51
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Nienhaus K, Nienhaus GU. Chromophore photophysics and dynamics in fluorescent proteins of the GFP family. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:443001. [PMID: 27604321 DOI: 10.1088/0953-8984/28/44/443001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Proteins of the green fluorescent protein (GFP) family are indispensable for fluorescence imaging experiments in the life sciences, particularly of living specimens. Their essential role as genetically encoded fluorescence markers has motivated many researchers over the last 20 years to further advance and optimize these proteins by using protein engineering. Amino acids can be exchanged by site-specific mutagenesis, starting with naturally occurring proteins as templates. Optical properties of the fluorescent chromophore are strongly tuned by the surrounding protein environment, and a targeted modification of chromophore-protein interactions requires a profound knowledge of the underlying photophysics and photochemistry, which has by now been well established from a large number of structural and spectroscopic experiments and molecular-mechanical and quantum-mechanical computations on many variants of fluorescent proteins. Nevertheless, such rational engineering often does not meet with success and thus is complemented by random mutagenesis and selection based on the optical properties. In this topical review, we present an overview of the key structural and spectroscopic properties of fluorescent proteins. We address protein-chromophore interactions that govern ground state optical properties as well as processes occurring in the electronically excited state. Special emphasis is placed on photoactivation of fluorescent proteins. These light-induced reactions result in large structural changes that drastically alter the fluorescence properties of the protein, which enables some of the most exciting applications, including single particle tracking, pulse chase imaging and super-resolution imaging. We also present a few examples of fluorescent protein application in live-cell imaging experiments.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang Gaede-Straße 1, 76131 Karlsruhe, Germany
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52
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Acharya A, Bogdanov AM, Grigorenko BL, Bravaya KB, Nemukhin AV, Lukyanov KA, Krylov AI. Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing? Chem Rev 2016; 117:758-795. [PMID: 27754659 DOI: 10.1021/acs.chemrev.6b00238] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Photoinduced reactions play an important role in the photocycle of fluorescent proteins from the green fluorescent protein (GFP) family. Among such processes are photoisomerization, photooxidation/photoreduction, breaking and making of covalent bonds, and excited-state proton transfer (ESPT). Many of these transformations are initiated by electron transfer (ET). The quantum yields of these processes vary significantly, from nearly 1 for ESPT to 10-4-10-6 for ET. Importantly, even when quantum yields are relatively small, at the conditions of repeated illumination the overall effect is significant. Depending on the task at hand, fluorescent protein photochemistry is regarded either as an asset facilitating new applications or as a nuisance leading to the loss of optical output. The phenomena arising due to phototransformations include (i) large Stokes shifts, (ii) photoconversions, photoactivation, and photoswitching, (iii) phototoxicity, (iv) blinking, (v) permanent bleaching, and (vi) formation of long-lived intermediates. The focus of this review is on the most recent experimental and theoretical work on photoinduced transformations in fluorescent proteins. We also provide an overview of the photophysics of fluorescent proteins, highlighting the interplay between photochemistry and other channels (fluorescence, radiationless relaxation, and intersystem crossing). The similarities and differences with photochemical processes in other biological systems and in dyes are also discussed.
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Affiliation(s)
- Atanu Acharya
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Ksenia B Bravaya
- Department of Chemistry, Boston University , Boston, Massachusetts United States
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
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53
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Chen F, Zeng Q, Zhuang W, Liang W. Characterizing the Structures, Spectra, and Energy Landscapes Involved in the Excited-State Proton Transfer Process of Red Fluorescent Protein LSSmKate1. J Phys Chem B 2016; 120:9833-42. [PMID: 27581731 DOI: 10.1021/acs.jpcb.6b04708] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
By applying molecular dynamics (MD) simulations and quantum chemical calculations, we have characterized the states and processes involved in the excited-state proton transfer (ESPT) of LSSmKate1. MD simulations identify two stable structures in the electronic ground state of LSSmKate1, one with a protonated chromophore and the other with a deprotonated chromophore, thus leading to two separate low-energy absorption maxima with a large energy spacing, as observed in the calculated and experimentally measured absorption spectra. Proton transfer is induced by electronic excitation. When LSSmKate1 is excited, the electrons in the chromophore are transferred from the phenol ring to the N-acylimine moiety; the acidity of a phenolic hydroxyl group is thus enhanced. The calculated potential energy curves (PECs) exhibit energetic feasibility in the generation of the fluorescent species in LSSmKate1, and the exact agreement between the calculated and experimentally measured values of the large Stokes shift further provides solid theoretical evidence for the ESPT process taking place in photoexcited LSSmKate1. The molecular environments play a significant role in the geometries and absorption/emission energies of the chromophores. Overall, TD-ωB97X-D/molecular mechanics (MM) provides a better description of the optical properties of LSSmKate1 than TD-B3LYP/MM, although it always overestimates the excitation energies.
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Affiliation(s)
- Fasheng Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - Qiao Zeng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences , Fuzhou, Fujian 350002, China
| | - WanZhen Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
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54
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Siriwardana K, Nettles CB, Vithanage BC, Zhou Y, Zou S, Zhang D. On-Resonance Fluorescence, Resonance Rayleigh Scattering, and Ratiometric Resonance Synchronous Spectroscopy of Molecular- and Quantum Dot-Fluorophores. Anal Chem 2016; 88:9199-206. [DOI: 10.1021/acs.analchem.6b02420] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Kumudu Siriwardana
- Department
of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Charles B. Nettles
- Department
of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Buddhini C.N. Vithanage
- Department
of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Yadong Zhou
- Department
of Chemistry, University of Central Florida, Orlando, Florida 32816, United States
| | - Shengli Zou
- Department
of Chemistry, University of Central Florida, Orlando, Florida 32816, United States
| | - Dongmao Zhang
- Department
of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
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55
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Ma C, Yang Y, Li C, Liu Y. The influence of π-conjugation framework on intramolecular proton transfer and Stokes shift in 1,8-Dihydroxydibenzo[a,c]phenazine molecule: a DFT and TD-DFT study. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1986-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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56
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Liu R, Liang QN, Du SQ, Hu XJ, Ding Y. The crystal structure of red fluorescent protein TagRFP-T reveals the mechanism of its superior photostability. Biochem Biophys Res Commun 2016; 477:229-34. [PMID: 27297107 DOI: 10.1016/j.bbrc.2016.06.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 06/09/2016] [Indexed: 10/21/2022]
Abstract
The red fluorescent protein variant TagRFP-T has greatly improved photostability over its parent molecule, TagRFP, but the underlying mechanism leading to this improvement is to date unknown. The 1.95 Å resolution crystallographic structure of TagRFP-T showed that its chromophore exists as a mixture of cis and trans coplanar isomers in roughly equal proportions. Interestingly, both isomers are able to fluoresce, a property that has never been observed in any other fluorescent protein. We propose a "circular restoration model" for TagRFP-T to explain its superior photostability: There are four co-existing chromophore states (cis/trans protonated/ionized state) that can be driven by light to transform from one state into another. This model also explains how TagRPF-T essentially eliminates the temporary dark state (reversible photobleaching).
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Affiliation(s)
- Rui Liu
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qing-Nan Liang
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shu-Qi Du
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiao-Jian Hu
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Yu Ding
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China.
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57
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Karanasios E, Walker SA, Okkenhaug H, Manifava M, Hummel E, Zimmermann H, Ahmed Q, Domart MC, Collinson L, Ktistakis NT. Autophagy initiation by ULK complex assembly on ER tubulovesicular regions marked by ATG9 vesicles. Nat Commun 2016; 7:12420. [PMID: 27510922 PMCID: PMC4987534 DOI: 10.1038/ncomms12420] [Citation(s) in RCA: 213] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 06/30/2016] [Indexed: 12/11/2022] Open
Abstract
Autophagosome formation requires sequential translocation of autophagy-specific proteins to membranes enriched in PI3P and connected to the ER. Preceding this, the earliest autophagy-specific structure forming de novo is a small punctum of the ULK1 complex. The provenance of this structure and its mode of formation are unknown. We show that the ULK1 structure emerges from regions, where ATG9 vesicles align with the ER and its formation requires ER exit and coatomer function. Super-resolution microscopy reveals that the ULK1 compartment consists of regularly assembled punctate elements that cluster in progressively larger spherical structures and associates uniquely with the early autophagy machinery. Correlative electron microscopy after live imaging shows tubulovesicular membranes present at the locus of this structure. We propose that the nucleation of autophagosomes occurs in regions, where the ULK1 complex coalesces with ER and the ATG9 compartment.
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Affiliation(s)
| | - Simon A. Walker
- Signalling Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Hanneke Okkenhaug
- Signalling Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Maria Manifava
- Signalling Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Eric Hummel
- Carl Zeiss Microscopy GmbH, Munich 81379, Germany
| | | | - Qashif Ahmed
- Signalling Programme, The Babraham Institute, Cambridge CB22 3AT, UK
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58
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Neena KK, Thilagar P. Conformational Restrictions in meso
-(2-Thiazolyl)-BODIPYs: Large Stokes Shift and pH-Dependent Optical Properties. Chempluschem 2016; 81:955-963. [DOI: 10.1002/cplu.201600254] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/21/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Kalluvettukuzhy K. Neena
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
| | - Pakkirisamy Thilagar
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
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59
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Paredes JM, Idilli AI, Mariotti L, Losi G, Arslanbaeva LR, Sato SS, Artoni P, Szczurkowska J, Cancedda L, Ratto GM, Carmignoto G, Arosio D. Synchronous Bioimaging of Intracellular pH and Chloride Based on LSS Fluorescent Protein. ACS Chem Biol 2016; 11:1652-60. [PMID: 27031242 DOI: 10.1021/acschembio.6b00103] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Ion homeostasis regulates critical physiological processes in the living cell. Intracellular chloride concentration not only contributes in setting the membrane potential of quiescent cells but it also plays a role in modulating the dynamic voltage changes during network activity. Dynamic chloride imaging demands new tools, allowing faster acquisition rates and correct accounting of concomitant pH changes. Joining a long-Stokes-shift red-fluorescent protein to a GFP variant with high sensitivity to pH and chloride, we obtained LSSmClopHensor, a genetically encoded fluorescent biosensor optimized for the simultaneous chloride and pH imaging and requiring only two excitation wavelengths (458 and 488 nm). LSSmClopHensor allowed us to monitor the dynamic changes of intracellular pH and chloride concentration during seizure like discharges in neocortical brain slices. Only cells with tightly controlled resting potential revealed a narrow distribution of chloride concentration peaking at about 5 and 8 mM, in neocortical neurons and SK-N-SH cells, respectively. We thus showed that LSSmClopHensor represents a new versatile tool for studying the dynamics of chloride and proton concentration in living systems.
