1
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Gałęcki K, Kowalska-Baron A, Nowak KE, Gajda A, Kolesińska B. Steady-State and Time-Resolved Fluorescence Study of Selected Tryptophan-Containing Peptides in an AOT Reverse Micelle Environment. Int J Mol Sci 2023; 24:15438. [PMID: 37895121 PMCID: PMC10607525 DOI: 10.3390/ijms242015438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
The aim of this study was to demonstrate the utility of time-resolved fluorescence spectroscopy in the detection of subtle changes in the local microenvironment of a tryptophan chromophore in a confined and crowded medium of AOT reverse micelles, which mimic biological membranes and cell compartmentalization. For this purpose, fluorescence properties of L-tryptophan and several newly synthesized tryptophan-containing peptides in buffer and in an AOT reverse micelle medium were determined. It was shown that insertion of tryptophan and its short di- and tripeptides inside micelles led to evident changes in both the steady-state emission spectra and in fluorescence decay kinetics. The observed differences in spectral characteristics, such as a blue shift in the emission maxima, changes in the average fluorescence lifetime, and the appearance of environmental-dependent fluorescent species, showed the utility of time-resolved fluorescence spectroscopy as a sensitive tool for detecting subtle conformational modifications in tryptophan and its peptides induced by changes in polarity, viscosity, and specific interactions between chromophores and water molecules/polar groups/ions that occur inside reverse micelles.
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Affiliation(s)
- Krystian Gałęcki
- Institute of Natural Products and Cosmetics, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego St. 2/22, 90-537 Lodz, Poland;
| | - Agnieszka Kowalska-Baron
- Institute of Natural Products and Cosmetics, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego St. 2/22, 90-537 Lodz, Poland;
| | - Katarzyna E. Nowak
- Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska St. 141/143, 90-236 Lodz, Poland;
| | - Anna Gajda
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego St. 114, 90-924 Lodz, Poland; (A.G.); (B.K.)
| | - Beata Kolesińska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego St. 114, 90-924 Lodz, Poland; (A.G.); (B.K.)
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2
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Li H, Cao S, Zhang S, Chen J, Xu J, Knutson JR. Ultrafast Förster resonance energy transfer from tyrosine to tryptophan in monellin: potential intrinsic spectroscopic ruler. Phys Chem Chem Phys 2023; 25:7239-7250. [PMID: 36853740 DOI: 10.1039/d2cp05842a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Ultrafast Förster Resonance Energy Transfer (FRET) between tyrosine (Tyr) and tryptophan (Trp) residues in the protein monellin has been investigated using picosecond and femtosecond time-resolved fluorescence spectroscopy. Decay associated spectra (DAS) and time-resolved emission spectra (TRES) taken with the different excitation wavelengths of 275, 290 and 295 nm were constructed via global analysis. At two of those three excitation loci (275 and 290 nm), earmarks of energy transfer from Tyr to Trp in monellin are seen, and particularly when the excitation is 275 nm, the energy transfer between Tyr and Trp clearly changes the signature emission DAS shape to that indicating excited state reaction (especially on the red side of fluorescence emission, near 380 nm). Those FRET signatures may overlap with the conventional signatory DAS in heterogeneous systems. When overlap and addition occur between FRET type DAS and "full positive" QSSQ (quasi-static self-quenching), mixed DAS shapes will emerge that still show "positive blue side and negative red sides", just with zero crossing shifted. In addition, excitation decay associated spectra (EDAS) taken with the different emission wavelengths of 330, 350 and 370 nm were constructed. In the study of protein dynamics, ultrafast FRET between Tyr and Trp could provide a basis for an intrinsic (non-perturbing) "spectroscopic ruler", potentially a powerful tool to detect even slight changes in protein structures.
