1
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Yang Q, Chen D. Na + Binding and Transport: Insights from Light-Driven Na +-Pumping Rhodopsin. Molecules 2023; 28:7135. [PMID: 37894614 PMCID: PMC10608830 DOI: 10.3390/molecules28207135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/07/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Na+ plays a vital role in numerous physiological processes across humans and animals, necessitating a comprehensive understanding of Na+ transmembrane transport. Among the various Na+ pumps and channels, light-driven Na+-pumping rhodopsin (NaR) has emerged as a noteworthy model in this field. This review offers a concise overview of the structural and functional studies conducted on NaR, encompassing ground/intermediate-state structures and photocycle kinetics. The primary focus lies in addressing key inquiries: (1) unraveling the translocation pathway of Na+; (2) examining the role of structural changes within the photocycle, particularly in the O state, in facilitating Na+ transport; and (3) investigating the timing of Na+ uptake/release. By delving into these unresolved issues and existing debates, this review aims to shed light on the future direction of Na+ pump research.
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Affiliation(s)
- Qifan Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Deliang Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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2
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Helbing J, Hamm P. Versatile Femtosecond Laser Synchronization for Multiple-Timescale Transient Infrared Spectroscopy. J Phys Chem A 2023. [PMID: 37478282 DOI: 10.1021/acs.jpca.3c03526] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Several ways to electronically synchronize different types of amplified femtosecond laser systems are presented based on a single freely programmable electronics hardware: arbitrary-detuning asynchronous optical sampling (ADASOPS), as well as actively locking two femtosecond laser oscillators, albeit not necessarily to the same round-trip frequency. They allow us to rapidly probe a very wide range of timescales, from picoseconds to potentially seconds, in a single transient absorption experiment without the need to move any delay stage. Experiments become possible that address a largely unexplored aspect of many photochemical reactions, in particular in the context of photo-catalysis as well as photoactive proteins, where an initial femtosecond trigger very often initiates a long-lasting cascade of follow-up processes. The approach is very versatile and allows us to synchronize very different lasers, such as a Ti:Sa amplifier and a 100 kHz Yb-laser system. The jitter of the synchronization, and therewith the time-resolution in the transient experiment, lies in the range from 1 to 3 ps, depending on the method. For illustration, transient IR measurements of the excited state solvation and decay of a metal carbonyl complex as well as the full reaction cycle of bacteriorhodopsin are shown. The pros and cons of the various methods are discussed, with regard to the scientific question one might want to address, and also with regard to the laser systems that might be already existent in a laser lab.
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Affiliation(s)
- Jan Helbing
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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3
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Hegemann P, Michel H. Dieter Oesterhelt (1940-2022): Life with light and color, pioneer of membrane protein research. Biophys Physicobiol 2023; 20:e201010. [PMID: 38362317 PMCID: PMC10865852 DOI: 10.2142/biophysico.bppb-v20.s010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 01/26/2023] Open
Affiliation(s)
| | - Hartmut Michel
- Max Planck Institute of Biophysics, Frankfurt 60438, Germany
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4
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Noji T, Ishikita H. Mechanism of Absorption Wavelength Shift of Bacteriorhodopsin During Photocycle. J Phys Chem B 2022; 126:9945-9955. [PMID: 36413506 DOI: 10.1021/acs.jpcb.2c04359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Bacteriorhodopsin, a light-driven proton pump, alters the absorption wavelengths in the range of 410-617 nm during the photocycle. Here, we report the absorption wavelengths, calculated using 12 bacteriorhodopsin crystal structures (including the BR, BR13-cis, J, K0, KE, KL, L, M, N, and O state structures) and a combined quantum mechanical/molecular mechanical/polarizable continuum model (QM/MM/PCM) approach. The QM/MM/PCM calculations reproduced the experimentally measured absorption wavelengths with a standard deviation of 4 nm. The shifts in the absorption wavelengths can be explained mainly by the following four factors: (i) retinal Schiff base deformation/twist induced by the protein environment, leading to a decrease in the electrostatic interaction between the protein environment and the retinal Schiff base; (ii) changes in the protonation state of the protein environment, directly altering the electrostatic interaction between the protein environment and the retinal Schiff base; (iii) changes in the protonation state; or (iv) isomerization of the retinal Schiff base, where the absorption wavelengths of the isomers originally differ.
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Affiliation(s)
- Tomoyasu Noji
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo153-8904, Japan
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo153-8904, Japan.,Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-8654, Japan
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5
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Kneuttinger AC. A guide to designing photocontrol in proteins: methods, strategies and applications. Biol Chem 2022; 403:573-613. [PMID: 35355495 DOI: 10.1515/hsz-2021-0417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/08/2022] [Indexed: 12/20/2022]
Abstract
Light is essential for various biochemical processes in all domains of life. In its presence certain proteins inside a cell are excited, which either stimulates or inhibits subsequent cellular processes. The artificial photocontrol of specifically proteins is of growing interest for the investigation of scientific questions on the organismal, cellular and molecular level as well as for the development of medicinal drugs or biocatalytic tools. For the targeted design of photocontrol in proteins, three major methods have been developed over the last decades, which employ either chemical engineering of small-molecule photosensitive effectors (photopharmacology), incorporation of photoactive non-canonical amino acids by genetic code expansion (photoxenoprotein engineering), or fusion with photoreactive biological modules (hybrid protein optogenetics). This review compares the different methods as well as their strategies and current applications for the light-regulation of proteins and provides background information useful for the implementation of each technique.
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Affiliation(s)
- Andrea C Kneuttinger
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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6
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A Light-Driven Integrated Bio-Capacitor with Single Nano-Channel Modulation. NANOMATERIALS 2022; 12:nano12040592. [PMID: 35214920 PMCID: PMC8879685 DOI: 10.3390/nano12040592] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 11/29/2022]
Abstract
Bioelectronics, an emerging discipline formed by the biology and electronic information disciplines, has maintained a state of rapid development since its birth. Amongst the various functional bioelectronics materials, bacteriorhodopsin (bR), with its directional proton pump function and favorable structural stability properties, has drawn wide attention. The main contents of the paper are as follows: Inspired by the capacitive properties of natural protoplast cell membranes, a new bio-capacitor based on bR and artificial nanochannels was constructed. As a point of innovation, microfluidic chips were integrated into our device as an ion transport channel, which made the bio-capacitor more stable. Meanwhile, a single nanopore structure was integrated to improve the accuracy of the device structure. Experiments observed that the size of the nanopore affected the ion transmission rate. Consequently, by making the single nanopore’s size change, the photocurrent duration time (PDT) of bR was effectively regulated. By using this specific phenomenon, the original transient photocurrent was successfully transformed into a square-like wave.
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7
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Chang C, Kuramochi H, Singh M, Abe‐Yoshizumi R, Tsukuda T, Kandori H, Tahara T. A Unified View on Varied Ultrafast Dynamics of the Primary Process in Microbial Rhodopsins. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Chun‐Fu Chang
- Molecular Spectroscopy Laboratory RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
- Department of Chemistry Graduate School of Science The University of Tokyo 7-3-1 Hongo Bunkyo-Ku Tokyo 113-0033 Japan
| | - Hikaru Kuramochi
- Molecular Spectroscopy Laboratory RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
- Ultrafast Spectroscopy Research Team RIKEN Center for Advanced Photonics (RAP), RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
- PRESTO (Japan) Science and Technology Agency 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
- Present address: Research Center of Integrative Molecular Systems Institute for Molecular Science 38 Nishigo-Naka Myodaiji Okazaki 444-8585 Japan
| | - Manish Singh
- Department of Life Science and Applied Chemistry Nagoya Institute of Technology, Showa-Ku Nagoya Aichi 466-8555 Japan
| | - Rei Abe‐Yoshizumi
- Department of Life Science and Applied Chemistry Nagoya Institute of Technology, Showa-Ku Nagoya Aichi 466-8555 Japan
| | - Tatsuya Tsukuda
- Department of Chemistry Graduate School of Science The University of Tokyo 7-3-1 Hongo Bunkyo-Ku Tokyo 113-0033 Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry Nagoya Institute of Technology, Showa-Ku Nagoya Aichi 466-8555 Japan
- OptoBioTechnology Research Center Nagoya Institute of Technology Showa-Ku, Nagoya Aichi 466-8555 Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
- Ultrafast Spectroscopy Research Team RIKEN Center for Advanced Photonics (RAP), RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
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8
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Chang CF, Kuramochi H, Singh M, Abe-Yoshizumi R, Tsukuda T, Kandori H, Tahara T. A Unified View on Varied Ultrafast Dynamics of the Primary Process in Microbial Rhodopsins. Angew Chem Int Ed Engl 2022; 61:e202111930. [PMID: 34670002 DOI: 10.1002/anie.202111930] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Indexed: 11/08/2022]
Abstract
All-trans to 13-cis photoisomerization of the protonated retinal Schiff base (PRSB) chromophore is the primary step that triggers various biological functions of microbial rhodopsins. While this ultrafast primary process has been extensively studied, it has been recognized that the relevant excited-state relaxation dynamics differ significantly from one rhodopsin to another. To elucidate the origin of the complicated ultrafast dynamics of the primary process in microbial rhodopsins, we studied the excited-state dynamics of proteorhodopsin, its D97N mutant, and bacteriorhodopsin by femtosecond time-resolved absorption (TA) spectroscopy in a wide pH range. The TA data showed that their excited-state relaxation dynamics drastically change when pH approaches the pKa of the counterion residue of the PRSB chromophore in the ground state. This result reveals that the varied excited-state relaxation dynamics in different rhodopsins mainly originate from the difference of the ground-state heterogeneity (i.e., protonation/deprotonation of the PRSB counterion).
