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Urui T, Hayashi K, Mizuno M, Inoue K, Kandori H, Mizutani Y. Cis- Trans Reisomerization Preceding Reprotonation of the Retinal Chromophore Is Common to the Schizorhodopsin Family: A Simple and Rational Mechanism for Inward Proton Pumping. J Phys Chem B 2024; 128:744-754. [PMID: 38204413 DOI: 10.1021/acs.jpcb.3c07510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
The creation of unidirectional ion transporters across membranes represents one of the greatest challenges in chemistry. Proton-pumping rhodopsins are composed of seven transmembrane helices with a retinal chromophore bound to a lysine side chain via a Schiff base linkage and provide valuable insights for designing such transporters. What makes these transporters particularly intriguing is the discovery of both outward and inward proton-pumping rhodopsins. Surprisingly, despite sharing identical overall structures and membrane topologies, these proteins facilitate proton transport in opposite directions, implying an underlying rational mechanism that can transport protons in different directions within similar protein structures. In this study, we unraveled this mechanism by examining the chromophore structures of deprotonated intermediates in schizorhodopsins, a recently discovered subfamily of inward proton-pumping rhodopsins, using time-resolved resonance Raman spectroscopy. The photocycle of schizorhodopsins revealed the cis-trans thermal isomerization that precedes reprotonation at the Schiff base of the retinal chromophore. Notably, this order has not been observed in other proton-pumping rhodopsins, but here, it was observed in all seven schizorhodopsins studied across the archaeal domain, strongly suggesting that cis-trans thermal isomerization preceding reprotonation is a universal feature of the schizorhodopsin family. Based on these findings, we propose a structural basis for the remarkable order of events crucial for facilitating inward proton transport. The mechanism underlying inward proton transport by schizorhodopsins is straightforward and rational. The insights obtained from this study hold great promise for the design of transmembrane unidirectional ion transporters.
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Affiliation(s)
- Taito Urui
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kouhei Hayashi
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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Otomo A, Mizuno M, Inoue K, Kandori H, Mizutani Y. Protein dynamics of a light-driven Na + pump rhodopsin probed using a tryptophan residue near the retinal chromophore. Biophys Physicobiol 2023; 20:e201016. [PMID: 38362331 PMCID: PMC10865881 DOI: 10.2142/biophysico.bppb-v20.s016] [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: 01/27/2023] [Accepted: 02/22/2023] [Indexed: 02/17/2024] Open
Abstract
Direct observation of protein structural changes during ion transport in ion pumps provides valuable insights into the mechanism of ion transport. In this study, we examined structural changes in the light-driven sodium ion (Na+) pump rhodopsin KR2 on the sub-millisecond time scale, corresponding with the uptake and release of Na+. We compared the ion-pumping activities and transient absorption spectra of WT and the W215F mutant, in which the Trp215 residue located near the retinal chromophore on the cytoplasmic side was replaced with a Phe residue. Our findings indicated that atomic contacts between the bulky side chain of Trp215 and the C20 methyl group of the retinal chromophore promote relaxation of the retinal chromophore from the 13-cis to the all-trans form. Since Trp215 is conserved in other ion-pumping rhodopsins, the present results suggest that this residue commonly acts as a mechanical transducer. In addition, we measured time-resolved ultraviolet resonance Raman (UVRR) spectra to show that the environment around Trp215 becomes less hydrophobic at 1 ms after photoirradiation and recovers to the unphotolyzed state with a time constant of around 10 ms. These time scales correspond to Na+ uptake and release, suggesting evolution of a transient ion channel at the cytoplasmic side for Na+ uptake, consistent with the alternating-access model of ion pumps. The time-resolved UVRR technique has potential for application to other ion-pumping rhodopsins and could provide further insights into the mechanism of ion transport.
