N. Gregory
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Allison M. Rice
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Mark D. Smith
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Sophya Garashchuk
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Karthikeyan Mythreye
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Natalia B. Shustova
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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23
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Deng H, Yu C, Yan D, Zhu X. Dual-Self-Restricted GFP Chromophore Analogues with Significantly Enhanced Emission. J Phys Chem B 2020; 124:871-880. [PMID: 31928005 DOI: 10.1021/acs.jpcb.9b11329] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The tremendous gap of fluorescence emission of synthetic green fluorescent protein (GFP) chromophore to the protein itself makes it impossible to use for applications in molecular and cellular imaging. Here, we developed an efficient methodology to enhance the photoluminescence response of synthetic GFP chromophore analogues by constructing dual-self-restricted chromophores. Single self-restricted chromophores were first generated with 2,5-dimethoxy substitution on the aromatic ring, which were further modified with phenyl or 2,5-dimethoxy phenyl to form dual-self-restricted chromophores. These two chromophores showed an obvious solvatofluorochromic color palette across blue to yellow with a maximum emission Stokes shift of 95 nm and dramatically enhanced fluorescence emission in various aprotic solvents, especially in hexane, where the QY reached around 0.6. Importantly, in acetonitrile and dimethyl sulfoxide, the fluorescence QYs of both chromophores were over 0.22, which were the highest reported so far in high polar organic solvents. Meanwhile, the fluorescence lifetimes also improved obviously with the maximum of around 4.5 ns. Theoretical calculations revealed a more favorable Mülliken atomic charge translocation over the double-bond bridge and illustrated much higher energy barriers for the Z/E photoisomerization together with larger bond orders compared with the GFP core chromophore, p-HBDI. Our work significantly improved the fluorescence emission of synthetic GFP chromophore analogues in polar solvents while reserved the multicolor emitting function, providing a solid molecular motif for engineering high-performance fluorescent probes.
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Affiliation(s)
- Hongping Deng
- School of Chemistry and Chemical Engineering, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, State Key Laboratory of Metal Matrix Composites , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , People's Republic of China
| | - Chunyang Yu
- School of Chemistry and Chemical Engineering, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, State Key Laboratory of Metal Matrix Composites , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , People's Republic of China
| | - Deyue Yan
- School of Chemistry and Chemical Engineering, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, State Key Laboratory of Metal Matrix Composites , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , People's Republic of China
| | - Xinyuan Zhu
- School of Chemistry and Chemical Engineering, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, State Key Laboratory of Metal Matrix Composites , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , People's Republic of China
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24
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Morgan E, Doh J, Beatty K, Reich N. VIPER nano: Improved Live Cell Intracellular Protein Tracking. ACS APPLIED MATERIALS & INTERFACES 2019; 11:36383-36390. [PMID: 31545582 PMCID: PMC7351371 DOI: 10.1021/acsami.9b12679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Tracking intracellular proteins in live cells has many challenges. The most widely used method, fluorescent protein fusions, can track proteins in their native cellular environment and has led to significant discoveries in cell biology. Fusion proteins add steric bulk to the target protein and can negatively affect native protein function. The use of exogenous probes such as antibodies or protein labels is problematic because these cannot cross the plasma membrane on their own and thus cannot label intracellular targets in cells. We developed a labeling platform, VIPERnano, for live cell imaging of intracellular proteins using a peptide fusion tag (CoilE) to the protein of interest and delivery of a fluorescently labeled probe peptide (CoilR). CoilR and CoilE form an α-helical heterodimer with the protein of interest, rendering a labeled protein. Delivery of CoilR into the cell uses hollow gold nanoshells (HGNs) as the primary delivery vehicle. The technology relies on the conjugation and light-activated release of the CoilR peptide on the surface of the HGNs. We demonstrate light-activated VIPERnano delivery and labeling with two intracellular proteins, localized either in the mitochondria or the nucleus. This technology has the ability to study intracellular protein dynamics and spatial tracking while lessening the steric bulk of tags associated with the protein of interest.
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Affiliation(s)
- Erin Morgan
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93117, United States
| | - Julia Doh
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Kimberly Beatty
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, United States
- OHSU Center for Spatial Systems Biomedicine, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Norbert Reich
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93117, United States
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25
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Nifosì R, Mennucci B, Filippi C. The key to the yellow-to-cyan tuning in the green fluorescent protein family is polarisation. Phys Chem Chem Phys 2019; 21:18988-18998. [PMID: 31464320 DOI: 10.1039/c9cp03722e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Computational approaches have to date failed to fully capture the large (about 0.4 eV) excitation energy tuning displayed by the nearly identical anionic chromophore in different green fluorescent protein (GFP) variants. Here, we present a thorough comparative study of a set of proteins in this sub-family, including the most red- (phiYFP) and blue-shifted (mTFP0.7) ones. We employ a classical polarisable embedding through induced dipoles and combine it with time-dependent density functional theory and multireference perturbation theory in order to capture both state-specific induction contributions and the coupling of the polarisation of the protein to the chromophore transition density. The obtained results show that only upon inclusion of both these two effects generated by the mutual polarisation between the chromophore and the protein can the full spectral tuning be replicated. We finally discuss how this mutual polarisation affects the correlation between excitation energies, dipole moment variation, and molecular electrostatic field.