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Affiliation(s)
- Haoyang Li
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.
| | - Simin Cao
- Key Laboratory of 3D Micro/Nano Fabrication and Characterization of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310024, China
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.
| | - Jay R Knutson
- Laboratory of Advanced Microscopy & Biophotonics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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3
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Li H, Cao S, Chen J, Zhang S, Xu J, Knutson JR. Ultrafast fluorescence dynamics of NADH in aprotic solvents: Quasi-static self-quenching unmasked. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2022.114384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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4
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Trachman RJ, Link KA, Knutson JR, Ferré-D'Amaré AR. Characterizing Fluorescence Properties of Turn-on RNA Aptamers. Methods Mol Biol 2023; 2568:25-36. [PMID: 36227560 PMCID: PMC9812286 DOI: 10.1007/978-1-0716-2687-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Fluorescent RNA aptamers are tools for studying RNA localization and interactions in vivo. The photophysical properties of these in vitro selected RNAs should be characterized prior to cellular imaging experiments. Here, we describe the process of determining the fluorophore affinity, fluorescence enhancement, and fluorescence lifetime(s) of the Mango-III fluorescence turn-on aptamer. Parameters determined through these protocols will aid in establishing conditions for live-cell imaging.
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Affiliation(s)
- Robert J Trachman
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Katie A Link
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Jay R Knutson
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA.
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5
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Determination of fluorescence quantum yields and decay times of NADH and FAD in water-alcohol mixtures: The analysis of radiative and nonradiative relaxation pathways. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.114388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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6
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Li H, Jiang G, Jia M, Cao S, Zhang S, Chen J, Sun H, Xu J, Knutson JR. Ultrafast Förster resonance energy transfer between tyrosine and tryptophan: potential contributions to protein-water dynamics measurements. Phys Chem Chem Phys 2022; 24:18055-18066. [PMID: 35861343 DOI: 10.1039/d2cp02139k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Ultrafast Förster Resonance Energy Transfer (FRET) between Tyrosine (Tyr, Y) and Tryptophan (Trp, W) in the model peptides Trp-(Pro)n-Tyr (WPnY) has been investigated using a femtosecond up-conversion spectrophotofluorometer. The ultrafast energy transfer process (<100 ps) in short peptides (WY, WPY and WP2Y) has been resolved. In fact, this FRET rate is found to be mixed with the rates of solvent relaxation (SR), ultrafast population decay (QSSQ) and other lifetime components. To further dissect and analyze the FRET, a spectral working model is constructed, and the contribution of a FRET lifetime is separated by reconciling the shapes of decay associated spectra (DAS). Surprisingly, FRET efficiency did not decrease monotonically with the growth of the peptide chain (as expected) but increased first and then decreased. The highest FRET efficiency occurred in peptide WPY. The kinetic results have been accompanied with molecular dynamics simulations that reconcile and explain this strange phenomenon: due to the strong interaction between amino acids, the distance between the donor and receptor in peptide WPY is actually closest, resulting in the fastest FRET. In addition, the FRET lifetimes (τcal) were estimated within the molecular dynamics simulations, and they were consistent with the lifetimes (τexp) separated out by the experimental measurements and the DAS working model. This benchmark study has implications for both previous and future studies of protein ultrafast dynamics. The approach taken can be generalized for the study of proximate tyrosine and tryptophan in proteins and it suggests spectral strategies for extracting mixed rates in other complex FRET problems.
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Affiliation(s)
- Haoyang Li
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.
| | - Guanyu Jiang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.
| | - Menghui Jia
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.
| | - Simin Cao
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.
| | - Haitao Sun
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.
| | - Jay R Knutson
- Laboratory of Advanced Microscopy & Biophotonics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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7
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Cao S, Li H, Zhao Z, Zhang S, Chen J, Xu J, Knutson JR, Brand L. Ultrafast Fluorescence Spectroscopy via Upconversion and Its Applications in Biophysics. Molecules 2021; 26:molecules26010211. [PMID: 33401638 PMCID: PMC7794851 DOI: 10.3390/molecules26010211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 11/25/2022] Open
Abstract
In this review, the experimental set-up and functional characteristics of single-wavelength and broad-band femtosecond upconversion spectrophotofluorometers developed in our laboratory are described. We discuss applications of this technique to biophysical problems, such as ultrafast fluorescence quenching and solvation dynamics of tryptophan, peptides, proteins, reduced nicotinamide adenine dinucleotide (NADH), and nucleic acids. In the tryptophan dynamics field, especially for proteins, two types of solvation dynamics on different time scales have been well explored: ~1 ps for bulk water, and tens of picoseconds for “biological water”, a term that combines effects of water and macromolecule dynamics. In addition, some proteins also show quasi-static self-quenching (QSSQ) phenomena. Interestingly, in our more recent work, we also find that similar mixtures of quenching and solvation dynamics occur for the metabolic cofactor NADH. In this review, we add a brief overview of the emerging development of fluorescent RNA aptamers and their potential application to live cell imaging, while noting how ultrafast measurement may speed their optimization.