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Affiliation(s)
- Akihiro Otomo
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Present address: Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, National Institutes of Natural Science, Okazaki, Aichi 444-8787, Japan
- Present address: Department of Functional Molecular Science, School of Physical Science, SOKENDAI, Hayama, Kanagawa 240-0193, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Hideki Kandori
- Department of Life Chemistry, Graduate School of Science, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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Borji S, Vahedpour M. A theoretical investigation of the possible mechanisms for detection the copper ions by a retinal-base sensor. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2022.114363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Shionoya T, Mizuno M, Kandori H, Mizutani Y. Contact-Mediated Retinal-Opsin Coupling Enables Proton Pumping in Gloeobacter Rhodopsin. J Phys Chem B 2022; 126:7857-7869. [PMID: 36173382 DOI: 10.1021/acs.jpcb.2c04208] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
When a chromophore embedded in a photoreceptive protein undergoes a reaction upon photoexcitation, the photoreaction triggers structural changes in the protein moiety that are necessary for the function of the protein. It is thus essential to elucidate the coupling between the chromophore and protein moiety to understand the functional mechanism for photoreceptive proteins, but the mechanism by which this coupling occurs remains poorly understood. Here, we show that nonbonded atomic contacts play an essential role in driving functionally important structural changes following photoisomerization of the chromophore in Gloeobacter rhodopsin (GR). Time-resolved ultraviolet resonance Raman spectroscopy revealed that the substitution of Trp222, which contacts with methyl groups of the retinal chromophore, with a Phe residue reduced the extent of structural change. The proton-pumping activity of the GR mutant was as small as 9% of that of the wild type. Time-resolved visible absorption and resonance Raman spectra showed that the photocycle of the mutant proceeded to the L intermediate following the all-trans to 13-cis photoisomerization step but did not result in the deprotonation of the chromophore. The present results demonstrate that the atomic contacts between the chromophore and the Trp222 side chain induce the structural changes necessary for proton transfer. The requirement for dense atomic packing in a protein structure for the efficient propagation of structural changes through a coupling mechanism is discussed.
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Affiliation(s)
- Tomomi Shionoya
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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Brown LS. Light-driven proton transfers and proton transport by microbial rhodopsins - A biophysical perspective. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183867. [PMID: 35051382 DOI: 10.1016/j.bbamem.2022.183867] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/30/2021] [Accepted: 01/10/2022] [Indexed: 12/31/2022]
Abstract
In the last twenty years, our understanding of the rules and mechanisms for the outward light-driven proton transport (and underlying proton transfers) by microbial rhodopsins has been changing dramatically. It transitioned from a very detailed atomic-level understanding of proton transport by bacteriorhodopsin, the prototypical proton pump, to a confounding variety of sequence motifs, mechanisms, directions, and modes of transport in its newly found homologs. In this review, we will summarize and discuss experimental data obtained on new microbial rhodopsin variants, highlighting their contribution to the refinement and generalization of the ideas crystallized in the previous century. In particular, we will focus on the proton transport (and transfers) vectoriality and their structural determinants, which, in many cases, remain unidentified.
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Affiliation(s)
- Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Ontario N1G 2W1, Canada.
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Nair AG, Perumalla DS, Anjukandi P. Towards solvent regulated self-activation of N-terminal disulfide bond oxidoreductase-D. Phys Chem Chem Phys 2022; 24:7691-7699. [PMID: 35311864 DOI: 10.1039/d1cp05819c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
N-terminal disulfide bond oxidoreductase-D (nDsbD), an essential redox enzyme in Gram-negative bacteria, consists of a single disulfide bond (Cys103-Cys109) in its active site. The enzymatic functions are believed to be regulated by an electron transfer mediated redox switching of the disulfide bond, which is vital in controlling bacterial virulence factors. In light of the disulfide bond's inclination towards nucleophilic cleavage, it is also plausible that an internal nucleophile could second the existing electron transfer mechanism in nDsbD. Using QM/MM MD metadynamics simulations, we explore different possibilities of generating an internal nucleophile near the nDsbD active site, which could serve as a fail-over mechanism in cleaving the disulfide bond. The simulations show the formation of the internal nucleophile Tyr42O- (F ≈ 9 kcal mol-1) and its stabilization through the solvent medium. The static gas-phase calculations show that Tyr42O- could be a potential nucleophile for cleaving the S-S bond. Most strikingly, it is also seen that Tyr42O- and Asp68OH communicate with each other through a proton-hole like water wire (F ≈ 12 kcal mol-1), thus modulating the nucleophile formation. Accordingly, we propose the role of a solvent in regulating the internal nucleophilic reactions and the subsequent self-activation of nDsbD. We believe that this could be deterministic while designing enzyme-targeted inhibitor compounds.
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Affiliation(s)
- Aparna G Nair
- Department of Chemistry, Indian Institute of Technology, Palakkad-678557, Kerala, India.
| | | | - Padmesh Anjukandi
- Department of Chemistry, Indian Institute of Technology, Palakkad-678557, Kerala, India.
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