1
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Qianzhu H, Abdelkader EH, Otting G, Huber T. Genetic Encoding of Fluoro-l-tryptophans for Site-Specific Detection of Conformational Heterogeneity in Proteins by NMR Spectroscopy. J Am Chem Soc 2024; 146:13641-13650. [PMID: 38687675 DOI: 10.1021/jacs.4c03743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The substitution of a single hydrogen atom in a protein by fluorine yields a site-specific probe for sensitive detection by 19F nuclear magnetic resonance (NMR) spectroscopy, where the absence of background signal from the protein facilitates the detection of minor conformational species. We developed genetic encoding systems for the site-selective incorporation of 4-fluorotryptophan, 5-fluorotryptophan, 6-fluorotryptophan, and 7-fluorotryptophan in response to an amber stop codon and used them to investigate conformational heterogeneity in a designed amino acid binding protein and in flaviviral NS2B-NS3 proteases. These proteases have been shown to present variable conformations in X-ray crystal structures, including flips of the indole side chains of tryptophan residues. The 19F NMR spectra of different fluorotryptophan isomers installed at the conserved site of Trp83 indicate that the indole ring flip is common in flaviviral NS2B-NS3 proteases in the apo state and suppressed by an active-site inhibitor.
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Affiliation(s)
- Haocheng Qianzhu
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Elwy H Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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2
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Babcock NS, Montes-Cabrera G, Oberhofer KE, Chergui M, Celardo GL, Kurian P. Ultraviolet Superradiance from Mega-Networks of Tryptophan in Biological Architectures. J Phys Chem B 2024; 128:4035-4046. [PMID: 38641327 DOI: 10.1021/acs.jpcb.3c07936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
Networks of tryptophan (Trp)─an aromatic amino acid with strong fluorescence response─are ubiquitous in biological systems, forming diverse architectures in transmembrane proteins, cytoskeletal filaments, subneuronal elements, photoreceptor complexes, virion capsids, and other cellular structures. We analyze the cooperative effects induced by ultraviolet (UV) excitation of several biologically relevant Trp mega-networks, thus giving insights into novel mechanisms for cellular signaling and control. Our theoretical analysis in the single-excitation manifold predicts the formation of strongly superradiant states due to collective interactions among organized arrangements of up to >105 Trp UV-excited transition dipoles in microtubule architectures, which leads to an enhancement of the fluorescence quantum yield (QY) that is confirmed by our experiments. We demonstrate the observed consequences of this superradiant behavior in the fluorescence QY for hierarchically organized tubulin structures, which increases in different geometric regimes at thermal equilibrium before saturation, highlighting the effect's persistence in the presence of disorder. Our work thus showcases the many orders of magnitude across which the brightest (hundreds of femtoseconds) and darkest (tens of seconds) states can coexist in these Trp lattices.
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Affiliation(s)
- N S Babcock
- Quantum Biology Laboratory, Howard University, Washington, D.C. 20060, United States
| | - G Montes-Cabrera
- Quantum Biology Laboratory, Howard University, Washington, D.C. 20060, United States
- Institute of Physics, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
| | - K E Oberhofer
- Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - M Chergui
- Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - G L Celardo
- Department of Physics and Astronomy, Università degli Studi di Firenze, Florence 50019, Italy
| | - P Kurian
- Quantum Biology Laboratory, Howard University, Washington, D.C. 20060, United States
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3
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Cui E, Liu H, Wang Z, Chen H, Weng YX. Femtosecond fluorescence conical optical parametric amplification spectroscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2024; 95:033008. [PMID: 38517256 DOI: 10.1063/5.0197254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/29/2024] [Indexed: 03/23/2024]
Abstract
Parametric superfluorescence (PSF), which originated from the optical amplification of vacuum quantum noise, is the primary noise source of femtosecond fluorescence non-collinear optical parametric amplification spectroscopy (FNOPAS). It severely affects the detection limit of FNOPAS to collect the femtosecond time-resolved spectra of extremely weak fluorescence. Here, we report the development of femtosecond fluorescence conical optical parametric amplification spectroscopy (FCOPAS), aimed at effectively suppressing the noise fluctuation from the PSF background. In contrast to traditional FNOPAS configurations utilizing lateral fluorescence collection and dot-like parametric amplification, FCOPAS employs an innovative conical fluorescence collection and ring-like amplification setup. This design enables effective cancellation of noise fluctuation across the entire PSF ring, resulting in an approximate order of magnitude reduction in PSF noise compared to prior FNOPAS outcomes. This advancement enables the resolution of transient fluorescence spectra of 4-dicyanomethylene-2-methyl-6-p-dimethylaminostyryl-4H-pyran (DCM) dye molecules in ethanol, even at an optically dilute concentration of 10-6 mol/l, with significantly enhanced signal-to-noise ratios. This improvement will be significant for extremely weak fluorescence detection on the femtosecond time scale.