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Affiliation(s)
- Simin Cao
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China; (S.C.); (H.L.); (Z.Z.); (S.Z.); (J.C.)
| | - Haoyang Li
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China; (S.C.); (H.L.); (Z.Z.); (S.Z.); (J.C.)
| | - Zenan Zhao
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China; (S.C.); (H.L.); (Z.Z.); (S.Z.); (J.C.)
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China; (S.C.); (H.L.); (Z.Z.); (S.Z.); (J.C.)
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China; (S.C.); (H.L.); (Z.Z.); (S.Z.); (J.C.)
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China; (S.C.); (H.L.); (Z.Z.); (S.Z.); (J.C.)
- Correspondence: (J.X.); (J.R.K.); Tel.: +86-21-6223-3936 (J.X.); +1-301-496-2557 (J.R.K.)
| | - Jay R. Knutson
- Laboratory for Advanced Microscopy and Biophotonics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Correspondence: (J.X.); (J.R.K.); Tel.: +86-21-6223-3936 (J.X.); +1-301-496-2557 (J.R.K.)
| | - Ludwig Brand
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA;
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8
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Gorbunova IA, Sasin ME, Beltukov YM, Semenov AA, Vasyutinskii OS. Anisotropic relaxation in NADH excited states studied by polarization-modulation pump-probe transient spectroscopy. Phys Chem Chem Phys 2020; 22:18155-18168. [PMID: 32766648 DOI: 10.1039/d0cp02496a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present the results of experimental and theoretical studies of fast anisotropic relaxation and rotational diffusion in the first electron excited state of biological coenzyme NADH in water-ethanol solutions. The experiments have been carried out by means of a novel polarization-modulation transient method and fluorescence polarization spectroscopy. For interpretation of the experimental results a model of the anisotropic relaxation in terms of scalar and vector properties of transition dipole moments has been developed based on the Born-Oppenheimer approximation. This model allows for the description of fast isotropic and anisotropic excited state relaxation under excitation of molecules by ultrafast laser pulses in transient absorption and upconversion experiments. The results obtained suggest that the dynamics of anisotropic rovibronic relaxation in NADH under excitation with 100 fs pump laser pulses can be characterised by a single vibrational relaxation time τv lying in the range of 2-15 ps and a single rotation diffusion time τr lying in the range of 100-450 ps, both depending on ethanol concentration. The dependence of the times τv and τr on the solution polarity (static permittivity) and viscosity has been determined and analyzed. Limiting values of the term P2(cos θ) describing the rotation of the transition dipole moment in the course of vibrational relaxation have been determined from experiments as a function of ethanol concentration and analyzed.
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Affiliation(s)
| | - Maxim E Sasin
- Ioffe Institute, Polytekhnicheskaya 26, St. Petersburg, Russia.
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9
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Cao S, Li H, Liu Y, Wang M, Zhang M, Zhang S, Chen J, Xu J, Knutson JR, Brand L. Dehydrogenase Binding Sites Abolish the "Dark" Fraction of NADH: Implication for Metabolic Sensing via FLIM. J Phys Chem B 2020; 124:6721-6727. [PMID: 32660250 PMCID: PMC7477841 DOI: 10.1021/acs.jpcb.0c04835] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The fluorescence of dinucleotide NADH has been exploited for decades to determine the redox state of cells and tissues in vivo and in vitro. Particularly, nanosecond (ns) fluorescence lifetime imaging microscopy (FLIM) of NADH (in free vs bound forms) has recently offered a label-free readout of mitochondrial function and allowed the different "pools" of NADH to be distinguished in living cells. In this study, the ultrafast fluorescence dynamics of NADH-dehydrogenase (MDH/LDH) complexes have been investigated by using both a femtosecond (fs) upconversion spectrophotofluorometer and a picosecond (ps) time-correlated single photon counting (TCSPC) apparatus. With these enhanced time-resolved tools, a few-picosecond decay process with a signatory spectrum was indeed found for bound NADH, and it can best be ascribed to the solvent relaxation originating in "bulk water". However, it is quite unlike our previously discovered ultrafast "dark" component (∼26 ps) that is prominent in free NADH (Chemical Physics Letters 2019, 726, 18-21). For these two critical protein-bound NADH exemplars, the decay transients lack the ultrafast quenching that creates the "dark" subpopulation of free NADH. Therefore, we infer that the apparent ratio of free to bound NADH recovered by ordinary (>50 ps) FLIM methods may be low, since the "dark" molecule subpopulation (lifetime too short for conventional FLIM), which effectively hides about a quarter of free molecules, is not present in the dehydrogenase-bound state.