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Affiliation(s)
- Jose M. Paredes
- Institute of Biophysics, CNR, Via
alla Cascata 56/C, 38123 Trento, Italy
- Bruno Kessler Foundation, Via
Sommarive 18, 38123 Trento, Italy
| | - Aurora I. Idilli
- Institute of Biophysics, CNR, Via
alla Cascata 56/C, 38123 Trento, Italy
| | - Letizia Mariotti
- Neuroscience Institute, CNR, Viale
G. Colombo 3, 35121 Padova, Italy
| | - Gabriele Losi
- Neuroscience Institute, CNR, Viale
G. Colombo 3, 35121 Padova, Italy
| | - Lyaysan R. Arslanbaeva
- Institute of Biophysics, CNR, Via
alla Cascata 56/C, 38123 Trento, Italy
- CIBIO, University of Trento, Via delle Regole 101, 38123 Trento, Italy
| | | | | | | | | | - Gian Michele Ratto
- Nanoscience Institute, CNR, Pisa, Italy
- Scuola Normale Superiore, Pisa, Italy
| | | | - Daniele Arosio
- Institute of Biophysics, CNR, Via
alla Cascata 56/C, 38123 Trento, Italy
- CIBIO, University of Trento, Via delle Regole 101, 38123 Trento, Italy
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60
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Chen JL, Voigt FF, Javadzadeh M, Krueppel R, Helmchen F. Long-range population dynamics of anatomically defined neocortical networks. eLife 2016; 5:e14679. [PMID: 27218452 PMCID: PMC4929001 DOI: 10.7554/elife.14679] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/21/2016] [Indexed: 12/12/2022] Open
Abstract
The coordination of activity across neocortical areas is essential for mammalian brain function. Understanding this process requires simultaneous functional measurements across the cortex. In order to dissociate direct cortico-cortical interactions from other sources of neuronal correlations, it is furthermore desirable to target cross-areal recordings to neuronal subpopulations that anatomically project between areas. Here, we combined anatomical tracers with a novel multi-area two-photon microscope to perform simultaneous calcium imaging across mouse primary (S1) and secondary (S2) somatosensory whisker cortex during texture discrimination behavior, specifically identifying feedforward and feedback neurons. We find that coordination of S1-S2 activity increases during motor behaviors such as goal-directed whisking and licking. This effect was not specific to identified feedforward and feedback neurons. However, these mutually projecting neurons especially participated in inter-areal coordination when motor behavior was paired with whisker-texture touches, suggesting that direct S1-S2 interactions are sensory-dependent. Our results demonstrate specific functional coordination of anatomically-identified projection neurons across sensory cortices.
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Affiliation(s)
- Jerry L Chen
- Brain Research Institute, University of Zurich, Zurich, Switzerland
| | - Fabian F Voigt
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, ETH Zurich, Zurich, Switzerland
| | - Mitra Javadzadeh
- Brain Research Institute, University of Zurich, Zurich, Switzerland
| | - Roland Krueppel
- Brain Research Institute, University of Zurich, Zurich, Switzerland
| | - Fritjof Helmchen
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, ETH Zurich, Zurich, Switzerland
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61
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Popov-Čeleketić D, Bianchi F, Ruiz SJ, Meutiawati F, Poolman B. A Plasma Membrane Association Module in Yeast Amino Acid Transporters. J Biol Chem 2016; 291:16024-37. [PMID: 27226538 DOI: 10.1074/jbc.m115.706770] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Indexed: 12/22/2022] Open
Abstract
Amino acid permeases (AAPs) in the plasma membrane (PM) of Saccharomyces cerevisiae are responsible for the uptake of amino acids and involved in regulation of their cellular levels. Here, we report on a strong and complex module for PM association found in the C-terminal tail of AAPs. Using in silico analyses and mutational studies we found that the C-terminal sequences of Gap1, Bap2, Hip1, Tat1, Tat2, Mmp1, Sam3, Agp1, and Gnp1 are about 50 residues long, associate with the PM, and have features that discriminate them from the termini of organellar amino acid transporters. We show that this sequence (named PMasseq) contains an amphipathic α-helix and the FWC signature, which is palmitoylated by palmitoyltransferase Pfa4. Variations of PMasseq, found in different AAPs, lead to different mobilities and localization patterns, whereas the disruption of the sequence has an adverse effect on cell viability. We propose that PMasseq modulates the function and localization of AAPs along the PM. PMasseq is one of the most complex protein signals for plasma membrane association across species and can be used as a delivery vehicle for the PM.
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Affiliation(s)
- Dušan Popov-Čeleketić
- From the Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Frans Bianchi
- From the Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Stephanie J Ruiz
- From the Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Febrina Meutiawati
- From the Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Bert Poolman
- From the Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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62
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Currier MG, Lee S, Stobart CC, Hotard AL, Villenave R, Meng J, Pretto CD, Shields MD, Nguyen MT, Todd SO, Chi MH, Hammonds J, Krumm SA, Spearman P, Plemper RK, Sakamoto K, Peebles RS, Power UF, Moore ML. EGFR Interacts with the Fusion Protein of Respiratory Syncytial Virus Strain 2-20 and Mediates Infection and Mucin Expression. PLoS Pathog 2016; 12:e1005622. [PMID: 27152417 PMCID: PMC4859522 DOI: 10.1371/journal.ppat.1005622] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 04/19/2016] [Indexed: 11/19/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the major cause of viral lower respiratory tract illness in children. In contrast to the RSV prototypic strain A2, clinical isolate RSV 2–20 induces airway mucin expression in mice, a clinically relevant phenotype dependent on the fusion (F) protein of the RSV strain. Epidermal growth factor receptor (EGFR) plays a role in airway mucin expression in other systems; therefore, we hypothesized that the RSV 2–20 F protein stimulates EGFR signaling. Infection of cells with chimeric strains RSV A2-2-20F and A2-2-20GF or over-expression of 2–20 F protein resulted in greater phosphorylation of EGFR than infection with RSV A2 or over-expression of A2 F, respectively. Chemical inhibition of EGFR signaling or knockdown of EGFR resulted in diminished infectivity of RSV A2-2-20F but not RSV A2. Over-expression of EGFR enhanced the fusion activity of 2–20 F protein in trans. EGFR co-immunoprecipitated most efficiently with RSV F proteins derived from “mucogenic” strains. RSV 2–20 F and EGFR co-localized in H292 cells, and A2-2-20GF-induced MUC5AC expression was ablated by EGFR inhibitors in these cells. Treatment of BALB/c mice with the EGFR inhibitor erlotinib significantly reduced the amount of RSV A2-2-20F-induced airway mucin expression. Our results demonstrate that RSV F interacts with EGFR in a strain-specific manner, EGFR is a co-factor for infection, and EGFR plays a role in RSV-induced mucin expression, suggesting EGFR is a potential target for RSV disease. Respiratory syncytial virus (RSV) is responsible for severe lower respiratory disease in infants and young children. Overabundant airway mucus contributes to airway obstruction in RSV bronchiolitis, and a better understanding of RSV pathogenesis may contribute to needed therapies and vaccines. We reported previously that RSV clinical isolate strain 2–20 induces more airway mucin expression in mice than prototypic RSV strains and that the 2–20 fusion (F) protein mediates mucin induction. Epidermal growth factor receptor (EGFR) has been shown to play a role in lung mucin expression. We identified a functional interaction between 2–20 F and EGFR, in that 2–20 F expression activated EGFR and, reciprocally, EGFR expression increased 2–20 F fusion activity. RSV F and EGFR co-localized in infected cells. EGFR co-immunoprecipitated with RSV F protein from various RSV strains, and the strength of this in vitro interaction correlated with strain-specific airway pathogenicity in mice. EGFR inhibition abrogated 2–20 F-mediated infection in vitro and mucin expression induction in vivo. These data identify EGFR as a novel strain-specific co-factor of RSV infection and suggest EGFR may be a target for ameliorating RSV disease.
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Affiliation(s)
- Michael G. Currier
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
| | - Sujin Lee
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
| | - Christopher C. Stobart
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
| | - Anne L. Hotard
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
| | - Remi Villenave
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, Northern Ireland
| | - Jia Meng
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
| | - Carla D. Pretto
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
| | - Michael D. Shields
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, Northern Ireland
- The Royal Belfast Hospital for Sick Children, Belfast, Northern Ireland
| | - Minh Trang Nguyen
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
| | - Sean O. Todd
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
| | - Michael H. Chi
- Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Jason Hammonds
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
| | - Stefanie A. Krumm
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, United States of America
| | - Paul Spearman
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
| | - Richard K. Plemper
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, United States of America
| | - Kaori Sakamoto
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - R. Stokes Peebles
- Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Ultan F. Power
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, Northern Ireland
| | - Martin L. Moore
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
- * E-mail:
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63
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Zhou S, Zhao Z, Lin Y, Gong S, Li F, Pan J, Li X, Gao Z, Zhao AZ. Suppression of pancreatic ductal adenocarcinoma growth by intratumoral delivery of attenuated Salmonella typhimurium using a dual fluorescent live tracking system. Cancer Biol Ther 2016; 17:732-40. [PMID: 27089121 PMCID: PMC4970537 DOI: 10.1080/15384047.2016.1177683] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has the poorest prognosis among all malignancies and is resistant to almost all current therapies. Attenuated Salmonella typhimurium strain VNP20009 has been deployed as powerful anticancer agent in a variety of animal cancer models, and previous phase 1 clinical trials have proven its safety profiles. However, thus far, little is known about its effect on PDAC. Here, we established CFPAC-1 cell lines expressing an mKate2 protein and thus emitting far-red fluorescence in the subsequent xenograft implant. VNP20009 strain was further engineered to carry a luciferase cDNA, which catalyzes the light-emitting reaction to allow the observation of salmonella distribution and accumulation within tumor with live imaging. Using such VNP20009 strain and intratumoral delivery, we could reduce the growth of pancreatic cancer by inducing apoptosis and severe necrosis in a dosage dependent manner. Consistent with this finding, intratumoral delivery of VNP20009 also increase caspase-3 activity and the expression of Bax protein. In summary, we revealed that VNP20009 is a promising bacterial agent for the treatment of PDAC, and that we have established a dual fluorescent imaging system as a valuable tool for noninvasive live imaging of solid tumor and engineered bacterial drug.