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Affiliation(s)
- Ennan Cui
- The Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Science, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Heyuan Liu
- The Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Science, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuan Wang
- The Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Hailong Chen
- The Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Science, University of the Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Yu-Xiang Weng
- The Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Science, University of the Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
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4
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Cosottini L, Zineddu S, Massai L, Ghini V, Turano P. 19F: A small probe for a giant protein. J Inorg Biochem 2023; 244:112236. [PMID: 37146532 DOI: 10.1016/j.jinorgbio.2023.112236] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 05/07/2023]
Abstract
Herein we describe a method for the efficient production (∼90% fluorination) of 5-F-Trp human H ferritin via the selective incorporation of 19F into the side chain of W93 using 5-fluoroindole as the fluorinated precursor of the amino acid. Human H ferritin is a nanocage composed of 24 identical subunits, each containing a single Trp belonging to a loop exposed on the external surface of the protein nanocage. This makes 5-F-Trp a potential probe for the study of intermolecular interactions in solution by exploiting its intrinsic fluorescence. More interestingly, albeit the large size of the cage (12 nm external diameter, ∼500 kDa molecular mass) we observe a broad but well defined NMR 19F resonance that can be used for the dual purpose of detecting solution intermolecular interactions via chemical shift perturbation mapping and monitoring the uptake of ferritin by cells treated with ferritin-based drug carriers, the latter being an application area of increasing importance.
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Affiliation(s)
- Lucrezia Cosottini
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Stefano Zineddu
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Lara Massai
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Veronica Ghini
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Paola Turano
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy.
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5
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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: 1] [Impact Index Per Article: 1.0] [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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6
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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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7
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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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8
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Jaiswal VK, Kabaciński P, Nogueira de Faria BE, Gentile M, de Paula AM, Borrego-Varillas R, Nenov A, Conti I, Cerullo G, Garavelli M. Environment-Driven Coherent Population Transfer Governs the Ultrafast Photophysics of Tryptophan. J Am Chem Soc 2022; 144:12884-12892. [PMID: 35796759 PMCID: PMC9305959 DOI: 10.1021/jacs.2c04565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
By combining UV transient
absorption spectroscopy with sub-30-fs
temporal resolution and CASPT2/MM calculations, we present a complete
description of the primary photoinduced processes in solvated tryptophan.
Our results shed new light on the role of the solvent in the relaxation
dynamics of tryptophan. We unveil two consecutive coherent population
transfer events involving the lowest two singlet excited states: a
sub-50-fs nonadiabatic La → Lb transfer
through a conical intersection and a subsequent 220 fs reverse Lb → La transfer due to solvent-assisted adiabatic
stabilization of the La state. Vibrational fingerprints
in the transient absorption spectra provide compelling evidence of
a vibronic coherence established between the two excited states from
the earliest times after photoexcitation and lasting until the back-transfer
to La is complete. The demonstration of response to the
environment as a driver of coherent population dynamics among the
excited states of tryptophan closes the long debate on its solvent-assisted
relaxation mechanisms and extends its application as a local probe
of protein dynamics to the ultrafast time scales.
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Affiliation(s)
- Vishal Kumar Jaiswal
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Piotr Kabaciński
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | | | - Marziogiuseppe Gentile
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Ana Maria de Paula
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte-MG, Brazil
| | - Rocio Borrego-Varillas
- Istituto di Fotonica e Nanotecnologie, CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Artur Nenov
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Irene Conti
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy.,Istituto di Fotonica e Nanotecnologie, CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Marco Garavelli
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
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9
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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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10
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Fluorine induced conformational switching and modulation in photophysical properties of 7-fluorotryptophan: Spectroscopic, quantum chemical calculation and molecular dynamics simulation studies. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2020. [DOI: 10.1016/j.jpap.2020.100011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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11
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Biswas B, Singh PC. The role of fluorocarbon group in the hydrogen bond network, photophysical and solvation dynamics of fluorinated molecules. J Fluor Chem 2020. [DOI: 10.1016/j.jfluchem.2019.109414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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12
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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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13
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Fukuda A, Oroguchi T, Nakasako M. Dipole-dipole interactions between tryptophan side chains and hydration water molecules dominate the observed dynamic stokes shift of lysozyme. Biochim Biophys Acta Gen Subj 2019; 1864:129406. [PMID: 31377191 DOI: 10.1016/j.bbagen.2019.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 07/24/2019] [Accepted: 07/29/2019] [Indexed: 10/26/2022]
Abstract
The fluorescence intensity of tryptophan residues in hen egg-white lysozyme was measured up to 500 ps after the excitation by irradiation pulses at 290 nm. From the time-dependent variation of fluorescence intensity in a wavelength range of 320-370 nm, the energy relaxation in the dynamic Stokes shift was reconstructed as the temporal variation in wavenumber of the estimated fluorescence maximum. The relaxation was approximated by two exponential curves with decay constants of 1.2 and 26.7 ps. To interpret the relaxation, a molecular dynamics simulation of 75 ns was conducted for lysozyme immersed in a water box. From the simulation, the energy relaxation in the electrostatic interactions of each tryptophan residue was evaluated by using a scheme derived from the linear response theory. Dipole-dipole interactions between each of the Trp62 and Trp123 residues and hydration water molecules displayed an energy relaxation similar to that experimentally observed regarding time constants and magnitudes. The side chains of these residues were partly or fully exposed to the solvent. In addition, by inspecting the variation in dipole moments of the hydration water molecules around lysozyme, it was suggested that the observed relaxation could be attributed to the orientational relaxation of hydration water molecules participating in the hydrogen-bond network formed around each of the two tryptophan residues.