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Affiliation(s)
- Riccardo Nifosì
- NEST, CNR - Istituto Nanoscienze and Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy.
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy
| | - Claudia Filippi
- MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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26
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Schmidt D, Stolte M, Süß J, Liess A, Stepanenko V, Würthner F. Protein-like Enwrapped Perylene Bisimide Chromophore as a Bright Microcrystalline Emitter Material. Angew Chem Int Ed Engl 2019; 58:13385-13389. [PMID: 31329325 PMCID: PMC6772080 DOI: 10.1002/anie.201907618] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Indexed: 01/01/2023]
Abstract
Strongly emissive solid‐state materials are mandatory components for many emerging optoelectronic technologies, but fluorescence is often quenched in the solid state owing to strong intermolecular interactions. The design of new organic pigments, which retain their optical properties despite their high tendency to crystallize, could overcome such limitations. Herein, we show a new material with monomer‐like absorption and emission profiles as well as fluorescence quantum yields over 90 % in its crystalline solid state. The material was synthesized by attaching two bulky tris(4‐tert‐butylphenyl)phenoxy substituents at the perylene bisimide bay positions. These substituents direct a packing arrangement with full enwrapping of the chromophore and unidirectional chromophore alignment within the crystal lattice to afford optical properties that resemble those of their natural pigment counterparts, in which chromophores are rigidly embedded in protein environments.
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Affiliation(s)
- David Schmidt
- Institut für Organische Chemie & Center for Nanosystems Chemistry, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Matthias Stolte
- Institut für Organische Chemie & Center for Nanosystems Chemistry, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Jasmin Süß
- Institut für Organische Chemie & Center for Nanosystems Chemistry, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Andreas Liess
- Institut für Organische Chemie & Center for Nanosystems Chemistry, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Vladimir Stepanenko
- Institut für Organische Chemie & Center for Nanosystems Chemistry, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Frank Würthner
- Institut für Organische Chemie & Center for Nanosystems Chemistry, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
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27
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Schmidt D, Stolte M, Süß J, Liess A, Stepanenko V, Würthner F. Protein‐like Enwrapped Perylene Bisimide Chromophore as a Bright Microcrystalline Emitter Material. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907618] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- David Schmidt
- Institut für Organische Chemie & Center for Nanosystems ChemistryUniversität Würzburg Am Hubland 97074 Würzburg Germany
| | - Matthias Stolte
- Institut für Organische Chemie & Center for Nanosystems ChemistryUniversität Würzburg Am Hubland 97074 Würzburg Germany
| | - Jasmin Süß
- Institut für Organische Chemie & Center for Nanosystems ChemistryUniversität Würzburg Am Hubland 97074 Würzburg Germany
| | - Andreas Liess
- Institut für Organische Chemie & Center for Nanosystems ChemistryUniversität Würzburg Am Hubland 97074 Würzburg Germany
| | - Vladimir Stepanenko
- Institut für Organische Chemie & Center for Nanosystems ChemistryUniversität Würzburg Am Hubland 97074 Würzburg Germany
| | - Frank Würthner
- Institut für Organische Chemie & Center for Nanosystems ChemistryUniversität Würzburg Am Hubland 97074 Würzburg Germany
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28
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Jancsó A, Kovács E, Cseri L, Rózsa BJ, Galbács G, Csizmadia IG, Mucsi Z. Synthesis and spectroscopic characterization of novel GFP chromophore analogues based on aminoimidazolone derivatives. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 218:161-170. [PMID: 30986708 DOI: 10.1016/j.saa.2019.03.111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
In order to improve the fluorescence properties of the green fluorescent protein chromophore, p‑HOBDI ((5‑(4‑hydroxybenzylidene)‑2,3‑dimethyl‑3,5‑dihydro‑4H‑imidazol‑4‑one), sixteen dihydroimidazolone derivates were synthesized from thiohydantoin and arylaldehydes. The synthesis developed is an efficient, novel, one-pot procedure. The study provides a detailed description of the spectroscopic characteristics of the newly synthesized compounds, using p‑HOBDI as a reference. The new compounds all exhibited significantly stronger fluorescence than p‑HOBDI, up to 28 times higher quantum yields. An experimental and theoretical investigation of the relationship of the fluorescence properties with the molecular structure was also carried out. A good correlation was found between the emission wavenumber and the Hammett constant of the functional group, which suggests the intermolecular charge transfer (ICT) mechanism between the aromatic groups.
