1
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Zangl R, Soravia S, Saft M, Löffler JG, Schulte J, Rosner CJ, Bredenbeck J, Essen LO, Morgner N. Time-Resolved Ion Mobility Mass Spectrometry to Solve Conformational Changes in a Cryptochrome. J Am Chem Soc 2024; 146:14468-14478. [PMID: 38757172 DOI: 10.1021/jacs.3c13818] [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: 05/18/2024]
Abstract
Many biological mechanisms rely on the precise control of conformational changes in proteins. Understanding such dynamic processes requires methods for determining structures and their temporal evolution. In this study, we introduce a novel approach to time-resolved ion mobility mass spectrometry. We validated the method on a simple photoreceptor model and applied it to a more complex system, the animal-like cryptochrome from Chlamydomonas reinhardtii (CraCRY), to determine the role of specific amino acids affecting the conformational dynamics as reaction to blue light activation. In our setup, using a high-power LED mounted in the source region of an ion mobility mass spectrometer, we allow a time-resolved evaluation of mass and ion mobility spectra. Cryptochromes like CraCRY are a widespread type of blue light photoreceptors and mediate various light-triggered biological functions upon excitation of their inbuilt flavin chromophore. Another hallmark of cryptochromes is their flexible carboxy-terminal extension (CTE), whose structure and function as well as the details of its interaction with the photolyase homology region are not yet fully understood and differ among different cryptochromes types. Here, we addressed the highly conserved C-terminal domain of CraCRY, to study the effects of single mutations on the structural transition of the C-terminal helix α22 and the attached CTE upon lit-state formation. We show that D321, the putative proton acceptor of the terminal proton-coupled electron transfer event from Y373, is essential for triggering the large-scale conformational changes of helix α22 and the CTE in the lit state, while D323 influences the timing.
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Affiliation(s)
- Rene Zangl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
| | - Sejla Soravia
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
| | - Martin Saft
- Department of Chemistry, Philipps University Marburg Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Jan Gerrit Löffler
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt/Main, Germany
| | - Jonathan Schulte
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
| | - Christian Joshua Rosner
- Department of Chemistry, Philipps University Marburg Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Jens Bredenbeck
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt/Main, Germany
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps University Marburg Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
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2
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Kim SS, Rhee YM. Potential energy interpolation with target-customized weighting coordinates: application to excited-state dynamics of photoactive yellow protein chromophore in water. Phys Chem Chem Phys 2024; 26:9021-9036. [PMID: 38440829 DOI: 10.1039/d3cp05643k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Interpolation of potential energy surfaces (PESs) can provide a practical route to performing molecular dynamics simulations with a reliability matching a high-level quantum chemical calculation. An obstacle to its widespread use is perhaps the lack of general and optimal interpolation settings that can be applied in a black-box manner for any given molecular system. How to set up the weights for interpolation is one such task, and we still need to diversify the approaches in order to treat various systems. Here, we develop a new interpolation weighting scheme, which allows us to choose the weighting coordinates in a system-specific manner, by amplifying the contribution from specific internal coordinates. The new weighting scheme with an appropriate selection of coordinates is proved to be effective in reducing the interpolation error along the reaction pathway. As a demonstration, we consider the photoactive yellow protein chromophore system, as it constitutes itself as an interesting target that bears long-standing questions related to excited-state dynamics inside protein environments. We build its two-state diabatic interpolated PES with the new weighting scheme. We indeed see the utility of our scheme by conducting nonadiabatic molecular dynamics simulations with the required semi-global PES based on a limited number of data points.
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Affiliation(s)
- Seung Soo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
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3
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Kuramochi H, Tsutsumi T, Saita K, Wei Z, Osawa M, Kumar P, Liu L, Takeuchi S, Taketsugu T, Tahara T. Ultrafast Raman observation of the perpendicular intermediate phantom state of stilbene photoisomerization. Nat Chem 2024; 16:22-27. [PMID: 38182762 DOI: 10.1038/s41557-023-01397-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 11/13/2023] [Indexed: 01/07/2024]
Abstract
Trans-cis photoisomerization is generally described by a model in which the reaction proceeds via a common intermediate having a perpendicular conformation around the rotating bond, irrespective of from which isomer the reaction starts. Nevertheless, such an intermediate has yet to be identified unambiguously, and it is often called the 'phantom' state. Here we present the structural identification of the common, perpendicular intermediate of stilbene photoisomerization using ultrafast Raman spectroscopy. Our results reveal ultrafast birth and decay of an identical, short-lived transient that exhibits a vibrational signature characteristic of the perpendicular state upon photoexcitation of the trans and cis forms. In combination with ab initio molecular dynamics simulations, it is shown that the photoexcited trans and cis forms are funnelled off to the ground state through the same, perpendicular intermediate.
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Affiliation(s)
- Hikaru Kuramochi
- Molecular Spectroscopy Laboratory, RIKEN, Wako, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), Wako, Japan
- JST, PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Japan
| | - Takuro Tsutsumi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Kenichiro Saita
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Zhengrong Wei
- Molecular Spectroscopy Laboratory, RIKEN, Wako, Japan
- Department of Physics, Hubei University, Wuhan, China
| | - Masahisa Osawa
- Department of Applied Chemistry, Nippon Institute of Technology, Miyashiro-Machi, Japan
| | - Pardeep Kumar
- Molecular Spectroscopy Laboratory, RIKEN, Wako, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), Wako, Japan
- Spiden AG, Pfäffikon, Switzerland
| | - Li Liu
- Molecular Spectroscopy Laboratory, RIKEN, Wako, Japan
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Satoshi Takeuchi
- Molecular Spectroscopy Laboratory, RIKEN, Wako, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), Wako, Japan
- Graduate School of Science, University of Hyogo, Kamigori, Ako, Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, Wako, Japan.
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), Wako, Japan.
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4
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Tsujimura M, Saito K, Ishikita H. Stretching vibrational frequencies and pK a differences in H-bond networks of protein environments. Biophys J 2023; 122:4336-4347. [PMID: 37838831 PMCID: PMC10722396 DOI: 10.1016/j.bpj.2023.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 08/22/2023] [Accepted: 10/12/2023] [Indexed: 10/16/2023] Open
Abstract
The experimentally measured stretching vibrational frequencies of O-D [νO-D(donor)] and C=O [νC=O(donor)] H-bond donor groups can provide valuable information about the H-bonds in proteins. Here, using a quantum mechanical/molecular mechanical approach, the relationship between these vibrational frequencies and the difference in pKa values between H-bond donor and acceptor groups [ΔpKa(donor … acceptor)] in bacteriorhodopsin and photoactive yellow protein environments was investigated. The results show that νO-D(donor) is correlated with ΔpKa(donor … acceptor), regardless of the specific protein environment. νC=O(donor) is also correlated with ΔpKa(donor … acceptor), although the correlation is weak because the C=O bond does not have a proton. Importantly, the shifts in νO-D(donor) and νC=O(donor) are not caused by changes in pKa(donor) alone, but rather by changes in ΔpKa(donor … acceptor). Specifically, a decrease in ΔpKa(donor … acceptor) can lead to proton release from the H-bond donor group toward the acceptor group, resulting in shifts in the vibrational frequencies of the protein environment. These findings suggest that changes in the stretching vibrational frequencies, in particular νO-D(donor), can be used to monitor proton transfer in protein environments.
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Affiliation(s)
- Masaki Tsujimura
- Department of Advanced Interdisciplinary Studies, The University of Tokyo, Meguro-ku, Tokyo, Japan.
| | - Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan.
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Krekic S, Mero M, Kuhl M, Balasubramanian K, Dér A, Heiner Z. Photoactive Yellow Protein Adsorption at Hydrated Polyethyleneimine and Poly-l-Glutamic Acid Interfaces. Molecules 2023; 28:molecules28104077. [PMID: 37241818 DOI: 10.3390/molecules28104077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Chiral and achiral vibrational sum-frequency generation (VSFG) spectroscopy was performed in the 1400-1700 and 2800-3800 cm-1 range to study the interfacial structure of photoactive yellow protein (PYP) adsorbed on polyethyleneimine (PEI) and poly-l-glutamic acid (PGA) surfaces. Nanometer-thick polyelectrolyte layers served as the substrate for PYP adsorption, with 6.5-pair layers providing the most homogeneous surfaces. When the topmost material was PGA, it acquired a random coil structure with a small number of β2-fibrils. Upon adsorption on oppositely charged surfaces, PYP yielded similar achiral spectra. However, the VSFG signal intensity increased for PGA surfaces with a concomitant redshift of the chiral Cα-H and N-H stretching bands, suggesting increased adsorption for PGA compared to PEI. At low wavenumbers, both the backbone and the side chains of PYP induced drastic changes to all measured chiral and achiral VSFG spectra. Decreasing ambient humidity led to the loss of tertiary structure with a re-orientation of α-helixes, evidenced by a strongly blue-shifted chiral amide I band of the β-sheet structure with a shoulder at 1654 cm-1. Our observations indicate that chiral VSFG spectroscopy is not only capable of determining the main type of secondary structure of PYP, i.e., β-scaffold, but is also sensitive to tertiary protein structure.
