Archaeal Lipids Regulating the Trimeric Structure Dynamics of Bacteriorhodopsin for Efficient Proton Release and Uptake

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Abstract
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.
Funding Information
  • Natural Science Foundation of Shanghai Municipality (19ZR1416300, 09PJ1404300, 30970657, 21475045, 22074040, GDW20123100086, 21922301, 21761132022, 2019YFA0905200, 2016YFA0501700)
  • Shanghai Pujiang Program (19ZR1416300, 09PJ1404300, 30970657, 21475045, 22074040, GDW20123100086, 21922301, 21761132022, 2019YFA0905200, 2016YFA0501700)
  • National Natural Science Foundation of China (19ZR1416300, 09PJ1404300, 30970657, 21475045, 22074040, GDW20123100086, 21922301, 21761132022, 2019YFA0905200, 2016YFA0501700)
  • State Administration of Foreign Experts Affairs of China through the High-End Foreign Experts Recruitment Program (19ZR1416300, 09PJ1404300, 30970657, 21475045, 22074040, GDW20123100086, 21922301, 21761132022, 2019YFA0905200, 2016YFA0501700)
  • National Natural Science Foundation of China (19ZR1416300, 09PJ1404300, 30970657, 21475045, 22074040, GDW20123100086, 21922301, 21761132022, 2019YFA0905200, 2016YFA0501700)
  • National Key R&D Program of China (19ZR1416300, 09PJ1404300, 30970657, 21475045, 22074040, GDW20123100086, 21922301, 21761132022, 2019YFA0905200, 2016YFA0501700)
  • Shanghai Frontiers Science Center of Molecule Intelligent Syntheses (19ZR1416300, 09PJ1404300, 30970657, 21475045, 22074040, GDW20123100086, 21922301, 21761132022, 2019YFA0905200, 2016YFA0501700)
  • Fundamental Research Funds for the Central Universities (19ZR1416300, 09PJ1404300, 30970657, 21475045, 22074040, GDW20123100086, 21922301, 21761132022, 2019YFA0905200, 2016YFA0501700)

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