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Affiliation(s)
- Attila Jancsó
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged H-6720, Hungary
| | - Ervin Kovács
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary; Department of Chemistry, Femtonics Inc., H-1094 Budapest, Hungary
| | - Levente Cseri
- Department of Chemistry, Femtonics Inc., H-1094 Budapest, Hungary; School of Chemical Engineering & Analytical Science, The University of Manchester, Manchester, United Kingdom
| | - Balázs J Rózsa
- Two-Photon Measurement Technology Research Group, The Faculty of Information Technology, Pázmány Péter Catholic University, Budapest H-1083, Hungary; Laboratory of 3D Functional Imaging of Neuronal Networks and Dendritic Integration, Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest H-1083, Hungary
| | - Gábor Galbács
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged H-6720, Hungary
| | - Imre G Csizmadia
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Zoltán Mucsi
- Department of Chemistry, Femtonics Inc., H-1094 Budapest, Hungary; Two-Photon Measurement Technology Research Group, The Faculty of Information Technology, Pázmány Péter Catholic University, Budapest H-1083, Hungary.
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29
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Pletneva NV, Goryacheva EA, Artemyev IV, Arkhipova SF, Pletnev VZ. Structure of Chromophores in GFP-Like Proteins: X-Ray Data. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s106816201903004x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Xu JJ, Sung R, Sung K. S 1/S 0 Potential Energy Surfaces Experience Different Types of Restricted Rotation: Restricted Z/ E Photoisomerization and E/ Z Thermoisomerization by an Out-of-Plane Benzyl Group or In-Plane m-Pyridinium Group? J Phys Chem A 2019; 123:4708-4716. [PMID: 31084005 DOI: 10.1021/acs.jpca.9b02924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Any method that can enhance the fluorescence of fluorophores is highly desirable. Fluorescence enhancement accomplished by restricted Z/ E photoisomerization through intramolecular steric hindrance or relatively high bond order of a C═C double bond in a S1 excited state has rarely been studied. In this article, we used green fluorescent protein (GFP) chromophore analogues as a model to get new physical insights into the restricted Z/ E photoisomerization and E/ Z thermoisomerization phenomena. We found that the S1 and S0 potential energy surfaces (PESs) of the GFP chromophore analogues experience two dramatically different types of restricted rotation, and 2b can be a representative example. In its S1 PES, it is not the intramolecular steric hindrance between the out-of-plane benzyl group and the in-plane m-pyridinium group but the relatively high bond order of the I-bond in the S1 excited state of 2b that makes it have a higher barrier for the Z/ E photoisomerization, a smaller Z/ E photoisomerization quantum yield, and a higher fluorescence quantum yield. In its S0 PES, it is not the reduced bond order of the I-bond in the S0 ground state of 2b but the intramolecular steric hindrance between the out-of-plane benzyl group and the in-plane m-pyridinium group that makes it have an extra higher barrier for E/ Z thermoisomerization and a much smaller E/ Z thermoisomerization rate constant.
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Affiliation(s)
- Jun-Jia Xu
- Department of Chemistry , National Cheng Kung University , Tainan , Taiwan
| | - Robert Sung
- Department of Chemistry , National Cheng Kung University , Tainan , Taiwan
| | - Kuangsen Sung
- Department of Chemistry , National Cheng Kung University , Tainan , Taiwan
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31
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Ferreira AV, Antunes E, Ribeiro A, Matamá T, Azoia NG, Cunha J, Cavaco-Paulo A. Design of a chromogenic substrate for elastase based on split GFP system-Proof of concept for colour switch sensors. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2019; 22:e00324. [PMID: 31049301 PMCID: PMC6479270 DOI: 10.1016/j.btre.2019.e00324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/15/2019] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
Recent studies have demonstrated that human neutrophil elastase (HNE) can be used as marker for inflammation/infection of chronic wounds since it was found to be present in high concentration in exudate collected from chronic wounds. Biosensors used in wound care benefit from a chromogenic signalling due to the readiness of signal interpretation, but the most common use faint yellow chromogenic molecules such as p-nitroaniline (pNa). In addition, if to be converted into smart dressings, the colour of the detection system should not be masked by the exudate's colour. In this work, we designed a chromogenic substrate for HNE aiming to be incorporated in a smart dressing as a colour switch sensor. The substrate was developed using the GFP-like chromoprotein ultramarine (UM), following the split GFP technology. The cleavage sequence for HNE (Ala-Ala-Pro-Val) was embedded into the sensing moiety of the substrate corresponding to the 11th β-sheet. In the presence of HNE, the 11th β-sheet is able to interact to the signalling moiety composed of the β1-β10 incomplete barrel, allowing the re-establishment of the chromophore environment and, hence, the colour production. Structural homology and molecular dynamics simulations were conducted to aid on the disclosure of the structural changes that are the base of the mechanism of action of this HNE switch substrate. Our findings explore the possible application of GFP-like chromogenic sensors in point-of-care devices for the evaluation of the wounds status, representing a major step in the medical field.