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Affiliation(s)
- Szilvia Krekic
- School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
- Institute of Biophysics, Biological Research Centre, 6726 Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, 6720 Szeged, Hungary
| | - Mark Mero
- Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy, 12489 Berlin, Germany
| | - Michel Kuhl
- School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
- Department of Chemistry and IRIS Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - Kannan Balasubramanian
- School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
- Department of Chemistry and IRIS Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - András Dér
- Institute of Biophysics, Biological Research Centre, 6726 Szeged, Hungary
| | - Zsuzsanna Heiner
- School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
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6
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Boichenko AN, Bochenkova AV. Accurate Vertical Electron Detachment Energies and Multiphoton Resonant Photoelectron Spectra of Biochromophore Anions in Aqueous Solution. J Chem Theory Comput 2023. [PMID: 37146177 DOI: 10.1021/acs.jctc.2c01082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We introduce a new methodology for calculating vertical electron detachment energies (VDEs) of biologically relevant chromophores in their deprotonated anionic forms in aqueous solution. It combines a large-scale mixed DFT/EFP/MD approach with the high-level multireference perturbation theory XMCQDPT2 and the Effective Fragment Potential (EFP) method. The methodology includes a multiscale flexible treatment of inner (∼1000 water molecules) and outer (∼18000 water molecules) water shells around a charged solute, capturing both the effects of specific solvation and the properties of bulk water. VDEs are calculated as a function of system size for getting a converged value at the DFT/EFP level of theory. The XMCQDPT2/EFP approach, adapted for calculating VDEs, supports the DFT/EFP results. When corrected for a solvent polarization contribution, the XMCQDPT2/EFP method yields the most accurate estimate to date of the first VDE for aqueous phenolate (7.3 ± 0.1 eV), which agrees well with liquid-jet X-ray photoelectron spectroscopy data (7.1 ± 0.1 eV). We show that the geometry of the water shell and its size are essential for accurate VDE calculations of aqueous phenolate and its biologically relevant derivatives. By simulating photoelectron spectra of aqueous phenolate upon two-photon excitation at wavelengths resonant with the S0 → S1 transition, we also provide interpretation of recent multiphoton UV liquid-microjet photoelectron spectroscopy experiments. We show that its first VDE is consistent with our estimate of 7.3 eV, when experimental two-photon binding energies are corrected for the resonant contribution.
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Affiliation(s)
- Anton N Boichenko
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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7
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Muramatsu S, Tokizane T, Inokuchi Y. One-Dimensionally Conjugated Carbocyanine Dyes Isolated under Cold Gas-Phase Conditions: Electronic Spectra and Photochemistry. J Phys Chem A 2022; 126:8127-8135. [DOI: 10.1021/acs.jpca.2c05111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Satoru Muramatsu
- Department of Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima-shi, Hiroshima739-8526, Japan
| | - Takayuki Tokizane
- Department of Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima-shi, Hiroshima739-8526, Japan
| | - Yoshiya Inokuchi
- Department of Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima-shi, Hiroshima739-8526, Japan
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8
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Ooka K, Liu R, Arai M. The Wako-Saitô-Muñoz-Eaton Model for Predicting Protein Folding and Dynamics. Molecules 2022; 27:molecules27144460. [PMID: 35889332 PMCID: PMC9319528 DOI: 10.3390/molecules27144460] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022] Open
Abstract
Despite the recent advances in the prediction of protein structures by deep neutral networks, the elucidation of protein-folding mechanisms remains challenging. A promising theory for describing protein folding is a coarse-grained statistical mechanical model called the Wako-Saitô-Muñoz-Eaton (WSME) model. The model can calculate the free-energy landscapes of proteins based on a three-dimensional structure with low computational complexity, thereby providing a comprehensive understanding of the folding pathways and the structure and stability of the intermediates and transition states involved in the folding reaction. In this review, we summarize previous and recent studies on protein folding and dynamics performed using the WSME model and discuss future challenges and prospects. The WSME model successfully predicted the folding mechanisms of small single-domain proteins and the effects of amino-acid substitutions on protein stability and folding in a manner that was consistent with experimental results. Furthermore, extended versions of the WSME model were applied to predict the folding mechanisms of multi-domain proteins and the conformational changes associated with protein function. Thus, the WSME model may contribute significantly to solving the protein-folding problem and is expected to be useful for predicting protein folding, stability, and dynamics in basic research and in industrial and medical applications.
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Affiliation(s)
- Koji Ooka
- Department of Physics, Graduate School of Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan;
- Komaba Organization for Educational Excellence, College of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Runjing Liu
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan;
| | - Munehito Arai
- Department of Physics, Graduate School of Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan;
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan;
- Correspondence:
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9
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van Wilderen LJGW, Blankenburg L, Bredenbeck J. Femtosecond-to-millisecond mid-IR spectroscopy of Photoactive Yellow Protein uncovers structural micro-transitions of the chromophore's protonation mechanism. J Chem Phys 2022; 156:205103. [DOI: 10.1063/5.0091918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Protein structural dynamics can span many orders of magnitude in time. Photoactive Yellow Protein's (PYP) reversible photocycle encompasses picosecond isomerization of the light-absorbing chromophore as well as large scale protein backbone motions occurring on a millisecond timescale. Femtosecond-to-millisecond time-resolved mid-Infrared (IR) spectroscopy is employed here to uncover structural details of photocycle intermediates up to chromophore protonation and the first structural changes leading to formation of the partially-unfolded signalling state pB. The data show that a commonly thought stable transient photocycle intermediate is actually formed after a sequence of several smaller structural changes. We provide residue-specific spectroscopic evidence that protonation of the chromophore on a hundreds of microseconds timescale is delayed with respect to deprotonation of the nearby E46 residue. That implies that the direct proton donor is not E46 but most likely a water molecule. Such details may assist ongoing photocycle and protein folding simulation efforts on the complex and wide time-spanning photocycle of the model system PYP.
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10
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Anstöter CS, Verlet JRR. A Hückel Model for the Excited-State Dynamics of a Protein Chromophore Developed Using Photoelectron Imaging. Acc Chem Res 2022; 55:1205-1213. [PMID: 35172580 PMCID: PMC9084545 DOI: 10.1021/acs.accounts.1c00780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Chemistry can be described as the movement of nuclei within molecules and the concomitant instantaneous change in electronic structure. This idea underpins the central chemical concepts of potential energy surfaces and reaction coordinates. To experimentally capture such chemical change therefore requires methods that can probe both the nuclear and electronic structure simultaneously and on the time scale of atomic motion. In this Account, we show how time-resolved photoelectron imaging can do exactly this and how it can be used to build a detailed and intuitive understanding of the electronic structure and excited-state dynamics of chromophores. The chromophore of the photoactive yellow protein (PYP) is used as a case study. This chromophore contains a para-substituted phenolate anion, where the substituent, R, can be viewed as an acrolein derivative. It is shown that the measured photoelectron angular distribution can be directly related to the electronic structure of the para-substituted phenolate anion. By incrementally considering differing R groups, it is also shown that these photoelectron angular distributions are exquisitely sensitive to the conformational flexibility of R and that when R contains a π-system the excited states of the chromophore can be viewed as a linear combination of the π* molecular orbitals on the phenolate (πPh*) and the R substituent (πR*). Such Hückel treatment shows that the S1 state of the PYP chromophore has predominantly πR* character and that it is essentially the same as the chromophore of the green fluorescent protein (GFP). The S1 excited-state dynamics of the PYP chromophore probed by time-resolved photoelectron imaging clearly reveals both structural (nuclear) dynamics through the energy spectrum and electronic dynamics through the photoelectron angular distributions. Both motions can be accurately assigned using quantum chemical calculations, and these are consistent with the intuitive Hückel treatment presented. The photoactive protein chromophores considered here are examples of where a chemists' intuitive Hückel view for ground-state chemistry appears to be transferable to the prediction of photochemical excited-state reactivity. While elegant and insightful, such models have limitations, including nonadiabatic dynamics, which is present in a related PYP chromophore, where a fraction of the S1 state population forms a nonvalence (dipole-bound) state of the anion.