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Affiliation(s)
- Chun-Fu Chang
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Hikaru Kuramochi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- PRESTO (Japan) Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama, 332-0012, Japan
- Present address: Research Center of Integrative Molecular Systems, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki, 444-8585, Japan
| | - Manish Singh
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, Aichi, 466-8555, Japan
| | - Rei Abe-Yoshizumi
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, Aichi, 466-8555, Japan
| | - Tatsuya Tsukuda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, Aichi, 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-Ku, Nagoya, Aichi, 466-8555, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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9
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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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10
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Chang CF, Kuramochi H, Singh M, Abe-Yoshizumi R, Tsukuda T, Kandori H, Tahara T. Acid-base equilibrium of the chromophore counterion results in distinct photoisomerization reactivity in the primary event of proteorhodopsin. Phys Chem Chem Phys 2019; 21:25728-25734. [PMID: 31720623 DOI: 10.1039/c9cp04991f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteorhodopsin (PR) is a proton-pumping rhodopsin, and it is known to exhibit a multi-phasic decay of the excited-state population in the primary process. So far, this complex excited-state decay has been attributed to the branching of the relaxation pathway on the excited-state potential energy surface. However, a recent ultrafast spectroscopic study on a sodium-pumping rhodopsin suggested that such a complex decay may originate from the heterogeneity in the ground state due to the acid-base equilibrium of the counterion of the protonated retinal Schiff base (PRSB). In this study, we studied the excited-state dynamics of PR at pH 11 and 4, in which the counterion of the PRSB, Asp97, is completely deprotonated and protonated, respectively. The obtained time-resolved absorption data revealed that the excited-state lifetime is decisively governed by the protonation state of Asp97, and the photoisomerization of the PRSB chromophore proceeds faster and more efficiently when Asp97 is deprotonated. This conclusion was further supported by high similarity of the excited-state dynamics between PR at pH 4 and the D97N mutant in which Asp97 is replaced with neutral Asn. The results of this study suggest that the protonation state of the PRSB counterion plays a decisive role in determining the excited-state dynamics and the photoisomerization reactivity of rhodopsins in general, by making a significant influence on the exited-state potential energy surface of the PRSB chromophore.
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Affiliation(s)
- Chun-Fu Chang
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.
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11
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Agathangelou D, Orozco-Gonzalez Y, Del Carmen Marín M, Roy PP, Brazard J, Kandori H, Jung KH, Léonard J, Buckup T, Ferré N, Olivucci M, Haacke S. Effect of point mutations on the ultrafast photo-isomerization of Anabaena sensory rhodopsin. Faraday Discuss 2019; 207:55-75. [PMID: 29388996 DOI: 10.1039/c7fd00200a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Anabaena sensory rhodopsin (ASR) is a particular microbial retinal protein for which light-adaptation leads to the ability to bind both the all-trans, 15-anti (AT) and the 13-cis, 15-syn (13C) isomers of the protonated Schiff base of retinal (PSBR). In the context of obtaining insight into the mechanisms by which retinal proteins catalyse the PSBR photo-isomerization reaction, ASR is a model system allowing to study, within the same protein, the protein-PSBR interactions for two different PSBR conformers at the same time. A detailed analysis of the vibrational spectra of AT and 13C, and their photo-products in wild-type ASR obtained through femtosecond (pump-) four-wave-mixing is reported for the first time, and compared to bacterio- and channelrhodopsin. As part of an extensive study of ASR mutants with blue-shifted absorption spectra, we present here a detailed computational analysis of the origin of the mutation-induced blue-shift of the absorption spectra, and identify electrostatic interactions as dominating steric effects that would entail a red-shift. The excited state lifetimes and isomerization reaction times (IRT) for the three mutants V112N, W76F, and L83Q are studied experimentally by femtosecond broadband transient absorption spectroscopy. Interestingly, in all three mutants, isomerization is accelerated for AT with respect to wild-type ASR, and this the more, the shorter the wavelength of maximum absorption. On the contrary, the 13C photo-reaction is slightly slowed down, leading to an inversion of the ESLs of AT and 13C, with respect to wt-ASR, in the blue-most absorbing mutant L83Q. Possible mechanisms for these mutation effects, and their steric and electrostatic origins are discussed.
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Affiliation(s)
- D Agathangelou
- University of Strasbourg, CNRS, Inst. de Physique et Chimie des Matériaux de Strasbourg, 67034 Strasbourg, France.
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12
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Tahara S, Takeuchi S, Abe-Yoshizumi R, Inoue K, Ohtani H, Kandori H, Tahara T. Origin of the Reactive and Nonreactive Excited States in the Primary Reaction of Rhodopsins: pH Dependence of Femtosecond Absorption of Light-Driven Sodium Ion Pump Rhodopsin KR2. J Phys Chem B 2018; 122:4784-4792. [DOI: 10.1021/acs.jpcb.8b01934] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | | | | | - Keiichi Inoue
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Hiroyuki Ohtani
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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13
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Li YT, Tian Y, Tian H, Tu T, Gou GY, Wang Q, Qiao YC, Yang Y, Ren TL. A Review on Bacteriorhodopsin-Based Bioelectronic Devices. SENSORS (BASEL, SWITZERLAND) 2018; 18:E1368. [PMID: 29702621 PMCID: PMC5982678 DOI: 10.3390/s18051368] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/06/2018] [Accepted: 04/18/2018] [Indexed: 11/24/2022]
Abstract
Bacteriorhodopsin protein extracted from Halobacterium salinarum is widely used in many biohybrid electronic devices and forms a research subject known as bioelectronics, which merges biology with electronic technique. The specific molecule structure and components of bR lead to its unique photocycle characteristic, which consists of several intermediates (bR, K, L, M, N, and O) and results in proton pump function. In this review, working principles and properties of bacteriorhodopsin are briefly introduced, as well as bR layer preparation method. After that, different bR-based devices divided into photochemical and photoelectric applications are shown. Finally, outlook and conclusions are drawn to inspire new design of high-performance bR-based biohybrid electronic devices.
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Affiliation(s)
- Yu-Tao Li
- Institute of Microelectronics, Tsinghua University, Beijing 100084, China.
- Tsinghua National Laboratory for Information Science and Technology (TNList), Tsinghua University, Beijing 100084, China.
| | - Ye Tian
- Institute of Microelectronics, Tsinghua University, Beijing 100084, China.
- Tsinghua National Laboratory for Information Science and Technology (TNList), Tsinghua University, Beijing 100084, China.
| | - He Tian
- Institute of Microelectronics, Tsinghua University, Beijing 100084, China.
- Tsinghua National Laboratory for Information Science and Technology (TNList), Tsinghua University, Beijing 100084, China.
| | - Tao Tu
- Institute of Microelectronics, Tsinghua University, Beijing 100084, China.
- Tsinghua National Laboratory for Information Science and Technology (TNList), Tsinghua University, Beijing 100084, China.
| | - Guang-Yang Gou
- Institute of Microelectronics, Tsinghua University, Beijing 100084, China.
