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Ultrafast Spectroscopies of Nitrophenols and Nitrophenolates in Solution: From Electronic Dynamics and Vibrational Structures to Photochemical and Environmental Implications. Molecules 2023; 28:molecules28020601. [PMID: 36677656 PMCID: PMC9866910 DOI: 10.3390/molecules28020601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/27/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Nitrophenols are a group of small organic molecules with significant environmental implications from the atmosphere to waterways. In this work, we investigate a series of nitrophenols and nitrophenolates, with the contrasting ortho-, meta-, and para-substituted nitro group to the phenolic hydroxy or phenolate oxygen site (2/3/4NP or NP-), implementing a suite of steady-state and time-resolved spectroscopic techniques that include UV/Visible spectroscopy, femtosecond transient absorption (fs-TA) spectroscopy with probe-dependent and global analysis, and femtosecond stimulated Raman spectroscopy (FSRS), aided by quantum calculations. The excitation-dependent (400 and 267 nm) electronic dynamics in water and methanol, for six protonated or deprotonated nitrophenol molecules (three regioisomers in each set), enable a systematic investigation of the excited-state dynamics of these functional "nanomachines" that can undergo nitro-group twisting (as a rotor), excited-state intramolecular or intermolecular proton transfer (donor-acceptor, ESIPT, or ESPT), solvation, and cooling (chromophore) events on molecular timescales. In particular, the meta-substituted compound 3NP or 3NP- exhibits the strongest charge-transfer character with FSRS signatures (e.g., C-N peak frequency), and thus, does not favor nitroaromatic twist in the excited state, while the ortho-substituted compound 2NP can undergo ESIPT in water and likely generate nitrous acid (HONO) after 267 nm excitation. The delineated mechanistic insights into the nitro-substituent-location-, protonation-, solvent-, and excitation-wavelength-dependent effects on nitrophenols, in conjunction with the ultraviolet-light-induced degradation of 2NP in water, substantiates an appealing discovery loop to characterize and engineer functional molecules for environmental applications.
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Lee SJ, Kim TW, Kim JG, Yang C, Yun SR, Kim C, Ren Z, Kumarapperuma I, Kuk J, Moffat K, Yang X, Ihee H. Light-induced protein structural dynamics in bacteriophytochrome revealed by time-resolved x-ray solution scattering. SCIENCE ADVANCES 2022; 8:eabm6278. [PMID: 35622911 PMCID: PMC9140987 DOI: 10.1126/sciadv.abm6278] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/13/2022] [Indexed: 05/25/2023]
Abstract
Bacteriophytochromes (BphPs) are photoreceptors that regulate a wide range of biological mechanisms via red light-absorbing (Pr)-to-far-red light-absorbing (Pfr) reversible photoconversion. The structural dynamics underlying Pfr-to-Pr photoconversion in a liquid solution phase are not well understood. We used time-resolved x-ray solution scattering (TRXSS) to capture light-induced structural transitions in the bathy BphP photosensory module of Pseudomonas aeruginosa. Kinetic analysis of the TRXSS data identifies three distinct structural species, which are attributed to lumi-F, meta-F, and Pr, connected by time constants of 95 μs and 21 ms. Structural analysis based on molecular dynamics simulations shows that the light activation of PaBphP accompanies quaternary structural rearrangements from an "II"-framed close form of the Pfr state to an "O"-framed open form of the Pr state in terms of the helical backbones. This study provides mechanistic insights into how modular signaling proteins such as BphPs transmit structural signals over long distances and regulate their downstream biological responses.
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Affiliation(s)
- Sang Jin Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Tae Wu Kim
- Department of Chemistry, Mokpo National University, Muan-gun, Jeollanam-do, 58554, Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Cheolhee Yang
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - So Ri Yun
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Changin Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Zhong Ren
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Indika Kumarapperuma
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jane Kuk
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Keith Moffat
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Ophthalmology and Vision Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
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Tang L, Fang C. Fluorescence Modulation by Ultrafast Chromophore Twisting Events: Developing a Powerful Toolset for Fluorescent-Protein-Based Imaging. J Phys Chem B 2021; 125:13610-13623. [PMID: 34883016 DOI: 10.1021/acs.jpcb.1c08570] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The advancement of modern life sciences has benefited tremendously from the discovery and development of fluorescent proteins (FPs), widely expressed in live cells to track a myriad of cellular events. The chromophores of various FPs can undergo many ultrafast photophysical and/or photochemical processes in the electronic excited state and emit fluorescence with different colors. However, the chromophore becomes essentially nonfluorescent in solution environment due to its intrinsic twisting capability upon photoexcitation. To study "microscopic" torsional events and their effects on "macroscopic" fluorescence, we have developed an integrated ultrafast characterization platform involving femtosecond transient absorption (fs-TA) and wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS). A wide range of naturally occurring, circularly permuted, non-canonical amino-acid-decorated FPs and FP-based optical highlighters with photochromicity, photoconversion, and/or photoswitching capabilities have been recently investigated in great detail. Twisting conformational motions were elucidated to exist in all of these systems but to various extents. The associated different ultrafast pathways can be monitored via frequency changes of characteristic Raman bands during primary events and functional processes. The mapped electronic and structural dynamics information is crucial and has shown great potential and initial success for the rational design of proteins and other photoreceptors with novel functions and fluorescence properties.