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Affiliation(s)
- Cate S. Anstöter
- Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Jan R. R. Verlet
- Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
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11
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Absorption wavelength along chromophore low-barrier hydrogen bonds. iScience 2022; 25:104247. [PMID: 35521532 PMCID: PMC9062252 DOI: 10.1016/j.isci.2022.104247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 03/18/2022] [Accepted: 04/07/2022] [Indexed: 11/22/2022] Open
Abstract
In low-barrier hydrogen bonds (H-bonds), the pKa values for the H-bond donor and acceptor moieties are nearly equal, whereas the redox potential values depend on the H+ position. Spectroscopic details of low-barrier H-bonds remain unclear. Here, we report the absorption wavelength along low-barrier H-bonds in protein environments, using a quantum mechanical/molecular mechanical approach. Low-barrier H-bonds form between Glu46 and p-coumaric acid (pCA) in the intermediate pRCW state of photoactive yellow protein and between Asp116 and the retinal Schiff base in the intermediate M-state of the sodium-pumping rhodopsin KR2. The H+ displacement of only ∼0.4 Å, which does not easily occur without low-barrier H-bonds, is responsible for the ∼50 nm-shift in the absorption wavelength. This may be a basis of how photoreceptor proteins have evolved to proceed photocycles using abundant protons. The low-barrier H-bond formation is a prerequisite for proton transfer How the absorption wavelength changes as H+ moves is an open question The H+ displacement of ∼0.4 Å leads to the absorption wavelength shift of ∼50 nm The localization of the molecular orbitals plays a key role in the wavelength shift
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12
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Tassone G, Paolino M, Pozzi C, Reale A, Salvini L, Giorgi G, Orlandini M, Galvagni F, Mangani S, Yang X, Carlotti B, Ortica F, Latterini L, Olivucci M, Cappelli A. Xanthopsin-Like Systems via Site-Specific Click-Functionalization of a Retinoic Acid Binding Protein. Chembiochem 2022; 23:e202100449. [PMID: 34647400 PMCID: PMC8934143 DOI: 10.1002/cbic.202100449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/12/2021] [Indexed: 01/07/2023]
Abstract
The use of light-responsive proteins to control both living or synthetic cells, is at the core of the expanding fields of optogenetics and synthetic biology. It is thus apparent that a richer reaction toolbox for the preparation of such systems is of fundamental importance. Here, we provide a proof-of-principle demonstration that Morita-Baylis-Hillman adducts can be employed to perform a facile site-specific, irreversible and diastereoselective click-functionalization of a lysine residue buried into a lipophilic binding pocket and yielding an unnatural chromophore with an extended π-system. In doing so we effectively open the path to the in vitro preparation of a library of synthetic proteins structurally reminiscent of xanthopsin eubacterial photoreceptors. We argue that such a library, made of variable unnatural chromophores inserted in an easy-to-mutate and crystallize retinoic acid transporter, significantly expand the scope of the recently introduced rhodopsin mimics as both optogenetic and "lab-on-a-molecule" tools.
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Affiliation(s)
| | - Marco Paolino
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Cecilia Pozzi
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Annalisa Reale
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Laura Salvini
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100 Siena, Italy
| | - Gianluca Giorgi
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Maurizio Orlandini
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Federico Galvagni
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Stefano Mangani
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Xuchun Yang
- Chemistry Department, Bowling Green State University, Overman Hall, Bowling Green, OH 43403, USA
| | - Benedetta Carlotti
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Fausto Ortica
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Loredana Latterini
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy,Chemistry Department, Bowling Green State University, Overman Hall, Bowling Green, OH 43403, USA
| | - Andrea Cappelli
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
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13
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Uratani H, Nakai H. Scalable Ehrenfest Molecular Dynamics Exploiting the Locality of Density-Functional Tight-Binding Hamiltonian. J Chem Theory Comput 2021; 17:7384-7396. [PMID: 34860019 DOI: 10.1021/acs.jctc.1c00950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
To explore the science behind excited-state dynamics in high-complexity chemical systems, a scalable nonadiabatic molecular dynamics (MD) technique is indispensable. In this study, by treating the electronic degrees of freedom at the density-functional tight-binding level, we developed and implemented a reduced scaling and multinode-parallelizable Ehrenfest MD method. To achieve this goal, we introduced a concept called patchwork approximation (PA), where the effective Hamiltonian for real-time propagation of the electronic density matrix is partitioned into a set of local parts. Numerical results for giant icosahedral fullerenes, which comprise up to 6000 atoms, suggest that the scaling of the present PA-based method is less than quadratic, which yields a significant advantage over the conventional cubic scaling method in terms of computational time. The acceleration by the parallelization on multiple nodes was also assessed. Furthermore, the electronic and structural dynamics resulting from the perturbation by the external electric field were accurately reproduced with the PA, even when the electronic excitation was spatially delocalized.
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Affiliation(s)
- Hiroki Uratani
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Waseda Research Institute for Science and Engineering (WISE), 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8245, Japan
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14
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Effect of Hydrated Ionic Liquid on Photocycle and Dynamics of Photoactive Yellow Protein. Molecules 2021; 26:molecules26154554. [PMID: 34361707 PMCID: PMC8348629 DOI: 10.3390/molecules26154554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/15/2021] [Accepted: 07/23/2021] [Indexed: 12/03/2022] Open
Abstract
The mechanism by which proteins are solvated in hydrated ionic liquids remains an open question. Herein, the photoexcitation dynamics of photoactive yellow protein dissolved in hydrated choline dihydrogen phosphate (Hy[ch][dhp]) were studied by transient absorption and transient grating spectroscopy. The photocyclic reaction of the protein in Hy[ch][dhp] was similar to that observed in the buffer solution, as confirmed by transient absorption spectroscopy. However, the structural change of the protein during the photocycle in Hy[ch][dhp] was found to be different from that observed in the buffer solution. The known change in the diffusion coefficient of the protein was apparently suppressed in high concentrations of [ch][dhp], plausibly due to stabilization of the secondary structure.
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15
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Kuramochi H, Takeuchi S, Kamikubo H, Kataoka M, Tahara T. Skeletal Structure of the Chromophore of Photoactive Yellow Protein in the Excited State Investigated by Ultraviolet Femtosecond Stimulated Raman Spectroscopy. J Phys Chem B 2021; 125:6154-6161. [PMID: 34102843 DOI: 10.1021/acs.jpcb.1c02828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We studied ultrafast structural dynamics of photoactive yellow protein (PYP) using ultraviolet femtosecond stimulated Raman spectroscopy. By employing the Raman pump and probe pulses in the ultraviolet region, resonantly enhanced, rich vibrational features of the excited-state chromophore were observed in the fingerprint region. In contrast to the marked spectral change reported for the excited-state chromophore in solution, in the protein, all of the observed Raman bands in the fingerprint region did not show any noticeable spectral shifts nor band shape changes during the excited-state lifetime of PYP. This indicates that the significant skeletal change does not occur on the chromophore in the excited state of PYP and that the trans conformation is retained in its lifetime. Based on the femtosecond Raman data of PYP obtained so far, we discuss a comprehensive picture of the excited-state structural dynamics of PYP.
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Affiliation(s)
- Hikaru Kuramochi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan.,PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Satoshi Takeuchi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
| | - Hironari Kamikubo
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Mikio Kataoka
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
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16
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Kuramochi H, Tahara T. Tracking Ultrafast Structural Dynamics by Time-Domain Raman Spectroscopy. J Am Chem Soc 2021; 143:9699-9717. [PMID: 34096295 PMCID: PMC9344463 DOI: 10.1021/jacs.1c02545] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
In traditional Raman spectroscopy,
narrow-band light is irradiated
on a sample, and its inelastic scattering, i.e., Raman scattering,
is detected. The energy difference between the Raman scattering and
the incident light corresponds to the vibrational energy of the molecule,
providing the Raman spectrum that contains rich information about
the molecular-level properties of the materials. On the other hand,
by using ultrashort optical pulses, it is possible to induce Raman-active
coherent nuclear motion of the molecule and to observe the molecular
vibration in real time. Moreover, this time-domain Raman measurement
can be combined with femtosecond photoexcitation, triggering chemical
changes, which enables tracking ultrafast structural dynamics in a
form of “time-resolved” time-domain Raman spectroscopy,
also known as time-resolved impulsive stimulated Raman spectroscopy.
With the advent of stable, ultrashort laser pulse sources, time-resolved
impulsive stimulated Raman spectroscopy now realizes high sensitivity
and a wide detection frequency window from THz to 3000 cm–1, and has seen success in unveiling the molecular mechanisms underlying
the efficient functions of complex molecular systems. In this Perspective,
we overview the present status of time-domain Raman spectroscopy,
particularly focusing on its application to the study of femtosecond
structural dynamics. We first explain the principle and a brief history
of time-domain Raman spectroscopy and then describe the apparatus
and recent applications to the femtosecond dynamics of complex molecular
systems, including proteins, molecular assemblies, and functional
materials. We also discuss future directions for time-domain Raman
spectroscopy, which has reached a status allowing a wide range of
applications.