- Tsinghua National Laboratory for Information Science and Technology (TNList), Tsinghua University, Beijing 100084, China.
| | - Qian Wang
- Institute of Microelectronics, Tsinghua University, Beijing 100084, China.
- Tsinghua National Laboratory for Information Science and Technology (TNList), Tsinghua University, Beijing 100084, China.
| | - Yan-Cong Qiao
- Institute of Microelectronics, Tsinghua University, Beijing 100084, China.
- Tsinghua National Laboratory for Information Science and Technology (TNList), Tsinghua University, Beijing 100084, China.
| | - Yi Yang
- Institute of Microelectronics, Tsinghua University, Beijing 100084, China.
- Tsinghua National Laboratory for Information Science and Technology (TNList), Tsinghua University, Beijing 100084, China.
| | - Tian-Ling Ren
- Institute of Microelectronics, Tsinghua University, Beijing 100084, China.
- Tsinghua National Laboratory for Information Science and Technology (TNList), Tsinghua University, Beijing 100084, China.
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14
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Köhler T, Weber I, Glaubitz C, Wachtveitl J. Proteorhodopsin Photocycle Kinetics Between pH 5 and pH 9. Photochem Photobiol 2017; 93:762-771. [DOI: 10.1111/php.12753] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/25/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas Köhler
- Institute of Physical and Theoretical Chemistry; Goethe Universität Frankfurt am Main; Frankfurt Germany
| | - Ingrid Weber
- Institut für Biophysikalische Chemie; Goethe Universität Frankfurt am Main; Frankfurt Germany
| | - Clemens Glaubitz
- Institut für Biophysikalische Chemie; Goethe Universität Frankfurt am Main; Frankfurt Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry; Goethe Universität Frankfurt am Main; Frankfurt Germany
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15
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Niho A, Yoshizawa S, Tsukamoto T, Kurihara M, Tahara S, Nakajima Y, Mizuno M, Kuramochi H, Tahara T, Mizutani Y, Sudo Y. Demonstration of a Light-Driven SO42– Transporter and Its Spectroscopic Characteristics. J Am Chem Soc 2017; 139:4376-4389. [DOI: 10.1021/jacs.6b12139] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Akiko Niho
- Faculty
of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Susumu Yoshizawa
- Atmosphere
and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan
| | - Takashi Tsukamoto
- Faculty
of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Marie Kurihara
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Shinya Tahara
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Yu Nakajima
- Atmosphere
and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan
| | - Misao Mizuno
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - 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
| | - 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
| | - Yasuhisa Mizutani
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yuki Sudo
- Faculty
of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
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16
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Kumpulainen T, Lang B, Rosspeintner A, Vauthey E. Ultrafast Elementary Photochemical Processes of Organic Molecules in Liquid Solution. Chem Rev 2016; 117:10826-10939. [DOI: 10.1021/acs.chemrev.6b00491] [Citation(s) in RCA: 249] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Tatu Kumpulainen
- Department of Physical Chemistry,
Sciences II, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - Bernhard Lang
- Department of Physical Chemistry,
Sciences II, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - Arnulf Rosspeintner
- Department of Physical Chemistry,
Sciences II, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - Eric Vauthey
- Department of Physical Chemistry,
Sciences II, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
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17
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Chiang HK, Chu LK. Wavelength-dependent photocycle activity of xanthorhodopsin in the visible region. Biochem Biophys Rep 2016; 7:347-352. [PMID: 28955925 PMCID: PMC5613640 DOI: 10.1016/j.bbrep.2016.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 07/10/2016] [Accepted: 07/12/2016] [Indexed: 12/02/2022] Open
Abstract
Xanthorhodopsin (xR) is a dual-chromophore proton-pump photosynthetic protein comprising one retinal Schiff base and one light-harvesting antenna salinixanthin (SX). The excitation wavelength-dependent transient population of the intermediate M demonstrates that the excitation of the retinal at 570 nm leads to the highest photocycle activity and the excitations of SX at 460 and 430 nm reduce the activity to ca. 37% relatively, suggesting an energy transfer pathway from the S2 state of the SX to the S1 state of the retinal and a quick internal vibrational relaxation in the S2 state of SX prior to the energy transfer from SX to retinal. Energy transfer efficiency from the salinixanthin (SX) to the retinal is ca. 37%. Energy transfer efficiency is not dependent on wavelength at 486–430 nm. Energy transfer from the S2 state of SX to the S2 state of retinal is less accessible.
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18
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Tahara S, Takeuchi S, Abe-Yoshizumi R, Inoue K, Ohtani H, Kandori H, Tahara T. Ultrafast photoreaction dynamics of a light-driven sodium-ion-pumping retinal protein from Krokinobacter eikastus revealed by femtosecond time-resolved absorption spectroscopy. J Phys Chem Lett 2015; 6:4481-4486. [PMID: 26582475 DOI: 10.1021/acs.jpclett.5b01994] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We report the first femtosecond time-resolved absorption study on ultrafast photoreaction dynamics of a recently discovered retinal protein, KR2, which functions as a light-driven sodium-ion pump. The obtained data show that the excited-state absorption around 460 nm and the stimulated emission around 720 nm decay concomitantly with a time constant of 180 fs. This demonstrates that the deactivation of the S1 state of KR2, which involves isomerization of the retinal chromophore, takes place three times faster than that of bacteriorhodopsin. In accordance with this rapid electronic relaxation, the photoproduct band assignable to the J intermediate grows up at ∼620 nm, indicating that the J intermediate is directly formed with the S1 → S0 internal conversion. The photoproduct band subsequently exhibits a ∼30 nm blue shift with a 500 fs time constant, corresponding to the conversion to the K intermediate. On the basis of the femtosecond absorption data obtained, we discuss the mechanism for the rapid photoreaction of KR2 and its relevance to the unique function of the sodium-ion pump.
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Affiliation(s)
- Shinya Tahara
- Molecular Spectroscopy Laboratory, RIKEN , 2-1 Hirosawa, Wako 351-0198, Japan
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology , Yokohama 226-8501, Japan
| | - Satoshi Takeuchi
- Molecular Spectroscopy Laboratory, RIKEN , 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN , 2-1 Hirosawa, Wako 351-0198, Japan
| | - Rei Abe-Yoshizumi
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
- PRESTO, Japan Science and Technology Agency , 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Hiroyuki Ohtani
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology , Yokohama 226-8501, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN , 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN , 2-1 Hirosawa, Wako 351-0198, Japan
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19
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Terpugov EL, Degtyareva OV. Photo-induced processes and the reaction dynamics of bacteriorhodopsin. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915020189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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20
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Cheminal A, Léonard J, Kim SY, Jung KH, Kandori H, Haacke S. 100 fs photo-isomerization with vibrational coherences but low quantum yield in Anabaena Sensory Rhodopsin. Phys Chem Chem Phys 2015; 17:25429-39. [DOI: 10.1039/c5cp04353k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Counter-intuitive photochemistry: in Anabaena Sensory Rhodopsin, the retinal 13-cis isomer isomerizes much faster than all-trans ASR, but with a 3-times lower quantum yield.
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Affiliation(s)
- Alexandre Cheminal
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE
- Université de Strasbourg – CNRS
- 67034 Strasbourg
- France
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE
- Université de Strasbourg – CNRS
- 67034 Strasbourg
- France
| | - So-Young Kim
- Department of Life Science and Institute of Biological Interfaces
- Sogang University
- Mapo-Gu
- South Korea
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces
- Sogang University
- Mapo-Gu
- South Korea
| | - Hideki Kandori
- Department of Frontier Materials
- Nagoya Institute of Technology
- Showa-ku
- Japan
| | - Stefan Haacke
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE
- Université de Strasbourg – CNRS
- 67034 Strasbourg
- France
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21
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Tavanti F, Tozzini V. A multi-scale-multi-stable model for the rhodopsin photocycle. Molecules 2014; 19:14961-78. [PMID: 25237751 PMCID: PMC6271392 DOI: 10.3390/molecules190914961] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 08/28/2014] [Accepted: 09/08/2014] [Indexed: 11/19/2022] Open
Abstract
We report a multi-scale simulation study of the photocycle of the rhodopsins. The quasi-atomistic representation ("united atoms" UA) of retinal is combined with a minimalist coarse grained (CG, one-bead-per amino acid) representation of the protein, in a hybrid UA/CG approach, which is the homolog of QM/MM, but at lower resolution. An accurate multi-stable parameterization of the model allows simulating each state and transition among them, and the combination of different scale representation allows addressing the entire photocycle. We test the model on bacterial rhodopsin, for which more experimental data are available, and then also report results for mammalian rhodopsins. In particular, the analysis of simulations reveals the spontaneous appearance of meta-stable states in quantitative agreement with experimental data.