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Affiliation(s)
- Sujin Zhou
- a Collaborative Innovation Center for Cancer Medicine, The Center of Metabolic Disease Research, Nanjing Medical University , Nanjing , Jiangsu Province , China
| | - Zhenggang Zhao
- a Collaborative Innovation Center for Cancer Medicine, The Center of Metabolic Disease Research, Nanjing Medical University , Nanjing , Jiangsu Province , China
| | - Yan Lin
- a Collaborative Innovation Center for Cancer Medicine, The Center of Metabolic Disease Research, Nanjing Medical University , Nanjing , Jiangsu Province , China
| | - Sijia Gong
- a Collaborative Innovation Center for Cancer Medicine, The Center of Metabolic Disease Research, Nanjing Medical University , Nanjing , Jiangsu Province , China
| | - Fanghong Li
- a Collaborative Innovation Center for Cancer Medicine, The Center of Metabolic Disease Research, Nanjing Medical University , Nanjing , Jiangsu Province , China
| | - Jinshun Pan
- a Collaborative Innovation Center for Cancer Medicine, The Center of Metabolic Disease Research, Nanjing Medical University , Nanjing , Jiangsu Province , China
| | - Xiaoxi Li
- a Collaborative Innovation Center for Cancer Medicine, The Center of Metabolic Disease Research, Nanjing Medical University , Nanjing , Jiangsu Province , China
| | - Zhuo Gao
- b Department of Clinical Laboratory , The Fourth Affiliated Hospital of Harbin Medical University , Harbin , Heilongjiang , China
| | - Allan Z Zhao
- a Collaborative Innovation Center for Cancer Medicine, The Center of Metabolic Disease Research, Nanjing Medical University , Nanjing , Jiangsu Province , China
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Barr AR, Heldt FS, Zhang T, Bakal C, Novák B. A Dynamical Framework for the All-or-None G1/S Transition. Cell Syst 2016; 2:27-37. [PMID: 27136687 PMCID: PMC4802413 DOI: 10.1016/j.cels.2016.01.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 11/09/2015] [Accepted: 01/04/2016] [Indexed: 01/24/2023]
Abstract
The transition from G1 into DNA replication (S phase) is an emergent behavior resulting from dynamic and complex interactions between cyclin-dependent kinases (Cdks), Cdk inhibitors (CKIs), and the anaphase-promoting complex/cyclosome (APC/C). Understanding the cellular decision to commit to S phase requires a quantitative description of these interactions. We apply quantitative imaging of single human cells to track the expression of G1/S regulators and use these data to parametrize a stochastic mathematical model of the G1/S transition. We show that a rapid, proteolytic, double-negative feedback loop between Cdk2:Cyclin and the Cdk inhibitor p27(Kip1) drives a switch-like entry into S phase. Furthermore, our model predicts that increasing Emi1 levels throughout S phase are critical in maintaining irreversibility of the G1/S transition, which we validate using Emi1 knockdown and live imaging of G1/S reporters. This work provides insight into the general design principles of the signaling networks governing the temporally abrupt transitions between cell-cycle phases.
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Affiliation(s)
- Alexis R Barr
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Frank S Heldt
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Tongli Zhang
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Chris Bakal
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
| | - Béla Novák
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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Abstract
The field of fluorescent proteins (FPs) is constantly developing. The use of FPs changed the field of life sciences completely, starting a new era of direct observation and quantification of cellular processes. The broad spectrum of FPs (see Fig. 1) with a wide range of characteristics allows their use in many different experiments. This review discusses the use of FPs for imaging in budding yeast (Saccharomyces cerevisiae) and fission yeast Schizosaccharomyces pombe). The information included in this review is relevant for both species unless stated otherwise.
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Affiliation(s)
- Maja Bialecka-Fornal
- Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA
| | - Tatyana Makushok
- Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, San Francisco, CA, 94158, USA
| | - Susanne M Rafelski
- Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA.
- Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA.
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66
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Randino C, Gelabert R, Moreno M, Lluch JM, Piatkevich KD. Molecular modelling of the pH influence in the geometry and the absorbance spectrum of near-infrared TagRFP675 fluorescent protein. Phys Chem Chem Phys 2015; 17:29363-73. [PMID: 26473582 DOI: 10.1039/c5cp04428f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Classical molecular dynamics (MD) simulations are carried out for the recently developed TagRFP675 fluorescent protein (FP), which is specifically designed to fully absorb and emit in the near infrared (NIR) region of the electromagnetic spectrum. Since the X-ray data of TagRFP675 reveal that the chromophore exists in both the cis and trans configuration and it can also be neutral (protonated) or anionic (deprotonated) depending on the pH of the media, a total of 8 molecular dynamic simulations have been run to simulate all the possible states of the chromophore. Time-dependent DFT (TDDFT) single point calculations are performed at selected points along the simulation to theoretically mimic the absorption spectrum of the protein. Our simulations compare well (within the expected error of the computational method) with the experimental results. Our theoretical procedure allows for an analysis of the molecular orbitals involved in the lowest energy electronic excitations of the chromophore and, more interestingly, for a full analysis of the H-bond interactions between the chromophore and its surrounding residues and solvent (water) molecules. This study does not support the hypothesis, exclusively based on the analysis of X-ray data, that the isomerization of nearby residues provokes the rearrangement of the hydrogen bonds in the chromophore's immediate environment leading to the observed red shift of the absorption bands at higher pHs. Instead, we attribute this shift mainly to the superposition of bands of the neutral and anionic chromophores that are expected to coexist at almost the full range of pHs experimentally analyzed. An additional factor that could contribute to this shift is the experimentally observed increase of the cis configuration of the chromophore at higher pHs.
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Affiliation(s)
- Carlos Randino
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Ricard Gelabert
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Miquel Moreno
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - José M Lluch
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain. and Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Kiryl D Piatkevich
- Departments of Biological Engineering and Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Fron E, De Keersmaecker H, Rocha S, Baeten Y, Lu G, Uji-i H, Van der Auweraer M, Hofkens J, Mizuno H. Mechanism Behind the Apparent Large Stokes Shift in LSSmOrange Investigated by Time-Resolved Spectroscopy. J Phys Chem B 2015; 119:14880-91. [PMID: 26529379 DOI: 10.1021/acs.jpcb.5b09189] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
LSSmOrange is a fluorescent protein with a large energy gap between the absorption and emission bands (5275 cm(-1)). The electronic structure of the LSSmOrange chromophore, 2-[(5-)-2-hydroxy-dihydrooxazole]-4-(p-hydroxybenzylidene)-5-imidazolinone, is affected by deprotonation of the p-hydroxybenzylidene group. We investigated LSSmOrange by time-resolved spectroscopy in the femtosecond and nanosecond range. The ground state chromophore was almost exclusively in the neutral form, which had a main absorption band at 437 nm with a small shoulder at 475 nm. The absorption at a wavelength within the former band promoted the protein to the excited state where excited state proton transfer (ESPT) could lead to deprotonation in 0.8 ps. Following ESPT, the chromophore emitted fluorescence with a maximum at 573 nm and a decay time of 3500 ps. Although deprotonation by ESPT occurs, we unexpectedly found a slow accumulation of the anionic form in the ground state upon repeated high intensity excitation. This accumulation of the anionic form was accompanied by a shift of the absorption band to 553 nm without changing the emission band. MALDI-MS revealed that this shift is accompanied by decarboxylation of E222, which is interacting with the imidazolinone ring of the chromophore. We concluded that the photoinduced decarboxylation induced a conformational change that affected local environment around the hydroxyl group, resulting in a stable deprotonated form of the chromophore.
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Affiliation(s)
- Eduard Fron
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven , Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Herlinde De Keersmaecker
- Laboratory of Biomolecular Network Dynamics, Biochemistry, Molecular and Structural Biology Section, Department of Chemistry, KU Leuven , Celestijnenlaan 200G, bus 2403, 3001 Heverlee, Belgium
| | - Susana Rocha
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven , Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Yannick Baeten
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven , Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Gang Lu
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven , Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Hiroshi Uji-i
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven , Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Mark Van der Auweraer
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven , Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Johan Hofkens
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven , Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Hideaki Mizuno
- Laboratory of Biomolecular Network Dynamics, Biochemistry, Molecular and Structural Biology Section, Department of Chemistry, KU Leuven , Celestijnenlaan 200G, bus 2403, 3001 Heverlee, Belgium
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68
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Faraji S, Krylov AI. On the Nature of an Extended Stokes Shift in the mPlum Fluorescent Protein. J Phys Chem B 2015; 119:13052-62. [PMID: 26402581 DOI: 10.1021/acs.jpcb.5b07724] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Far-red fluorescent proteins (FPs) enable deep-tissue in vivo imaging. Combining FPs with large and small Stokes shifts enables single-excitation/dual-emission multicolor applications. Using a quantum mechanics/molecular mechanics (QM/MM) scheme, we carried out a series of simulations to identify the origin of an extended Stokes shift (0.2 eV) observed in mPlum, one of the most far-red-shifted FPs. We demonstrated that the red shift of emission is largely due to the excited-state relaxation of the chromophore itself. Rigid protein environment suppresses the relaxation; however, if the hydrogen-bond network around the chromophore is sufficiently flexible, it can rearrange upon electronic excitation, allowing the chromophore to relax. The reorganization of the hydrogen-bond network is driven by changes in bonding and charge distributions of the chromophore in the excited state. The ILE65 and GLU16 residues play the most important role. The MD simulations reveal two ground-state populations with the direct (Chro-ILE65···GLU16) and water-mediated (Chro-ILE65···Wat321···GLU16) hydrogen-bond patterns. In the excited state, both populations relax to a single emitting state with the water-mediated (Chro-ILE65···Wat321···GLU16) hydrogen-bond pattern, which provides a better match for the excited-state charge distribution (the acylimine's oxygen has a larger negative charge in S1 than in S0). The extended Stokes shift arises due to the conversion of the direct hydrogen-bond pattern to the water-mediated one accompanied by large structural relaxation of the electronically excited chromophore. This conclusion is supported by calculations for the GLU16LEU mutant, which has only one hydrogen-bond pattern. Consequently, no interconversion is possible, and the computed Stokes shift is small, in agreement with the experiment. Our theoretical findings provide support to a recent study of the Stokes shifts in mPlum and its mutants.