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Affiliation(s)
- Simin Cao
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Haoyang Li
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Yangyi Liu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Mengyu Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Mengjie Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Jay R Knutson
- Laboratory for Advanced Microscopy and Biophotonics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ludwig Brand
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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10
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Cao S, Li H, Liu Y, Zhang M, Wang M, Zhou Z, Chen J, Zhang S, Xu J, Knutson JR. Femtosecond Fluorescence Spectra of NADH in Solution: Ultrafast Solvation Dynamics. J Phys Chem B 2020; 124:771-776. [PMID: 31941277 PMCID: PMC7477843 DOI: 10.1021/acs.jpcb.9b10656] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ultrafast solvation dynamics of reduced nicotinamide adenine dinucleotide (NADH) free in solution has been investigated, using both a femtosecond upconversion spectrophotofluorometer and a picosecond time-correlated single-photon counting (TCSPC) apparatus. The familiar time constant of solvent relaxation originating in "bulk water" was found to be ∼1.4 ps, revealing ultrafast solvent reorientation upon excitation. We also found a slower spectral relaxation process with an apparent time of 27 ps, suggesting there could either be dissociable "biological water" hydration sites on the surface of NADH or internal dielectric rearrangements of the flexible solvated molecule on that timescale. In contrast, the femtosecond fluorescence anisotropy measurement revealed that rotational diffusion happened on two different timescales (3.6 ps (local) and 141 ps (tumbling)); thus, any dielectric rearrangement scenario for the 27 ps relaxation must occur without significant chromophore oscillator rotation. The coexistence of quasi-static self quenching (QSSQ) with the slower relaxation is also discussed.
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Affiliation(s)
- Simin Cao
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai 200062 , China
| | - Haoyang Li
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai 200062 , China
| | - Yangyi Liu
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai 200062 , China
| | - Mengjie Zhang
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai 200062 , China
| | - Mengyu Wang
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai 200062 , China
| | - Zhongneng Zhou
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai 200062 , China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai 200062 , China
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai 200062 , China
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai 200062 , China
| | - Jay R Knutson
- Laboratory for Advanced Microscopy and Biophotonics, National Heart, Lung and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
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11
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Cao S, Zhou Z, Li H, Jia M, Liu Y, Wang M, Zhang M, Zhang S, Chen J, Xu J, Knutson JR. A fraction of NADH in solution is "dark": Implications for metabolic sensing via fluorescence lifetime. Chem Phys Lett 2019; 726:18-21. [PMID: 32921799 PMCID: PMC7486008 DOI: 10.1016/j.cplett.2019.04.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The metabolic cofactor and energy carrier NADH (nicotinamide adenine dinucleotide, reduced) has fluorescence yield and lifetime that depends strongly on conformation, a fact that has enabled metabolic monitoring of cells via FLIM (Fluorescence Lifetime Microscopy). Using femtosecond fluorescence upconversion, we show that this molecule in solution participates in ultrafast self-quenching along with both bulk solvent relaxation and spectral relaxation on 1.4 and 26 ps timescales. This, in effect, means up to a third of NADH is effectively "dark" for FLIM in the 400-500 nm observation window commonly employed. Methods to compensate for, avoid or measure dark species corrections are outlined.
