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Malakar P, Gholami S, Aarabi M, Rivalta I, Sheves M, Garavelli M, Ruhman S. Retinal photoisomerization versus counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct. Nat Commun 2024; 15:2136. [PMID: 38459010 PMCID: PMC10923925 DOI: 10.1038/s41467-024-46061-w] [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: 09/20/2023] [Accepted: 02/08/2024] [Indexed: 03/10/2024] Open
Abstract
Discovered over 50 years ago, bacteriorhodopsin is the first recognized and most widely studied microbial retinal protein. Serving as a light-activated proton pump, it represents the archetypal ion-pumping system. Here we compare the photochemical dynamics of bacteriorhodopsin light and dark-adapted forms with that of the first metastable photocycle intermediate known as "K". We observe that following thermal double isomerization of retinal in the dark from bio-active all-trans 15-anti to 13-cis, 15-syn, photochemistry proceeds even faster than the ~0.5 ps decay of the former, exhibiting ballistic wave packet curve crossing to the ground state. In contrast, photoexcitation of K containing a 13-cis, 15-anti chromophore leads to markedly multi-exponential excited state decay including much slower stages. QM/MM calculations, aimed to interpret these results, highlight the crucial role of protonation, showing that the classic quadrupole counterion model poorly reproduces spectral data and dynamics. Single protonation of ASP212 rectifies discrepancies and predicts triple ground state structural heterogeneity aligning with experimental observations. These findings prompt a reevaluation of counter ion protonation in bacteriorhodopsin and contribute to the broader understanding of its photochemical dynamics.
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Affiliation(s)
- Partha Malakar
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Samira Gholami
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy
| | - Mohammad Aarabi
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy
| | - Ivan Rivalta
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy
- ENSL, CNRS, Laboratoire de Chimie UMR 5182, 46 allée d'Italie, 69364, Lyon, France
| | - Mordechai Sheves
- Department of Molecular Chemistry and Materials Science, The Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Marco Garavelli
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy.
| | - Sanford Ruhman
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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Malakar P, Das I, Bhattacharya S, Harris A, Sheves M, Brown LS, Ruhman S. Bidirectional Photochemistry of Antarctic Microbial Rhodopsin: Emerging Trend of Ballistic Photoisomerization from the 13- cis Resting State. J Phys Chem Lett 2022; 13:8134-8140. [PMID: 36000820 PMCID: PMC9442786 DOI: 10.1021/acs.jpclett.2c01974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
The decades-long ultrafast examination of nearly a dozen microbial retinal proteins, ion pumps, and sensory photoreceptors has not identified structure-function indicators which predict photoisomerization dynamics, whether it will be sub-picosecond and ballistic or drawn out with complex curve-crossing kinetics. Herein, we report the emergence of such an indicator. Using pH control over retinal isomer ratios, photoinduced transient absorption is recorded in an inward proton pumping Antarctic microbial rhodopsin (AntR) for 13-cis and all-trans retinal resting states. The all-trans fluorescent state decays with 1 ps exponential kinetics. In contrast, in 13-cis it decays within ∼300 fs accompanied by continuous spectral evolution, indicating ballistic internal conversion. The coherent wave packet nature of 13-cis isomerization in AntR matches published results for bacteriorhodopsin (BR) and Anabaena sensory rhodopsin (ASR), which also accommodate both all-trans and 13-cis retinal resting states, marking the emergence of a first structure-photodynamics indicator which holds for all three tested pigments.
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Affiliation(s)
- Partha Malakar
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ishita Das
- Department
of Molecular Chemistry and Materials Science, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sudeshna Bhattacharya
- Department
of Molecular Chemistry and Materials Science, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Andrew Harris
- Department
of Physics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Mordechai Sheves
- Department
of Molecular Chemistry and Materials Science, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Leonid S. Brown
- Department
of Physics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Sanford Ruhman
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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Roy P, Sardjan AS, Cnossen A, Browne WR, Feringa BL, Meech SR. Excited State Structure Correlates with Efficient Photoconversion in Unidirectional Motors. J Phys Chem Lett 2021; 12:3367-3372. [PMID: 33784091 DOI: 10.1021/acs.jpclett.1c00710] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The design of unidirectional photomolecular motors demands a critical understanding of an ultrafast photochemical isomerization. An intermediate dark excited state mediates the reaction via a conical intersection (CI) with the ground state, but a correlation between molecular structure and photoisomerization efficiency has remained elusive. Here femtosecond stimulated Raman spectroscopy captures vibrational spectra of the dark state in a set of molecular motors bearing different substituents. A direct correlation between isomerization quantum yield, dark state lifetime, and excited state vibrational spectrum is found. Electron withdrawing substituents lead to activity in lower frequency modes, which we correlate with a pyramidalization distortion at the ethylenic axle occurring within 100 fs. This structure is not formed with an electron donating substituent, where the axle retains double bond character. Further structural reorganization is observed and assigned to excited state reorganization and charge redistribution on the sub-picosecond time scale. The correlation of the dark state structure with photoconversion performance suggests guidelines for developing new more efficient motor derivatives.
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Affiliation(s)
- Palas Roy
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Andy S Sardjan
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Arjen Cnossen
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Wesley R Browne
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Ben L Feringa
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Stephen R Meech
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
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Abstract
This is a review of relevant Raman spectroscopy (RS) techniques and their use in structural biology, biophysics, cells, and tissues imaging towards development of various medical diagnostic tools, drug design, and other medical applications. Classical and contemporary structural studies of different water-soluble and membrane proteins, DNA, RNA, and their interactions and behavior in different systems were analyzed in terms of applicability of RS techniques and their complementarity to other corresponding methods. We show that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases. In particular, the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS), which would help to further the development of protein structural crystallography and would result in a number of novel high-resolution structures of membrane proteins—drug targets; and, structural studies of photoactive membrane proteins (rhodopsins, photoreceptors, etc.) for the development of new optogenetic tools. Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed. All of these techniques have been extensively developed during recent several decades. A number of interesting applications of CARS, resonant, and surface-enhanced Raman spectroscopy methods are also discussed.
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Buhrke D, Hildebrandt P. Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy. Chem Rev 2019; 120:3577-3630. [PMID: 31814387 DOI: 10.1021/acs.chemrev.9b00429] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.
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Affiliation(s)
- David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
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