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Affiliation(s)
- Shirin Faraji
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
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69
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Shen Y, Lai T, Campbell RE. Red fluorescent proteins (RFPs) and RFP-based biosensors for neuronal imaging applications. NEUROPHOTONICS 2015; 2:031203. [PMID: 26158012 PMCID: PMC4478792 DOI: 10.1117/1.nph.2.3.031203] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 05/19/2015] [Indexed: 05/23/2023]
Abstract
The inherent advantages of red-shifted fluorescent proteins and fluorescent protein-based biosensors for the study of signaling processes in neurons and other tissues have motivated the development of a plethora of new tools. Relative to green fluorescent proteins (GFPs) and other blue-shifted alternatives, red fluorescent proteins (RFPs) provide the inherent advantages of lower phototoxicity, lower autofluorescence, and deeper tissue penetration associated with longer wavelength excitation light. All other factors being the same, the multiple benefits of using RFPs make these tools seemingly ideal candidates for use in neurons and, ultimately, the brain. However, for many applications, the practical utility of RFPs still falls short of the preferred GFPs. We present an overview of RFPs and RFP-based biosensors, with an emphasis on their reported applications in neuroscience.
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Affiliation(s)
- Yi Shen
- University of Alberta, Department of Chemistry, Edmonton, Alberta T6G 2G2, Canada
| | - Tiffany Lai
- University of Alberta, Department of Chemistry, Edmonton, Alberta T6G 2G2, Canada
| | - Robert E. Campbell
- University of Alberta, Department of Chemistry, Edmonton, Alberta T6G 2G2, Canada
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70
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Guan Y, Meurer M, Raghavan S, Rebane A, Lindquist JR, Santos S, Kats I, Davidson MW, Mazitschek R, Hughes TE, Drobizhev M, Knop M, Shah JV. Live-cell multiphoton fluorescence correlation spectroscopy with an improved large Stokes shift fluorescent protein. Mol Biol Cell 2015; 26:2054-66. [PMID: 25877871 PMCID: PMC4472016 DOI: 10.1091/mbc.e14-10-1473] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 04/03/2015] [Accepted: 04/07/2015] [Indexed: 11/11/2022] Open
Abstract
We report an improved variant of mKeima, a monomeric long Stokes shift red fluorescent protein, hmKeima8.5. The increased intracellular brightness and large Stokes shift (∼180 nm) make it an excellent partner with teal fluorescent protein (mTFP1) for multiphoton, multicolor applications. Excitation of this pair by a single multiphoton excitation wavelength (MPE, 850 nm) yields well-separable emission peaks (∼120-nm separation). Using this pair, we measure homo- and hetero-oligomerization interactions in living cells via multiphoton excitation fluorescence correlation spectroscopy (MPE-FCS). Using tandem dimer proteins and small-molecule inducible dimerization domains, we demonstrate robust and quantitative detection of intracellular protein-protein interactions. We also use MPE-FCCS to detect drug-protein interactions in the intracellular environment using a Coumarin 343 (C343)-conjugated drug and hmKeima8.5 as a fluorescence pair. The mTFP1/hmKeima8.5 and C343/hmKeima8.5 combinations, together with our calibration constructs, provide a practical and broadly applicable toolbox for the investigation of molecular interactions in the cytoplasm of living cells.
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Affiliation(s)
- Yinghua Guan
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115 Renal Division, Brigham and Women's Hospital, Boston, MA 02115
| | - Matthias Meurer
- Zentrum für Molekulare Biologie der Universität Heidelberg and Deutsches Krebsforschungszentrum, DKFZ-ZMBH-Allianz, 69120 Heidelberg, Germany
| | - Sarada Raghavan
- Zentrum für Molekulare Biologie der Universität Heidelberg and Deutsches Krebsforschungszentrum, DKFZ-ZMBH-Allianz, 69120 Heidelberg, Germany
| | | | - Jake R Lindquist
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717
| | - Sofia Santos
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114 Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisbon 1640-003, Portugal
| | - Ilia Kats
- Zentrum für Molekulare Biologie der Universität Heidelberg and Deutsches Krebsforschungszentrum, DKFZ-ZMBH-Allianz, 69120 Heidelberg, Germany
| | - Michael W Davidson
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114 Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | - Thomas E Hughes
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717
| | | | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg and Deutsches Krebsforschungszentrum, DKFZ-ZMBH-Allianz, 69120 Heidelberg, Germany
| | - Jagesh V Shah
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115 Renal Division, Brigham and Women's Hospital, Boston, MA 02115
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71
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Sladitschek HL, Neveu PA. MXS-Chaining: A Highly Efficient Cloning Platform for Imaging and Flow Cytometry Approaches in Mammalian Systems. PLoS One 2015; 10:e0124958. [PMID: 25909630 PMCID: PMC4409215 DOI: 10.1371/journal.pone.0124958] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/19/2015] [Indexed: 11/25/2022] Open
Abstract
The continuous improvement of imaging technologies has driven the development of sophisticated reporters to monitor biological processes. Such constructs should ideally be assembled in a flexible enough way to allow for their optimization. Here we describe a highly reliable cloning method to efficiently assemble constructs for imaging or flow cytometry applications in mammalian cell culture systems. We bioinformatically identified a list of restriction enzymes whose sites are rarely found in human and mouse cDNA libraries. From the best candidates, we chose an enzyme combination (MluI, XhoI and SalI: MXS) that enables iterative chaining of individual building blocks. The ligation scar resulting from the compatible XhoI- and SalI-sticky ends can be translated and hence enables easy in-frame cloning of coding sequences. The robustness of the MXS-chaining approach was validated by assembling constructs up to 20 kb long and comprising up to 34 individual building blocks. By assessing the success rate of 400 ligation reactions, we determined cloning efficiency to be 90% on average. Large polycistronic constructs for single-cell imaging or flow cytometry applications were generated to demonstrate the versatility of the MXS-chaining approach. We devised several constructs that fluorescently label subcellular structures, an adapted version of FUCCI (fluorescent, ubiquitination-based cell cycle indicator) optimized to visualize cell cycle progression in mouse embryonic stem cells and an array of artificial promoters enabling dosage of doxycyline-inducible transgene expression. We made publicly available through the Addgene repository a comprehensive set of MXS-building blocks comprising custom vectors, a set of fluorescent proteins, constitutive promoters, polyadenylation signals, selection cassettes and tools for inducible gene expression. Finally, detailed guidelines describe how to chain together prebuilt MXS-building blocks and how to generate new customized MXS-building blocks.
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Affiliation(s)
- Hanna L. Sladitschek
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg, Germany
| | - Pierre A. Neveu
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg, Germany
- * E-mail:
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72
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D'Angelis do E. S. Barbosa C, Corrêa JR, Medeiros GA, Barreto G, Magalhães KG, de Oliveira AL, Spencer J, Rodrigues MO, Neto BAD. Carbon Dots (C-dots) from Cow Manure with Impressive Subcellular Selectivity Tuned by Simple Chemical Modification. Chemistry 2015; 21:5055-60. [DOI: 10.1002/chem.201406330] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Indexed: 11/11/2022]
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73
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Zhang GR, Zhao H, Abdul-Muneer PM, Cao H, Li X, Geller AI. Neurons can be labeled with unique hues by helper virus-free HSV-1 vectors expressing Brainbow. J Neurosci Methods 2015; 240:77-88. [PMID: 25448383 PMCID: PMC4670084 DOI: 10.1016/j.jneumeth.2014.11.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 11/11/2014] [Accepted: 11/12/2014] [Indexed: 12/30/2022]
Abstract
BACKGROUND A central problem in neuroscience is elucidating synaptic connections, the connectome. Because mammalian forebrains contain many neurons, labeling specific neurons with unique tags is desirable. A novel technology, Brainbow, creates hundreds of hues by combinatorial expression of multiple fluorescent proteins (FPs). NEW METHOD We labeled small numbers of neurons, and their axons, with unique hues, by expressing Brainbow from a helper virus-free Herpes Simplex Virus (HSV-1) vector. RESULTS The vector expresses a Brainbow cassette containing four FPs from a glutamatergic-specific promoter. Packaging HSV-Brainbow produced arrays of seven to eight Brainbow cassettes, and using Cre, each FP gene was in a position to be expressed, in different cassettes. Delivery into rat postrhinal (POR) cortex or hippocampus labeled small numbers of neurons with different, often unique, hues. An area innervated by POR cortex, perirhinal (PER) cortex, contained axons with different hues. Specific axons in PER cortex were matched to specific cell bodies in POR cortex, using hue. COMPARISON WITH EXISTING METHODS HSV-Brainbow is the only technology for labeling small numbers of neurons with unique hues. In Brainbow mice, many neurons contain the same hue. Brainbow-adeno-associated virus vectors require transduction of the same neuron with multiple vector particles, confounding neuroanatomical studies. Replication-competent Brainbow-pseudorabies virus vectors label multiple neurons with the same hue. CONCLUSIONS Attractive properties of HSV-Brainbow include each vector particle contains multiple cassettes, representing numerous hues, recombination products are stabile, and experimental control of the number of labeled neurons. Labeling neurons with unique hues will benefit mapping forebrain circuits.
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Affiliation(s)
- Guo-Rong Zhang
- New Jersey Neuroscience Institute, JFK Medical Center, Edison, NJ 08818, USA
| | - Hua Zhao
- New Jersey Neuroscience Institute, JFK Medical Center, Edison, NJ 08818, USA
| | - P M Abdul-Muneer
- New Jersey Neuroscience Institute, JFK Medical Center, Edison, NJ 08818, USA
| | - Haiyan Cao
- New Jersey Neuroscience Institute, JFK Medical Center, Edison, NJ 08818, USA
| | - Xu Li
- New Jersey Neuroscience Institute, JFK Medical Center, Edison, NJ 08818, USA
| | - Alfred I Geller
- New Jersey Neuroscience Institute, JFK Medical Center, Edison, NJ 08818, USA.
