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Mehl BP, Vairaprakash P, Li L, Hinde E, MacNevin CJ, Hsu CW, Gratton E, Liu B, Hahn KM. Live-cell biosensors based on the fluorescence lifetime of environment-sensing dyes. CELL REPORTS METHODS 2024; 4:100734. [PMID: 38503289 PMCID: PMC10985238 DOI: 10.1016/j.crmeth.2024.100734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/13/2023] [Accepted: 02/26/2024] [Indexed: 03/21/2024]
Abstract
In this work, we examine the use of environment-sensitive fluorescent dyes in fluorescence lifetime imaging microscopy (FLIM) biosensors. We screened merocyanine dyes to find an optimal combination of environment-induced lifetime changes, photostability, and brightness at wavelengths suitable for live-cell imaging. FLIM was used to monitor a biosensor reporting conformational changes of endogenous Cdc42 in living cells. The ability to quantify activity using phasor analysis of a single fluorophore (e.g., rather than ratio imaging) eliminated potential artifacts. We leveraged these properties to determine specific concentrations of activated Cdc42 across the cell.
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Affiliation(s)
- Brian P Mehl
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Pothiappan Vairaprakash
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Li Li
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Elizabeth Hinde
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California at Irvine, Irvine, CA 92617, USA
| | - Christopher J MacNevin
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chia-Wen Hsu
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California at Irvine, Irvine, CA 92617, USA
| | - Bei Liu
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Klaus M Hahn
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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2
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MacNevin CJ, Watanabe T, Weitzman M, Gulyani A, Fuehrer S, Pinkin NK, Tian X, Liu F, Jin J, Hahn KM. Membrane-Permeant, Environment-Sensitive Dyes Generate Biosensors within Living Cells. J Am Chem Soc 2019; 141:7275-7282. [PMID: 30994345 DOI: 10.1021/jacs.8b09841] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Dyes with environment-sensitive fluorescence have proven useful to study the spatiotemporal dynamics of protein activity in living cells. When attached to proteins, their fluorescence can reflect protein conformational changes, post-translational modifications, or protein interactions. However, the utility of such dye-protein conjugates has been limited because it is difficult to load them into cells. They usually must be introduced using techniques that perturb cell physiology, limit throughput, or generate fluorescent vesicles (e.g., electroporation, microinjection, or membrane transduction peptides). Here we circumvent these problems by modifying a proven, environment-sensitive biosensor fluorophore so that it can pass through cell membranes without staining intracellular compartments and can be attached to proteins within living cells using unnatural amino acid (UAA) mutagenesis. Reactive groups were incorporated for attachment to UAAs or small molecules (mero166, azide; mero167, alkyne; mero76, carboxylic acid). These dyes are bright and fluoresce at long wavelengths (reaching ε = 100 000 M-1 cm-1, ϕ = 0.24, with excitation 565 nm and emission 594 nm). The utility of mero166 was demonstrated by in-cell labeling of a UAA to generate a biosensor for the small GTPase Cdc42. In addition, conjugation of mero166 to a small molecule produced a membrane-permeable probe that reported the localization of the DNA methyltransferase G9a in cells. This approach provides a strategy to access biosensors for many targets and to more practically harness the varied environmental sensitivities of synthetic dyes.
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Affiliation(s)
- Christopher J MacNevin
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Takashi Watanabe
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Matthew Weitzman
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Akash Gulyani
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Sheryl Fuehrer
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Nicholas K Pinkin
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Xu Tian
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Feng Liu
- Center for Integrative Chemical Biology and Drug Discovery, School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Jian Jin
- Center for Integrative Chemical Biology and Drug Discovery, School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Klaus M Hahn
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
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3
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Zhang X, Liu T, Wang B, Gao Y, Liu P, Li M, Du L. Astemizole-based turn-on fluorescent probes for imaging hERG potassium channel. MEDCHEMCOMM 2019; 10:513-516. [PMID: 31057730 DOI: 10.1039/c8md00562a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/25/2019] [Indexed: 11/21/2022]
Abstract
Based on the scaffold of astemizole, three novel turn-on fluorescent probes (N1-N3) for human ether-a-go-go-related gene (hERG) potassium channel were developed herein. These probes have reasonable fluorescence properties, acceptable cell toxicity, and potent inhibitory activity, all of which contribute to cell imaging at the nanomolar level. Overall, these probes have the potential for setting up a screening system for hERG channels.