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Affiliation(s)
- Francesco Tavanti
- NEST-Istituto Nanoscienze, CNR, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Valentina Tozzini
- NEST-Istituto Nanoscienze, CNR, Piazza San Silvestro 12, 56127 Pisa, Italy.
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22
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Kochendoerfer GG, Mathies RA. Ultrafast Spectroscopy of Rhodopsins - Photochemistry at Its Best! Isr J Chem 2013. [DOI: 10.1002/ijch.199500028] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Althaus T, Eisfeld W, Lohrmann R, Stockburger M. Application of Raman Spectroscopy to Retinal Proteins. Isr J Chem 2013. [DOI: 10.1002/ijch.199500029] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Luck M, Mathes T, Bruun S, Fudim R, Hagedorn R, Tran Nguyen TM, Kateriya S, Kennis JTM, Hildebrandt P, Hegemann P. A photochromic histidine kinase rhodopsin (HKR1) that is bimodally switched by ultraviolet and blue light. J Biol Chem 2012; 287:40083-90. [PMID: 23027869 DOI: 10.1074/jbc.m112.401604] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rhodopsins are light-activated chromoproteins that mediate signaling processes via transducer proteins or promote active or passive ion transport as ion pumps or directly light-activated channels. Here, we provide spectroscopic characterization of a rhodopsin from the Chlamydomonas eyespot. It belongs to a recently discovered but so far uncharacterized family of histidine kinase rhodopsins (HKRs). These are modular proteins consisting of rhodopsin, a histidine kinase, a response regulator, and in some cases an effector domain such as an adenylyl or guanylyl cyclase, all encoded in a single protein as a two-component system. The recombinant rhodopsin fragment, Rh, of HKR1 is a UVA receptor (λ(max) = 380 nm) that is photoconverted by UV light into a stable blue light-absorbing meta state Rh-Bl (λ(max) = 490 nm). Rh-Bl is converted back to Rh-UV by blue light. Raman spectroscopy revealed that the Rh-UV chromophore is in an unusual 13-cis,15-anti configuration, which explains why the chromophore is deprotonated. The excited state lifetime of Rh-UV is exceptionally stable, probably caused by a relatively unpolar retinal binding pocket, converting into the photoproduct within about 100 ps, whereas the blue form reacts 100 times faster. We propose that the photochromic HKR1 plays a role in the adaptation of behavioral responses in the presence of UVA light.
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Affiliation(s)
- Meike Luck
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
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25
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Schoepp-Cothenet B, van Lis R, Atteia A, Baymann F, Capowiez L, Ducluzeau AL, Duval S, ten Brink F, Russell MJ, Nitschke W. On the universal core of bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:79-93. [PMID: 22982447 DOI: 10.1016/j.bbabio.2012.09.005] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 01/05/2023]
Abstract
Living cells are able to harvest energy by coupling exergonic electron transfer between reducing and oxidising substrates to the generation of chemiosmotic potential. Whereas a wide variety of redox substrates is exploited by prokaryotes resulting in very diverse layouts of electron transfer chains, the ensemble of molecular architectures of enzymes and redox cofactors employed to construct these systems is stunningly small and uniform. An overview of prominent types of electron transfer chains and of their characteristic electrochemical parameters is presented. We propose that basic thermodynamic considerations are able to rationalise the global molecular make-up and functioning of these chemiosmotic systems. Arguments from palaeogeochemistry and molecular phylogeny are employed to discuss the evolutionary history leading from putative energy metabolisms in early life to the chemiosmotic diversity of extant organisms. Following the Occam's razor principle, we only considered for this purpose origin of life scenarios which are contiguous with extant life. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.
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Affiliation(s)
- Barbara Schoepp-Cothenet
- Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 CNRS/AMU, FR3479, F-13402 Marseille Cedex 20, France.
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26
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Scholz F, Bamberg E, Bamann C, Wachtveitl J. Tuning the primary reaction of channelrhodopsin-2 by imidazole, pH, and site-specific mutations. Biophys J 2012; 102:2649-57. [PMID: 22713581 DOI: 10.1016/j.bpj.2012.04.034] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 03/12/2012] [Accepted: 04/19/2012] [Indexed: 01/11/2023] Open
Abstract
Femtosecond time-resolved absorption measurements were performed to investigate the influence of the pH, imidazole concentration, and point mutations on the isomerization process of Channelrhodopsin-2. Apart from the typical spectral characteristics of retinal isomerization, an additional absorption feature rises for the wild-type (wt) on a timescale from tens of ps to 1 ns within the spectral range of the photoproduct and is attributed to an equilibration between different K-intermediates. Remarkably, this absorption feature vanishes upon addition of imidazole or lowering the pH. In the latter case, the isomerization is dramatically slowed down, due to protonation of negatively charged amino acids within the retinal binding pocket, e.g., E123 and D253. Moreover, we investigated the influence of several point mutations within the retinal binding pocket E123T, E123D, C128T, and D156C. For E123T, the isomerization is retarded compared to wt and E123D, indicating that a negatively charged residue at this position functions as an effective catalyst in the isomerization process. In the case of the C128T mutant, all primary processes are slightly accelerated compared to the wt, whereas the isomerization dynamics for the D156C mutant is similar to wt after addition of imidazole.
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Affiliation(s)
- Frank Scholz
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Frankfurt/Main, Germany
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27
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Verhoefen MK, Bamann C, Blöcher R, Förster U, Bamberg E, Wachtveitl J. The photocycle of channelrhodopsin-2: ultrafast reaction dynamics and subsequent reaction steps. Chemphyschem 2011; 11:3113-22. [PMID: 20730849 DOI: 10.1002/cphc.201000181] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The photocycle of channelrhodopsin-2 is investigated in a comprehensive study by ultrafast absorption and fluorescence spectroscopy as well as flash photolysis in the visible spectral range. The ultrafast techniques reveal an excited-state decay mechanism analogous to that of the archaeal bacteriorhodopsin and sensory rhodopsin II from Natronomonas pharaonis. After a fast vibrational relaxation of the excited-state population with 150 fs its decay with mainly 400 fs is observed. Hereby, both the initial all-trans retinal ground state and the 13-cis-retinal K photoproduct are populated. The reaction proceeds with a 2.7 ps component assigned to cooling processes. Small spectral shifts are observed on a 200 ps timescale. They are attributed to conformational rearrangements in the retinal binding pocket. The subsequent dynamics progresses with the formation of an M-like intermediate (7 and 120 μs), which decays into red-shifted states within 3 ms. Ground-state recovery including channel closing and reisomerization of the retinal chromophore occurs in a triexponential manner (6 ms, 33 ms, 3.4 s). To learn more about the energy barriers between the different photocycle intermediates, temperature-dependent flash photolysis measurements are performed between 10 and 30°C. The first five time constants decrease with increasing temperature. The calculated thermodynamic parameters indicate that the closing mechanism is controlled by large negative entropy changes. The last time constant is temperature independent, which demonstrates that the photocycle is most likely completed by a series of individual steps recovering the initial structure.
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Affiliation(s)
- Mirka-Kristin Verhoefen
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe University Frankfurt, Max von Laue-Straße 7, 60438 Frankfurt am Main, Germany
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Song L, El-Sayed MA, Lanyi JK. Protein catalysis of the retinal subpicosecond photoisomerization in the primary process of bacteriorhodopsin photosynthesis. Science 2010; 261:891-4. [PMID: 17783735 DOI: 10.1126/science.261.5123.891] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The rate of retinal photoisomerization in wild-type bacteriorhodopsin (wt bR) is compared with that in a number of mutants in which a positively charged (Arg(82)), a negatively charged (Asp(85) or Asp(212)), or neutral hydrogen bonding (Asp(115) or Tyr(185)) amino acid residue known to be functionally important within the retinal cavity is replaced by a neutral, non-hydrogen bonding one. Only the replacements of the charged residues reduced the photoisomerization rate of the 13-cis and all-trans isomers present in these mutants by factors of approximately 1/4 and approximately 1/20, respectively. Retinal photo- and thermal isomerization catalysis and selectivity in wt bR by charged residues is discussed in terms of the known protein structure, the valence-bond wave functions of the ground and excited state of the retinal, and the electrostatic stabilization interactions within the retinal cavity.