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Albrecht T, Zhao Y, Nguyen TH, Campbell RE, Johnson JD. Fluorescent biosensors illuminate calcium levels within defined beta-cell endosome subpopulations. Cell Calcium 2015; 57:263-74. [PMID: 25682167 DOI: 10.1016/j.ceca.2015.01.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 12/26/2014] [Accepted: 01/19/2015] [Indexed: 11/18/2022]
Abstract
Live cell imaging has revealed that calcium ions (Ca(2+)) pass in and out of many cellular organelles. However, technical hurdles have limited measurements of Ca(2+) in acidic organelles, such as endosomes. Although evidence hints that endosomes play a role in Ca(2+) signaling, direct measurements within endosomal lumina represent one of the final frontiers in organelle imaging. To measure Ca(2+) in a TiVAMP-positive endosome sub-population, the pH-resistant ratiometric Ca(2+) biosensor GEM-GECO1 and the ratiometric pH biosensor mKeima were used. A positive correlation between acidic endosomal pH and higher Ca(2+) was observed within these Rab5a- and Rab7-positive compartments. Ca(2+) concentration in most endosomes was estimated to be below 2μM, lower than Ca(2+) levels in several other intracellular stores, indicating that endosomes may take up Ca(2+) during physiological stimulation. Indeed, endosomes accumulated Ca(2+) during glucose-stimulation, a condition where endosomal pH did not change. Our biosensors permitted the first measurements revealing a role for endosomes in cellular Ca(2+) homeostasis during physiological stimulation.
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Affiliation(s)
- Tobias Albrecht
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Yongxin Zhao
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Trang Hai Nguyen
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - James D Johnson
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada.
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75
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Wu J, Abdelfattah AS, Miraucourt LS, Kutsarova E, Ruangkittisakul A, Zhou H, Ballanyi K, Wicks G, Drobizhev M, Rebane A, Ruthazer ES, Campbell RE. A long Stokes shift red fluorescent Ca2+ indicator protein for two-photon and ratiometric imaging. Nat Commun 2014; 5:5262. [PMID: 25358432 PMCID: PMC4920544 DOI: 10.1038/ncomms6262] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 09/12/2014] [Indexed: 11/09/2022] Open
Abstract
The introduction of calcium ion (Ca(2+)) indicators based on red fluorescent proteins (RFPs) has created new opportunities for multicolour visualization of intracellular Ca(2+) dynamics. However, one drawback of these indicators is that they have optimal two-photon excitation outside the near-infrared window (650-1,000 nm) where tissue is most transparent to light. To address this shortcoming, we developed a long Stokes shift RFP-based Ca(2+) indicator, REX-GECO1, with optimal two-photon excitation at <1,000 nm. REX-GECO1 fluoresces at 585 nm when excited at 480 nm or 910 nm by a one- or two-photon process, respectively. We demonstrate that REX-GECO1 can be used as either a ratiometric or intensiometric Ca(2+) indicator in organotypic hippocampal slice cultures (one- and two-photon) and the visual system of albino tadpoles (two-photon). Furthermore, we demonstrate single excitation wavelength two-colour Ca(2+) and glutamate imaging in organotypic cultures.
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Affiliation(s)
- Jiahui Wu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Ahmed S Abdelfattah
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Loïs S Miraucourt
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, Neuroengineering Program, McGill University, Montreal, Quebec, Canada H3A 2B4
| | - Elena Kutsarova
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, Neuroengineering Program, McGill University, Montreal, Quebec, Canada H3A 2B4
| | | | - Hang Zhou
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Klaus Ballanyi
- Department of Physiology, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Geoffrey Wicks
- Department of Physics, Montana State University, Bozeman, Montana 59717, USA
| | - Mikhail Drobizhev
- Department of Physics, Montana State University, Bozeman, Montana 59717, USA
| | - Aleksander Rebane
- 1] Department of Physics, Montana State University, Bozeman, Montana 59717, USA [2] National Institute of Chemical Physics and Biophysics, Tallinn, Estonia 12618
| | - Edward S Ruthazer
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, Neuroengineering Program, McGill University, Montreal, Quebec, Canada H3A 2B4
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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76
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Piatkevich KD, English BP, Malashkevich VN, Xiao H, Almo SC, Singer RH, Verkhusha VV. Photoswitchable red fluorescent protein with a large Stokes shift. CHEMISTRY & BIOLOGY 2014; 21:1402-1414. [PMID: 25242289 PMCID: PMC4224599 DOI: 10.1016/j.chembiol.2014.08.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 08/08/2014] [Accepted: 08/13/2014] [Indexed: 11/24/2022]
Abstract
A subclass of fluorescent proteins (FPs), large Stokes shift (LSS) FP, are characterized by increased spread between excitation and emission maxima. We report a photoswitchable variant of a red FP with an LSS, PSLSSmKate, which initially exhibits excitation and emission at 445 and 622 nm, but violet irradiation photoswitches PSLSSmKate into a common red form with excitation and emission at 573 and 621 nm. We characterize spectral, photophysical, and biochemical properties of PSLSSmKate in vitro and in mammalian cells and determine its crystal structure in the LSS form. Mass spectrometry, mutagenesis, and spectroscopy of PSLSSmKate allow us to propose molecular mechanisms for the LSS, pH dependence, and light-induced chromophore transformation. We demonstrate the applicability of PSLSSmKate to superresolution photoactivated localization microscopy and protein dynamics in live cells. Given its promising properties, we expect that PSLSSmKate-like phenotype will be further used for photoactivatable imaging and tracking multiple populations of intracellular objects.
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Affiliation(s)
- Kiryl D Piatkevich
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Brian P English
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | | | - Hui Xiao
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Vladislav V Verkhusha
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Biochemistry and Developmental Biology, Institute of Biomedicine, University of Helsinki, Helsinki 00290, Finland.
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77
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Ritsma L, Ponsioen B, van Rheenen J. Intravital imaging of cell signaling in mice. INTRAVITAL 2014. [DOI: 10.4161/intv.20802] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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78
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Nienhaus K, Nienhaus GU. Fluorescent proteins for live-cell imaging with super-resolution. Chem Soc Rev 2014; 43:1088-106. [PMID: 24056711 DOI: 10.1039/c3cs60171d] [Citation(s) in RCA: 256] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorescent proteins (FPs) from the GFP family have become indispensable as marker tools for imaging live cells, tissues and entire organisms. A wide variety of these proteins have been isolated from natural sources and engineered to optimize their properties as genetically encoded markers. Here we review recent developments in this field. A special focus is placed on photoactivatable FPs, for which the fluorescence emission can be controlled by light irradiation at specific wavelengths. They enable regional optical marking in pulse-chase experiments on live cells and tissues, and they are essential marker tools for live-cell optical imaging with super-resolution. Photoconvertible FPs, which can be activated irreversibly via a photo-induced chemical reaction that either turns on their emission or changes their emission wavelength, are excellent markers for localization-based super-resolution microscopy (e.g., PALM). Patterned illumination microscopy (e.g., RESOLFT), however, requires markers that can be reversibly photoactivated many times. Photoswitchable FPs can be toggled repeatedly between a fluorescent and a non-fluorescent state by means of a light-induced chromophore isomerization coupled to a protonation reaction. We discuss the mechanistic origins of the effect and illustrate how photoswitchable FPs are employed in RESOLFT imaging. For this purpose, special FP variants with low switching fatigue have been introduced in recent years. Despite nearly two decades of FP engineering by many laboratories, there is still room for further improvement of these important markers for live cell imaging.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Straβe 1, 76131 Karlsruhe, Germany
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79
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Arosio D, Ratto GM. Twenty years of fluorescence imaging of intracellular chloride. Front Cell Neurosci 2014; 8:258. [PMID: 25221475 PMCID: PMC4148895 DOI: 10.3389/fncel.2014.00258] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/12/2014] [Indexed: 11/23/2022] Open
Abstract
Chloride homeostasis has a pivotal role in controlling neuronal excitability in the adult brain and during development. The intracellular concentration of chloride is regulated by the dynamic equilibrium between passive fluxes through membrane conductances and the active transport mediated by importers and exporters. In cortical neurons, chloride fluxes are coupled to network activity by the opening of the ionotropic GABAA receptors that provides a direct link between the activity of interneurons and chloride fluxes. These molecular mechanisms are not evenly distributed and regulated over the neuron surface and this fact can lead to a compartmentalized control of the intracellular concentration of chloride. The inhibitory drive provided by the activity of the GABAA receptors depends on the direction and strength of the associated currents, which are ultimately dictated by the gradient of chloride, the main charge carrier flowing through the GABAA channel. Thus, the intracellular distribution of chloride determines the local strength of ionotropic inhibition and influences the interaction between converging excitation and inhibition. The importance of chloride regulation is also underlined by its involvement in several brain pathologies, including epilepsy and disorders of the autistic spectra. The full comprehension of the physiological meaning of GABAergic activity on neurons requires the measurement of the spatiotemporal dynamics of chloride fluxes across the membrane. Nowadays, there are several available tools for the task, and both synthetic and genetically encoded indicators have been successfully used for chloride imaging. Here, we will review the available sensors analyzing their properties and outlining desirable future developments.