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Affiliation(s)
- Longteng Tang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, United States
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, United States
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Fischer T, van Wilderen LJGW, Gnau P, Bredenbeck J, Essen LO, Wachtveitl J, Slavov C. Ultrafast Photoconversion Dynamics of the Knotless Phytochrome SynCph2. Int J Mol Sci 2021; 22:ijms221910690. [PMID: 34639031 PMCID: PMC8508867 DOI: 10.3390/ijms221910690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 12/03/2022] Open
Abstract
The family of phytochrome photoreceptors contains proteins with different domain architectures and spectral properties. Knotless phytochromes are one of the three main subgroups classified by their distinct lack of the PAS domain in their photosensory core module, which is in contrast to the canonical PAS-GAF-PHY array. Despite intensive research on the ultrafast photodynamics of phytochromes, little is known about the primary kinetics in knotless phytochromes. Here, we present the ultrafast Pr ⇆ Pfr photodynamics of SynCph2, the best-known knotless phytochrome. Our results show that the excited state lifetime of Pr* (~200 ps) is similar to bacteriophytochromes, but much longer than in most canonical phytochromes. We assign the slow Pr* kinetics to relaxation processes of the chromophore-binding pocket that controls the bilin chromophore’s isomerization step. The Pfr photoconversion dynamics starts with a faster excited state relaxation than in canonical phytochromes, but, despite the differences in the respective domain architectures, proceeds via similar ground state intermediate steps up to Meta-F. Based on our observations, we propose that the kinetic features and overall dynamics of the ultrafast photoreaction are determined to a great extent by the geometrical context (i.e., available space and flexibility) within the binding pocket, while the general reaction steps following the photoexcitation are most likely conserved among the red/far-red phytochromes.
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Affiliation(s)
- Tobias Fischer
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Straße 7, 60438 Frankfurt, Germany;
| | - Luuk J. G. W. van Wilderen
- Institute of Biophysics, Goethe University Frankfurt am Main, Max-von-Laue Straße 1, 60438 Frankfurt, Germany; (L.J.G.W.v.W.); (J.B.)
| | - Petra Gnau
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany; (P.G.); (L.-O.E.)
| | - Jens Bredenbeck
- Institute of Biophysics, Goethe University Frankfurt am Main, Max-von-Laue Straße 1, 60438 Frankfurt, Germany; (L.J.G.W.v.W.); (J.B.)
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany; (P.G.); (L.-O.E.)
- Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Straße 6, 35032 Marburg, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Straße 7, 60438 Frankfurt, Germany;
- Correspondence: (J.W.); (C.S.)
| | - Chavdar Slavov
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Straße 7, 60438 Frankfurt, Germany;
- Correspondence: (J.W.); (C.S.)
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Buhrke D. The impact of chromophore choice on the assembly kinetics and primary photochemistry of a red/green cyanobacteriochrome. Phys Chem Chem Phys 2021; 23:20867-20874. [PMID: 34374395 PMCID: PMC8479780 DOI: 10.1039/d1cp02696h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/04/2021] [Indexed: 11/24/2022]
Abstract
Cyanobacteriochromes (CBCRs) are bi-stable photoreceptor proteins with high potential for biotechnological applications. Most of these proteins utilize phycocyanobilin (PCB) as a light-sensing co-factor, which is unique to cyanobacteria, but some variants also incorporate biliverdin (BV). The latter are of particular interest for biotechnology due to the natural abundance and red-shifted absorption of BV. Here, AmI-g2 was investigated, a CBCR capable of binding both PCB and BV. The assembly kinetics and primary photochemistry of AmI-g2 with both chromophores were studied in vitro. The assembly reaction with PCB is roughly 10× faster than BV, and the formation of a non-covalent intermediate was identified as the rate-limiting step in the case of BV. This step is fast for PCB, where the formation of the covalent thioether bond between AmI-g2 and PCB becomes rate-limiting. The photochemical quantum yields of the forward and backward reactions of AmI-g2 were estimated and discussed in the context of homologous CBCRs.