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Affiliation(s)
- Simin Cao
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Zhongneng Zhou
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Haoyang Li
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Menghui Jia
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Yangyi Liu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Mengyu Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Mengjie Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Jay R. Knutson
- Laboratory for Advanced Microscopy and Biophotonics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, United States
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12
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Trachman RJ, Autour A, Jeng SCY, Abdolahzadeh A, Andreoni A, Cojocaru R, Garipov R, Dolgosheina EV, Knutson JR, Ryckelynck M, Unrau PJ, Ferré-D'Amaré AR. Structure and functional reselection of the Mango-III fluorogenic RNA aptamer. Nat Chem Biol 2019; 15:472-479. [PMID: 30992561 DOI: 10.1038/s41589-019-0267-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 03/06/2019] [Indexed: 11/09/2022]
Abstract
Several turn-on RNA aptamers that activate small-molecule fluorophores have been selected in vitro. Among these, the ~30 nucleotide Mango-III is notable because it binds the thiazole orange derivative TO1-Biotin with high affinity and fluoresces brightly (quantum yield 0.55). Uniquely among related aptamers, Mango-III exhibits biphasic thermal melting, characteristic of molecules with tertiary structure. We report crystal structures of TO1-Biotin complexes of Mango-III, a structure-guided mutant Mango-III(A10U), and a functionally reselected mutant iMango-III. The structures reveal a globular architecture arising from an unprecedented pseudoknot-like connectivity between a G-quadruplex and an embedded non-canonical duplex. The fluorophore is restrained into a planar conformation by the G-quadruplex, a lone, long-range trans Watson-Crick pair (whose A10U mutation increases quantum yield to 0.66), and a pyrimidine perpendicular to the nucleobase planes of those motifs. The improved iMango-III and Mango-III(A10U) fluoresce ~50% brighter than enhanced green fluorescent protein, making them suitable tags for live cell RNA visualization.
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Affiliation(s)
- Robert J Trachman
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Alexis Autour
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, Strasbourg, France
| | - Sunny C Y Jeng
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Amir Abdolahzadeh
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Alessio Andreoni
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Razvan Cojocaru
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Ramil Garipov
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Elena V Dolgosheina
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jay R Knutson
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Michael Ryckelynck
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, Strasbourg, France
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD, USA.
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13
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Zelent B, Bialas C, Gryczynski I, Chen P, Chib R, Lewerissa K, Corradini MG, Ludescher RD, Vanderkooi JM, Matschinsky FM. Tryptophan Fluorescence Yields and Lifetimes as a Probe of Conformational Changes in Human Glucokinase. J Fluoresc 2017; 27:1621-1631. [PMID: 28432632 PMCID: PMC6025808 DOI: 10.1007/s10895-017-2099-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 04/04/2017] [Indexed: 10/19/2022]
Abstract
Five variants of glucokinase (ATP-D-hexose-6-phosphotransferase, EC 2.7.1.1) including wild type and single Trp mutants with the Trp residue at positions 65, 99, 167 and 257 were prepared. The fluorescence of Trp in all locations studied showed intensity changes when glucose bound, indicating that conformational change occurs globally over the entire protein. While the fluorescence quantum yield changes upon glucose binding, the enzyme's absorption spectra, emission spectra and fluorescence lifetimes change very little. These results are consistent with the existence of a dark complex for excited state Trp. Addition of glycerol, L-glucose, sucrose, or trehalose increases the binding affinity of glucose to the enzyme and increases fluorescence intensity. The effect of these osmolytes is thought to shift the protein conformation to a condensed, high affinity form. Based upon these results, we consider the nature of quenching of the Trp excited state. Amide groups are known to quench indole fluorescence and amides of the polypeptide chain make interact with excited state Trp in the relatively unstructured, glucose-free enzyme. Also, removal of water around the aromatic ring by addition of glucose substrate or osmolyte may reduce the quenching.
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Affiliation(s)
- Bogumil Zelent
- Department of Biochemistry and Biophysics and Diabetes Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Food Science, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.