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Affiliation(s)
- Daniele Arosio
- Institute of Biophysics, National Research Council and Bruno Kessler Foundation Trento, Italy ; Centre for Integrative Biology, University of Trento Trento, Italy
| | - Gian Michele Ratto
- Nanoscience Institute, National Research Council of Italy Pisa, Italy ; NEST, Scuola Normale Superiore Pisa, Italy
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80
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Drobizhev M, Stoltzfus C, Topol I, Collins J, Wicks G, Mikhaylov A, Barnett L, Hughes T, Rebane A. Multiphoton photochemistry of red fluorescent proteins in solution and live cells. J Phys Chem B 2014; 118:9167-79. [PMID: 25004113 PMCID: PMC4126731 DOI: 10.1021/jp502477c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/02/2014] [Indexed: 12/13/2022]
Abstract
Genetically encoded fluorescent proteins (FPs), and biosensors based on them, provide new insights into how living cells and tissues function. Ultimately, the goal of the bioimaging community is to use these probes deep in tissues and even in entire organisms, and this will require two-photon laser scanning microscopy (TPLSM), with its greater tissue penetration, lower autofluorescence background, and minimum photodamage in the out-of-focus volume. However, the extremely high instantaneous light intensities of femtosecond pulses in the focal volume dramatically increase the probability of further stepwise resonant photon absorption, leading to highly excited, ionizable and reactive states, often resulting in fast bleaching of fluorescent proteins in TPLSM. Here, we show that the femtosecond multiphoton excitation of red FPs (DsRed2 and mFruits), both in solution and live cells, results in a chain of consecutive, partially reversible reactions, with individual rates driven by a high-order (3-5 photon) absorption. The first step of this process corresponds to a three- (DsRed2) or four-photon (mFruits) induced fast isomerization of the chromophore, yielding intermediate fluorescent forms, which then subsequently transform into nonfluorescent products. Our experimental data and model calculations are consistent with a mechanism in which ultrafast electron transfer from the chromophore to a neighboring positively charged amino acid residue triggers the first step of multiphoton chromophore transformations in DsRed2 and mFruits, consisting of decarboxylation of a nearby deprotonated glutamic acid residue.
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Affiliation(s)
- Mikhail Drobizhev
- Department of Physics and Department of
Cell Biology and Neuroscience, Montana State
University, Bozeman, Montana 59717, United
States
| | - Caleb Stoltzfus
- Department of Physics and Department of
Cell Biology and Neuroscience, Montana State
University, Bozeman, Montana 59717, United
States
| | - Igor Topol
- Leidos
Biomedical Research, Inc., Frederick National Laboratory for Cancer
Research, Frederick, Maryland 21702-1201, United States
| | - Jack Collins
- Leidos
Biomedical Research, Inc., Frederick National Laboratory for Cancer
Research, Frederick, Maryland 21702-1201, United States
| | - Geoffrey Wicks
- Department of Physics and Department of
Cell Biology and Neuroscience, Montana State
University, Bozeman, Montana 59717, United
States
| | - Alexander Mikhaylov
- Department of Physics and Department of
Cell Biology and Neuroscience, Montana State
University, Bozeman, Montana 59717, United
States
| | - Lauren Barnett
- Department of Physics and Department of
Cell Biology and Neuroscience, Montana State
University, Bozeman, Montana 59717, United
States
| | - Thomas
E. Hughes
- Department of Physics and Department of
Cell Biology and Neuroscience, Montana State
University, Bozeman, Montana 59717, United
States
| | - Aleksander Rebane
- Department of Physics and Department of
Cell Biology and Neuroscience, Montana State
University, Bozeman, Montana 59717, United
States
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81
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Kong W, Liu R, Li H, Liu J, Huang H, Liu Y, Kang Z. High-bright fluorescent carbon dots and their application in selective nucleoli staining. J Mater Chem B 2014; 2:5077-5082. [DOI: 10.1039/c4tb00579a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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82
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Pletnev S, Shcherbakova DM, Subach OM, Pletneva NV, Malashkevich VN, Almo SC, Dauter Z, Verkhusha VV. Orange fluorescent proteins: structural studies of LSSmOrange, PSmOrange and PSmOrange2. PLoS One 2014; 9:e99136. [PMID: 24960050 PMCID: PMC4068994 DOI: 10.1371/journal.pone.0099136] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 05/08/2014] [Indexed: 11/22/2022] Open
Abstract
A structural analysis of the recently developed orange fluorescent proteins with novel phenotypes, LSSmOrange (λex/λem at 437/572 nm), PSmOrange (λex/λem at 548/565 nm and for photoconverted form at 636/662 nm) and PSmOrange2 (λex/λem at 546/561 nm and for photoconverted form at 619/651 nm), is presented. The obtained crystallographic structures provide an understanding of how the ensemble of a few key mutations enabled special properties of the orange FPs. While only a single Ile161Asp mutation, enabling excited state proton transfer, is critical for LSSmOrange, other substitutions provide refinement of its special properties and an exceptional 120 nm large Stokes shift. Similarly, a single Gln64Leu mutation was sufficient to cause structural changes resulting in photoswitchability of PSmOrange, and only one additional substitution (Phe65Ile), yielding PSmOrange2, was enough to greatly decrease the energy of photoconversion and increase its efficiency of photoswitching. Fluorescence of photoconverted PSmOrange and PSmOrange2 demonstrated an unexpected bathochromic shift relative to the fluorescence of classic red FPs, such as DsRed, eqFP578 and zFP574. The structural changes associated with this fluorescence shift are of considerable value for the design of advanced far-red FPs. For this reason the chromophore transformations accompanying photoconversion of the orange FPs are discussed.
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Affiliation(s)
- Sergei Pletnev
- Leidos Biomedical Research Inc., Basic Research Program, Argonne, Illinois, United States of America
- Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, Illinois, United States of America
| | - Daria M. Shcherbakova
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Oksana M. Subach
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Nano, Bio, Information and Cognitive Technologies, Moscow Institute of Physics and Technology, Moscow, Russian Federation
| | - Nadya V. Pletneva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir N. Malashkevich
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Zbigniew Dauter
- Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, Illinois, United States of America
| | - Vladislav V. Verkhusha
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
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83
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Zeng Q, Liu J, Liang W. Molecular properties of excited electronic state: formalism, implementation, and applications of analytical second energy derivatives within the framework of the time-dependent density functional theory/molecular mechanics. J Chem Phys 2014; 140:18A506. [PMID: 24832314 DOI: 10.1063/1.4863563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
This work extends our previous works [J. Liu and W. Z. Liang, J. Chem. Phys. 135, 014113 (2011); J. Liu and W. Z. Liang, J. Chem. Phys. 135, 184111 (2011)] on analytical excited-state energy Hessian within the framework of time-dependent density functional theory (TDDFT) to couple with molecular mechanics (MM). The formalism, implementation, and applications of analytical first and second energy derivatives of TDDFT/MM excited state with respect to the nuclear and electric perturbations are presented. Their performances are demonstrated by the calculations of adiabatic excitation energies, and excited-state geometries, harmonic vibrational frequencies, and infrared intensities for a number of benchmark systems. The consistent results with the full quantum mechanical method and other hybrid theoretical methods indicate the reliability of the current numerical implementation of developed algorithms. The computational accuracy and efficiency of the current analytical approach are also checked and the computational efficient strategies are suggested to speed up the calculations of complex systems with many MM degrees of freedom. Finally, we apply the current analytical approach in TDDFT/MM to a realistic system, a red fluorescent protein chromophore together with part of its nearby protein matrix. The calculated results indicate that the rearrangement of the hydrogen bond interactions between the chromophore and the protein matrix is responsible for the large Stokes shift.
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Affiliation(s)
- Qiao Zeng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Province Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jie Liu
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - WanZhen Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Province Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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84
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Birsa N, Norkett R, Wauer T, Mevissen TET, Wu HC, Foltynie T, Bhatia K, Hirst WD, Komander D, Plun-Favreau H, Kittler JT. Lysine 27 ubiquitination of the mitochondrial transport protein Miro is dependent on serine 65 of the Parkin ubiquitin ligase. J Biol Chem 2014; 289:14569-82. [PMID: 24671417 PMCID: PMC4031514 DOI: 10.1074/jbc.m114.563031] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mitochondrial transport plays an important role in matching mitochondrial distribution to localized energy production and calcium buffering requirements. Here, we demonstrate that Miro1, an outer mitochondrial membrane (OMM) protein crucial for the regulation of mitochondrial trafficking and distribution, is a substrate of the PINK1/Parkin mitochondrial quality control system in human dopaminergic neuroblastoma cells. Moreover, Miro1 turnover on damaged mitochondria is altered in Parkinson disease (PD) patient-derived fibroblasts containing a pathogenic mutation in the PARK2 gene (encoding Parkin). By analyzing the kinetics of Miro1 ubiquitination, we further demonstrate that mitochondrial damage triggers rapid (within minutes) and persistent Lys-27-type ubiquitination of Miro1 on the OMM, dependent on PINK1 and Parkin. Proteasomal degradation of Miro1 is then seen on a slower time scale, within 2-3 h of the onset of ubiquitination. We find Miro ubiquitination in dopaminergic neuroblastoma cells is independent of Miro1 phosphorylation at Ser-156 but is dependent on the recently identified Ser-65 residue within Parkin that is phosphorylated by PINK1. Interestingly, we find that Miro1 can stabilize phospho-mutant versions of Parkin on the OMM, suggesting that Miro is also part of a Parkin receptor complex. Moreover, we demonstrate that Ser-65 in Parkin is critical for regulating Miro levels upon mitochondrial damage in rodent cortical neurons. Our results provide new insights into the ubiquitination-dependent regulation of the Miro-mediated mitochondrial transport machinery by PINK1/Parkin and also suggest that disruption of this regulation may be implicated in Parkinson disease pathogenesis.
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Affiliation(s)
- Nicol Birsa
- From the Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Rosalind Norkett
- From the Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Tobias Wauer
- the Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Tycho E T Mevissen
- the Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Hsiu-Chuan Wu
- the University College London Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom, and
| | - Thomas Foltynie
- the University College London Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom, and
| | - Kailash Bhatia
- the University College London Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom, and
| | - Warren D Hirst
- the Neuroscience Research Unit, Pfizer, Cambridge, Massachusetts 02139
| | - David Komander
- the Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Helene Plun-Favreau
- the University College London Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom, and
| | - Josef T Kittler
- From the Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London WC1E 6BT, United Kingdom,
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85
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Piatkevich KD, Subach FV, Verkhusha VV. Far-red light photoactivatable near-infrared fluorescent proteins engineered from a bacterial phytochrome. Nat Commun 2014; 4:2153. [PMID: 23842578 PMCID: PMC3749836 DOI: 10.1038/ncomms3153] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Accepted: 06/15/2013] [Indexed: 01/11/2023] Open
Abstract
Ability to modulate fluorescence of optical probes can be used to enhance signal-to-noise ratio for imaging within highly autofluorescent environments, such as intact tissues and living organisms. Here we report two phytochrome-based photoactivatable near-infrared fluorescent proteins, named PAiRFP1 and PAiRFP2. PAiRFPs utilize heme-derived biliverdin, ubiquitous in mammalian tissues, as the chromophore. Initially weakly fluorescent PAiRFPs undergo photoconversion into a highly fluorescent state with excitation/emission at 690 nm/717 nm following a brief irradiation with far-red light. After photoactivation, PAiRFPs slowly revert back to initial state, enabling multiple photoactivation-relaxation cycles. Low-temperature optical spectroscopy reveals several intermediates involved in PAiRFP photocycles, which all differ from that of the bacteriophytochrome precursor. PAiRFPs can be photoactivated in a spatially selective manner in mouse tissues, and optical modulation of their fluorescence allows for substantial contrast enhancement, making PAiRFPs advantageous over permanently fluorescent probes for in vivo imaging conditions of high autofluorescence and low signal levels.