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Affiliation(s)
- David Buhrke
- Department of Chemistry, University of Zürich, Zürich, Switzerland.
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Boulanger SA, Chen C, Tang L, Zhu L, Baleeva NS, Myasnyanko IN, Baranov MS, Fang C. Shedding light on ultrafast ring-twisting pathways of halogenated GFP chromophores from the excited to ground state. Phys Chem Chem Phys 2021; 23:14636-14648. [PMID: 34212170 DOI: 10.1039/d1cp02140k] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Since green fluorescent protein (GFP) has revolutionized molecular and cellular biology for about three decades, there has been a keen interest in understanding, designing, and controlling the fluorescence properties of GFP chromophore (i.e., HBDI) derivatives from the protein matrix to solution. Amongst these cross-disciplinary efforts, the elucidation of excited-state dynamics of HBDI derivatives holds the key to correlating the light-induced processes and fluorescence quantum yield (FQY). Herein, we implement steady-state electronic spectroscopy, femtosecond transient absorption (fs-TA), femtosecond stimulated Raman spectroscopy (FSRS), and quantum calculations to study a series of mono- and dihalogenated HBDI derivatives (X = F, Cl, Br, 2F, 2Cl, and 2Br) in basic aqueous solution, gaining new insights into the photophysical reaction coordinates. In the excited state, the halogenated "floppy" chromophores exhibit an anti-heavy atom effect, reflected by strong correlations between FQY vs. Franck-Condon energy (EFC) or Stokes shift, and knrvs. EFC, as well as a swift bifurcation into the I-ring (major) and P-ring (minor) twisting motions. In the ground state, both ring-twisting motions become more susceptible to sterics and exhibit spectral signatures from the halogen-dependent hot ground-state absorption band decay in TA data. We envision this type of systematic analysis of the halogenated HBDI derivatives to provide guiding principles for the site-specific modification of GFP chromophores, and expand design space for brighter and potentially photoswitchable organic chemical probes in aqueous solution with discernible spectral signatures throughout the photocycle.
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Affiliation(s)
- Sean A Boulanger
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, USA.
| | - Cheng Chen
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, USA.
| | - Longteng Tang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, USA.
| | - Liangdong Zhu
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, USA.
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia and Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia and Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia and Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, USA.
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An Engineered Biliverdin-Compatible Cyanobacteriochrome Enables a Unique Ultrafast Reversible Photoswitching Pathway. Int J Mol Sci 2021; 22:ijms22105252. [PMID: 34065754 PMCID: PMC8156171 DOI: 10.3390/ijms22105252] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/09/2021] [Accepted: 05/14/2021] [Indexed: 11/17/2022] Open
Abstract
Cyanobacteriochromes (CBCRs) are promising optogenetic tools for their diverse absorption properties with a single compact cofactor-binding domain. We previously uncovered the ultrafast reversible photoswitching dynamics of a red/green photoreceptor AnPixJg2, which binds phycocyanobilin (PCB) that is unavailable in mammalian cells. Biliverdin (BV) is a mammalian cofactor with a similar structure to PCB but exhibits redder absorption. To improve the AnPixJg2 feasibility in mammalian applications, AnPixJg2_BV4 with only four mutations has been engineered to incorporate BV. Herein, we implemented femtosecond transient absorption (fs-TA) and ground state femtosecond stimulated Raman spectroscopy (GS-FSRS) to uncover transient electronic dynamics on molecular time scales and key structural motions responsible for the photoconversion of AnPixJg2_BV4 with PCB (Bpcb) and BV (Bbv) cofactors in comparison with the parent AnPixJg2 (Apcb). Bpcb adopts the same photoconversion scheme as Apcb, while BV4 mutations create a less bulky environment around the cofactor D ring that promotes a faster twist. The engineered Bbv employs a reversible clockwise/counterclockwise photoswitching that requires a two-step twist on ~5 and 35 picosecond (ps) time scales. The primary forward Pfr → Po transition displays equal amplitude weights between the two processes before reaching a conical intersection. In contrast, the primary reverse Po → Pfr transition shows a 2:1 weight ratio of the ~35 ps over 5 ps component, implying notable changes to the D-ring-twisting pathway. Moreover, we performed pre-resonance GS-FSRS and quantum calculations to identify the Bbv vibrational marker bands at ~659,797, and 1225 cm-1. These modes reveal a stronger H-bonding network around the BV cofactor A ring with BV4 mutations, corroborating the D-ring-dominant reversible photoswitching pathway in the excited state. Implementation of BV4 mutations in other PCB-binding GAF domains like AnPixJg4, AM1_1870g3, and NpF2164g5 could promote similar efficient reversible photoswitching for more directional bioimaging and optogenetic applications, and inspire other bioengineering advances.
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