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Nagasaka Y, Hososhima S, Kubo N, Nagata T, Kandori H, Inoue K, Yawo H. Gate-keeper of ion transport-a highly conserved helix-3 tryptophan in a channelrhodopsin chimera, C1C2/ChRWR. Biophys Physicobiol 2020; 17:59-70. [PMID: 33173715 PMCID: PMC7593130 DOI: 10.2142/biophysico.bsj-2020007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/27/2020] [Indexed: 12/01/2022] Open
Abstract
Microbial rhodopsin is a large family of membrane proteins having seven transmembrane helices (TM1-7) with an all-trans retinal (ATR) chromophore that is covalently bound to Lys in the TM7. The Trp residue in the middle of TM3, which is homologous to W86 of bacteriorhodopsin (BR), is highly conserved among microbial rhodopsins with various light-driven functions. However, the significance of this Trp for the ion transport function of microbial rhodopsins has long remained unknown. Here, we replaced the W163 (BR W86 counterpart) of a channelrhodopsin (ChR), C1C2/ChRWR, which is a chimera between ChR1 and 2, with a smaller aromatic residue, Phe to verify its role in the ion transport. Under whole-cell patch clamp recordings from the ND7/23 cells that were transfected with the DNA plasmid coding human codon optimized C1C2/ChRWR (hWR) or its W163F mutant (hWR-W163F), the photocurrents were evoked by a pulsatile light at 475 nm. The ion-transporting activity of hWR was strongly altered by the W163F mutation in 3 points: (1) the H+ leak at positive membrane potential (Vm) and its light-adaptation, (2) the attenuation of cation channel activity and (3) the manifestation of outward H+ pump activity. All of these results strongly suggest that W163 has a role in stabilizing the structure involved in the gating-on and -off of the cation channel, the role of “gate keeper”. We can attribute the attenuation of cation channel activity to the incomplete gating-on and the H+ leak to the incomplete gating-off.
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Affiliation(s)
- Yujiro Nagasaka
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan.,Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Shoko Hososhima
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Naoko Kubo
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan.,Department of Physiology, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO) , Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Hiromu Yawo
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
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Tu CH, Yi HP, Hsieh SY, Lin HS, Yang CS. Overexpression of Different Types of Microbial Rhodopsins with a Highly Expressible Bacteriorhodopsin from Haloarcula marismortui as a Single Protein in E. coli. Sci Rep 2018; 8:14026. [PMID: 30232361 PMCID: PMC6145879 DOI: 10.1038/s41598-018-32399-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 09/06/2018] [Indexed: 11/09/2022] Open
Abstract
Microbial rhodopsins (M-Rho) are found in Archaea, Bacteria and some species of Eukarya and serve as light-driven ion pumps or mediate phototaxis responses in various biological systems. We previously reported an expression system using a highly expressible mutant, D94N-HmBRI (HEBR) from Haloarcula marismortui, as a leading tag to assist in the expression of membrane proteins that were otherwise difficult to express in E. coli. In this study, we show a universal strategy for the expression of two M-Rho proteins, either the same or different types, as one fusion protein with the HEBR system. One extra transmembrane domain was engineered to the C-terminal of HEBR to express another target M-Rho. The average expression yield in this new system reached a minimum of 2 mg/L culture, and the maximum absorbance of the target M-Rho remained unaltered in the fusion forms. The fusion protein showed a combined absorbance spectrum of a lone HEBR and target M-Rho. The function of the target M-Rho was not affected after examination with functional tests, including the photocycle and proton pumping activity of fusion proteins. In addition, an otherwise unstable sensory rhodopsin, HmSRM, showed the same or even improved stability under various temperatures, salt concentrations, and a wide range of pH conditions. This HEBR platform provides the possibility to construct multi-functional, stoichiometric and color-tuning fusion proteins using M-Rho from haloarchaea.
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Affiliation(s)
- Cheng-Hong Tu
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10616, Taiwan
| | - Hsiu-Ping Yi
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10616, Taiwan
| | - Shiang-Yuan Hsieh
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10616, Taiwan
| | - Hong-Syuan Lin
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10616, Taiwan
| | - Chii-Shen Yang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10616, Taiwan.
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Hsu MF, Fu HY, Cai CJ, Yi HP, Yang CS, Wang AHJ. Structural and Functional Studies of a Newly Grouped Haloquadratum walsbyi Bacteriorhodopsin Reveal the Acid-resistant Light-driven Proton Pumping Activity. J Biol Chem 2015; 290:29567-77. [PMID: 26483542 PMCID: PMC4705956 DOI: 10.1074/jbc.m115.685065] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Indexed: 11/23/2022] Open
Abstract
Retinal bound light-driven proton pumps are widespread in eukaryotic and prokaryotic organisms. Among these pumps, bacteriorhodopsin (BR) proteins cooperate with ATP synthase to convert captured solar energy into a biologically consumable form, ATP. In an acidic environment or when pumped-out protons accumulate in the extracellular region, the maximum absorbance of BR proteins shifts markedly to the longer wavelengths. These conditions affect the light-driven proton pumping functional exertion as well. In this study, wild-type crystal structure of a BR with optical stability under wide pH range from a square halophilic archaeon, Haloquadratum walsbyi (HwBR), was solved in two crystal forms. One crystal form, refined to 1.85 Å resolution, contains a trimer in the asymmetric unit, whereas another contains an antiparallel dimer was refined at 2.58 Å. HwBR could not be classified into any existing subgroup of archaeal BR proteins based on the protein sequence phylogenetic tree, and it showed unique absorption spectral stability when exposed to low pH values. All structures showed a unique hydrogen-bonding network between Arg82 and Thr201, linking the BC and FG loops to shield the retinal-binding pocket in the interior from the extracellular environment. This result was supported by R82E mutation that attenuated the optical stability. The negatively charged cytoplasmic side and the Arg82–Thr201 hydrogen bond may play an important role in the proton translocation trend in HwBR under acidic conditions. Our findings have unveiled a strategy adopted by BR proteins to solidify their defenses against unfavorable environments and maintain their optical properties associated with proton pumping.