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van den Berg R, Du-Jeon-Jang, Bitting HC, El-Sayed MA. Subpicosecond resonance Raman spectra of the early intermediates in the photocycle of bacteriorhodopsin. Biophys J 2010; 58:135-41. [PMID: 19431759 DOI: 10.1016/s0006-3495(90)82359-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The resonance Raman spectra are presented for the species formed during the photocycle of bacteriorhodopsin (bR) on a timescale of 800-900 fs. In the ethylenic stretch region two intermediates were found with frequencies of 1,510 and 1,518 cm(-1), corresponding to species with optical absorption maxima at 660 and 625 nm, respectively. This leads to the assignment of the 1,518 cm(-1) band to the J(625) intermediate. In the fingerprint region, the appearance of a vibration at 1,195 cm(-1) strongly suggests that the isomerization indeed has taken place in a time less than the pulsewidth of our laser. This supports the previous proposals made on the basis of the optical spectra. The spectra are compared with those observed in tens of picoseconds up to nanoseconds.
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Affiliation(s)
- R van den Berg
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90024-1569 USA
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Abstract
Values in the literature for the quantum efficiency of the photochemical cycle of bacteriorhodopsin (bR) range from 0.25 to 0.79 and the sum of the quantum yields of the forward and back photoreactions [Formula: see text] has been proposed to be 1. In the present work, low intensity laser flashes (532 nm) and kinetic spectroscopy were used to determine the quantum efficiency of bR photoconversion, [UNK](bR), by measuring transient bleaching of bR at 610 nm in the millisecond time scale. Bovine rhodopsin (R) in 2% ammonyx LO was used as a photon counter. We find that the ratio of the quantum yields of bacteriorhodopsin photoconversion and bleaching of rhodopsin, [UNK](bR)/[UNK](R), is 0.96 +/- 0.04. Based on the quantum yield of the photobleaching of rhodopsin, 0.67, the quantum efficiency of bR photoconversion was determined to be 0.64 +/- 0.04. The quantum yield of M formation was found to be 0.65 +/- 0.06. From the transient bleaching of bR at 610 nm with a saturating laser flash (28 mJ/cm(2)) the maximum amount of bR cycling was estimated to be 47 +/- 3%. From this value and the spectrum of K published in the literature, the ratio of the efficiencies of the forward and back light reactions, [UNK](1)/[UNK](2), was estimated to be 0.67 +/- 0.06 and so [UNK](2) approximately 1 (0.94 +/- 0.06). The sum of [UNK](1) + [UNK](2) approximately 1.6. It was found that repeated high-intensity laser flashes (>20 mJ/cm(2)) irreversibly transformed bR into two stable photoproducts. One has its absorption maximum at 605 nm and the other has a well-resolved vibronic spectrum with maxima at 342, 359 (main peak), and 379 nm. The quantum yield of the formation of the photoproducts is approximately 10(-4).
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31
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Delaney JK, Brack TL, Atkinson GH. Time-resolved absorption and fluorescence from the bacteriorhodopsin photocycle in the nanosecond time regime. Biophys J 2010; 64:1512-9. [PMID: 19431895 DOI: 10.1016/s0006-3495(93)81520-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Picosecond transient absorption (PTA) in the 568-660-nm region is measured over the initial 80 ns of the bacteriorhodopsin photocycle. After photocycle initiation with 573-nm excitation (7-ps pulsewidth), these PTA data reflect the formation during the initial 40 ps of two long-recognized intermediates with red-shifted (relative to that of BR-570) absorption bands, namely J-625 and K-590. PTA signals at 568, 628, and 652 nm are unchanged for the remainder of the 80-ns photocycle interval measured, demonstrating that no other intermediates, including the proposed KL, are observable by absorption changes. Picosecond time-resolved fluorescence (PTRF), measured at 740 nm, is initiated by 7 ps excitation of the species present at various time delays after the photocycle begins. PTRF signals change rapidly over the initial 40 ps, reflecting, first, the depletion of the ground state BR-570 population and, subsequently, the formation of K-590. The PTRF signal then decreases monotonically with a time constant of 5.5 +/- 0.5 ns from its maximum near a 50-ps delay until it reaches a minimum at a delay of approximately 13 ns. For time delays between 13 and 80 ns, the PTRF signal remains unchanged and slightly higher than that measured from BR-570 alone. The rapid decrease in PTRF signals over the same photocycle interval in which the PTA signals remain unchanged suggests that the retinal-protein interactions involving electronically excited K-590 (K*) are being significantly altered.
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Affiliation(s)
- J K Delaney
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721 USA
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Dioumaev AK, Wang JM, Lanyi JK. Low-temperature FTIR study of multiple K intermediates in the photocycles of bacteriorhodopsin and xanthorhodopsin. J Phys Chem B 2010; 114:2920-31. [PMID: 20136108 PMCID: PMC3820168 DOI: 10.1021/jp908698f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Low-temperature FTIR spectroscopy of bacteriorhodopsin and xanthorhodopsin was used to elucidate the number of K-like bathochromic states, their sequence, and their contributions to the photoequilibrium mixtures created by illumination at 80-180 K. We conclude that in bacteriorhodopsin the photocycle includes three distinct K-like states in the sequence bR (hv)--> I* --> J --> K(0) --> K(E) --> L --> ..., and similarly in xanthorhodopsin. K(0) is the main fraction in the mixture at 77 K that is formed from J. K(0) becomes thermally unstable above approximately 50 K in both proteins. At 77 K, both J-to-K(0) and K(0)-to-K(E) transitions occur and, contrarily to long-standing belief, cryogenic trapping at 77 K does not produce a pure K state but a mixture of the two states, K(0) and K(E), with contributions from K(E) of approximately 15 and approximately 10% in the two retinal proteins, respectively. Raising the temperature leads to increasing conversion of K(0) to K(E), and the two states coexist (without contamination from non-K-like states) in the 80-140 K range in bacteriorhodopsin, and in the 80-190 K range in xanthorhodopsin. Temperature perturbation experiments in these regions of coexistence revealed that, in spite of the observation of apparently stable mixtures of K(0) and K(E), the two states are not in thermally controlled equilibrium. The K(0)-to-K(E) transition is unidirectional, and the partial transformation to K(E) is due to distributed kinetics, which governs the photocycle dynamics at temperatures below approximately 245 K (Dioumaev and Lanyi, Biochemistry 2008, 47, 11125-11133). From spectral deconvolution, we conclude that the K(E) state, which is increasingly present at higher temperatures, is the same intermediate that is detected by time-resolved FTIR prior to its decay, on a time scale of hundreds of nanoseconds at ambient temperature (Dioumaev and Braiman, J. Phys. Chem. B 1997, 101, 1655-1662), into the K(L) state. We were unable to trap the latter separately from K(E) at low temperature, due to the slow distributed kinetics and the increasingly faster overlapping formation of the L state. Formation of the two consecutive K-like states in both proteins is accompanied by distortion of two different weakly bound water molecules: one in K(0), the other in K(E). The first, well-documented in bacteriorhodopsin at 77 K where K(0) dominates, was assigned to water 401 in bacteriorhodopsin. The other water molecule, whose participation has not been described previously, is disturbed on the next step of the photocycle, in K(E), in both proteins. In bacteriorhodopsin, the most likely candidate is water 407. However, unlike bacteriorhodopsin, the crystal structure of xanthorhodopsin lacks homologous weakly bound water molecules.
