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Wangamnuayporn S, Kinoshita M, Kawai T, Matsumori N. Gold nanoparticle-powered screening of membrane protein-specific lipids from complex lipid mixtures. Anal Biochem 2024; 687:115447. [PMID: 38141800 DOI: 10.1016/j.ab.2023.115447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/25/2023]
Abstract
Membrane proteins (MPs) are affected by binding of specific lipids. We previously developed a methodology for systematically analyzing MP-lipid interactions leveraging surface plasmon resonance (SPR). In this method, the gold sensor chip surface was modified with a self-assembled monolayer (SAM), which allowed for a larger amount of MP-immobilization. However, the laborious lipid purification step remained a bottleneck. To address this issue, a new strategy has been developed utilizing gold nanoparticles (AuNPs) instead of the gold sensor chip. AuNPs were coated with SAM, on which MP was covalently anchored. The MP-immobilized AuNPs were mixed with a lipid mixture, and the recovered lipids were quantified by LC-MS. Bacteriorhodopsin (bR) was used as an MP to demonstrate this concept. We optimized immobilization conditions and confirmed the efficient immobilization of bR by dynamic light scattering and electron micrographs. Washing conditions for pulldown experiments were optimized to efficiently remove non-specific lipids. A new binding index was introduced to qualitatively reproduce the known affinity of lipids for bR. Consequently, the low-abundant and least-studied lipid S-TeGD was identified as a candidate for bR-specific lipids. This technique can skip the laborious lipid purification process, accelerating the screening of MP-specific lipids from complex lipid mixtures.
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Affiliation(s)
- Supakorn Wangamnuayporn
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Masanao Kinoshita
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Takayuki Kawai
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
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2
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Zhong YR, Yu TY, Chu LK. Roles of functional lipids in bacteriorhodopsin photocycle in various delipidated purple membranes. Biophys J 2022; 121:1789-1798. [PMID: 35440419 DOI: 10.1016/j.bpj.2022.04.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 04/07/2022] [Accepted: 04/15/2022] [Indexed: 11/30/2022] Open
Abstract
Purple membrane (PM) is composed of several native lipids and the transmembrane protein bacteriorhodopsin (bR) in trimeric configuration. The delipidated PM (dPM) samples can be prepared by treating PM with CHAPS (3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate) to partially remove native lipids while maintaining bR in the trimeric configuration. By correlating the photocycle kinetics of bR and the exact lipid compositions of the various dPM samples, one can reveal the roles of native PM lipids. However, it is challenging to compare the lipid compositions of the various dPM samples quantitatively. Here, we utilized the absorbances of extracted retinal at 382 nm to normalize the concentrations of the remaining lipids in each dPM sample, which were then quantified by mass spectrometry, allowing us to compare the lipid compositions of different samples in a quantitative manner. The corresponding photocycle kinetics of bR were probed by transient difference absorption spectroscopy. We found that the removal rate of the polar lipids follows the order of BPG ≈ GlyC < S-TGD-1 ≈ PG < PGP-Me ≈ PGS. Since BPG and GlyC have more nonpolar phytanyl groups than other lipids at the hydrophobic tail, causing a higher affinity with the hydrophobic surface of bR, the corresponding removal rates are slowest. In addition, as the reaction period of PM and CHAPS increases, the residual amounts of PGS and PGP-Me significantly decrease, in concomitance with the decelerated rates of the recovery of ground state and the decay of intermediate M, and the reduced transient population of intermediate O. PGS and PGP-Me are the lipids with the highest correlation to the photocycle activity among the six polar lipids of PM. From a practical viewpoint, combining optical spectroscopy and mass spectrometry appears a promising approach to simultaneously track the functions and the concomitant active components in a given biological system.
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Affiliation(s)
- Yi-Rui Zhong
- Department of Chemistry, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu 30013, Taiwan
| | - Tsyr-Yan Yu
- Institute of Atomic and Molecular Sciences, Academia Sinica, 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan; International Graduate Program of Molecular Science and Technology, National Taiwan University, Taipei, Taiwan.
| | - Li-Kang Chu
- Department of Chemistry, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu 30013, Taiwan.