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Affiliation(s)
- Kiryl D Piatkevich
- Department of Anatomy and Structural Biology, Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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86
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Adjili S, Favier A, Massin J, Bretonnière Y, Lacour W, Lin YC, Chatre E, Place C, Favard C, Muriaux D, Andraud C, Charreyre MT. Synthesis of multifunctional lipid–polymer conjugates: application to the elaboration of bright far-red fluorescent lipid probes. RSC Adv 2014. [DOI: 10.1039/c4ra01334d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Well-defined multifunctional lipid-polymer conjugates as new tools for the functionalization of lipid assemblies.
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Affiliation(s)
- Salim Adjili
- École Normale Supérieure de Lyon
- Laboratoire Joliot-Curie
- CNRS USR 3010
- F-69364 Lyon, France
- INSA-Lyon
| | - Arnaud Favier
- École Normale Supérieure de Lyon
- Laboratoire Joliot-Curie
- CNRS USR 3010
- F-69364 Lyon, France
- INSA-Lyon
| | - Julien Massin
- École Normale Supérieure de Lyon
- Laboratoire de Chimie
- CNRS UMR 5182
- Université Lyon 1
- Lyon, France
| | - Yann Bretonnière
- École Normale Supérieure de Lyon
- Laboratoire de Chimie
- CNRS UMR 5182
- Université Lyon 1
- Lyon, France
| | - William Lacour
- École Normale Supérieure de Lyon
- Laboratoire Joliot-Curie
- CNRS USR 3010
- F-69364 Lyon, France
- INSA-Lyon
| | - Yi-Chun Lin
- École Normale Supérieure de Lyon
- Laboratoire Joliot-Curie
- CNRS USR 3010
- F-69364 Lyon, France
- INSA-Lyon
| | - Elodie Chatre
- École Normale Supérieure de Lyon
- Laboratoire Joliot-Curie
- CNRS USR 3010
- F-69364 Lyon, France
| | - Christophe Place
- École Normale Supérieure de Lyon
- Laboratoire Joliot-Curie
- CNRS USR 3010
- F-69364 Lyon, France
| | - Cyril Favard
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé
- CNRS UMR 5236
- Montpellier, France
| | - Delphine Muriaux
- École Normale Supérieure de Lyon
- Laboratoire de Virologie Humaine
- F-69364 Lyon, France
| | - Chantal Andraud
- École Normale Supérieure de Lyon
- Laboratoire de Chimie
- CNRS UMR 5182
- Université Lyon 1
- Lyon, France
| | - Marie-Thérèse Charreyre
- École Normale Supérieure de Lyon
- Laboratoire Joliot-Curie
- CNRS USR 3010
- F-69364 Lyon, France
- INSA-Lyon
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87
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Zhang MY, Xu C, Lin CS, Guan X, Cheng WD. Theoretical study of the proton transfer wires influence on the one- and two-photon absorption properties of green fluorescent protein chromophore. Org Biomol Chem 2013; 11:1414-22. [PMID: 23338242 DOI: 10.1039/c2ob26914g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The excited-state proton transfer (ESPT) via proton transfer wires in green fluorescent protein (GFP) plays an important role on the spectroscopic of GFP. In this work, we use the proton transfer wires and the chromophore complex to simulate the tautomer structures of neutral state and the intermediate state in wt-GFP. And we employ the time-dependent density functional theory combined with the sum-over-states method to calculate the one- and two-photon absorption properties of these complexes in GFP. We obtain the large stokes shift from 383 nm to 500 nm in GFP when simulating the ESPT process by these isomerous H-bonding complexes. We find that the TPA spectrum of the H-bonding complex of the intermediate state agrees more with experimental measurement than that of the H-bonding complex of the neutral state. The TPA spectrum of GFP might be mainly dominated by the structure which is similar to the H-bonding complex of intermediate state. Further, we simulate another kind of complex which possess short-strong hydrogen bonds in proton transfer wires, and find that TPA properties of these complexes are much stronger than that of the complexes with the long distance proton wires from GFP.
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Affiliation(s)
- Min-Yi Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
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88
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Nobis M, Carragher NO, McGhee EJ, Morton JP, Sansom OJ, Anderson KI, Timpson P. Advanced intravital subcellular imaging reveals vital three-dimensional signalling events driving cancer cell behaviour and drug responses in live tissue. FEBS J 2013; 280:5177-97. [PMID: 23678945 DOI: 10.1111/febs.12348] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 05/13/2013] [Accepted: 05/14/2013] [Indexed: 12/18/2022]
Abstract
The integration of signal transduction pathways plays a fundamental role in governing disease initiation, progression and outcome. It is therefore necessary to understand disease at the signalling level to enable effective treatment and to intervene in its progression. The recent extension of in vitro subcellular image-based analysis to live in vivo modelling of disease is providing a more complete picture of real-time, dynamic signalling processes or drug responses in live tissue. Intravital imaging offers alternative strategies for studying disease and embraces the biological complexities that govern disease progression. In the present review, we highlight how three-dimensional or live intravital imaging has uncovered novel insights into biological mechanisms or modes of drug action. Furthermore, we offer a prospective view of how imaging applications may be integrated further with the aim of understanding disease in a more physiological and functional manner within the framework of the drug discovery process.
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Affiliation(s)
- Max Nobis
- The Beatson Institute for Cancer Research, Glasgow, UK
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89
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Smurthwaite CA, Hilton BJ, O'Hanlon R, Stolp ZD, Hancock BM, Abbadessa D, Stotland A, Sklar LA, Wolkowicz R. Fluorescent genetic barcoding in mammalian cells for enhanced multiplexing capabilities in flow cytometry. Cytometry A 2013; 85:105-13. [DOI: 10.1002/cyto.a.22406] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 10/01/2013] [Accepted: 10/04/2013] [Indexed: 01/19/2023]
Affiliation(s)
| | - Brett J. Hilton
- Department of Biology; San Diego State University; San Diego California 92182
| | - Ryan O'Hanlon
- Department of Biology; San Diego State University; San Diego California 92182
| | - Zachary D. Stolp
- Department of Biology; San Diego State University; San Diego California 92182
| | - Bryan M. Hancock
- Department of Biology; San Diego State University; San Diego California 92182
| | - Darin Abbadessa
- Department of Biology; San Diego State University; San Diego California 92182
| | - Aleksandr Stotland
- Department of Biology; San Diego State University; San Diego California 92182
| | - Larry A. Sklar
- UNM Center for Molecular Discovery; University of New Mexico School of Medicine; Albuquerque New Mexico 87131
- Department of Pathology; University of New Mexico School of Medicine; Albuquerque New Mexico 87131
| | - Roland Wolkowicz
- Department of Biology; San Diego State University; San Diego California 92182
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90
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Wickstrum J, Sammons LR, Restivo KN, Hefty PS. Conditional gene expression in Chlamydia trachomatis using the tet system. PLoS One 2013; 8:e76743. [PMID: 24116144 PMCID: PMC3792055 DOI: 10.1371/journal.pone.0076743] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 08/23/2013] [Indexed: 01/25/2023] Open
Abstract
Chlamydia trachomatis is maintained through a complex bi-phasic developmental cycle that incorporates numerous processes that are poorly understood. This is reflective of the previous paucity of genetic tools available. The recent advent of a method for transforming Chlamydia has enabled the development of essential molecular tools to better study these medically important bacteria. Critical for the study of Chlamydia biology and pathogenesis, is a system for tightly controlled inducible gene expression. To accomplish this, a new shuttle vector was generated with gene expression controlled by the Tetracycline repressor and anhydryotetracycline. Evaluation of GFP expression by this system demonstrated tightly controlled gene regulation with rapid protein expression upon induction and restoration of transcription repression following inducer removal. Additionally, induction of expression could be detected relatively early during the developmental cycle and concomitant with conversion into the metabolically active form of Chlamydia. Uniform and strong GFP induction was observed during middle stages of the developmental cycle. Interestingly, variable induced GFP expression by individual organisms within shared inclusions during later stages of development suggesting metabolic diversity is affecting induction and/or expression. These observations support the strong potential of this molecular tool to enable numerous experimental analyses for a better understanding of the biology and pathogenesis of Chlamydia.
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Affiliation(s)
- Jason Wickstrum
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Lindsay R. Sammons
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Keasha N. Restivo
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - P. Scott Hefty
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
- * E-mail:
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91
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Gaytán P, Roldán-Salgado A. Elimination of redundant and stop codons during the chemical synthesis of degenerate oligonucleotides. Combinatorial testing on the chromophore region of the red fluorescent protein mKate. ACS Synth Biol 2013; 2:453-62. [PMID: 23654278 DOI: 10.1021/sb3001326] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although some strategies have been reported for the elimination of stop and redundant codons during the chemical synthesis of degenerate oligonucleotides, incorporating an expensive cocktail of 20 trimer-phosphoramidites is currently a commonly employed and straightforward approach. As an alternative option, we describe here a cheaper strategy based on standard monomer-phosphoramidites and a simplified resin-splitting procedure. The accurate division of the resin, containing the growing oligonucleotide, into four columns represents the key step in this approach. The synthesis of the degenerate codon NDT in column 1, loaded with 60% of the resin, produces 12 codons, while a degenerate codon VMA in column 2, loaded with 30% of the resin, produces 6 codons. Codons ATG and TGG, independently synthesized in columns 3 and 4, respectively, and loaded with 5% each, completes the 20 different codons. The experimental frequency of each mutant codon in the library was assessed by randomizing 12 contiguous codons that encode for amino acids located in the chromophore region of the enhanced red fluorescent protein mKate-S158A. Furthermore, randomization of three contiguous codons that encode for the amino acids Phe62, Met63, and Tyr64, which are equivalent to Phe64, Ser65, and Tyr66 in GFP, gave rise to some red and golden yellow fluorescent mutants displaying interesting phenotypes and spectroscopic properties. The absorption and emission spectra of two of these mutants also suggested that the complete maturation of the red and golden yellow chromophores in mKate proceeds via the formation of a green-type chromophore and a cyan-type chromophore, respectively.