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Affiliation(s)
- Min-Feng Hsu
- From the Institute of Biological Chemistry and Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 11529 and
| | - Hsu-Yuan Fu
- the Department of Biochemical Science and Technology, College of Life Science, Yen Tjing Ling Industrial Research Institute, and
| | - Chun-Jie Cai
- the Department of Biochemical Science and Technology, College of Life Science
| | - Hsiu-Pin Yi
- the Department of Biochemical Science and Technology, College of Life Science
| | - Chii-Shen Yang
- the Department of Biochemical Science and Technology, College of Life Science, Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Andrew H-J Wang
- From the Institute of Biological Chemistry and Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 11529 and
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Computational studies of membrane proteins: models and predictions for biological understanding. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:927-41. [PMID: 22051023 DOI: 10.1016/j.bbamem.2011.09.026] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 09/22/2011] [Accepted: 09/26/2011] [Indexed: 01/26/2023]
Abstract
We discuss recent progresses in computational studies of membrane proteins based on physical models with parameters derived from bioinformatics analysis. We describe computational identification of membrane proteins and prediction of their topology from sequence, discovery of sequence and spatial motifs, and implications of these discoveries. The detection of evolutionary signal for understanding the substitution pattern of residues in the TM segments and for sequence alignment is also discussed. We further discuss empirical potential functions for energetics of inserting residues in the TM domain, for interactions between TM helices or strands, and their applications in predicting lipid-facing surfaces of the TM domain. Recent progresses in structure predictions of membrane proteins are also reviewed, with further discussions on calculation of ensemble properties such as melting temperature based on simplified state space model. Additional topics include prediction of oligomerization state of membrane proteins, identification of the interfaces for protein-protein interactions, and design of membrane proteins. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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Imasheva ES, Balashov SP, Choi AR, Jung KH, Lanyi JK. Reconstitution of Gloeobacter violaceus rhodopsin with a light-harvesting carotenoid antenna. Biochemistry 2009; 48:10948-55. [PMID: 19842712 DOI: 10.1021/bi901552x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We show that salinixanthin, the light-harvesting carotenoid antenna of xanthorhodopsin, can be reconstituted into the retinal protein from Gloeobacter violaceus expressed in Escherichia coli. Reconstitution of gloeobacter rhodopsin with the carotenoid is accompanied by characteristic absorption changes and the appearance of CD bands similar to those observed for xanthorhodopsin that indicate immobilization and twist of the carotenoid in the binding site. As in xanthorhodopsin, the carotenoid functions as a light-harvesting antenna. The excitation spectrum for retinal fluorescence emission shows that ca. 36% of the energy absorbed by the carotenoid is transferred to the retinal. From excitation anisotropy, we calculate the angle between the two chromophores as being ca. 50 degrees , similar to that in xanthorhodopsin. The results indicate that gloeobacter rhodopsin binds salinixanthin in a manner similar to that of xanthorhodopsin and suggest that it might bind a carotenoid also in vivo. In the crystallographic structure of xanthorhodopsin, the conjugated chain of the carotenoid lies on the surface of helices E and F, and the 4-keto ring is immersed in the protein at van der Waals distance from the ionone ring of the retinal. The 4-keto ring is in the space occupied by a tryptophan in bacteriorhodopsin, which is replaced by the smaller glycine in xanthorhodopsin and gloeobacter rhodopsin. Specific binding of the carotenoid and its light-harvesting function are eliminated by a single mutation of the gloeobacter protein that replaces this glycine with a tryptophan. This indicates that the 4-keto ring is critically involved in carotenoid binding and suggests that a number of other recently identified retinal proteins, from a diverse group of organisms, could also contain carotenoid antenna since they carry the homologous glycine near the retinal.
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Affiliation(s)
- Eleonora S Imasheva
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA
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Liang J, Tseng YY, Dundas J, Binkowski TA, Joachimiak A, Ouyang Z, Adamian L. Chapter 4. Predicting and characterizing protein functions through matching geometric and evolutionary patterns of binding surfaces. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2009; 75:107-41. [PMID: 20731991 PMCID: PMC2882714 DOI: 10.1016/s0065-3233(07)75004-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
Predicting protein functions from structures is an important and challenging task. Although proteins are often thought to be packed as tightly as solids, closer examination based on geometric computation reveals that they contain numerous voids and pockets. Most of them are of random nature, but some are binding sites providing surfaces to interact with other molecules. A promising approach for function prediction is to infer functions through discovery of similarity in local binding pockets, as proteins binding to similar substrates/ligands and carrying out similar functions have similar physical constraints for binding and reactions. In this chapter, we describe computational methods to distinguish those surface pockets that are likely to be involved in important biological functions, and methods to identify key residues in these pockets. We further describe how to predict protein functions at large scale from structures by detecting binding surfaces similar in residue make-ups, shape, and orientation. We also describe a Bayesian Monte Carlo method that can separate selection pressure due to biological function from pressure due to protein folding. We show how this method can be used to reconstruct the evolutionary history of binding surfaces for detecting similar binding surfaces. In addition, we briefly discuss how the negative image of a binding pocket can be casted, and how such information can be used to facilitate drug discovery.
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Affiliation(s)
- Jie Liang
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 200240, China
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