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Affiliation(s)
- Andrei K. Dioumaev
- Department of Physiology & Biophysics, University of California, Irvine, CA 92697
| | - Jennifer M. Wang
- Department of Physiology & Biophysics, University of California, Irvine, CA 92697
| | - Janos K. Lanyi
- Department of Physiology & Biophysics, University of California, Irvine, CA 92697
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Müller WEG, Wang X, Schröder HC, Korzhev M, Grebenjuk VA, Markl JS, Jochum KP, Pisignano D, Wiens M. A cryptochrome-based photosensory system in the siliceous sponge Suberites domuncula (Demospongiae). FEBS J 2010; 277:1182-201. [DOI: 10.1111/j.1742-4658.2009.07552.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Zgrablić G, Ricci M, Novello AM, Parmigiani F. Dependence of Photochemical Reactivity of the All-trans Retinal Protonated Schiff Base on the Solvent and the Excitation Wavelength. Photochem Photobiol 2010; 86:507-12. [DOI: 10.1111/j.1751-1097.2009.00697.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Dioumaev AK, Lanyi JK. Two bathointermediates of the bacteriorhodopsin photocycle, from time-resolved nanosecond spectra in the visible. J Phys Chem B 2009; 113:16643-53. [PMID: 19994879 PMCID: PMC3808455 DOI: 10.1021/jp907393m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Time-resolved measurements were performed on wild-type bacteriorhodopsin with an optical multichannel analyzer in the spectral range 350-735 nm, from 100 ns to the photocycle completion, at four temperatures in the 5-30 degrees C range. The intent was to examine the possibility of two K-like bathochromic intermediates and to obtain their spectra and kinetics in the visible. The existence of a second K-like intermediate, termed KL, had been postulated (Shichida et al., Biochim. Biophys. Acta 1983, 723, 240-246) to reconcile inconsistencies in data in the pico- and microsecond time domains. However, introduction of KL led to a controversy, since neither its visible spectrum nor its kinetics could be confirmed. Infrared data (Dioumaev and Braiman, J. Phys. Chem. B 1997, 101, 1655-1662) revealed a state which might have been considered a homologue to KL, but it had a kinetic pattern different from that of the earlier proposed KL. Here, we characterize two distinct K-like intermediates, K(E) ("early") and K(L) ("late"), by their spectra and kinetics in the visible as revealed by global kinetic analysis. The K(E)-to-K(L) transition has a time constant of approximately 250 ns at 20 degrees C, and describes a shift from K(E) with lambda(max) at approximately 600 nm and extinction of approximately 56,000 M(-1) x cm(-1) to K(L) with lambda(max) at approximately 590 nm and extinction of approximately 50,000 M(-1) x cm(-1). The temperature dependence of this transition is characterized by an enthalpy of activation of DeltaH(++) approximately 40 kJ/mol and a positive entropy of activation of DeltaS(++)/R approximately 4. The consequences of multiple K-like states for interpreting the spectral evolution in the early stages of the photocycle are discussed.
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Affiliation(s)
- Andrei K Dioumaev
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, California 92697, USA.
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Mizuno M, Shibata M, Yamada J, Kandori H, Mizutani Y. Picosecond Time-Resolved Ultraviolet Resonance Raman Spectroscopy of Bacteriorhodopsin: Primary Protein Response to the Photoisomerization of Retinal. J Phys Chem B 2009; 113:12121-8. [DOI: 10.1021/jp904388w] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 454-8555, Japan
| | - Mikihiro Shibata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 454-8555, Japan
| | - Junya Yamada
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 454-8555, Japan
| | - Hideki Kandori
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 454-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 454-8555, Japan
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Sobotta C, Braun M, Tittor J, Oesterhelt D, Zinth W. Influence of the charge at D85 on the initial steps in the photocycle of bacteriorhodopsin. Biophys J 2009; 97:267-76. [PMID: 19580764 DOI: 10.1016/j.bpj.2009.04.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 03/25/2009] [Accepted: 04/06/2009] [Indexed: 10/20/2022] Open
Abstract
Studies have shown that trans-cis isomerization of retinal is the primary photoreaction in the photocycle of the light-driven proton pump bacteriorhodopsin (BR) from Halobacterium salinarum, as well as in the photocycle of the chloride pump halorhodopsin (HR). The transmembrane proteins HR and BR show extensive structural similarities, but differ in the electrostatic surroundings of the retinal chromophore near the protonated Schiff base. Point mutation of BR of the negatively charged aspartate D85 to a threonine T (D85T) in combination with variation of the pH value and anion concentration is used to study the ultrafast photoisomerization of BR and HR for well-defined electrostatic surroundings of the retinal chromophore. Variations of the pH value and salt concentration allow a switch in the isomerization dynamics of the BR mutant D85T between BR-like and HR-like behaviors. At low salt concentrations or a high pH value (pH 8), the mutant D85T shows a biexponential initial reaction similar to that of HR. The combination of high salt concentration and a low pH value (pH 6) leads to a subpopulation of 25% of the mutant D85T whose stationary and dynamic absorption properties are similar to those of native BR. In this sample, the combination of low pH and high salt concentration reestablishes the electrostatic surroundings originally present in native BR, but only a minor fraction of the D85T molecules have the charge located exactly at the position required for the BR-like fast isomerization reaction. The results suggest that the electrostatics in the native BR protein is optimized by evolution. The accurate location of the fixed charge at the aspartate D85 near the Schiff base in BR is essential for the high efficiency of the primary reaction.
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Affiliation(s)
- Constanze Sobotta
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik, Ludwig-Maximilians-Universität München, Munich, Germany
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Zgrablić G, Haacke S, Chergui M. Heterogeneity and Relaxation Dynamics of the Photoexcited Retinal Schiff Base Cation in Solution. J Phys Chem B 2009; 113:4384-93. [DOI: 10.1021/jp8077216] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Goran Zgrablić
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, Faculté des Sciences de Base, BSP, CH-1015 Lausanne-Dorigny, Switzerland, Sincrotrone Trieste Elettra, S.S. 14 km 163.5 in Area Science Park, 34012 Basovizza, Trieste, Italy, and Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS-ULP, 67034 Strasbourg Cédex, France
| | - Stefan Haacke
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, Faculté des Sciences de Base, BSP, CH-1015 Lausanne-Dorigny, Switzerland, Sincrotrone Trieste Elettra, S.S. 14 km 163.5 in Area Science Park, 34012 Basovizza, Trieste, Italy, and Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS-ULP, 67034 Strasbourg Cédex, France
| | - Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, Faculté des Sciences de Base, BSP, CH-1015 Lausanne-Dorigny, Switzerland, Sincrotrone Trieste Elettra, S.S. 14 km 163.5 in Area Science Park, 34012 Basovizza, Trieste, Italy, and Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS-ULP, 67034 Strasbourg Cédex, France
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Abstract
Functions of biologically active molecules are frequently initiated by elementary chemical reactions such as energy and electron transfer, cis-trans isomerizations, and proton transfer. The nature of these reactions generally makes them very fast and efficient, occurring on picosecond and femtosecond timescales. Ultrafast spectroscopy has played an important role in the study of a number of biological processes and has provided unique information about several of nature's responses to light. Here I review the current understanding of light-energy collection and conversion in photosynthesis, the function of carotenoid molecules in photosynthesis, and the primary light-initiated reactions of the photoreceptors rhodopsin, bacteriorhodopsin, photoactive yellow protein, phytochrome, and a new type of blue-light receptor based on flavin chromophores.
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Affiliation(s)
- Villy Sundström
- Department of Chemical Physics, Lund University, S-221 00 Lund, Sweden.