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Affiliation(s)
- Asahi Fukuda
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokihama 223-8522, Japan
| | - Tomotaka Oroguchi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokihama 223-8522, Japan
| | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokihama 223-8522, Japan.
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14
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Nandy T, Mondal S, Singh PC. Solvent organization around the noncanonical part of tyrosine modulates its fluorescence properties. Phys Chem Chem Phys 2019; 21:6042-6050. [DOI: 10.1039/c8cp06410e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Solvent interactions with the fluorocarbon group of noncanonical amino acids are the cause of their diverse fluorescence behaviors, which implies their usefulness as solvent-sensitive environmental sensors in many biological processes.
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Affiliation(s)
- Tonima Nandy
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Saptarsi Mondal
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata
- India
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Mondal S, Chaterjee S, Halder R, Jana B, Singh PC. Role of Dispersive Fluorous Interaction in the Solvation Dynamics of the Perfluoro Group Containing Molecules. J Phys Chem B 2017; 121:7681-7688. [PMID: 28737391 DOI: 10.1021/acs.jpcb.7b03420] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Perfluoro group containing molecules possess an important self-aggregation property through the fluorous (F···F) interaction which makes them useful for diverse applications such as medicinal chemistry, separation techniques, polymer technology, and biology. In this article, we have investigated the solvation dynamics of coumarin-153 (C153) and coumarin-6H (C6H) in ethanol (ETH), 2-fluoroethanol (MFE), and 2,2,2-trifluoroethanol (TFE) using the femtosecond upconversion technique and molecular dynamics (MD) simulation to understand the role of fluorous interaction between the solute and solvent molecules in the solvation dynamics of perfluoro group containing molecules. The femtosecond upconversion data show that the time scales of solvation dynamics of C6H in ETH, MFE, and TFE are approximately the same whereas the solvation dynamics of C153 in TFE is slow as compared to that of ETH and MFE. It has also been observed that the time scale of solvation dynamics of C6H in ETH and MFE is higher than that of C153 in the same solvents. MD simulation results show a qualitative agreement with the experimental data in terms of the time scale of the slow components of the solvation for all the systems. The experimental and simulation studies combined lead to the conclusion that the solvation dynamics of C6H in all solvents as well as C153 in ETH and MFE is mostly governed by the charge distribution of ester moieties (C═O and O) of dye molecules whereas the solvation of C153 in TFE is predominantly due to the dispersive fluorous interaction (F···F) between the perfluoro groups of the C153 and solvent molecules.
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Affiliation(s)
- Saptarsi Mondal
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Soumit Chaterjee
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Ritaban Halder
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Biman Jana
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Prashant Chandra Singh
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
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Rolinski OJ, McLaughlin D, Birch DJS, Vyshemirsky V. Resolving environmental microheterogeneity and dielectric relaxation in fluorescence kinetics of protein. Methods Appl Fluoresc 2016; 4:024001. [PMID: 28809166 DOI: 10.1088/2050-6120/4/2/024001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The fluorescence intensity decay of protein is easily measurable and reports on the intrinsic fluorophore-local environment interactions on the sub-nm spatial and sub-ns temporal scales, which are consistent with protein activity in numerous biomedical and industrial processes. This makes time-resolved fluorescence a perfect tool for understanding, monitoring and controlling these processes at the molecular level, but the complexity of the decay, which has been traditionally fitted to multi-exponential functions, has hampered the development of this technique over the last few decades. Using the example of tryptophan in HSA we present the alternative to the conventional approach to modelling intrinsic florescence intensity decay in protein where the key factors determining fluorescence decay, i.e. the excited-state depopulation and the dielectric relaxation (Toptygin and Brand 2000 Chem. Phys. Lett. 322 496-502), are represented by the individual relaxation functions. This allows quantification of both effects separately by determining their parameters from the global analysis of a series of fluorescence intensity decays measured at different detection wavelengths. Moreover, certain pairs of the recovered parameters of tryptophan were found to be correlated, indicating the influence of the dielectric relaxation on the transient rate of the electronic transitions. In this context the potential for the dual excited state depopulation /dielectric relaxation fluorescence lifetime sensing is discussed.