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Affiliation(s)
- Hikaru Kuramochi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi 332-0012, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
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17
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Schmalzbauer M, Marcon M, König B. Excited State Anions in Organic Transformations. Angew Chem Int Ed Engl 2021; 60:6270-6292. [PMID: 33002265 PMCID: PMC7986118 DOI: 10.1002/anie.202009288] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/17/2020] [Indexed: 02/06/2023]
Abstract
Utilizing light is a smart way to fuel chemical transformations as it allows the energy to be selectively focused on certain molecules. Many reactions involving electronically excited species proceed via open-shell intermediates, which offer novel and unique routes to expand the hitherto used synthetic toolbox in organic chemistry. The direct conversion of non-prefunctionalized, less activated compounds is a highly desirable goal to pave the way towards more sustainable and atom-economic chemical processes. Photoexcited closed-shell anions have been shown to reach extreme potentials in single electron transfer reactions and reveal unusual excited-state reactivity. It is, therefore, surprising that their use as a reagent or photocatalyst is limited to a few examples. In this Review, we briefly discuss the characteristics of anionic photochemistry, highlight pioneering work, and show recent progress which has been made by utilizing photoexcited anionic species in organic synthesis.
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Affiliation(s)
- Matthias Schmalzbauer
- Faculty of Chemistry and PharmacyUniversity of RegensburgUniversitätsstrasse 3193053RegensburgGermany
| | - Michela Marcon
- Faculty of Chemistry and PharmacyUniversity of RegensburgUniversitätsstrasse 3193053RegensburgGermany
| | - Burkhard König
- Faculty of Chemistry and PharmacyUniversity of RegensburgUniversitätsstrasse 3193053RegensburgGermany
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18
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Schmalzbauer M, Marcon M, König B. Photoangeregte Anionen in organischen Reaktionen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009288] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Matthias Schmalzbauer
- Fakultät für Chemie und Pharmazie Universität Regensburg Universitätsstraße 31 93053 Regensburg Deutschland
| | - Michela Marcon
- Fakultät für Chemie und Pharmazie Universität Regensburg Universitätsstraße 31 93053 Regensburg Deutschland
| | - Burkhard König
- Fakultät für Chemie und Pharmazie Universität Regensburg Universitätsstraße 31 93053 Regensburg Deutschland
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19
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Kim S, Nakasone Y, Takakado A, Yamazaki Y, Kamikubo H, Terazima M. Wavelength-Dependent Photoreaction of PYP from Rhodobacter capsulatus. Biochemistry 2020; 59:4810-4821. [DOI: 10.1021/acs.biochem.0c00821] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Suhyang Kim
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Akira Takakado
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoichi Yamazaki
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Hironari Kamikubo
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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20
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Anstöter CS, Curchod BFE, Verlet JRR. Geometric and electronic structure probed along the isomerisation coordinate of a photoactive yellow protein chromophore. Nat Commun 2020; 11:2827. [PMID: 32499507 PMCID: PMC7272410 DOI: 10.1038/s41467-020-16667-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/15/2020] [Indexed: 01/29/2023] Open
Abstract
Understanding the connection between the motion of the nuclei in a molecule and the rearrangement of its electrons lies at the heart of chemistry. While many experimental methods have been developed to probe either the electronic or the nuclear structure on the timescale of atomic motion, very few have been able to capture both these changes in concert. Here, we use time-resolved photoelectron imaging to probe the isomerisation coordinate on the excited state of an isolated model chromophore anion of the photoactive yellow protein. By probing both the electronic structure changes as well as nuclear dynamics, we are able to uniquely measure isomerisation about a specific bond. Our results demonstrate that the photoelectron signal dispersed in time, energy and angle combined with calculations can track the evolution of both electronic and geometric structure along the adiabatic state, which in turn defines that chemical transformation. Resolving concerted nuclear and electronic motion in real-time is a primary goal in chemistry. The authors monitor nuclear and valence electronic dynamics in the excited state single-bond isomerisation of a chromophore of photoactive yellow protein, using time-resolved photoelectron imaging and electronic structure calculations.
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Affiliation(s)
- Cate S Anstöter
- Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | | | - Jan R R Verlet
- Department of Chemistry, Durham University, Durham, DH1 3LE, UK.
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21
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Mustalahti S, Morozov D, Luk HL, Pallerla RR, Myllyperkiö P, Pettersson M, Pihko PM, Groenhof G. Photoactive Yellow Protein Chromophore Photoisomerizes around a Single Bond if the Double Bond Is Locked. J Phys Chem Lett 2020; 11:2177-2181. [PMID: 32109070 PMCID: PMC7145348 DOI: 10.1021/acs.jpclett.0c00060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/28/2020] [Indexed: 06/10/2023]
Abstract
Photoactivation in the Photoactive Yellow Protein, a bacterial blue-light photoreceptor, proceeds via photoisomerization of the double C═C bond in the covalently attached chromophore. Quantum chemistry calculations, however, have suggested that in addition to double-bond photoisomerization, the isolated chromophore and many of its analogues can isomerize around a single C-C bond as well. Whereas double-bond photoisomerization has been observed with X-ray crystallography, experimental evidence of single-bond photoisomerization is currently lacking. Therefore, we have synthesized a chromophore analogue, in which the formal double bond is covalently locked in a cyclopentenone ring, and carried out transient absorption spectroscopy experiments in combination with nonadiabatic molecular dynamics simulations to reveal that the locked chromophore isomerizes around the single bond upon photoactivation. Our work thus provides experimental evidence of single-bond photoisomerization in a photoactive yellow protein chromophore analogue and suggests that photoisomerization is not restricted to the double bonds in conjugated systems. This insight may be useful for designing light-driven molecular switches or motors.
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22
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Schmidt-Engler JM, Blankenburg L, Zangl R, Hoffmann J, Morgner N, Bredenbeck J. Local dynamics of the photo-switchable protein PYP in ground and signalling state probed by 2D-IR spectroscopy of –SCN labels. Phys Chem Chem Phys 2020; 22:22963-22972. [DOI: 10.1039/d0cp04307a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We employ 2D-IR spectroscopy of the protein label –SCN to describe the local dynamics in the photo-switchable protein PYP in its dark state (pG) and after photoactivation, concomitant with vast structural rearrangements, in its signalling state (pB).
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Affiliation(s)
| | - Larissa Blankenburg
- Johann Wolfgang Goethe-University
- Institute of Biophysics
- 60438 Frankfurt am Main
- Germany
| | - Rene Zangl
- Johann Wolfgang Goethe-University
- Institute of Physical and Theoretical Chemistry
- Frankfurt am Main
- Germany
| | - Jan Hoffmann
- Johann Wolfgang Goethe-University
- Institute of Physical and Theoretical Chemistry
- Frankfurt am Main
- Germany
| | - Nina Morgner
- Johann Wolfgang Goethe-University
- Institute of Physical and Theoretical Chemistry
- Frankfurt am Main
- Germany
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University
- Institute of Biophysics
- 60438 Frankfurt am Main
- Germany
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23
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Gromov EV, Domratcheva T. Four resonance structures elucidate double-bond isomerisation of a biological chromophore. Phys Chem Chem Phys 2020; 22:8535-8544. [DOI: 10.1039/d0cp00814a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Four resonance structures determining the electronic structure of the chromophore’s ground and first excited states. Changing the relative energies of the structures by hydrogen-bonding interactions tunes all chromophore’s photochemical properties.
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Affiliation(s)
- Evgeniy V. Gromov
- Max-Planck Institute for Medical Research
- Jahnstraße 29
- 69120 Heidelberg
- Germany
| | - Tatiana Domratcheva
- Max-Planck Institute for Medical Research
- Jahnstraße 29
- 69120 Heidelberg
- Germany
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24
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Schmidt-Engler JM, Blankenburg L, Błasiak B, van Wilderen LJGW, Cho M, Bredenbeck J. Vibrational Lifetime of the SCN Protein Label in H 2O and D 2O Reports Site-Specific Solvation and Structure Changes During PYP's Photocycle. Anal Chem 2019; 92:1024-1032. [PMID: 31769286 DOI: 10.1021/acs.analchem.9b03997] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The application of vibrational labels such as thiocyanate (-S-C≡N) for studying protein structure and dynamics is thriving. Absorption spectroscopy is usually employed to obtain wavenumber and line shape of the label. An observable of great significance might be the vibrational lifetime, which can be obtained by pump probe or 2D-IR spectroscopy. Due to the insulating effect of the heavy sulfur atom in the case of the SCN label, the lifetime of the C≡N oscillator is expected to be particularly sensitive to its surrounding as it is not dominated by through-bond relaxation. We therefore investigate the vibrational lifetime of the SCN label at various positions in the blue light sensor protein Photoactive Yellow Protein (PYP) in the ground state and signaling state of the photoreceptor. We find that the vibrational lifetime of the C≡N stretching mode is strongly affected both by its protein environment and by the degree of exposure to the solvent. Even for label positions where the line shape and wavenumber observed by FTIR are barely changing upon activation of the photoreceptor, we find that the lifetime can change considerably. To obtain an unambiguous measure for the solvent exposure of the labeled site, we show that it is imperative to compare the lifetimes in H2O and D2O. Importantly, the lifetimes shorten in H2O as compared to D2O for water exposed labels, while they stay largely the same for buried labels. We quantify this effect by defining a solvent exclusion coefficient (SEC). The response of the label's vibrational lifetime to its solvent exposure renders it a suitable universal probe for protein investigations. This applies even to systems that are otherwise hard to address, such as transient or short-lived states, which could be created during a protein's working cycle (as here in PYP) or during protein folding. It is also applicable to flexible systems (intrinsically disordered proteins), protein-protein and protein-membrane interactions.