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Affiliation(s)
| | | | | | | | | | | | - Artur Cavaco-Paulo
- Centre of Biological Engineering (CEB), University of Minho, Campus of Gualtar, 4710-057, Braga, Portugal
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32
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Taylor MA, Zhu L, Rozanov ND, Stout KT, Chen C, Fang C. Delayed vibrational modulation of the solvated GFP chromophore into a conical intersection. Phys Chem Chem Phys 2019; 21:9728-9739. [PMID: 31032505 DOI: 10.1039/c9cp01077g] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Green fluorescent protein (GFP) has revolutionized bioimaging and life sciences. Its successes have inspired modification of the chromophore structure and environment to tune emission properties, but outside the protein cage, the chromophore is essentially non-fluorescent. In this study, we employ the tunable femtosecond stimulated Raman spectroscopy (FSRS) and transient absorption (TA) to map the energy dissipation pathways of GFP model chromophore (HBDI) in basic aqueous solution. Strategic tuning of the Raman pump to 550 nm exploits the stimulated emission band to enhance excited state vibrational motions as HBDI navigates the non-equilibrium potential energy landscape to pass through a conical intersection. The time-resolved FSRS uncovers prominent anharmonic couplings between a global out-of-plane bending mode of ∼227 cm-1 and two modes at ∼866 and 1572 cm-1 before HBDI reaches the twisted intramolecular charge transfer (TICT) state on the ∼3 ps time scale. Remarkably, the wavelet transform analysis reveals a ∼500 fs delayed onset of the coupling peaks, in correlation with the emergence of an intermediate charge-separated state en route to the TICT state. This mechanism is corroborated by the altered coupling matrix for the HBDI Raman modes in the 50% (v/v) water-glycerol mixture, and a notable lengthening of the picosecond time constant. The real-time molecular "movie" of the general rotor-like HBDI isomerization reaction following photoexcitation represents a significant advance in comprehending the photochemical reaction pathways of the solvated GFP chromophore, therefore providing a crucial foundation to enable rational design of diverse nanomachines from efficient molecular rotors to bright fluorescent probes.
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Affiliation(s)
- Miles A Taylor
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, USA.
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33
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Kinoshita N, Huang AJY, McHugh TJ, Suzuki SC, Masai I, Kim IH, Soderling SH, Miyawaki A, Shimogori T. Genetically Encoded Fluorescent Indicator GRAPHIC Delineates Intercellular Connections. iScience 2019; 15:28-38. [PMID: 31026667 PMCID: PMC6482341 DOI: 10.1016/j.isci.2019.04.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/05/2019] [Accepted: 04/06/2019] [Indexed: 12/19/2022] Open
Abstract
Intercellular contacts are essential for precise organ morphogenesis, function, and maintenance; however, spatiotemporal information of cell-cell contacts or adhesions remains elusive in many systems. We developed a genetically encoded fluorescent indicator for intercellular contacts with optimized intercellular GFP reconstitution using glycosylphosphatidylinositol (GPI) anchor, GRAPHIC (GPI anchored reconstitution-activated proteins highlight intercellular connections), which can be used for an expanded number of cell types. We observed a robust GFP signal specifically at the interface between cultured cells, without disrupting natural cell contact. Application of GRAPHIC to the fish retina specifically delineated cone-bipolar connection sites. Moreover, we showed that GRAPHIC can be used in the mouse central nervous system to delineate synaptic sites in the thalamocortical circuit. Finally, we generated GRAPHIC color variants, enabling detection of multiple convergent contacts simultaneously in cell culture system. We demonstrated that GRAPHIC has high sensitivity and versatility, which will facilitate the analysis of the complex multicellular connections without previous limitations. Development of GRAPHIC to visualize intercellular contact site GPI anchor and different split site provides stronger fluorescent signal GRAPHIC can be used to delineate synaptic site in mouse CNS and zebrafish retina GRAPHIC color variants for multi–contact site visualization
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Affiliation(s)
- Nagatoki Kinoshita
- Molecular Mechanisms of Brain Development, Center for Brain Science (CBS), RIKEN, Saitama, Japan; Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Agency (JST), Tokyo, Japan
| | | | - Thomas J McHugh
- Circuit and Behavioral Physiology, CBS, RIKEN, Saitama, Japan
| | - Sachihiro C Suzuki
- Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, Japan
| | - Ichiro Masai
- Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, Japan
| | - Il Hwan Kim
- Department of Cell Biology, Duke University Medical School, Durham, NC, USA
| | - Scott H Soderling
- Department of Cell Biology, Duke University Medical School, Durham, NC, USA
| | - Atsushi Miyawaki
- Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Agency (JST), Tokyo, Japan; Cell Function Dynamics, CBS, RIKEN, Saitama, Japan
| | - Tomomi Shimogori
- Molecular Mechanisms of Brain Development, Center for Brain Science (CBS), RIKEN, Saitama, Japan.