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Affiliation(s)
- Xiaomeng Zhang
- Department of Medicinal Chemistry , Key Laboratory of Chemical Biology (MOE) , School of Pharmacy , Shandong University , Jinan , Shandong 250012 , China .
| | - Tingting Liu
- Department of Medicinal Chemistry , Key Laboratory of Chemical Biology (MOE) , School of Pharmacy , Shandong University , Jinan , Shandong 250012 , China .
| | - Beilei Wang
- Department of Medicinal Chemistry , Key Laboratory of Chemical Biology (MOE) , School of Pharmacy , Shandong University , Jinan , Shandong 250012 , China .
| | - Yuqi Gao
- Department of Medicinal Chemistry , Key Laboratory of Chemical Biology (MOE) , School of Pharmacy , Shandong University , Jinan , Shandong 250012 , China .
| | - Pan Liu
- Department of Medicinal Chemistry , Key Laboratory of Chemical Biology (MOE) , School of Pharmacy , Shandong University , Jinan , Shandong 250012 , China .
| | - Minyong Li
- Department of Medicinal Chemistry , Key Laboratory of Chemical Biology (MOE) , School of Pharmacy , Shandong University , Jinan , Shandong 250012 , China .
| | - Lupei Du
- Department of Medicinal Chemistry , Key Laboratory of Chemical Biology (MOE) , School of Pharmacy , Shandong University , Jinan , Shandong 250012 , China .
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4
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Raja SO, Sivaraman G, Mukherjee A, Duraisamy C, Gulyani A. Facile Synthesis of Highly Sensitive, Red-Emitting, Fluorogenic Dye for Microviscosity and Mitochondrial Imaging in Embryonic Stem Cells. ChemistrySelect 2017. [DOI: 10.1002/slct.201700463] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Sufi O. Raja
- Institute for Stem Cell Biology & Regenerative Medicine; Bengaluru 560065 India
| | - Gandhi Sivaraman
- Institute for Stem Cell Biology & Regenerative Medicine; Bengaluru 560065 India
| | - Ananya Mukherjee
- Institute for Stem Cell Biology & Regenerative Medicine; Bengaluru 560065 India
- SASTRA University; Thanjavur- 613401 India
| | | | - Akash Gulyani
- Institute for Stem Cell Biology & Regenerative Medicine; Bengaluru 560065 India
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5
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MacNevin CJ, Toutchkine A, Marston DJ, Hsu CW, Tsygankov D, Li L, Liu B, Qi T, Nguyen DV, Hahn KM. Ratiometric Imaging Using a Single Dye Enables Simultaneous Visualization of Rac1 and Cdc42 Activation. J Am Chem Soc 2016; 138:2571-5. [PMID: 26863024 DOI: 10.1021/jacs.5b09764] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biosensors that report endogenous protein activity in vivo can be based on environment-sensing fluorescent dyes. The dyes can be attached to reagents that bind selectively to a specific conformation of the targeted protein, such that binding leads to a fluorescence change. Dyes that are sufficiently bright for use at low, nonperturbing intracellular concentrations typically undergo changes in intensity rather than the shifts in excitation or emission maxima that would enable precise quantitation through ratiometric imaging. We report here mero199, an environment-sensing dye that undergoes a 33 nm solvent-dependent shift in excitation. The dye was used to generate a ratiometric biosensor of Cdc42 (CRIB199) without the need for additional fluorophores. CRIB199 was used in the same cell with a FRET sensor of Rac1 activation to simultaneously observe Cdc42 and Rac1 activity in cellular protrusions, indicating that Rac1 but not Cdc42 activity was reduced during tail retraction, and specific protrusions had reduced Cdc42 activity. A novel program (EdgeProps) used to correlate localized activation with cell edge dynamics indicated that Rac1 was specifically reduced during retraction.