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Affiliation(s)
- Julian M Schmidt-Engler
- Johann Wolfgang Goethe-University , Institute of Biophysics , Max-von-Laue-Straße 1 , 60438 Frankfurt am Main , Germany
| | - Larissa Blankenburg
- Johann Wolfgang Goethe-University , Institute of Biophysics , Max-von-Laue-Straße 1 , 60438 Frankfurt am Main , Germany
| | - Bartosz Błasiak
- Johann Wolfgang Goethe-University , Institute of Biophysics , Max-von-Laue-Straße 1 , 60438 Frankfurt am Main , Germany
| | - Luuk J G W van Wilderen
- Johann Wolfgang Goethe-University , Institute of Biophysics , Max-von-Laue-Straße 1 , 60438 Frankfurt am Main , Germany
| | - Minhaeng Cho
- Institute of Basic Science , Center of Molecular Spectroscopy and Dynamics , 145 Anam-ro , Seongbuk-gu , Seoul 02841 , Republic of Korea.,Korea University , Department of Chemistry , 145 Anam-ro , Seongbuk-gu , Seoul 02841 , Republic of Korea
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University , Institute of Biophysics , Max-von-Laue-Straße 1 , 60438 Frankfurt am Main , Germany
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25
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Maiuri M, Garavelli M, Cerullo G. Ultrafast Spectroscopy: State of the Art and Open Challenges. J Am Chem Soc 2019; 142:3-15. [DOI: 10.1021/jacs.9b10533] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margherita Maiuri
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
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26
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Fang C, Tang L, Chen C. Unveiling coupled electronic and vibrational motions of chromophores in condensed phases. J Chem Phys 2019; 151:200901. [PMID: 31779327 DOI: 10.1063/1.5128388] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The quest for capturing molecular movies of functional systems has motivated scientists and engineers for decades. A fundamental understanding of electronic and nuclear motions, two principal components of the molecular Schrödinger equation, has the potential to enable the de novo rational design for targeted functionalities of molecular machines. We discuss the development and application of a relatively new structural dynamics technique, femtosecond stimulated Raman spectroscopy with broadly tunable laser pulses from the UV to near-IR region, in tracking the coupled electronic and vibrational motions of organic chromophores in solution and protein environments. Such light-sensitive moieties hold broad interest and significance in gaining fundamental knowledge about the intramolecular and intermolecular Hamiltonian and developing effective strategies to control macroscopic properties. Inspired by recent experimental and theoretical advances, we focus on the in situ characterization and spectroscopy-guided tuning of photoacidity, excited state proton transfer pathways, emission color, and internal conversion via a conical intersection.
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Affiliation(s)
- Chong Fang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Longteng Tang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Cheng Chen
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
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27
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Kuramochi H, Takeuchi S, Kamikubo H, Kataoka M, Tahara T. Fifth-order time-domain Raman spectroscopy of photoactive yellow protein for visualizing vibrational coupling in its excited state. SCIENCE ADVANCES 2019; 5:eaau4490. [PMID: 31187055 PMCID: PMC6555629 DOI: 10.1126/sciadv.aau4490] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 04/26/2019] [Indexed: 05/15/2023]
Abstract
We report fifth-order time-domain Raman spectroscopy of photoactive yellow protein (PYP), with the aim to visualize vibrational coupling in its excited state. After the ultrashort actinic pump pulse prepared the vibrational coherence and population in the excited state, the evolving vibrational structure was tracked by time-resolved impulsive stimulated Raman spectroscopy using sub-7-fs pulses. The obtained fifth-order time-domain Raman data were translated to a two-dimensional (2D) frequency-frequency correlation map, which visualizes the correlation between low- and high-frequency vibrational modes of the excited state. The 2D map of PYP reveals a cross peak, indicating the coupling between the phenolic C─O stretch mode of the chromophore and the low-frequency modes (~160 cm-1), assignable to the intermolecular motions involving the surrounding hydrogen-bonded amino acids. The unveiled coupling suggests the importance of the low-frequency vibrational motion in the primary photoreaction of PYP, highlighting the unique capability of this spectroscopic approach for studying ultrafast reaction dynamics.
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Affiliation(s)
- Hikaru Kuramochi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi 332-0012, Japan
| | - Satoshi Takeuchi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
- Corresponding author. (S.T.); (T.T.)
| | - Hironari Kamikubo
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Mikio Kataoka
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
- Corresponding author. (S.T.); (T.T.)
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28
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Blankenburg L, Schroeder L, Habenstein F, Błasiak B, Kottke T, Bredenbeck J. Following local light-induced structure changes and dynamics of the photoreceptor PYP with the thiocyanate IR label. Phys Chem Chem Phys 2019; 21:6622-6634. [PMID: 30855039 DOI: 10.1039/c8cp05399e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoactive Yellow Protein (PYP) is a bacterial blue light receptor that enters a photocycle after excitation. The intermediate states are formed on time scales ranging from femtoseconds up to hundreds of milliseconds, after which the signaling state with a lifetime of about 1 s is reached. To investigate structural changes and dynamics, we incorporated the SCN IR label at distinct positions of the photoreceptor via cysteine mutation and cyanylation. FT-IR measurements of the SCN label at different sites of the well-established dark state structure of PYP characterized the spectral response of the label to differences in the environment. Under constant blue light irradiation, we observed the formation of the signaling state with significant changes of wavenumber and lineshape of the SCN bands. Thereby we deduced light-induced structural changes in the local environment of the labels. These results were supported by molecular dynamics simulations on PYP providing the solvent accessible surface area (SASA) at the different positions. To follow protein dynamics via the SCN label during the photocycle, we performed step-scan FT-IR measurements with a time resolution of 10 μs. Global analysis yielded similar time constants of τ1 = 70 μs, τ2 = 640 μs, and τ3 > 20 ms for the wild type and τ1 = 36 μs, τ2 = 530 μs, and τ3 > 20 ms for the SCN-labeled mutant PYP-A44C*, a mutant which provided a sufficiently large SCN difference signal to measure step-scan FT-IR spectra. In comparison to the protein (amide, E46) and chromophore bands the dynamics of the SCN label show a different behavior. This result indicates that the local kinetics sensed by the label are different from the global protein kinetics.
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Affiliation(s)
- Larissa Blankenburg
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany.
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29
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Krekic S, Nagy D, Taneva SG, Fábián L, Zimányi L, Dér A. Spectrokinetic characterization of photoactive yellow protein films for integrated optical applications. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:465-473. [PMID: 30905045 PMCID: PMC6647221 DOI: 10.1007/s00249-019-01353-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/19/2019] [Accepted: 03/04/2019] [Indexed: 11/02/2022]
Abstract
In this paper, the photocycle of the dried photoactive yellow protein film has been investigated in different humidity environments, in order to characterize its nonlinear optical properties for possible integrated optical applications. The light-induced spectral changes of the protein films were monitored by an optical multichannel analyser set-up, while the accompanying refractive index changes were measured with the optical waveguide lightmode spectroscopy method. To determine the number and kinetics of spectral intermediates in the photocycle, the absorption kinetic data were analysed by singular value decomposition and multiexponential fitting methods, whose results were used in a subsequent step of fitting a photocycle model to the data. The absorption signals of the films were found to be in strong correlation with the measured light-induced refractive index changes, whose size and kinetics imply that photoactive yellow protein may be a good alternative for utilization as an active nonlinear optical material in future integrated optical applications.