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34
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Orozco-Gonzalez Y, Kabir MP, Gozem S. Electrostatic Spectral Tuning Maps for Biological Chromophores. J Phys Chem B 2019; 123:4813-4824. [DOI: 10.1021/acs.jpcb.9b00489] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - Mohammad Pabel Kabir
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
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35
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Abstract
Many proteins can be split into fragments that spontaneously reassemble, without covalent linkage, into a functional protein. For split green fluorescent proteins (GFPs), fragment reassembly leads to a fluorescent readout, which has been widely used to investigate protein-protein interactions. We review the scope and limitations of this approach as well as other diverse applications of split GFPs as versatile sensors, molecular glues, optogenetic tools, and platforms for photophysical studies.
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Affiliation(s)
- Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, California 94305, USA; ,
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA; ,
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36
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Cycles of protein condensation and discharge in nuclear organelles studied by fluorescence lifetime imaging. Nat Commun 2019; 10:455. [PMID: 30692529 PMCID: PMC6349932 DOI: 10.1038/s41467-019-08354-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 01/03/2019] [Indexed: 02/07/2023] Open
Abstract
Nuclear organelles are viscous droplets, created by concentration-dependent condensation and liquid–liquid phase separation of soluble proteins. Nuclear organelles have been actively investigated for their role in cellular regulation and disease. However, these studies are highly challenging to perform in live cells, and therefore, their physico-chemical properties are still poorly understood. In this study, we describe a fluorescence lifetime imaging approach for real-time monitoring of protein condensation in nuclear organelles of live cultured cells. This approach unravels surprisingly large cyclic changes in concentration of proteins in major nuclear organelles including nucleoli, nuclear speckles, Cajal bodies, as well as in the clusters of heterochromatin. Remarkably, protein concentration changes are synchronous for different organelles of the same cells. We propose a molecular mechanism responsible for synchronous accumulations of proteins in the nuclear organelles. This mechanism can serve for general regulation of cellular metabolism and contribute to coordination of gene expression. Studying the condensation of proteins into membraneless organelles in live cells is highly challenging. Here the authors develop a fluorescence lifetime imaging approach to monitor the condensation of proteins in nuclear organelles and report coordinated and cyclic changes in several nuclear organelles.
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Grünewald J, Brock A, Geierstanger BH. Site-Specific Antibody Labeling Using Phosphopantetheinyl Transferase-Catalyzed Ligation. Methods Mol Biol 2019; 2012:237-278. [PMID: 31161512 DOI: 10.1007/978-1-4939-9546-2_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
4'-Phosphopantetheinyl transferases (PPTases) have been employed by researchers as versatile biocatalysts for the site-specific modification of numerous protein targets with structurally diverse molecules. Here we describe the use of these enzymes for the production of homogeneous antibody-drug conjugates (ADCs), which have garnered much attention as innovative anticancer drugs. The exceptionally broad substrate tolerance of PPTases allows for one-step and two-step conjugation strategies for site-specific ADC synthesis. While one-step conjugation involves direct coupling of a drug molecule to an antibody, two-step conjugation provides increased flexibility and efficiency of the conjugation process by first attaching a bioorthogonal chemical handle that is then used for drug molecule attachment in a second step. The aim of this chapter is to outline detailed protocols for both labeling procedures, as well as to provide guidance on enzyme and substrate preparation.
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Affiliation(s)
- Jan Grünewald
- Biotherapeutics, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA.