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Affiliation(s)
- Christopher J MacNevin
- Department of Pharmacology, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Alexei Toutchkine
- Department of Pharmacology, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Daniel J Marston
- Department of Pharmacology, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Chia-Wen Hsu
- Department of Pharmacology, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Denis Tsygankov
- Department of Pharmacology, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Li Li
- Department of Pharmacology, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Bei Liu
- Department of Pharmacology, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Timothy Qi
- Department of Pharmacology, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Dan-Vinh Nguyen
- Department of Pharmacology, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Klaus M Hahn
- Department of Pharmacology, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
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Bekere L, Larina N, Lokshin V, Ellern A, Sigalov M, Khodorkovsky V. A new class of spirocyclic photochromes reacting with light of both UV and visible ranges. NEW J CHEM 2016. [DOI: 10.1039/c6nj00666c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Deep coloration of weakly colored spirocyclic derivatives (R = NMe2, NEt2, and OMe) can be achieved by irradiation with light of any wavelength between 254 and 642 nm.
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Affiliation(s)
- Laura Bekere
- Aix Marseille Université
- CNRS
- CINaM UMR 7325
- Marseille
- France
| | - Nina Larina
- Aix Marseille Université
- CNRS
- CINaM UMR 7325
- Marseille
- France
| | | | | | - Mark Sigalov
- Department of Chemistry
- Ben Gurion University of the Negev
- Beer Sheva
- Israel
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7
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Masunov AE, Anderson D, Freidzon AY, Bagaturyants AA. Symmetry-Breaking in Cationic Polymethine Dyes: Part 2. Shape of Electronic Absorption Bands Explained by the Thermal Fluctuations of the Solvent Reaction Field. J Phys Chem A 2015; 119:6807-15. [DOI: 10.1021/acs.jpca.5b03877] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | | | - Alexandra Ya. Freidzon
- Photochemistry
Center RAS, ul. Novatorov 7a, Moscow, 119421, Russia
- National Research Nuclear University MEPhI, Kashirskoye shosse 31, Moscow, 115409, Russia
| | - Alexander A. Bagaturyants
- Photochemistry
Center RAS, ul. Novatorov 7a, Moscow, 119421, Russia
- National Research Nuclear University MEPhI, Kashirskoye shosse 31, Moscow, 115409, Russia
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8
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Zhekova H, Krykunov M, Autschbach J, Ziegler T. Applications of Time Dependent and Time Independent Density Functional Theory to the First π to π* Transition in Cyanine Dyes. J Chem Theory Comput 2014; 10:3299-307. [DOI: 10.1021/ct500292c] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hristina Zhekova
- Department of Chemistry, University of Calgary, University Drive 2500, Calgary AB T2N-1N4, Canada
| | - Mykhaylo Krykunov
- Department of Chemistry, University of Calgary, University Drive 2500, Calgary AB T2N-1N4, Canada
| | - Jochen Autschbach
- Department of Chemistry, State University of New York, 312 Natural
Sciences Complex, Buffalo, New York 14260-3000, United States
| | - Tom Ziegler
- Department of Chemistry, University of Calgary, University Drive 2500, Calgary AB T2N-1N4, Canada
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9
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MacNevin CJ, Gremyachinskiy D, Hsu CW, Li L, Rougie M, Davis TT, Hahn KM. Environment-sensing merocyanine dyes for live cell imaging applications. Bioconjug Chem 2013; 24:215-23. [PMID: 23297747 DOI: 10.1021/bc3005073] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescent biosensors based on environmentally sensitive dyes enable visualization and quantification of endogenous protein activation within living cells. Merocyanine dyes are especially useful for live cell imaging applications, as they are extraordinarily bright, have long wavelengths of excitation and emission, and can exhibit readily detectable fluorescence changes in response to environment. We sought to systematically examine the effects of structural features on key photophysical properties, including dye brightness, environmental responsiveness, and photostability, through the synthesis of a library of 25 merocyanine dyes, derived from combinatorial reaction of 5 donor and 5 acceptor heterocycles. Four of these dyes showed optimal properties for specific imaging applications and were subsequently prepared with reactive side chains and enhanced aqueous solubility using a one-pot synthetic method. The new dyes were then applied within a biosensor design for Cdc42 activation, where dye mero60 showed a remarkable 1470% increase in fluorescence intensity on binding activated Cdc42 in vitro. The dye-based biosensors were used to report activation of endogenous Cdc42 in living cells.