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Affiliation(s)
- Szilvia Krekic
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, P.O. Box 521, Szeged, 6701, Hungary.
| | - Dávid Nagy
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, P.O. Box 521, Szeged, 6701, Hungary
| | - Stefka G Taneva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 21, Sofia, 1113, Bulgaria
| | - László Fábián
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, P.O. Box 521, Szeged, 6701, Hungary
| | - László Zimányi
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, P.O. Box 521, Szeged, 6701, Hungary
| | - András Dér
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, P.O. Box 521, Szeged, 6701, Hungary
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30
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Zhao L, Liu J, Zhou P. Does the wavelength dependent photoisomerization process of the p‑coumaric acid come out from the electronic state dependent pathways? SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 211:203-211. [PMID: 30544011 DOI: 10.1016/j.saa.2018.12.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Similar to the anion photoactive yellow protein (PYP) chromophore, the neutral form of the PYP chromophore was also found to exhibit a the wavelength-dependent photoisomerization quantum yield. The isomerization quantum yield increases with the increasing excitation energy on the S1 state, while decreases when being excited to the S2 state. Does this wavelength dependent product yield come out from the specific reaction pathways of the S1 and S2 states? This would mean that, the relaxation pathway of the S2 state is distinct from that of the S1 state and does not involve twisting motion. Does it break Kasha's rule by exhibiting a direct transition from the S2 state to the ground state? The underlying mechanism needs further in. In this article, we employed the on-the-fly dynamics simulations and static electronic structure calculations to reveal the deactivation mechanism of the neutral form of the PYP chromophore. Our results indicated that the CC twisting motion dominates the S1 state decay process. In contrast, for the decay process of the S2 state, an ultrafast transition from the S2 to the S1 state through a planar conical intersection is observed, and the excess energy activates a new reaction channel to the ground state characterized by a puckering distortion of the ring. This pathway competes with the photoisomerization channel. No direct transition from S2 to S0 is observed, hence Kasha's rule is valid for this process. Our calcualtions can provide a reasonable explanation of the wavelength-dependent isomerization quantum yield of neutral PYP chromophore, and we hope it can provide theoretical foundations for comparing the effect of protonation state on the dynamcal behaviors of PYP chromophore.
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Affiliation(s)
- Li Zhao
- School of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China.
| | - Jianyong Liu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Panwang Zhou
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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31
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Affiliation(s)
- Alice Henley
- Department of Chemistry, University College London, London, UK
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32
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Henley A, Patel AM, Parkes MA, Anderson JC, Fielding HH. Role of Photoisomerization on the Photodetachment of the Photoactive Yellow Protein Chromophore. J Phys Chem A 2018; 122:8222-8228. [PMID: 30234981 DOI: 10.1021/acs.jpca.8b07770] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photocycle of photoactive yellow protein (PYP) is initiated by a photoinduced trans-cis isomerization around a C═C bond in the chromophore that lies at the heart of the protein; however, in addition to the desired photochemical pathway, the chromophore can undergo competing electronic relaxation processes. Here we combine gas-phase anion photoelectron spectroscopy and quantum chemistry calculations to investigate how locking the C═C bond in the chromophore controls the competition between these electronic relaxation processes following photoexcitation in the range 400-310 nm. We find evidence to suggest that preventing trans-cis isomerization effectively turns off internal conversion to the ground electronic state and enhances electron emission from the first electronically excited state.
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Affiliation(s)
- Alice Henley
- Department of Chemistry , University College London , London WC1H 0AJ , United Kingdom
| | - Anand M Patel
- Department of Chemistry , University College London , London WC1H 0AJ , United Kingdom
| | - Michael A Parkes
- Department of Chemistry , University College London , London WC1H 0AJ , United Kingdom
| | - James C Anderson
- Department of Chemistry , University College London , London WC1H 0AJ , United Kingdom
| | - Helen H Fielding
- Department of Chemistry , University College London , London WC1H 0AJ , United Kingdom
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33
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Spectroscopic ruler for measuring active-site distortions based on Raman optical activity of a hydrogen out-of-plane vibration. Proc Natl Acad Sci U S A 2018; 115:8671-8675. [PMID: 30104345 DOI: 10.1073/pnas.1806491115] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Photoactive yellow protein (PYP), from the phototrophic bacterium Halorhodospira halophila, is a small water-soluble photoreceptor protein and contains p-coumaric acid (pCA) as a chromophore. PYP has been an attractive model for studying the physical chemistry of protein active sites. Here, we explore how Raman optical activity (ROA) can be used to extract quantitative information on distortions of the pCA chromophore at the active site in PYP. We use 13C8-pCA to assign an intense signal at 826 cm-1 in the ROA spectrum of PYP to a hydrogen out-of-plane vibration of the ethylenic moiety of the chromophore. Quantum-chemical calculations based on density functional theory demonstrate that the sign of this ROA band reports the direction of the distortion in the dihedral angle about the ethylenic C=C bond, while its amplitude is proportional to the dihedral angle. These results document the ability of ROA to quantify structural deformations of a cofactor molecule embedded in a protein moiety.
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Abstract
The first stage in biological signaling is based on changes in the functional state of a receptor protein triggered by interaction of the receptor with its ligand(s). The light-triggered nature of photoreceptors allows studies on the mechanism of such changes in receptor proteins using a wide range of biophysical methods and with superb time resolution. Here, we critically evaluate current understanding of proton and electron transfer in photosensory proteins and their involvement both in primary photochemistry and subsequent processes that lead to the formation of the signaling state. An insight emerging from multiple families of photoreceptors is that ultrafast primary photochemistry is followed by slower proton transfer steps that contribute to triggering large protein conformational changes during signaling state formation. We discuss themes and principles for light sensing shared by the six photoreceptor families: rhodopsins, phytochromes, photoactive yellow proteins, light-oxygen-voltage proteins, blue-light sensors using flavin, and cryptochromes.
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Affiliation(s)
- Tilman Kottke
- Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Aihua Xie
- Department of Physics, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Delmar S. Larsen
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Wouter D. Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, USA
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, USA
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35
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Goian V, Schumann FO, Widdra W. Growth and lattice dynamics of ultrathin BaO films on Pt(0 0 1). JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:095001. [PMID: 29350619 DOI: 10.1088/1361-648x/aaa94a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report on the surface phonons of long-range ordered BaO thin films grown on Pt(0 0 1). In the thickness range between 4 and 28 ML, we find unstrained BaO(0 0 1)-([Formula: see text]) bulk-like terminated films which coincide with a Pt(0 0 1)-c([Formula: see text]) lattice periodicity. The dipole-active lattice vibrations were determined using high-resolution electron energy loss spectroscopy. For all BaO film thicknesses, a single Fuchs-Kliewer phonon-polariton is observed. Its intensity increases and its frequency softens with increasing film thickness. These thickness-dependent properties and the spectral shape are quantitatively discussed on the basis of dielectric theory, where a proper modeling requires three components: the dielectric response of the BaO film itself, the plasmonic response of the metallic substrate, and a weak damping due to a defect-induced doping within the oxide film. For a full description, also the quantization of the phonon wavevector due to the confinement within the film of finite thickness has to be taken into account.
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Affiliation(s)
- Veronica Goian
- Institute of Physics, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
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36
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Mix LT, Carroll EC, Morozov D, Pan J, Gordon WR, Philip A, Fuzell J, Kumauchi M, van Stokkum I, Groenhof G, Hoff WD, Larsen DS. Excitation-Wavelength-Dependent Photocycle Initiation Dynamics Resolve Heterogeneity in the Photoactive Yellow Protein from Halorhodospira halophila. Biochemistry 2018; 57:1733-1747. [PMID: 29465990 DOI: 10.1021/acs.biochem.7b01114] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photoactive yellow proteins (PYPs) make up a diverse class of blue-light-absorbing bacterial photoreceptors. Electronic excitation of the p-coumaric acid chromophore covalently bound within PYP results in triphasic quenching kinetics; however, the molecular basis of this behavior remains unresolved. Here we explore this question by examining the excitation-wavelength dependence of the photodynamics of the PYP from Halorhodospira halophila via a combined experimental and computational approach. The fluorescence quantum yield, steady-state fluorescence emission maximum, and cryotrapping spectra are demonstrated to depend on excitation wavelength. We also compare the femtosecond photodynamics in PYP at two excitation wavelengths (435 and 475 nm) with a dual-excitation-wavelength-interleaved pump-probe technique. Multicompartment global analysis of these data demonstrates that the excited-state photochemistry of PYP depends subtly, but convincingly, on excitation wavelength with similar kinetics with distinctly different spectral features, including a shifted ground-state beach and altered stimulated emission oscillator strengths and peak positions. Three models involving multiple excited states, vibrationally enhanced barrier crossing, and inhomogeneity are proposed to interpret the observed excitation-wavelength dependence of the data. Conformational heterogeneity was identified as the most probable model, which was supported with molecular mechanics simulations that identified two levels of inhomogeneity involving the orientation of the R52 residue and different hydrogen bonding networks with the p-coumaric acid chromophore. Quantum calculations were used to confirm that these inhomogeneities track to altered spectral properties consistent with the experimental results.