| | - Ansgar Brock
- Biotherapeutics, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
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Laporte A, Nordenbrock A, Lenzen S, Elsner M. Light-induced intracellular hydrogen peroxide generation through genetically encoded photosensitizer KillerRed-SOD1. Free Radic Res 2018; 52:1170-1181. [DOI: 10.1080/10715762.2018.1540042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Anna Laporte
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Anke Nordenbrock
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Sigurd Lenzen
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
- Institute of Experimental Diabetes, Research Hannover Medical School, Hannover, Germany
| | - Matthias Elsner
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
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Wang S, Shuai Y, Sun C, Xue B, Hou Y, Su X, Sun Y. Lighting Up Live Cells with Smart Genetically Encoded Fluorescence Probes from GMars Family. ACS Sens 2018; 3:2269-2277. [PMID: 30346738 DOI: 10.1021/acssensors.8b00449] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As a special kind of delicate light-controllable genetically encoded optical device, reversibly photoswitchable fluorescent proteins (RSFPs) have been widely applied in many fields, especially various kinds of advanced nanoscopy approaches in recent years. However, there are still necessities for exploring novel RSFPs with specific biochemical or photophysical properties not only for bioimaging or biosensing applications but also for fluorescent protein (FP) mechanisms study and further knowledge-based molecular sensors or optical actuators' rational design and evolution. Besides previously reported GMars-Q and GMars-T variants, herein, we reported the development and applications of other RSFPs from GMars family, especially some featured RSFPs with desired optical properties. In the current work, in vitro FP purification, spectra measurements, and live-cell RESOLFT nanoscopy approaches were applied to characterize the basic properties and test the imaging performances of the selected RSFPs. As demonstrated, GMars variants such as GMars-A, GMars-G, or remarkable photofatigue-resistant GMars-L were found with beneficial properties to be capable of parallelized RESOLFT nanoscopy in living cells, while other featured GMars variants such as dark GMars-P may be a good candidate for further biosensor or actuator design and applications.
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Affiliation(s)
- Sheng Wang
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
| | - Yao Shuai
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Chaoying Sun
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
| | - Boxin Xue
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
| | - Yingping Hou
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
| | - Xiaodong Su
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Yujie Sun
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
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40
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Genetically encoded fluorescent indicators for live cell pH imaging. Biochim Biophys Acta Gen Subj 2018; 1862:2924-2939. [PMID: 30279147 DOI: 10.1016/j.bbagen.2018.09.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/17/2018] [Accepted: 09/17/2018] [Indexed: 02/04/2023]
Abstract
BACKGROUND Intracellular pH underlies most cellular processes. There is emerging evidence of a pH-signaling role in plant cells and microorganisms. Dysregulation of pH is associated with human diseases, such as cancer and Alzheimer's disease. SCOPE OF REVIEW In this review, we attempt to provide a summary of the progress that has been made in the field during the past two decades. First, we present an overview of the current state of the design and applications of fluorescent protein (FP)-based pH indicators. Then, we turn our attention to the development and applications of hybrid pH sensors that combine the capabilities of non-GFP fluorophores with the advantages of genetically encoded tags. Finally, we discuss recent advances in multicolor pH imaging and the applications of genetically encoded pH sensors in multiparameter imaging. MAJOR CONCLUSIONS Genetically encoded pH sensors have proven to be indispensable noninvasive tools for selective targeting to different cellular locations. Although a variety of genetically encoded pH sensors have been designed and applied at the single cell level, there is still much room for improvements and future developments of novel powerful tools for pH imaging. Among the most pressing challenges in this area is the design of brighter redshifted sensors for tissue research and whole animal experiments. GENERAL SIGNIFICANCE The design of precise pH measuring instruments is one of the important goals in cell biochemistry and may give rise to the development of new powerful diagnostic tools for various diseases.
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Abstract
A half century of studying protein folding in vitro and modeling it in silico has not provided us with a reliable computational method to predict the native conformations of proteins de novo, let alone identify the intermediates on their folding pathways. In this Opinion article, we suggest that the reason for this impasse is the over-reliance on current physical models of protein folding that are based on the assumption that proteins are able to fold spontaneously without assistance. These models arose from studies conducted in vitro on a biased sample of smaller, easier-to-isolate proteins, whose native structures appear to be thermodynamically stable. Meanwhile, the vast empirical data on the majority of larger proteins suggests that once these proteins are completely denatured in vitro, they cannot fold into native conformations without assistance. Moreover, they tend to lose their native conformations spontaneously and irreversibly in vitro, and therefore such conformations must be metastable. We propose a model of protein folding that is based on the notion that the folding of all proteins in the cell is mediated by the actions of the "protein folding machine" that includes the ribosome, various chaperones, and other components involved in co-translational or post-translational formation, maintenance and repair of protein native conformations in vivo. The most important and universal component of the protein folding machine consists of the ribosome in complex with the welcoming committee chaperones. The concerted actions of molecular machinery in the ribosome peptidyl transferase center, in the exit tunnel, and at the surface of the ribosome result in the application of mechanical and other forces to the nascent peptide, reducing its conformational entropy and possibly creating strain in the peptide backbone. The resulting high-energy conformation of the nascent peptide allows it to fold very fast and to overcome high kinetic barriers along the folding pathway. The early folding intermediates in vivo are stabilized by interactions with the ribosome and welcoming committee chaperones and would not be able to exist in vitro in the absence of such cellular components. In vitro experiments that unfold proteins by heat or chemical treatment produce denaturation ensembles that are very different from folding intermediates in vivo and therefore have very limited use in reconstructing the in vivo folding pathways. We conclude that computational modeling of protein folding should deemphasize the notion of unassisted thermodynamically controlled folding, and should focus instead on the step-by-step reverse engineering of the folding process as it actually occurs in vivo. REVIEWERS This article was reviewed by Eugene Koonin and Frank Eisenhaber.