| | - Chris Bialas
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ignacy Gryczynski
- Department of Cell Biology and Immunology, Center for Fluorescence Technologies and Nanomedicine, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Pan Chen
- Department of Biochemistry and Biophysics and Diabetes Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Rahul Chib
- Department of Food Science, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Karina Lewerissa
- Department of Food Science, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Maria G Corradini
- Department of Food Science, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Department of Food Science, University of Massachusetts Amherst, Massachusetts, MA, USA
| | - Richard D Ludescher
- Department of Food Science, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Jane M Vanderkooi
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Franz M Matschinsky
- Department of Biochemistry and Biophysics and Diabetes Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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14
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Sousa G, Gaulier G, Bonacina L, Wolf JP. Discriminating Bio-aerosols from Non-Bio-aerosols in Real-Time by Pump-Probe Spectroscopy. Sci Rep 2016; 6:33157. [PMID: 27619546 PMCID: PMC5020503 DOI: 10.1038/srep33157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/22/2016] [Indexed: 11/09/2022] Open
Abstract
The optical identification of bioaerosols in the atmosphere and its discrimination against combustion related particles is a major issue for real-time, field compatible instruments. In the present paper, we show that by embedding advanced pump-probe depletion spectroscopy schemes in a portable instrument, it is possible to discriminate amino acid containing airborne particles (bacteria, humic particles, etc.) from poly-cyclic aromatic hydrocarbon containing combustion particles (Diesel droplets, soot, vehicle exhausts) with high selectivity. Our real-time, multi-modal device provides, in addition to the pump-probe depletion information, fluorescence spectra (over 32 channels), fluorescence lifetime and Mie scattering patterns of each individually flowing particle in the probed air.
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Affiliation(s)
- Gustavo Sousa
- Université de Genève, GAP-Biophotonics, 22 chemin de Pinchat, Carouge, 1211 Geneva 4, Switzerland
| | - Geoffrey Gaulier
- Université de Genève, GAP-Biophotonics, 22 chemin de Pinchat, Carouge, 1211 Geneva 4, Switzerland
| | - Luigi Bonacina
- Université de Genève, GAP-Biophotonics, 22 chemin de Pinchat, Carouge, 1211 Geneva 4, Switzerland
| | - Jean-Pierre Wolf
- Université de Genève, GAP-Biophotonics, 22 chemin de Pinchat, Carouge, 1211 Geneva 4, Switzerland
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15
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Li L, Yi H, Chang M, Cao X, Zhou Z, Qin C, Zhang S, Pan H, Chen Y, Xu J. Fluorescence dynamics of N-terminal Trp–Trp residues in polypeptide: intrinsic indicators for monitoring pH. Sci Bull (Beijing) 2015. [DOI: 10.1007/s11434-015-0942-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Jia M, Yi H, Chang M, Cao X, Li L, Zhou Z, Pan H, Chen Y, Zhang S, Xu J. Fluorescence kinetics of Trp-Trp dipeptide and its derivatives in water via ultrafast fluorescence spectroscopy. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 149:243-8. [PMID: 26111991 DOI: 10.1016/j.jphotobiol.2015.06.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 05/23/2015] [Accepted: 06/16/2015] [Indexed: 11/18/2022]
Abstract
Ultrafast fluorescence dynamics of Tryptophan-Tryptophan (Trp-Trp/Trp2) dipeptide and its derivatives in water have been investigated using a picosecond resolved time correlated single photon counting (TCSPC) apparatus together with a femtosecond resolved upconversion spectrophotofluorometer. The fluorescence decay profiles at multiple wavelengths were fitted by a global analysis technique. Nanosecond fluorescence kinetics of Trp2, N-tert-butyl carbonyl oxygen-N'-aldehyde group-l-tryptophan-l-tryptophan (NBTrp2), l-tryptophan-l-tryptophan methyl ester (Trp2Me), and N-acetyl-l-tryptophan-l-tryptophan methyl ester (NATrp2Me) exhibit multi-exponential decays with the average lifetimes of 1.99, 3.04, 0.72 and 1.22ns, respectively. Due to the intramolecular interaction between two Trp residues, the "water relaxation" lifetime was observed around 4ps, and it is noticed that Trp2 and its derivatives also exhibit a new decay with a lifetime of ∼100ps, while single-Trp fluorescence decay in dipeptides/proteins shows 20-30ps. The intramolecular interaction lifetime constants of Trp2, NBTrp2, Trp2Me and NATrp2Me were then calculated to be 3.64, 0.93, 11.52 and 2.40ns, respectively. Candidate mechanisms (including heterogeneity, solvent relaxation, quasi static self-quenching or ET/PT quenching) have been discussed.