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Backus EHG, Nguyen PH, Botan V, Pfister R, Moretto A, Crisma M, Toniolo C, Stock G, Hamm P. Energy Transport in Peptide Helices: A Comparison between High- and Low-Energy Excitations. J Phys Chem B 2008; 112:9091-9. [DOI: 10.1021/jp711046e] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ellen H. G. Backus
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, I-35131 Padova, Italy, and Institut für Physikalische and Theoretische Chemie, J. W. Goethe Unversität, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Phuong H. Nguyen
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, I-35131 Padova, Italy, and Institut für Physikalische and Theoretische Chemie, J. W. Goethe Unversität, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Virgiliu Botan
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, I-35131 Padova, Italy, and Institut für Physikalische and Theoretische Chemie, J. W. Goethe Unversität, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Rolf Pfister
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, I-35131 Padova, Italy, and Institut für Physikalische and Theoretische Chemie, J. W. Goethe Unversität, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Alessandro Moretto
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, I-35131 Padova, Italy, and Institut für Physikalische and Theoretische Chemie, J. W. Goethe Unversität, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Marco Crisma
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, I-35131 Padova, Italy, and Institut für Physikalische and Theoretische Chemie, J. W. Goethe Unversität, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Claudio Toniolo
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, I-35131 Padova, Italy, and Institut für Physikalische and Theoretische Chemie, J. W. Goethe Unversität, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Gerhard Stock
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, I-35131 Padova, Italy, and Institut für Physikalische and Theoretische Chemie, J. W. Goethe Unversität, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Peter Hamm
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland, Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, I-35131 Padova, Italy, and Institut für Physikalische and Theoretische Chemie, J. W. Goethe Unversität, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
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41
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Wu Y, Zhong S, Ai X, Hu K, Zhang J. Ultrafast isomerization dynamics of retinal in bacteriorhodopsin as revealed by femtosecond absorption spectroscopy. Sci Bull (Beijing) 2008. [DOI: 10.1007/s11434-008-0283-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Müller MG, Lindner I, Martin I, Gärtner W, Holzwarth AR. Femtosecond kinetics of photoconversion of the higher plant photoreceptor phytochrome carrying native and modified chromophores. Biophys J 2008. [PMID: 18199671 DOI: 10.1529/biophysj.106.0916521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
The photoprocesses of native (phyA of oat), and of C-terminally truncated recombinant phytochromes, assembled instead of the native phytochromobilin with phycocyanobilin (PCB-65 kDa-phy) and iso-phycocyanobilin (iso-PCB-65 kDa-phy) chromophores, have been studied by femtosecond transient absorption spectroscopy in both their red absorbing phytochrome (P(r)) and far-red absorbing phytochrome (P(fr)) forms. Native P(r) phytochrome shows an excitation wavelength dependence of the kinetics with three main picosecond components. The formation kinetics of the first ground-state intermediate I(700), absorbing at approximately 690 nm, is mainly described by 28 ps or 40 ps components in native and PCB phytochrome, respectively, whereas additional approximately 15 and 50 ps components describe conformational dynamics and equilibria among different local minima on the excited-state hypersurface. No significant amount of I(700) formation can be observed on our timescale for iso-PCB phytochrome. We suggest that iso-PCB-65 kDa-phy either interacts with the protein differently leading to a more twisted and/or less protonated configuration, or undergoes P(r) to P(fr) isomerization primarily via a different configurational pathway, largely circumventing I(700) as an intermediate. The isomerization process is accompanied by strong coherent oscillations due to wavepacket motion on the excited-state surface for both phytochrome forms. The femto- to (sub-)nanosecond kinetics of the P(fr) forms is again quite similar for the native and the PCB phytochromes. After an ultrafast excited-state relaxation within approximately 150 fs, the chromophores return to the first ground-state intermediate in 400-800 fs followed by two additional ground-state intermediates which are formed with 2-3 ps and approximately 400 ps lifetimes. We call the first ground-state intermediate in native phytochrome I(fr 750), due to its pronounced absorption at that wavelength. The other intermediates are termed I(fr 675) and pseudo-P(r). The absorption spectrum of the latter already closely resembles the absorption of the P(r) chromophore. PCB-65 kDa-phy shows a very similar kinetics, although many of the detailed spectral features in the transients seen in native phy are blurred, presumably due to wider inhomogeneous distribution of the chromophore conformation. Iso-PCB-65 kDa-phy shows similar features to the PCB-65 kDa-phy, with some additional blue-shift of the transient spectra of approximately 10 nm. The sub-200 fs component is, however, absent, and the picosecond lifetimes are somewhat longer than in 124 kDa phytochrome or in PCB-65 kDa-phy. We interpret the data within the framework of two- and three-dimensional potential energy surface diagrams for the photoisomerization processes and the ground-state intermediates involved in the two photoconversions.
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Affiliation(s)
- Marc G Müller
- Max-Planck-Institut für Bioanorganische Chemie, D-45470 Mülheim a.d. Ruhr, Germany
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43
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Braun-Sand S, Sharma PK, Chu ZT, Pisliakov AV, Warshel A. The energetics of the primary proton transfer in bacteriorhodopsin revisited: it is a sequential light-induced charge separation after all. BIOCHIMICA ET BIOPHYSICA ACTA 2008; 1777:441-52. [PMID: 18387356 PMCID: PMC2443747 DOI: 10.1016/j.bbabio.2008.03.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2007] [Revised: 02/29/2008] [Accepted: 03/03/2008] [Indexed: 11/26/2022]
Abstract
The light-induced proton transport in bacteriorhodopsin has been considered as a model for other light-induced proton pumps. However, the exact nature of this process is still unclear. For example, it is not entirely clear what the driving force of the initial proton transfer is and, in particular, whether it reflects electrostatic forces or other effects. The present work simulates the primary proton transfer (PT) by a specialized combination of the EVB and the QCFF/PI methods. This combination allows us to obtain sufficient sampling and a quantitative free energy profile for the PT at different protein configurations. The calculated profiles provide new insight about energetics of the primary PT and its coupling to the protein conformational changes. Our finding confirms the tentative analysis of an earlier work (A. Warshel, Conversion of light energy to electrostatic energy in the proton pump of Halobacterium halobium, Photochem. Photobiol. 30 (1979) 285-290) and determines that the overall PT process is driven by the energetics of the charge separation between the Schiff base and its counterion Asp85. Apparently, the light-induced relaxation of the steric energy of the chromophore leads to an increase in the ion-pair distance, and this drives the PT process. Our use of the linear response approximation allows us to estimate the change in the protein conformational energy and provides the first computational description of the coupling between the protein structural changes and the PT process. It is also found that the PT is not driven by twist-modulated changes of the Schiff base's pKa, changes in the hydrogen bond directionality, or other non-electrostatic effects. Overall, based on a consistent use of structural information as the starting point for converging free energy calculations, we conclude that the primary event should be described as a light-induced formation of an unstable ground state, whose relaxation leads to charge separation and to the destabilization of the ion-pair state. This provides the driving force for the subsequent PT steps.
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Affiliation(s)
- Sonja Braun-Sand
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
- Department of Chemistry, University of Colorado at Colorado Springs (UCCS), Colorado Springs, CO 80918
| | - Pankaz K. Sharma
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
| | - Zhen T. Chu
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
| | - Andrei V. Pisliakov
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
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44
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Femtosecond kinetics of photoconversion of the higher plant photoreceptor phytochrome carrying native and modified chromophores. Biophys J 2008; 94:4370-82. [PMID: 18199671 DOI: 10.1529/biophysj.106.091652] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The photoprocesses of native (phyA of oat), and of C-terminally truncated recombinant phytochromes, assembled instead of the native phytochromobilin with phycocyanobilin (PCB-65 kDa-phy) and iso-phycocyanobilin (iso-PCB-65 kDa-phy) chromophores, have been studied by femtosecond transient absorption spectroscopy in both their red absorbing phytochrome (P(r)) and far-red absorbing phytochrome (P(fr)) forms. Native P(r) phytochrome shows an excitation wavelength dependence of the kinetics with three main picosecond components. The formation kinetics of the first ground-state intermediate I(700), absorbing at approximately 690 nm, is mainly described by 28 ps or 40 ps components in native and PCB phytochrome, respectively, whereas additional approximately 15 and 50 ps components describe conformational dynamics and equilibria among different local minima on the excited-state hypersurface. No significant amount of I(700) formation can be observed on our timescale for iso-PCB phytochrome. We suggest that iso-PCB-65 kDa-phy either interacts with the protein differently leading to a more twisted and/or less protonated configuration, or undergoes P(r) to P(fr) isomerization primarily via a different configurational pathway, largely circumventing I(700) as an intermediate. The isomerization process is accompanied by strong coherent oscillations due to wavepacket motion on the excited-state surface for both phytochrome forms. The femto- to (sub-)nanosecond kinetics of the P(fr) forms is again quite similar for the native and the PCB phytochromes. After an ultrafast excited-state relaxation within approximately 150 fs, the chromophores return to the first ground-state intermediate in 400-800 fs followed by two additional ground-state intermediates which are formed with 2-3 ps and approximately 400 ps lifetimes. We call the first ground-state intermediate in native phytochrome I(fr 750), due to its pronounced absorption at that wavelength. The other intermediates are termed I(fr 675) and pseudo-P(r). The absorption spectrum of the latter already closely resembles the absorption of the P(r) chromophore. PCB-65 kDa-phy shows a very similar kinetics, although many of the detailed spectral features in the transients seen in native phy are blurred, presumably due to wider inhomogeneous distribution of the chromophore conformation. Iso-PCB-65 kDa-phy shows similar features to the PCB-65 kDa-phy, with some additional blue-shift of the transient spectra of approximately 10 nm. The sub-200 fs component is, however, absent, and the picosecond lifetimes are somewhat longer than in 124 kDa phytochrome or in PCB-65 kDa-phy. We interpret the data within the framework of two- and three-dimensional potential energy surface diagrams for the photoisomerization processes and the ground-state intermediates involved in the two photoconversions.