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42
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Chen F, Zhao X, Liang W. One- and two-photon absorption spectra of the yellow fluorescent protein citrine: effects of intramolecular electron-vibrational coupling and intermolecular interactions. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1426130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Fasheng Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, China
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Xinyi Zhao
- Department of Science and Technology for Inspection, Xiamen Huaxia University, Xiamen, China
| | - WanZhen Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, China
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
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43
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Freeley M, Worthy HL, Ahmed R, Bowen B, Watkins D, Macdonald JE, Zheng M, Jones DD, Palma M. Site-Specific One-to-One Click Coupling of Single Proteins to Individual Carbon Nanotubes: A Single-Molecule Approach. J Am Chem Soc 2017; 139:17834-17840. [PMID: 29148737 DOI: 10.1021/jacs.7b07362] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report the site-specific coupling of single proteins to individual carbon nanotubes (CNTs) in solution and with single-molecule control. Using an orthogonal Click reaction, Green Fluorescent Protein (GFP) was engineered to contain a genetically encoded azide group and then bound to CNT ends in different configurations: in close proximity or at longer distances from the GFP's functional center. Atomic force microscopy and fluorescence analysis in solution and on surfaces at the single-protein level confirmed the importance of bioengineering optimal protein attachment sites to achieve direct protein-nanotube communication and bridging.
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Affiliation(s)
- Mark Freeley
- School of Biological and Chemical Sciences, Institute of Bioengineering, and Materials Research Institute, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
| | - Harley L Worthy
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University , Cardiff, Wales CF10 3AX, United Kingdom
| | - Rochelle Ahmed
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University , Cardiff, Wales CF10 3AX, United Kingdom
| | - Ben Bowen
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University , Cardiff, Wales CF10 3AX, United Kingdom
| | - Daniel Watkins
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University , Cardiff, Wales CF10 3AX, United Kingdom
| | - J Emyr Macdonald
- School of Physics and Astronomy, Cardiff University , Queens's Building, The Parade, Cardiff CF24 3AA, United Kingdom
| | - Ming Zheng
- Materials Science and Engineering Division, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899-8542, United States
| | - D Dafydd Jones
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University , Cardiff, Wales CF10 3AX, United Kingdom
| | - Matteo Palma
- School of Biological and Chemical Sciences, Institute of Bioengineering, and Materials Research Institute, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
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Liu Y, Liu Y, Wang M. Design, Optimization and Application of Small Molecule Biosensor in Metabolic Engineering. Front Microbiol 2017; 8:2012. [PMID: 29089935 PMCID: PMC5651080 DOI: 10.3389/fmicb.2017.02012] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/29/2017] [Indexed: 11/13/2022] Open
Abstract
The development of synthetic biology and metabolic engineering has painted a great future for the bio-based economy, including fuels, chemicals, and drugs produced from renewable feedstocks. With the rapid advance of genome-scale modeling, pathway assembling and genome engineering/editing, our ability to design and generate microbial cell factories with various phenotype becomes almost limitless. However, our lack of ability to measure and exert precise control over metabolite concentration related phenotypes becomes a bottleneck in metabolic engineering. Genetically encoded small molecule biosensors, which provide the means to couple metabolite concentration to measurable or actionable outputs, are highly promising solutions to the bottleneck. Here we review recent advances in the design, optimization and application of small molecule biosensor in metabolic engineering, with particular focus on optimization strategies for transcription factor (TF) based biosensors.
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Affiliation(s)
- Yang Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ye Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Meng Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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45
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Pakhomov AA, Martynov VI, Orsa AN, Bondarenko AA, Chertkova RV, Lukyanov KA, Petrenko AG, Deyev IE. Fluorescent protein Dendra2 as a ratiometric genetically encoded pH-sensor. Biochem Biophys Res Commun 2017; 493:1518-1521. [PMID: 28986251 DOI: 10.1016/j.bbrc.2017.09.170] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 09/30/2017] [Indexed: 10/18/2022]
Abstract
Fluorescent protein Dendra2 is a monomeric GFP-like protein that belongs to the group of Kaede-like photoconvertible fluorescent proteins with irreversible photoconversion from a green- to red-emitting state when exposed to violet-blue light. In an acidic environment, photoconverted Dendra2 turns green due to protonation of the phenolic group of the chromophore with pKa of about 7.5. Thus, photoconverted form of Dendra2 can be potentially used as a ratiometric pH-sensor in the physiological pH range. However, incomplete photoconversion makes ratiometric measurements irreproducible when using standard filter sets. Here, we describe the method to detect fluorescence of only photoconverted Dendra2 form, but not nonconverted green Dendra2. We show that the 350 nm excitation light induces solely the fluorescence of photoconverted protein. By measuring the red to green fluorescence ratio, we determined intracellular pH in live CHO and HEK 293 cells. Thus, Dendra2 can be used as a novel ratiometric genetically encoded pH sensor with emission maxima in the green-red spectral region, which is suitable for application in live cells.