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Affiliation(s)
- Menghui Jia
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Hua Yi
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Mengfang Chang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Xiaodan Cao
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Lei Li
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Zhongneng Zhou
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Haifeng Pan
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Yan Chen
- Tongji Hospital Affiliated to Tongji University, 389 Xincun Road, Shanghai 200065, China
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
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17
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Mora AK, Murudkar S, Singh PK, Nath S. Effect of fibrillation on the excited state dynamics of tryptophan in serum protein – A time-resolved fluorescence study. J Photochem Photobiol A Chem 2015. [DOI: 10.1016/j.jphotochem.2014.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Callis PR. Binding phenomena and fluorescence quenching. II: Photophysics of aromatic residues and dependence of fluorescence spectra on protein conformation. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.04.051] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Binding phenomena and fluorescence quenching. I: Descriptive quantum principles of fluorescence quenching using a supermolecule approach. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.04.050] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Biesso A, Xu J, Muíño PL, Callis PR, Knutson JR. Charge invariant protein-water relaxation in GB1 via ultrafast tryptophan fluorescence. J Am Chem Soc 2014; 136:2739-47. [PMID: 24456037 PMCID: PMC4004251 DOI: 10.1021/ja406126a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
The
protein–water interface is a critical determinant of
protein structure and function, yet the precise nature of dynamics
in this complex system remains elusive. Tryptophan fluorescence has
become the probe of choice for such dynamics on the picosecond time
scale (especially via fluorescence “upconversion”).
In the absence of ultrafast (“quasi-static”) quenching
from nearby groups, the TDFSS (time-dependent fluorescence Stokes
shift) for exposed Trp directly reports on dipolar relaxation near
the interface (both water and polypeptide). The small protein GB1
contains a single Trp (W43) of this type, and its structure is refractory
to pH above 3. Thus, it can be used to examine the dependence of dipolar
relaxation upon charge reconfiguration with titration. Somewhat surprisingly,
the dipolar dynamics in the 100 fs to 100 ps range were unchanged
with pH, although nanosecond yield, rates, and access all changed.
These results were rationalized with the help of molecular dynamics
(including QM-MM) simulations that reveal a balancing, sometimes even
countervailing influence of protein and water dipoles. Interestingly,
these simulations also showed the dominant influence of water molecules
which are associated with the protein interface for up to 30 ps yet
free to rotate at approximately “bulk” water rates.
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Affiliation(s)
- Arianna Biesso
- Optical Spectroscopy Section, Laboratory of Molecular Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
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21
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Biesso A, Xu J, Knutson JR. Upconversion spectrophotofluorometry. Methods Mol Biol 2014; 1076:303-319. [PMID: 24108631 PMCID: PMC4196937 DOI: 10.1007/978-1-62703-649-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
As the other chapters attest, sensitivity of fluorescent molecules to their local environment has created powerful tools in the study of molecular biology, particularly in the study of protein, DNA, and lipid dynamics. Surprisingly, even events faster than the nanosecond lifetimes of fluorophores are important in protein function, and in particular, events lasting just a few ps reflect on water motion and the coupled dynamics of proteins. These ultrafast phenomena can best be studied by using the same laser that excites fluorescence to also "strobe" the emission, providing sub-picosecond time slices of the action. We explain the strobing "upconversion" technique and some limits on its execution.
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22
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Maity I, Mukherjee TK, Das AK. Photophysical study of a π-stacked β-sheet nanofibril forming peptide bolaamphiphile hydrogel. NEW J CHEM 2014. [DOI: 10.1039/c3nj00814b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Meng X, Harricharran T, Juszczak LJ. A spectroscopic survey of substituted indoles reveals consequences of a stabilized 1Lb transition. Photochem Photobiol 2012; 89:40-50. [PMID: 22882557 DOI: 10.1111/j.1751-1097.2012.01219.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Accepted: 07/31/2012] [Indexed: 11/28/2022]
Abstract
Although tryptophan is a natural probe of protein structure, interpretation of its fluorescence emission spectrum is complicated by the presence of two electronic transitions, (1)L(a) and (1)L(b). Theoretical calculations show that a point charge adjacent to either ring of the indole can shift the emission maximum. This study explores the effect of pyrrole and benzyl ring substitutions on the transitions' energy via absorption and fluorescence spectroscopy, and anisotropy and lifetime measurements. The survey of indole derivatives shows that methyl substitutions on the pyrrole ring effect (1)L(a) and (1)L(b) energies in tandem, whereas benzyl ring substitutions with electrophilic groups lift the (1)L(a)/(1)L(b) degeneracy. For 5- and 6-hydroxyindole in cyclohexane, (1)L(a) and (1)L(b) transitions are resolved. This finding provides for (1)L(a) origin assignment in the absorption and excitation spectra for indole vapor. The 5- and 6-hydroxyindole excitation spectra show that despite a blue-shifted emission spectrum, both the (1)L(a) and (1)L(b) transitions contribute to emission. Fluorescence lifetimes of 1(0) ns for 5-hydroxyindole are consistent with a charge acceptor-induced increase in the nonradiative rate (1).