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Affiliation(s)
- L Tyler Mix
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Elizabeth C Carroll
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Dmitry Morozov
- Department of Chemistry and NanoScience Center , University of Jyväskylä , P.O. Box 35, 40014 Jyväskylä , Finland
| | - Jie Pan
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | | | | | - Jack Fuzell
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Masato Kumauchi
- Department of Microbiology and Molecular Genetics , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Ivo van Stokkum
- Faculty of Sciences , Vrije Universiteit Amsterdam , De Boelelaan 1081 , 1081 HV Amsterdam , The Netherlands
| | - Gerrit Groenhof
- Department of Chemistry and NanoScience Center , University of Jyväskylä , P.O. Box 35, 40014 Jyväskylä , Finland
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Delmar S Larsen
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
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37
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KOMOTO N, YOSHIKAWA T, ONO J, NAKAI H. Development of the Divide-and-Conquer Time-Dependent Density Functional Tight-Binding Method for Photoreceptor Protein. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2018. [DOI: 10.2477/jccj.2018-0032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Nana KOMOTO
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University,3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, JAPAN
| | - Takeshi YOSHIKAWA
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University,3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, JAPAN
| | - Junichi ONO
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, JAPAN
| | - Hiromi NAKAI
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University,3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, JAPAN
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, JAPAN
- ESICB Kyoto University, Kyotodaigaku-Katsura, Nishigyo-ku, Kyoto, Kyoto 615-8520, JAPAN
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38
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Henley A, Diveky ME, Patel AM, Parkes MA, Anderson JC, Fielding HH. Electronic structure and dynamics of torsion-locked photoactive yellow protein chromophores. Phys Chem Chem Phys 2017; 19:31572-31580. [PMID: 29165495 DOI: 10.1039/c7cp06950b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photocycle of photoactive yellow protein (PYP) begins with small-scale torsional motions of the chromophore leading to large-scale movements of the protein scaffold triggering a biological response. The role of single-bond torsional molecular motions of the chromophore in the initial steps of the PYP photocycle are not fully understood. Here, we employ anion photoelectron spectroscopy measurements and quantum chemistry calculations to investigate the electronic relaxation dynamics following photoexcitation of four model chromophores, para-coumaric acid, its methyl ester, and two analogues with aliphatic bridges hindering torsional motions around the single bonds adjacent to the alkene group. Following direct photoexcitation of S1 at 400 nm, we find that both single bond rotations play a role in steering the PYP chromophore through the S1/S0 conical intersection but that rotation around the single bond between the alkene moiety and the phenoxide group is particularly important. Following photoexcitation of higher lying electronic states in the range 346-310 nm, we find that rotation around the single bond between the alkene and phenoxide groups also plays a key role in the electronic relaxation from higher lying states to the S1 state. These results have potential applications in tuning the photoresponse of photoactive proteins and materials with chromophores based on PYP.
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Affiliation(s)
- Alice Henley
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
| | - Matus E Diveky
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
| | - Anand M Patel
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
| | - Michael A Parkes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
| | - James C Anderson
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
| | - Helen H Fielding
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
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39
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Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017; 117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hoi Ling Luk
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, 53100 Siena, Italy
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40
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Yang C, Kim TW, Kim Y, Choi J, Lee SJ, Ihee H. Kinetics of the E46Q mutant of photoactive yellow protein investigated by transient grating spectroscopy. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.03.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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41
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Ikeda T, Tanimura Y. Probing photoisomerization processes by means of multi-dimensional electronic spectroscopy: The multi-state quantum hierarchical Fokker-Planck equation approach. J Chem Phys 2017; 147:014102. [DOI: 10.1063/1.4989537] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Tatsushi Ikeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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42
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Hirano K, Nakano H, Nakao Y, Sato H, Sakaki S. Photo absorption of
p-coumaric acid in aqueous solution: RISM-SCF-SEDD theory approach. J Comput Chem 2017; 38:1567-1573. [DOI: 10.1002/jcc.24784] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 02/01/2017] [Accepted: 02/22/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Kenji Hirano
- Department of Molecular Engineering; Kyoto University; Kyoto 615-8510 Japan
| | - Hiroshi Nakano
- Department of Molecular Engineering; Kyoto University; Kyoto 615-8510 Japan
| | - Yoshihide Nakao
- Department of Molecular Engineering; Kyoto University; Kyoto 615-8510 Japan
| | - Hirofumi Sato
- Department of Molecular Engineering; Kyoto University; Kyoto 615-8510 Japan
| | - Shigeyoshi Sakaki
- Department of Molecular Engineering; Kyoto University; Kyoto 615-8510 Japan
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43
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García-Prieto FF, Muñoz-Losa A, Fdez Galván I, Sánchez ML, Aguilar MA, Martín ME. QM/MM Study of Substituent and Solvent Effects on the Excited State Dynamics of the Photoactive Yellow Protein Chromophore. J Chem Theory Comput 2017; 13:737-748. [PMID: 28072537 DOI: 10.1021/acs.jctc.6b01069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Substituent and solvent effects on the excited state dynamics of the Photoactive Yellow Protein chromophore are studied using the average solvent electrostatic potential from molecular dynamics (ASEP/MD) method. Four molecular models were considered: the ester and thioester derivatives of the p-coumaric acid anion and their methylated derivatives. We found that the solvent produces dramatic modifications on the free energy profile of the S1 state: 1) Two twisted structures that are minima in the gas phase could not be located in aqueous solution. 2) Conical intersections (CIs) associated with the rotation of the single bond adjacent to the phenyl group are found for the four derivatives in water solution but only for thio derivatives in the gas phase. 3) The relative stability of minima and CIs is reverted with respect to the gas phase values, affecting the prevalent de-excitation paths. As a consequence of these changes, three competitive de-excitation channels are open in aqueous solution: the fluorescence emission from a planar minimum on S1, the trans-cis photoisomerization through a CI that involves the rotation of the vinyl double bond, and the nonradiative, nonreactive, de-excitation through the CI associated with the rotation of the single bond adjacent to the phenyl group. In the gas phase, the minima are the structures with the lower energy, while in solution these are the conical intersections. In solution, the de-excitation prevalent path seems to be the photoisomerization for oxo compounds, while thio compounds return to the initial trans ground state without emission.
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Affiliation(s)
- Francisco F García-Prieto
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - Aurora Muñoz-Losa
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - Ignacio Fdez Galván
- Department of Chemistry-Ångström, The Theoretical Chemistry Programme, Uppsala University , Box 518, 751 20 Uppsala, Sweden
| | - M Luz Sánchez
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - Manuel A Aguilar
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - M Elena Martín
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
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44
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Hutchison CD, van Thor JJ. Populations and coherence in femtosecond time resolved X-ray crystallography of the photoactive yellow protein. INT REV PHYS CHEM 2017. [DOI: 10.1080/0144235x.2017.1276726] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | - Jasper J. van Thor
- Molecular Biophysics, Imperial College London, South Kensington Campus, London, UK
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45
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Kim TW, Yang C, Kim Y, Kim JG, Kim J, Jung YO, Jun S, Lee SJ, Park S, Kosheleva I, Henning R, van Thor JJ, Ihee H. Combined probes of X-ray scattering and optical spectroscopy reveal how global conformational change is temporally and spatially linked to local structural perturbation in photoactive yellow protein. Phys Chem Chem Phys 2017; 18:8911-8919. [PMID: 26960811 DOI: 10.1039/c6cp00476h] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Real-time probing of structural transitions of a photoactive protein is challenging owing to the lack of a universal time-resolved technique that can probe the changes in both global conformation and light-absorbing chromophores of the protein. In this work, we combine time-resolved X-ray solution scattering (TRXSS) and transient absorption (TA) spectroscopy to investigate how the global conformational changes involved in the photoinduced signal transduction of photoactive yellow protein (PYP) is temporally and spatially related to the local structural change around the light-absorbing chromophore. In particular, we examine the role of internal proton transfer in developing a signaling state of PYP by employing its E46Q mutant (E46Q-PYP), where the internal proton transfer is inhibited by the replacement of a proton donor. The comparison of TRXSS and TA spectroscopy data directly reveals that the global conformational change of the protein, which is probed by TRXSS, is temporally delayed by tens of microseconds from the local structural change of the chromophore, which is probed by TA spectroscopy. The molecular shape of the signaling state reconstructed from the TRXSS curves directly visualizes the three-dimensional conformations of protein intermediates and reveals that the smaller structural change in E46Q-PYP than in wild-type PYP suggested by previous studies is manifested in terms of much smaller protrusion, confirming that the signaling state of E46Q-PYP is only partially developed compared with that of wild-type PYP. This finding provides direct evidence of how the environmental change in the vicinity of the chromophore alters the conformational change of the entire protein matrix.