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Hashimoto M, Murai Y, Morita K, Kikukawa T, Takagi T, Takahashi H, Yokoyama Y, Amii H, Sonoyama M. Comparison of functionality and structural stability of bacteriorhodopsin reconstituted in partially fluorinated dimyristoylphosphatidylcholine liposomes with different perfluoroalkyl chain lengths. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183686. [PMID: 34175295 DOI: 10.1016/j.bbamem.2021.183686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 11/19/2022]
Abstract
Amphiphilic molecules with one or more perfluoroalkyl groups (Rf, CnF2n+1), which show peculiar interfacial properties, are attracting much attention in membrane protein science. We recently have developed a partially fluorinated dimyristoylphosphatidylcholine (DMPC) with a perfluorobutyl group in the hydrophobic chain terminal (F4-DMPC) and demonstrated that F4-DMPC is a promising material for incorporating membrane proteins. Moreover, we have found out that membrane properties of a series of partially fluorinated DMPCs with different Rf chain lengths (Fn-DMPCs) vary in a significant Rf chain length-dependent manner. In the present study, structural and functional properties of a membrane protein bacteriorhodopsin (bR) in the Fn-DMPC (n = 4, 6, and 8) membranes (bR/Fn-DMPC) are investigated using several physicochemical techniques. Regardless of the Rf chain lengths, bR/Fn-DMPCs retain native-like structural and functional properties at 30 °C, unlike bR molecules in DMPC vesicles. In particular, bR/F6-DMPC, which is in the fluid phase at 30 °C, shows flash-induced transient absorption changes very similar to the native purple membrane (PM) and very high thermal stability of bR trimers comparable to the PM. Structural and functional properties of bR/Fn-DMPCs are discussed compared to the PM and bR/DMPC.
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Affiliation(s)
- Mami Hashimoto
- Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Yuka Murai
- Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Kohei Morita
- Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Takashi Kikukawa
- Department of Functional Life Science, Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Toshiyuki Takagi
- Cellular and Molecular Biotechnology Research Institute, AIST, Tsukuba, Ibaraki 305-8565, Japan.
| | - Hiroshi Takahashi
- Division of Pure and Applied Science, Faculty of Science and Technology, Gunma University, Maebashi, Gunma 371-8510, Japan.
| | - Yasunori Yokoyama
- Department of Applied Physics, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Hideki Amii
- Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan; Gunma University Initiative for Advanced Research (GIAR), Kiryu, Gunma 376-8515, Japan
| | - Masashi Sonoyama
- Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan; Gunma University Initiative for Advanced Research (GIAR), Kiryu, Gunma 376-8515, Japan; Gunma University Center for Food Science and Wellness (GUCFW), Gunma University, Kiryu, Gunma 376-8515, Japan.
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4
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Inada M, Kinoshita M, Matsumori N. Archaeal Glycolipid S-TGA-1 Is Crucial for Trimer Formation and Photocycle Activity of Bacteriorhodopsin. ACS Chem Biol 2020; 15:197-204. [PMID: 31647217 DOI: 10.1021/acschembio.9b00756] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although it has been demonstrated that membrane proteins (MPs) require lipids to ensure their structural and functional integrity, details on how lipid-MP interactions regulate MPs are still unclear. Recently, we developed a concise method for quantitatively evaluating lipid-MP interactions and applied it to bacteriorhodopsin (bR), a halobacterial MP that forms trimers and acts as a light-driven proton pump. Consequently, we found that the halobacterial glycolipid, S-TGA-1, has the highest affinity for bR, among other lipids. In this study, we examined the effects of S-TGA-1 on bR via visible circular dichroism spectroscopy, flash photolysis, and proton influx measurement. The results showed that S-TGA-1 efficiently promotes trimer formation, photocycle, and proton pumping in bR. Our data also suggested that the bR photocycle is restored as a consequence of the trimerization induced by the lipid. This study demonstrates clearly that lipids specifically interacting with MPs can have significant impacts on MP structure and/or function. The methodology adopted in our studies can be applied to other MPs and will help elucidate the physiological functions of lipids in terms of lipid-MP interactions, thus accelerating "lipid chemical biology" studies.
