Archaeal Lipids Regulating the Trimeric Structure Dynamics of Bacteriorhodopsin for Efficient Proton Release and Uptake
S-TGA-1 and PGP-Me are native archaeal lipids associated with the bacteriorhodopsin (bR) trimer and contribute to protein stabilization and native dynamics for proton transfer. However, little is known about the underlying molecular mechanism of how these lipids regulate bR trimerization and efficie...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-06-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/23/13/6913 |
| _version_ | 1797479841530904576 |
|---|---|
| author | Sijin Chen Xiaoyan Ding Chao Sun Fei Wang Xiao He Anthony Watts Xin Zhao |
| author_facet | Sijin Chen Xiaoyan Ding Chao Sun Fei Wang Xiao He Anthony Watts Xin Zhao |
| author_sort | Sijin Chen |
| collection | DOAJ |
| description | S-TGA-1 and PGP-Me are native archaeal lipids associated with the bacteriorhodopsin (bR) trimer and contribute to protein stabilization and native dynamics for proton transfer. However, little is known about the underlying molecular mechanism of how these lipids regulate bR trimerization and efficient photocycling. Here, we explored the specific binding of S-TGA-1 and PGP-Me with the bR trimer and elucidated how specific interactions modulate the bR trimeric structure and proton release and uptake using long-term atomistic molecular dynamic simulations. Our results showed that S-TGA-1 and PGP-Me are essential for stabilizing the bR trimer and maintaining the coherent conformational dynamics necessary for proton transfer. The specific binding of S-TGA-1 with W80 and K129 regulates proton release on the extracellular surface by forming a “Glu-shared” model. The interaction of PGP-Me with K40 ensures proton uptake by accommodating the conformation of the helices to recruit enough water molecules on the cytoplasmic side. The present study results could fill in the theoretical gaps of studies on the functional role of archaeal lipids and could provide a reference for other membrane proteins containing similar archaeal lipids. |
| first_indexed | 2024-03-09T21:52:35Z |
| format | Article |
| id | doaj.art-2e4f8800ee5a4dba9de7b69ff6421546 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T21:52:35Z |
| publishDate | 2022-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-2e4f8800ee5a4dba9de7b69ff64215462023-11-23T20:04:44ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-06-012313691310.3390/ijms23136913Archaeal Lipids Regulating the Trimeric Structure Dynamics of Bacteriorhodopsin for Efficient Proton Release and UptakeSijin Chen0Xiaoyan Ding1Chao Sun2Fei Wang3Xiao He4Anthony Watts5Xin Zhao6Department of Physics, School of Physics and Electronic Science, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, ChinaDepartment of Physics, School of Physics and Electronic Science, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, ChinaDepartment of Physics, School of Physics and Electronic Science, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, ChinaDepartment of Physics, School of Physics and Electronic Science, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, ChinaShanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, ChinaDepartment of Biochemistry, University of Oxford, South Park Road, Oxford OX1 3QU, UKDepartment of Physics, School of Physics and Electronic Science, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, ChinaS-TGA-1 and PGP-Me are native archaeal lipids associated with the bacteriorhodopsin (bR) trimer and contribute to protein stabilization and native dynamics for proton transfer. However, little is known about the underlying molecular mechanism of how these lipids regulate bR trimerization and efficient photocycling. Here, we explored the specific binding of S-TGA-1 and PGP-Me with the bR trimer and elucidated how specific interactions modulate the bR trimeric structure and proton release and uptake using long-term atomistic molecular dynamic simulations. Our results showed that S-TGA-1 and PGP-Me are essential for stabilizing the bR trimer and maintaining the coherent conformational dynamics necessary for proton transfer. The specific binding of S-TGA-1 with W80 and K129 regulates proton release on the extracellular surface by forming a “Glu-shared” model. The interaction of PGP-Me with K40 ensures proton uptake by accommodating the conformation of the helices to recruit enough water molecules on the cytoplasmic side. The present study results could fill in the theoretical gaps of studies on the functional role of archaeal lipids and could provide a reference for other membrane proteins containing similar archaeal lipids.https://www.mdpi.com/1422-0067/23/13/6913bacteriorhodopsinarchaeal lipidsS-TGA-1 and PGP-Melipid–protein interactionstrimer stabilityproton release and uptake |
| spellingShingle | Sijin Chen Xiaoyan Ding Chao Sun Fei Wang Xiao He Anthony Watts Xin Zhao Archaeal Lipids Regulating the Trimeric Structure Dynamics of Bacteriorhodopsin for Efficient Proton Release and Uptake International Journal of Molecular Sciences bacteriorhodopsin archaeal lipids S-TGA-1 and PGP-Me lipid–protein interactions trimer stability proton release and uptake |
| title | Archaeal Lipids Regulating the Trimeric Structure Dynamics of Bacteriorhodopsin for Efficient Proton Release and Uptake |
| title_full | Archaeal Lipids Regulating the Trimeric Structure Dynamics of Bacteriorhodopsin for Efficient Proton Release and Uptake |
| title_fullStr | Archaeal Lipids Regulating the Trimeric Structure Dynamics of Bacteriorhodopsin for Efficient Proton Release and Uptake |
| title_full_unstemmed | Archaeal Lipids Regulating the Trimeric Structure Dynamics of Bacteriorhodopsin for Efficient Proton Release and Uptake |
| title_short | Archaeal Lipids Regulating the Trimeric Structure Dynamics of Bacteriorhodopsin for Efficient Proton Release and Uptake |
| title_sort | archaeal lipids regulating the trimeric structure dynamics of bacteriorhodopsin for efficient proton release and uptake |
| topic | bacteriorhodopsin archaeal lipids S-TGA-1 and PGP-Me lipid–protein interactions trimer stability proton release and uptake |
| url | https://www.mdpi.com/1422-0067/23/13/6913 |
| work_keys_str_mv | AT sijinchen archaeallipidsregulatingthetrimericstructuredynamicsofbacteriorhodopsinforefficientprotonreleaseanduptake AT xiaoyanding archaeallipidsregulatingthetrimericstructuredynamicsofbacteriorhodopsinforefficientprotonreleaseanduptake AT chaosun archaeallipidsregulatingthetrimericstructuredynamicsofbacteriorhodopsinforefficientprotonreleaseanduptake AT feiwang archaeallipidsregulatingthetrimericstructuredynamicsofbacteriorhodopsinforefficientprotonreleaseanduptake AT xiaohe archaeallipidsregulatingthetrimericstructuredynamicsofbacteriorhodopsinforefficientprotonreleaseanduptake AT anthonywatts archaeallipidsregulatingthetrimericstructuredynamicsofbacteriorhodopsinforefficientprotonreleaseanduptake AT xinzhao archaeallipidsregulatingthetrimericstructuredynamicsofbacteriorhodopsinforefficientprotonreleaseanduptake |