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Affiliation(s)
- Tae Wu Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Cheolhee Yang
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Youngmin Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Jong Goo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Jeongho Kim
- Department of Chemistry, Inha University, Incheon 402-751, Korea
| | - Yang Ouk Jung
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Sunhong Jun
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Sang Jin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Sungjun Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago IL 60637, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Chicago IL 60637, USA
| | - Jasper J van Thor
- Division of Molecular Biosciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Hyotcherl Ihee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
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46
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Yamazaki K, Miyazaki Y, Harabuchi Y, Taketsugu T, Maeda S, Inokuchi Y, Kinoshita SN, Sumida M, Onitsuka Y, Kohguchi H, Ehara M, Ebata T. Multistep Intersystem Crossing Pathways in Cinnamate-Based UV-B Sunscreens. J Phys Chem Lett 2016; 7:4001-4007. [PMID: 27657500 DOI: 10.1021/acs.jpclett.6b01643] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The nonradiative decay pathways of jet-cooled para-methoxy methylcinnamate (p-MMC) and para-methoxy ethylcinnamate (p-MEC) have been investigated by picosecond pump-probe and nanosecond UV-Deep UV pump-probe spectroscopy. The possible relaxation pathways were calculated by the (time-dependent) density functional theory. We found that p-MMC and p-MEC at low excess energy undergo multistep intersystem crossing (ISC) from the bright S1 (1ππ*) state to the lowest triplet T1 (3ππ*) state via two competing pathways through the T2 state in the time scale of 100 ps: (a) stepwise ISC followed after the internal conversion (IC) from S1 to the dark 1nπ* state; (b) direct ISC from the S1 to T2 states. These picosecond multistep ISCs result in the torsion of C═C double bond by ∼95° in the T1 state, whose measured adiabatic energy and lifetime are 16577 cm-1 and ∼20 ns, respectively, for p-MMC. These results suggest that the ISC processes play an indispensable role in the photoprotecting sunscreens in natural plants.
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Affiliation(s)
- Kaoru Yamazaki
- Department of Chemistry, Faculty of Science, Hokkaido University , Sapporo 060-0810, Japan
| | - Yasunori Miyazaki
- Department of Chemistry, Graduate School of Science, Hiroshima University , Higashi-Hiroshima 739-8526, Japan
| | - Yu Harabuchi
- Department of Chemistry, Faculty of Science, Hokkaido University , Sapporo 060-0810, Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University , Sapporo 060-0810, Japan
| | - Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University , Sapporo 060-0810, Japan
| | - Yoshiya Inokuchi
- Department of Chemistry, Graduate School of Science, Hiroshima University , Higashi-Hiroshima 739-8526, Japan
| | - Shin-Nosuke Kinoshita
- Department of Chemistry, Graduate School of Science, Hiroshima University , Higashi-Hiroshima 739-8526, Japan
| | - Masataka Sumida
- Department of Chemistry, Graduate School of Science, Hiroshima University , Higashi-Hiroshima 739-8526, Japan
| | - Yuuki Onitsuka
- Department of Chemistry, Graduate School of Science, Hiroshima University , Higashi-Hiroshima 739-8526, Japan
| | - Hiroshi Kohguchi
- Department of Chemistry, Graduate School of Science, Hiroshima University , Higashi-Hiroshima 739-8526, Japan
| | - Masahiro Ehara
- Institute for Molecular Science and Research Center for Computational Science , 38 Myodaiji, Okazaki 444-8585, Japan
- Elements Strategy for Catalysts and Batteries, Kyoto University Katsura , Kyoto 615-8520, Japan
| | - Takayuki Ebata
- Department of Chemistry, Graduate School of Science, Hiroshima University , Higashi-Hiroshima 739-8526, Japan
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47
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Taenzler PJ, Sadeghian K, Ochsenfeld C. A Dynamic Equilibrium of Three Hydrogen-Bond Conformers Explains the NMR Spectrum of the Active Site of Photoactive Yellow Protein. J Chem Theory Comput 2016; 12:5170-5178. [DOI: 10.1021/acs.jctc.6b00359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Phillip Johannes Taenzler
- Chair of Theoretical Chemistry,
Department of Chemistry, University of Munich (LMU), Butenandtstrasse
7, D-81377 Munich, Germany
- Center for Integrated Protein
Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 Muenchen, Germany
| | - Keyarash Sadeghian
- Chair of Theoretical Chemistry,
Department of Chemistry, University of Munich (LMU), Butenandtstrasse
7, D-81377 Munich, Germany
- Center for Integrated Protein
Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 Muenchen, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry,
Department of Chemistry, University of Munich (LMU), Butenandtstrasse
7, D-81377 Munich, Germany
- Center for Integrated Protein
Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 Muenchen, Germany
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48
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Cho HS, Schotte F, Dashdorj N, Kyndt J, Henning R, Anfinrud PA. Picosecond Photobiology: Watching a Signaling Protein Function in Real Time via Time-Resolved Small- and Wide-Angle X-ray Scattering. J Am Chem Soc 2016; 138:8815-23. [PMID: 27305463 DOI: 10.1021/jacs.6b03565] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The capacity to respond to environmental changes is crucial to an organism's survival. Halorhodospira halophila is a photosynthetic bacterium that swims away from blue light, presumably in an effort to evade photons energetic enough to be genetically harmful. The protein responsible for this response is believed to be photoactive yellow protein (PYP), whose chromophore photoisomerizes from trans to cis in the presence of blue light. We investigated the complete PYP photocycle by acquiring time-resolved small and wide-angle X-ray scattering patterns (SAXS/WAXS) over 10 decades of time spanning from 100 ps to 1 s. Using a sequential model, global analysis of the time-dependent scattering differences recovered four intermediates (pR0/pR1, pR2, pB0, pB1), the first three of which can be assigned to prior time-resolved crystal structures. The 1.8 ms pB0 to pB1 transition produces the PYP signaling state, whose radius of gyration (Rg = 16.6 Å) is significantly larger than that for the ground state (Rg = 14.7 Å) and is therefore inaccessible to time-resolved protein crystallography. The shape of the signaling state, reconstructed using GASBOR, is highly anisotropic and entails significant elongation of the long axis of the protein. This structural change is consistent with unfolding of the 25 residue N-terminal domain, which exposes the β-scaffold of this sensory protein to a potential binding partner. This mechanistically detailed description of the complete PYP photocycle, made possible by time-resolved crystal and solution studies, provides a framework for understanding signal transduction in proteins and for assessing and validating theoretical/computational approaches in protein biophysics.
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Affiliation(s)
- Hyun Sun Cho
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Friedrich Schotte
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Naranbaatar Dashdorj
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - John Kyndt
- College of Science and Technology, Bellevue University , Bellevue, Nebraska 68005, United States
| | - Robert Henning
- Center for Advanced Radiation Sources, University of Chicago , Chicago, Illinois 60637, United States
| | - Philip A Anfinrud
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
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49
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Hutchison CD, Kaucikas M, Tenboer J, Kupitz C, Moffat K, Schmidt M, van Thor JJ. Photocycle populations with femtosecond excitation of crystalline photoactive yellow protein. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.04.087] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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50
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Parkes MA, Phillips C, Porter MJ, Fielding HH. Controlling electron emission from the photoactive yellow protein chromophore by substitution at the coumaric acid group. Phys Chem Chem Phys 2016; 18:10329-36. [PMID: 27025529 DOI: 10.1039/c6cp00565a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Understanding how the interactions between a chromophore and its surrounding protein control the function of a photoactive protein remains a challenge. Here, we present the results of photoelectron spectroscopy measurements and quantum chemistry calculations aimed at investigating how substitution at the coumaryl tail of the photoactive yellow protein chromophore controls competing relaxation pathways following photoexcitation of isolated chromophores in the gas phase with ultraviolet light in the range 350-315 nm. The photoelectron spectra are dominated by electrons resulting from direct detachment and fast detachment from the 2(1)ππ* state but also have a low electron kinetic energy component arising from autodetachment from lower lying electronically excited states or thermionic emission from the electronic ground state. We find that substituting the hydrogen atom of the carboxylic acid group with a methyl group lowers the threshold for electron detachment but has very little effect on the competition between the different relaxation pathways, whereas substituting with a thioester group raises the threshold for electron detachment and appears to 'turn off' the competing electron emission processes from lower lying electronically excited states. This has potential implications in terms of tuning the light-induced electron donor properties of photoactive yellow protein.
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Affiliation(s)
- Michael A Parkes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
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