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10
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Jacquemin D, Zhao Y, Valero R, Adamo C, Ciofini I, Truhlar DG. Verdict: Time-Dependent Density Functional Theory "Not Guilty" of Large Errors for Cyanines. J Chem Theory Comput 2012; 8:1255-9. [PMID: 26596742 DOI: 10.1021/ct200721d] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We assess the accuracy of eight Minnesota density functionals (M05 through M08-SO) and two others (PBE and PBE0) for the prediction of electronic excitation energies of a family of four cyanine dyes. We find that time-dependent density functional theory (TDDFT) with the five most recent of these functionals (from M06-HF through M08-SO) is able to predict excitation energies for cyanine dyes within 0.10-0.36 eV accuracy with respect to the most accurate available Quantum Monte Carlo calculations, providing a comparable accuracy to the latest generation of CASPT2 calculations, which have errors of 0.16-0.34 eV. Therefore previous conclusions that TDDFT cannot treat cyanine dyes reasonably accurately must be revised.
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Affiliation(s)
- Denis Jacquemin
- Laboratoire CEISAM - UMR CNRS 6230, Université de Nantes , 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Yan Zhao
- Commercial Printing Engine Lab, HP Laboratories, Hewlett-Packard Co. , 1501 Page Mill Road, Palo Alto, California 94304, United States
| | - Rosendo Valero
- Department of Chemistry, University of Coimbra , 3004-535 Coimbra, Portugal
| | - Carlo Adamo
- École Nationale Supérieure de Chimie de Paris - Chimie ParisTech , LECIME, UMR 7575 CNRS, 11 rue Pierre et Marie Curie, 75005 Paris, France
| | - Ilaria Ciofini
- École Nationale Supérieure de Chimie de Paris - Chimie ParisTech , LECIME, UMR 7575 CNRS, 11 rue Pierre et Marie Curie, 75005 Paris, France
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota , Minneapolis, Minnesota 55455-0431, United States
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11
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Kowalczyk T, Yost SR, Voorhis TV. Assessment of the ΔSCF density functional theory approach for electronic excitations in organic dyes. J Chem Phys 2011; 134:054128. [DOI: 10.1063/1.3530801] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Kulinich AV, Derevyanko NA, Mikitenko EK, Ishchenko AA. Merocyanines based on 1,3-indanedione: electronic structure and solvatochromism. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1821] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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Han WG, Giammona DA, Bashford D, Noodleman L. Density functional theory analysis of structure, energetics, and spectroscopy for the Mn-Fe active site of Chlamydia trachomatis ribonucleotide reductase in four oxidation states. Inorg Chem 2010; 49:7266-81. [PMID: 20604534 PMCID: PMC2919573 DOI: 10.1021/ic902051t] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Models for the Mn-Fe active site structure of ribonucleotide reductase (RNR) from pathogenic bacteria Chlamydia trachomatis (Ct) in different oxidation states have been studied in this paper, using broken-symmetry density functional theory (DFT) incorporated with the conductor like screening (COSMO) solvation model and also with finite-difference Poisson-Boltzmann self-consistent reaction field (PB-SCRF) calculations. The detailed structures for the reduced Mn(II)-Fe(II), the met Mn(III)-Fe(III), the oxidized Mn(IV)-Fe(III) and the superoxidized Mn(IV)-Fe(IV) states are predicted. The calculated properties, including geometries, (57)Fe Mossbauer isomer shifts and quadrupole splittings, and (57)Fe and (55)Mn electron nuclear double resonance (ENDOR) hyperfine coupling constants, are compared with the available experimental data. The Mössbauer and energetic calculations show that the (mu-oxo, mu-hydroxo) models better represent the structure of the Mn(IV)-Fe(III) state