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Affiliation(s)
- Olaf J Rolinski
- Photophysics Group, Centre for Molecular Nanometrology, Department of Physics, Scottish Universities Physics Alliance, University of Strathclyde, 107 Rottenrow, Glasgow G4 0NG, UK
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Markiewicz BN, Mukherjee D, Troxler T, Gai F. Utility of 5-Cyanotryptophan Fluorescence as a Sensitive Probe of Protein Hydration. J Phys Chem B 2016; 120:936-44. [PMID: 26783936 DOI: 10.1021/acs.jpcb.5b12233] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tryptophan (Trp) fluorescence has been widely used to interrogate the structure, dynamics, and function of proteins. In particular, it provides a convenient and site-specific means to probe a protein's hydration status and dynamics. Herein, we show that a tryptophan analogue, 5-cyanotryptophan (TrpCN), can also be used for this purpose, but with the benefit of enhanced sensitivity to hydration. This conclusion is reached based on measurements of the static and time-resolved fluorescence properties of 5-cyanoindole, TrpCN, and TrpCN-containing peptides in different solvents, which indicate that upon dehydration the fluorescence quantum yield (QY) and lifetime (τF) of TrpCN undergo a much greater change in comparison to those of Trp. For example, in H2O the QY of TrpCN is less than 0.01, which increases to 0.11 in 1,4-dioxane. Consistently, the fluorescence decay kinetics of TrpCN in H2O are dominated by a 0.4 ns component, whereas in 1,4-dioxane the kinetics are dominated by a 6.0 ns component. The versatile utility of TrpCN as a sensitive fluorescence reporter is further demonstrated in three applications, where we used it (1) to probe the solvent property of a binary mixture consisting of dimethyl sulfoxide and H2O, (2) to monitor the binding interaction of an antimicrobial peptide with lipid membranes, and (3) to differentiate two differently hydrated environments in a folded protein.
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Affiliation(s)
- Beatrice N Markiewicz
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Debopreeti Mukherjee
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Thomas Troxler
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Feng Gai
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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Rahamim G, Chemerovski-Glikman M, Rahimipour S, Amir D, Haas E. Resolution of Two Sub-Populations of Conformers and Their Individual Dynamics by Time Resolved Ensemble Level FRET Measurements. PLoS One 2015; 10:e0143732. [PMID: 26699718 PMCID: PMC4689530 DOI: 10.1371/journal.pone.0143732] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/08/2015] [Indexed: 11/19/2022] Open
Abstract
Most active biopolymers are dynamic structures; thus, ensembles of such molecules should be characterized by distributions of intra- or intermolecular distances and their fast fluctuations. A method of choice to determine intramolecular distances is based on Förster resonance energy transfer (FRET) measurements. Major advances in such measurements were achieved by single molecule FRET measurements. Here, we show that by global analysis of the decay of the emission of both the donor and the acceptor it is also possible to resolve two sub-populations in a mixture of two ensembles of biopolymers by time resolved FRET (trFRET) measurements at the ensemble level. We show that two individual intramolecular distance distributions can be determined and characterized in terms of their individual means, full width at half maximum (FWHM), and two corresponding diffusion coefficients which reflect the rates of fast ns fluctuations within each sub-population. An important advantage of the ensemble level trFRET measurements is the ability to use low molecular weight small-sized probes and to determine nanosecond fluctuations of the distance between the probes. The limits of the possible resolution were first tested by simulation and then by preparation of mixtures of two model peptides. The first labeled polypeptide was a relatively rigid Pro7 and the second polypeptide was a flexible molecule consisting of (Gly-Ser)7 repeats. The end to end distance distributions and the diffusion coefficients of each peptide were determined. Global analysis of trFRET measurements of a series of mixtures of polypeptides recovered two end-to-end distance distributions and associated intramolecular diffusion coefficients, which were very close to those determined from each of the pure samples. This study is a proof of concept study demonstrating the power of ensemble level trFRET based methods in resolution of subpopulations in ensembles of flexible macromolecules.
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Affiliation(s)
- Gil Rahamim
- The Goodman Faculty of Life Sciences Bar Ilan University, Ramat Gan Israel 52900
| | | | - Shai Rahimipour
- Department of Chemistry, Bar-Ilan University, Ramat Gan Israel 52900
| | - Dan Amir
- The Goodman Faculty of Life Sciences Bar Ilan University, Ramat Gan Israel 52900
| | - Elisha Haas
- The Goodman Faculty of Life Sciences Bar Ilan University, Ramat Gan Israel 52900
- * E-mail:
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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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