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45
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46
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Amsden JJ, Kralj JM, Chieffo LR, Wang X, Erramilli S, Spudich EN, Spudich JL, Ziegler LD, Rothschild KJ. Subpicosecond protein backbone changes detected during the green-absorbing proteorhodopsin primary photoreaction. J Phys Chem B 2007; 111:11824-31. [PMID: 17880126 DOI: 10.1021/jp073490r] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Recent studies demonstrate that photoactive proteins can react within several picoseconds to photon absorption by their chromophores. Faster subpicosecond protein responses have been suggested to occur in rhodopsin-like proteins where retinal photoisomerization may impulsively drive structural changes in nearby protein groups. Here, we test this possibility by investigating the earliest protein structural changes occurring in proteorhodopsin (PR) using ultrafast transient infrared (TIR) spectroscopy with approximately 200 fs time resolution combined with nonperturbing isotope labeling. PR is a recently discovered microbial rhodopsin similar to bacteriorhodopsin (BR) found in marine proteobacteria and functions as a proton pump. Vibrational bands in the retinal fingerprint (1175-1215 cm(-1)) and ethylenic stretching (1500-1570 cm(-1)) regions characteristic of all-trans to 13-cis chromophore isomerization and formation of a red-shifted photointermediate appear with a 500-700 fs time constant after photoexcitation. Bands characteristic of partial return to the ground state evolve with a 2.0-3.5 ps time constant. In addition, a negative band appears at 1548 cm(-1) with a time constant of 500-700 fs, which on the basis of total-15N and retinal C15D (retinal with a deuterium on carbon 15) isotope labeling is assigned to an amide II peptide backbone mode that shifts to near 1538 cm(-1) concomitantly with chromophore isomerization. Our results demonstrate that one or more peptide backbone groups in PR respond with a time constant of 500-700 fs, almost coincident with the light-driven retinylidene chromophore isomerization. The protein changes we observe on a subpicosecond time scale may be involved in storage of the absorbed photon energy subsequently utilized for proton transport.
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Affiliation(s)
- Jason J Amsden
- Department of Physics, Boston University, Boston, MA 02215, USA
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47
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Prokhorenko VI, Nagy AM, Waschuk SA, Brown LS, Birge RR, Miller RJD. Coherent Control of Retinal Isomerization in Bacteriorhodopsin. Science 2006; 313:1257-61. [PMID: 16946063 DOI: 10.1126/science.1130747] [Citation(s) in RCA: 217] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Optical control of the primary step of photoisomerization of the retinal molecule in bacteriorhodopsin from the all-trans to the 13-cis state was demonstrated under weak field conditions (where only 1 of 300 retinal molecules absorbs a photon during the excitation cycle) that are relevant to understanding biological processes. By modulating the phases and amplitudes of the spectral components in the photoexcitation pulse, we showed that the absolute quantity of 13-cis retinal formed upon excitation can be enhanced or suppressed by +/-20% of the yield observed using a short transform-limited pulse having the same actinic energy. The shaped pulses were shown to be phase-sensitive at intensities too low to access different higher electronic states, and so these pulses apparently steer the isomerization through constructive and destructive interference effects, a mechanism supported by observed signatures of vibrational coherence. These results show that the wave properties of matter can be observed and even manipulated in a system as large and complex as a protein.
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Affiliation(s)
- Valentyn I Prokhorenko
- Institute for Optical Sciences, Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, M5S3H6, Toronto, Ontario, Canada
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48
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Zgrablić G, Voïtchovsky K, Kindermann M, Haacke S, Chergui M. Ultrafast excited state dynamics of the protonated Schiff base of all-trans retinal in solvents. Biophys J 2005; 88:2779-88. [PMID: 15792984 PMCID: PMC1305373 DOI: 10.1529/biophysj.104.046094] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a comparative study of the ultrafast photophysics of all-trans retinal in the protonated Schiff base form in solvents with different polarities and viscosities. Steady-state spectra of retinal in the protonated Schiff base form show large absorption-emission Stokes shifts (6500-8100 cm(-1)) for both polar and nonpolar solvents. Using a broadband fluorescence up-conversion experiment, the relaxation kinetics of fluorescence is investigated with 120 fs time resolution. The time-zero spectra already exhibit a Stokes-shift of approximately 6000 cm(-1), indicating depopulation of the Franck-Condon region in < or =100 fs. We attribute it to relaxation along skeletal stretching. A dramatic spectral narrowing is observed on a 150 fs timescale, which we assign to relaxation from the S(2) to the S(1) state. Along with the direct excitation of S(1), this relaxation populates different quasistationary states in S(1), as suggested from the existence of three distinct fluorescence decay times with different decay associated spectra. A 0.5-0.65 ps decay component is observed, which may reflect the direct repopulation of the ground state, in line with the small isomerization yield in solvents. Two longer decay components are observed and are attributed to torsional motion leading to photo-isomerization. The various decay channels show little or no dependence with respect to the viscosity or dielectric constant of the solvents. This suggests that in the protein, the bond selectivity of isomerization is mainly governed by steric effects.
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Affiliation(s)
- Goran Zgrablić
- Laboratoire de Spectroscopie Ultrarapide, Ecole Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, FSB-BSP, CH-1015 Lausanne-Dorigny, Switzerland
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Fischer T, Hampp NA. Two-photon absorption of bacteriorhodopsin: formation of a red-shifted thermally stable photoproduct F620. Biophys J 2005; 89:1175-82. [PMID: 15894635 PMCID: PMC1366602 DOI: 10.1529/biophysj.104.055806] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
By means of high-intensity 532 nm laser pulses, a photochemical conversion of the initial B(570) state of bacteriorhodopsin (BR) to a stable photoproduct absorbing maximally at approximately 620 nm in BR suspensions and at approximately 610 nm in BR films is induced. This state, which we named F(620), is photochemically further converted to a group of three products with maximal absorptions in the wavelength range from 340 nm to 380 nm, which show identical spectral properties to the so-called P(360) state reported in the literature. The photoconversion from B(570) to F(620) is most likely a resonant two-photon absorption induced step. The formation of F(620) and P(360) leads to a distinguished photo-induced permanent optical anisotropy in BR films. The spectral dependence of the photo-induced anisotropy and the anisotropy orientations at the educt (B(570)) and product (F(620)) wavelengths are strong indicators that F(620) is formed in a direct photochemical step from B(570). The chemical nature of the P(360) products probably is that of a retro-retinal containing BR, but the structural characteristics of the F(620) state are still unclear. The photo-induced permanent anisotropy induced by short laser pulses in BR films helps to better understand the photochemical pathways related to this transition, and it is interesting in view of potential applications as this feature is the molecular basis for permanent optical data storage using BR films.
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Schmidt B, Sobotta C, Heinz B, Laimgruber S, Braun M, Gilch P. Excited-state dynamics of bacteriorhodopsin probed by broadband femtosecond fluorescence spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1706:165-73. [PMID: 15620377 DOI: 10.1016/j.bbabio.2004.10.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2004] [Revised: 10/04/2004] [Accepted: 10/20/2004] [Indexed: 10/26/2022]
Abstract
The impact of varying excitation densities (approximately 0.3 to approximately 40 photons per molecule) on the ultrafast fluorescence dynamics of bacteriorhodopsin has been studied in a wide spectral range (630-900 nm). For low excitation densities, the fluorescence dynamics can be approximated biexponentially with time constants of <0.15 and approximately 0.45 ps. The spectrum associated with the fastest time constant peaks at 650 nm, while the 0.45 ps component is most prominent at 750 nm. Superimposed on these kinetics is a shift of the fluorescence maximum with time (dynamic Stokes shift). Higher excitation densities alter the time constants and their amplitudes. These changes are assigned to multi-photon absorptions.
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Affiliation(s)
- B Schmidt
- Department für Physik, Ludwig-Maximilians-Universität, Oettingenstr. 67, D-80538 Munich, Germany
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