than the di-mu-oxo models. The predicted Mn(IV)-Fe(III) distances (2.95 and 2.98 A) in the (mu-oxo, mu-hydroxo) models are in agreement with the extended X-ray absorption fine structure (EXAFS) experimental value of 2.92 A (Younker et al. J. Am. Chem. Soc. 2008, 130, 15022-15027). The effect of the protein and solvent environment on the assignment of the Mn metal position is examined by comparing the relative energies of alternative mono-Mn(II) active site structures. It is proposed that if the Mn(II)-Fe(II) protein is prepared with prior addition of Mn(II) or with Mn(II) richer than Fe(II), Mn is likely positioned at metal site 2, which is further from Phe127.
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Affiliation(s)
- Wen-Ge Han
- Department of Molecular Biology, TPC15, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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14
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Han WG, Noodleman L. DFT calculations of comparative energetics and ENDOR/Mössbauer properties for two protonation states of the iron dimer cluster of ribonucleotide reductase intermediate X. Dalton Trans 2009:6045-57. [PMID: 19623405 PMCID: PMC2746754 DOI: 10.1039/b903847g] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two models (I and II) for the active site structure of class-I ribonucleotide reductase (RNR) intermediate X in subunit R2 have been studied in this paper, using broken-symmetry density functional theory (DFT) incorporated with the conductor like screening (COSMO) solvation model and with the finite-difference Poisson-Boltzmann self-consistent reaction field (PB-SCRF) calculations. Only one of the bridging groups between the two iron centers is different between model-I and model-II. Model-I contains two mu-oxo bridges, while model-II has one bridging oxo and one bridging hydroxo. These are large active site models including up to the fourth coordination shell H-bonding residues. Mössbauer and ENDOR hyperfine property calculations show that model-I is more likely to represent the active site structure of RNR-X. However, energetically our pK(a) calculations at first highly favored the bridging oxo and hydroxo (in model-II) structure of the diiron center rather than having the di-oxo bridge (in model-I). Since the Arg236 and the nearby Lys42, which are very close to the diiron center, are on the protein surface of RNR-R2, it is highly feasible that one or two anion groups in solution would interact with the positively charged side chains of Arg236 and Lys42. The anion group(s) can be a reductant, phosphate, sulfate, nitrate, and other negatively charged groups existing in biological environments or in the buffer of the experiment. Since sulfate ions certainly exist in the buffer of the ENDOR experiment, we have examined the effect of the sulfate (SO(4)(2-), surrounded by explicit water molecules) H-bonding to the side chain of Arg236. We find that when sulfate interacts with Arg236, the carboxylate group of Asp237 tends to be protonated, and once Asp237 is protonated, the Fe(iii)Fe(iv) center in X favors the di-oxo bridge (model-I). This would explain that the ENDOR observed RNR-X active site structure is likely to be represented by model-I rather than model-II.
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Affiliation(s)
- Wen-Ge Han
- Department of Molecular Biology TPC15 The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, California 92037
| | - Louis Noodleman
- Department of Molecular Biology TPC15 The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, California 92037
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15
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Kulinich AV, Ishchenko AA. Merocyanine dyes: synthesis, structure, properties and applications. RUSSIAN CHEMICAL REVIEWS 2009. [DOI: 10.1070/rc2009v078n02abeh003900] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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