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Affiliation(s)
- Paul Gaytán
- Instituto de Biotecnología-Universidad Nacional Autónoma de México, Ap. Postal 510-3 Cuernavaca, Morelos 62250, México.
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92
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Weber T, Köster R. Genetic tools for multicolor imaging in zebrafish larvae. Methods 2013; 62:279-91. [DOI: 10.1016/j.ymeth.2013.07.028] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 07/08/2013] [Accepted: 07/16/2013] [Indexed: 02/06/2023] Open
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93
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Filonov GS, Verkhusha VV. A near-infrared BiFC reporter for in vivo imaging of protein-protein interactions. ACTA ACUST UNITED AC 2013; 20:1078-86. [PMID: 23891149 DOI: 10.1016/j.chembiol.2013.06.009] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 06/11/2013] [Accepted: 06/17/2013] [Indexed: 11/28/2022]
Abstract
Studies of protein-protein interactions deep in organs and in whole mammals have been hindered by a lack of genetically encoded fluorescent probes in near-infrared region for which mammalian tissues are the most transparent. We have used a near-infrared fluorescent protein iRFP engineered from a bacterial phytochrome as the template to develop an in vivo split fluorescence complementation probe. The domain architecture-based rational design resulted in an iSplit reporter with the spectra optimal for whole-body imaging, high photostability, and high complementation contrast, which compares favorably to that of other available split fluorescent protein-based probes. Successful visualization of interaction of two known protein partners in a living mouse model suggests iSplit as the probe of choice for noninvasive detection of protein-protein interactions in vivo, whereas its fast intracellular degradation enables time-resolved monitoring of repetitive binding events.
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Affiliation(s)
- Grigory S Filonov
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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94
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Lee S, Lim WA, Thorn KS. Improved blue, green, and red fluorescent protein tagging vectors for S. cerevisiae. PLoS One 2013; 8:e67902. [PMID: 23844123 PMCID: PMC3699464 DOI: 10.1371/journal.pone.0067902] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 05/22/2013] [Indexed: 12/21/2022] Open
Abstract
Fluorescent protein fusions are a powerful tool to monitor the localization and trafficking of proteins. Such studies are particularly easy to carry out in the budding yeast Saccharomyces cerevisiae due to the ease with which tags can be introduced into the genome by homologous recombination. However, the available yeast tagging plasmids have not kept pace with the development of new and improved fluorescent proteins. Here, we have constructed yeast optimized versions of 19 different fluorescent proteins and tested them for use as fusion tags in yeast. These include two blue, seven green, and seven red fluorescent proteins, which we have assessed for brightness, photostability and perturbation of tagged proteins. We find that EGFP remains the best performing green fluorescent protein, that TagRFP-T and mRuby2 outperform mCherry as red fluorescent proteins, and that mTagBFP2 can be used as a blue fluorescent protein tag. Together, the new tagging vectors we have constructed provide improved blue and red fluorescent proteins for yeast tagging and three color imaging.
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Affiliation(s)
- Sidae Lee
- UCSF Center for Systems and Synthetic Biology, University of California San Francisco, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
| | - Wendell A. Lim
- UCSF Center for Systems and Synthetic Biology, University of California San Francisco, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, San Francisco, California, United States of America
| | - Kurt S. Thorn
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
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95
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Yang J, Wang L, Yang F, Luo H, Xu L, Lu J, Zeng S, Zhang Z. mBeRFP, an improved large stokes shift red fluorescent protein. PLoS One 2013; 8:e64849. [PMID: 23840310 PMCID: PMC3688735 DOI: 10.1371/journal.pone.0064849] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 04/19/2013] [Indexed: 11/28/2022] Open
Abstract
Herein, we describe the generation of a monomeric large Stokes shift (LSS) red fluorescent protein, mBeRFP, with excitation and emission peaks at 446 and 615 nm, respectively. Compared with two previously reported LSS-RFPs (mKeima and LSS-mKate2), mBeRFP is approximately three times brighter. In addition, mBeRFP is characterized by improved photostability, rapid maturation, an extended lifetime, and a monomeric nature. Additionally, mBeRFP can be paired with the Alexa 647 dye as a FRET donor to detect caspase 3 activity. This FRET pair has an extremely dynamic range and a large Förster radius (approximately 6.5 nm). To demonstrate the applicability of mBeRFP for imaging in living cells, we performed dual-color imaging of mBeRFP and CFP simultaneously excited by a single excitation source, and we demonstrated that these fluorescent proteins allow the clear visualization of the dynamics of Bax during cancer cell apoptosis. Thus, mBeRFP appears to be particularly useful for cellular imaging applications.
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Affiliation(s)
- Jie Yang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Liang Wang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fei Yang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Haiming Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lingling Xu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jinling Lu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shaoqun Zeng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhihong Zhang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, China
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96
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Entenberg D, Kedrin D, Wyckoff J, Sahai E, Condeelis J, Segall JE. Imaging tumor cell movement in vivo. CURRENT PROTOCOLS IN CELL BIOLOGY 2013; Chapter 19:19.7.1-19.7.19. [PMID: 23456602 PMCID: PMC3722061 DOI: 10.1002/0471143030.cb1907s58] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This unit describes the methods that we have been developing for analyzing tumor cell motility in mouse and rat models of breast cancer metastasis. Rodents are commonly used both to provide a mammalian system for studying human tumor cells (as xenografts in immunocompromised mice) as well as for following the development of tumors from a specific tissue type in transgenic lines. The Basic Protocol in this unit describes the standard methods used for generation of mammary tumors and imaging them. Additional protocols for labeling macrophages, blood vessel imaging, and image analysis are also included.
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Affiliation(s)
- David Entenberg
- Albert Einstein College of Medicine, Bronx, New York
- These authors contributed equally to this work
| | - Dmitriy Kedrin
- Albert Einstein College of Medicine, Bronx, New York
- These authors contributed equally to this work
| | | | - Erik Sahai
- London Research Institute, London, United Kingdom
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97
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Nadal-Ferret M, Gelabert R, Moreno M, Lluch JM. How Does the Environment Affect the Absorption Spectrum of the Fluorescent Protein mKeima? J Chem Theory Comput 2013; 9:1731-42. [DOI: 10.1021/ct301003t] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Marc Nadal-Ferret
- Departament
de Química and ‡Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Ricard Gelabert
- Departament
de Química and ‡Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Miquel Moreno
- Departament
de Química and ‡Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - José M. Lluch
- Departament
de Química and ‡Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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98
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A time-dependent DFT/molecular dynamics study of the proton-wire responsible for the red fluorescence in the LSSmKate2 protein. Theor Chem Acc 2013. [DOI: 10.1007/s00214-012-1327-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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99
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Stepanenko OV, Stepanenko OV, Kuznetsova IM, Verkhusha VV, Turoverov KK. Beta-barrel scaffold of fluorescent proteins: folding, stability and role in chromophore formation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 302:221-78. [PMID: 23351712 DOI: 10.1016/b978-0-12-407699-0.00004-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review focuses on the current view of the interaction between the β-barrel scaffold of fluorescent proteins and their unique chromophore located in the internal helix. The chromophore originates from the polypeptide chain and its properties are influenced by the surrounding protein matrix of the β-barrel. On the other hand, it appears that a chromophore tightens the β-barrel scaffold and plays a crucial role in its stability. Furthermore, the presence of a mature chromophore causes hysteresis of protein unfolding and refolding. We survey studies measuring protein unfolding and refolding using traditional methods as well as new approaches, such as mechanical unfolding and reassembly of truncated fluorescent proteins. We also analyze models of fluorescent protein unfolding and refolding obtained through different approaches, and compare the results of protein folding in vitro to co-translational folding of a newly synthesized polypeptide chain.
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Affiliation(s)
- Olesya V Stepanenko
- Institute of Cytology of Russian Academy of Sciences, St. Petersburg, Russia
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100
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Piatkevich KD, Malashkevich VN, Morozova KS, Nemkovich NA, Almo SC, Verkhusha VV. Extended Stokes shift in fluorescent proteins: chromophore-protein interactions in a near-infrared TagRFP675 variant. Sci Rep 2013; 3:1847. [PMID: 23677204 PMCID: PMC3654500 DOI: 10.1038/srep01847] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 04/29/2013] [Indexed: 12/11/2022] Open
Abstract
Most GFP-like fluorescent proteins exhibit small Stokes shifts (10-45 nm) due to rigidity of the chromophore environment that excludes non-fluorescent relaxation to a ground state. An unusual near-infrared derivative of the red fluorescent protein mKate, named TagRFP675, exhibits the Stokes shift, which is 30 nm extended comparing to that of the parental protein. In physiological conditions, TagRFP675 absorbs at 598 nm and emits at 675 nm that makes it the most red-shifted protein of the GFP-like protein family. In addition, its emission maximum strongly depends on the excitation wavelength. Structures of TagRFP675 revealed the common DsRed-like chromophore, which, however, interacts with the protein matrix via an extensive network of hydrogen bonds capable of large flexibility. Based on the spectroscopic, biochemical, and structural analysis we suggest that the rearrangement of the hydrogen bond interactions between the chromophore and the protein matrix is responsible for the TagRFP675 spectral properties.
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Affiliation(s)
- Kiryl D. Piatkevich
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Bronx, New York 10461, United States
| | - Vladimir N. Malashkevich
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Kateryna S. Morozova
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Bronx, New York 10461, United States
| | - Nicolai A. Nemkovich
- B. I. Stepanov Institute of Physics, National Academy of Sciences of Belarus, 68 Independence Avenue, Minsk 220072, Belarus
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Vladislav V. Verkhusha
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Bronx, New York 10461, United States
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