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Affiliation(s)
- Alexey A Pakhomov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Vladimir I Martynov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexander N Orsa
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alena A Bondarenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Rita V Chertkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexander G Petrenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Igor E Deyev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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46
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Villa JK, Tran HA, Vipani M, Gianturco S, Bhasin K, Russell BL, Harbron EJ, Young DD. Fluorescence Modulation of Green Fluorescent Protein Using Fluorinated Unnatural Amino Acids. Molecules 2017; 22:molecules22071194. [PMID: 28714902 PMCID: PMC5806519 DOI: 10.3390/molecules22071194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 11/28/2022] Open
Abstract
The ability to modulate protein function through minimal perturbations to amino acid structure represents an ideal mechanism to engineer optimized proteins. Due to the novel spectroscopic properties of green fluorescent protein, it has found widespread application as a reporter protein throughout the fields of biology and chemistry. Using site-specific amino acid mutagenesis, we have incorporated various fluorotyrosine residues directly into the fluorophore of the protein, altering the fluorescence and shifting the pKa of the phenolic proton associated with the fluorophore. Relative to wild type GFP, the fluorescence spectrum of the protein is altered with each additional fluorine atom, and the mutant GFPs have the potential to be employed as pH sensors due to the altered electronic properties of the fluorine atoms.
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Affiliation(s)
- Jordan K Villa
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Hong-Anh Tran
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Megha Vipani
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Stephanie Gianturco
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Konark Bhasin
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Brent L Russell
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Elizabeth J Harbron
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Douglas D Young
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
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47
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Molecular evolution of versatile derivatives from a GFP-like protein in the marine copepod Chiridius poppei. PLoS One 2017; 12:e0181186. [PMID: 28700734 PMCID: PMC5507436 DOI: 10.1371/journal.pone.0181186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/26/2017] [Indexed: 12/20/2022] Open
Abstract
Fluorescent proteins are now indispensable tools in molecular research. They have also been adapted for a wide variety of uses in cases involving creative applications, including textiles, aquarium fish, and ornamental plants. Our colleagues have previously cloned a yellow GFP-like protein derived from the marine copepod Chiridius poppei (YGFP), and moreover, succeeded in generating transgenic flowers with clearly visible fluorescence, without the need for high-sensitivity imaging equipment. However, due to the low Stokes shift of YGFP (10 nm), it is difficult to separate emitted light of a labeled object from the light used for excitation; hence, limitations for various applications remain. In this study, which was aimed at developing YGFP mutants with increased Stokes shifts, we conducted stepwise molecular evolution experiments on YGFP by screening random mutations at three key amino acids, based on their fluorescent characteristics and structural stabilities, followed by optimization of their fluorescence output by DNA shuffling of the entire coding sequence. We successfully identified an eYGFPuv that had an excitation maximum in UV wavelengths and a 24-fold increase in fluorescence intensity compared to the previously reported YGFP mutant (H52D). In addition, eYGFPuv exhibited almost 9-fold higher fluorescence intensity compared to the commercially available GFPuv when expressed in human colon carcinoma HCT116 cells and without any differences in cytotoxicity. Thus, this novel mutant with the desirable characteristics of bright fluorescence, long Stokes shift, and low cytotoxity, may be particularly well suited to a variety of molecular and biological applications.
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48
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Liu R, Hu XJ, Ding Y. Rational design of a pH-insensitive cyan fluorescent protein CyPet2 based on the CyPet crystal structure. FEBS Lett 2017; 591:1761-1769. [DOI: 10.1002/1873-3468.12678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/02/2017] [Accepted: 05/09/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Rui Liu
- Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai China
| | - Xiao-Jian Hu
- Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai China
| | - Yu Ding
- Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai China
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49
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Bose S, Chakrabarty S, Ghosh D. Electrostatic Origin of the Red Solvatochromic Shift of DFHBDI in RNA Spinach. J Phys Chem B 2017; 121:4790-4798. [DOI: 10.1021/acs.jpcb.7b02445] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samik Bose
- Physical and Materials
Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Suman Chakrabarty
- Physical and Materials
Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Debashree Ghosh
- Physical and Materials
Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
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50
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Pakhomov AA, Chertkova RV, Deyev IE, Petrenko AG, Martynov VI. Generation of photoactivatable fluorescent protein from photoconvertible ancestor. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s106816201703013x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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