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Affiliation(s)
- Masataka Inada
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Masanao Kinoshita
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
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Hanashima S, Yano Y, Murata M. Enantiomers of phospholipids and cholesterol: A key to decipher lipid‐lipid interplay in membrane. Chirality 2020; 32:282-298. [DOI: 10.1002/chir.23171] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 12/23/2019] [Accepted: 12/26/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Shinya Hanashima
- Department of Chemistry, Graduate School of ScienceOsaka University Toyonaka Japan
| | - Yo Yano
- Department of Chemistry, Graduate School of ScienceOsaka University Toyonaka Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of ScienceOsaka University Toyonaka Japan
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Yamagami M, Tsuchikawa H, Cui J, Umegawa Y, Miyazaki Y, Seo S, Shinoda W, Murata M. Average Conformation of Branched Chain Lipid PGP-Me That Accounts for the Thermal Stability and High-Salinity Resistance of Archaeal Membranes. Biochemistry 2019; 58:3869-3879. [DOI: 10.1021/acs.biochem.9b00469] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Masaki Yamagami
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- JST ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Jin Cui
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- JST ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yuichi Umegawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- JST ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yusuke Miyazaki
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Sangjae Seo
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Wataru Shinoda
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- JST ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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7
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Stability of the two-dimensional lattice of bacteriorhodopsin reconstituted in partially fluorinated phosphatidylcholine bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:631-642. [DOI: 10.1016/j.bbamem.2018.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/27/2018] [Accepted: 12/20/2018] [Indexed: 11/21/2022]
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Kao YM, Cheng CH, Syue ML, Huang HY, Chen IC, Yu TY, Chu LK. Photochemistry of Bacteriorhodopsin with Various Oligomeric Statuses in Controlled Membrane Mimicking Environments: A Spectroscopic Study from Femtoseconds to Milliseconds. J Phys Chem B 2019; 123:2032-2039. [DOI: 10.1021/acs.jpcb.9b01224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu-Min Kao
- Department of Chemistry, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Chung-Hao Cheng
- Department of Chemistry, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Ming-Lun Syue
- Department of Chemistry, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Hsin-Yu Huang
- Department of Chemistry, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - I-Chia Chen
- Department of Chemistry, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Tsyr-Yan Yu
- Institute of Atomic and Molecular Sciences, Academia Sinica, 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
- International Graduate Program of Molecular Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Li-Kang Chu
- Department of Chemistry, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
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Palanco ME, Skovgaard N, Hansen JS, Berg-Sørensen K, Hélix-Nielsen C. Tuning biomimetic membrane barrier properties by hydrocarbon, cholesterol and polymeric additives. BIOINSPIRATION & BIOMIMETICS 2017; 13:016005. [PMID: 29019793 DOI: 10.1088/1748-3190/aa92be] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The barrier properties of cellular membranes are increasingly attracting attention as a source of inspiration for designing biomimetic membranes. The broad range of potential technological applications makes the use of lipid and lately also polymeric materials a popular choice for constructing biomimetic membranes, where the barrier properties can be controlled by the composition of the membrane constituent elements. Here we investigate the membrane properties reported by the light-induced proton pumping activity of bacteriorhodopsin (bR) reconstituted in three vesicle systems of different membrane composition. Specifically we quantify how the resulting proton influx and efflux rates are influenced by the membrane composition using a variety of membrane modulators. We demonstrate that by adding hydrocarbons to vesicles with reconstituted bR formed from asolectin lipids the resulting transmembrane proton fluxes changes proportional to the carbon chain length when compared against control. We observe a similar proportionality in single-component 1,2-Dioleoyl-sn-glycero-3-phosphocholine model membranes when using cholesterol. Lastly we investigate the effects of adding the amphiphilic di-block co-polymer polybutadiene-polyethyleneoxide (PB12-PEO10) to phospholipid membranes formed from 1,2-Dioleoyl-sn-glycero-3-phosphocholine, 1,2-Dioleoyl-sn-glycero-3-phosphatidylethanolamine, and 1,2-Dioleoyl-sn-glycero-3-phosphatidylserine. The proton pumping activity of bR (measured as a change in extra-vesicular pH) in mixed lipid/PB12-PEO10 lipid systems is up to six-fold higher compared to that observed for bR containing vesicles made from PB12-PEO10 alone. Interestingly, bR inserts with apparent opposite orientation in pure PB12-PEO10 vesicles as compared to pure lipid vesicles. Addition of equimolar amounts of lipids to PB12-PEO10 results in bR orientation similar to that observed for pure lipids. In conclusion our results show how the barrier properties of the membranes can be controlled by the composition of the membrane. In particular the use of mixed lipid-polymer systems may pave the way for constructing biomimetic membranes tailored for optimal properties in various applications including drug delivery systems, biosensors and energy conservation technology.
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Affiliation(s)
- Marta Espina Palanco
- Department of Physics, Technical University of Denmark (DTU), 2800 Kgs. Lyngby, Denmark. These authors contributed equally to this work
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