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Affiliation(s)
- Xianwei Meng
- Brooklyn College, The City University of New York, New York, NY, USA
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24
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Messina F, El-Zohry AM, Mohammed OF, Chergui M. The Role of Site-Specific Hydrogen Bonding Interactions in the Solvation Dynamics of N-Acetyltryptophanamide. J Phys Chem B 2012; 116:10730-8. [DOI: 10.1021/jp305363y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Fabrizio Messina
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide
(LSU), ISIC, Faculté des Sciences de Base, station 6, CH-1015
Lausanne-Dorigny, Switzerland
| | - Ahmed M. El-Zohry
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide
(LSU), ISIC, Faculté des Sciences de Base, station 6, CH-1015
Lausanne-Dorigny, Switzerland
- Chemistry Department, Faculty of Science, Assiut University, Assiut 71516, Egypt
| | - Omar F. Mohammed
- Chemistry Department, Faculty of Science, Assiut University, Assiut 71516, Egypt
| | - Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide
(LSU), ISIC, Faculté des Sciences de Base, station 6, CH-1015
Lausanne-Dorigny, Switzerland
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25
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Rondi A, Bonacina L, Trisorio A, Hauri C, Wolf JP. Coherent manipulation of free amino acids fluorescence. Phys Chem Chem Phys 2012; 14:9317-22. [PMID: 22395710 DOI: 10.1039/c2cp23357f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coherent manipulation of molecular wavepackets in biomolecules might contribute to the quest towards label-free cellular imaging and protein identification. We report the use of optimally tailored UV laser pulses in pump-probe depletion experiments that selectively enhance or decrease fluorescence between two aromatic amino acids: tryptophan (Trp) and tyrosine (Tyr). Selective fluorescence modulation is achieved with a contrast of ~35%. A neat modification of the time-dependent fluorescence depletion signal of Trp is observed, while the Tyr transient trace remains unchanged. The mechanism invoked for explaining the change of the depletion of Trp is a less efficient coupling between the fluorescing state and the higher non-radiative excited states by the optimally shaped pulse, than by the reference pulse.
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Affiliation(s)
- A Rondi
- GAP-Biophotonics, University of Geneva, 22 ch. de Pinchat, CH-1211 Geneva 4, Switzerland
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26
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Pan CP, Muiño PL, Barkley MD, Callis PR. Correlation of Tryptophan Fluorescence Spectral Shifts and Lifetimes Arising Directly from Heterogeneous Environment. J Phys Chem B 2011; 115:3245-53. [PMID: 21370844 DOI: 10.1021/jp111925w] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Chia-Pin Pan
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Pedro L. Muiño
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Mary D. Barkley
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Patrik R. Callis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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27
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Kwon OH, Yoo TH, Othon CM, Van Deventer JA, Tirrell DA, Zewail AH. Hydration dynamics at fluorinated protein surfaces. Proc Natl Acad Sci U S A 2010; 107:17101-6. [PMID: 20855583 PMCID: PMC2951393 DOI: 10.1073/pnas.1011569107] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Water-protein interactions dictate many processes crucial to protein function including folding, dynamics, interactions with other biomolecules, and enzymatic catalysis. Here we examine the effect of surface fluorination on water-protein interactions. Modification of designed coiled-coil proteins by incorporation of 5,5,5-trifluoroleucine or (4S)-2-amino-4-methylhexanoic acid enables systematic examination of the effects of side-chain volume and fluorination on solvation dynamics. Using ultrafast fluorescence spectroscopy, we find that fluorinated side chains exert electrostatic drag on neighboring water molecules, slowing water motion at the protein surface.
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Affiliation(s)
- Oh-Hoon Kwon
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125
| | - Tae Hyeon Yoo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
| | - Christina M. Othon
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125
| | - James A. Van Deventer
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
| | - David A. Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
| | - Ahmed H. Zewail
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125
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