Collective exchange processes reveal an active site proton cage in bacteriorhodopsin.,Communications Biology

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Collective exchange processes reveal an active site proton cage in bacteriorhodopsin.
Communications Biology ( IF 5.2 ) Pub Date : 2020-01-03 , DOI: 10.1038/s42003-019-0733-7
Daniel Friedrich _{1,

2,

3,

4} , Florian N Brünig ₅ , Andrew J Nieuwkoop _{1,

6} , Roland R Netz ₅ , Peter Hegemann ₇ , Hartmut Oschkinat _{1,

2}

Affiliation

Proton translocation across membranes is vital to all kingdoms of life. Mechanistically, it relies on characteristic proton flows and modifications of hydrogen bonding patterns, termed protonation dynamics, which can be directly observed by fast magic angle spinning (MAS) NMR. Here, we demonstrate that reversible proton displacement in the active site of bacteriorhodopsin already takes place in its equilibrated dark-state, providing new information on the underlying hydrogen exchange processes. In particular, MAS NMR reveals proton exchange at D85 and the retinal Schiff base, suggesting a tautomeric equilibrium and thus partial ionization of D85. We provide evidence for a proton cage and detect a preformed proton path between D85 and the proton shuttle R82. The protons at D96 and D85 exchange with water, in line with ab initio molecular dynamics simulations. We propose that retinal isomerization makes the observed proton exchange processes irreversible and delivers a proton towards the extracellular release site.

中文翻译：

集体交换过程揭示了细菌视紫红质中的一个活性位点质子笼。

质子跨膜移位对于所有生命王国都是至关重要的。从机理上讲，它依赖于特征质子流和氢键键合模式的修饰，即质子化动力学，可以通过快速魔角旋转（MAS）NMR直接观察到。在这里，我们证明了细菌视紫红质活性位点中的可逆质子置换已经在其平衡的暗态下发生，从而提供了有关潜在氢交换过程的新信息。尤其是，MAS NMR揭示了D85和视网膜席夫碱的质子交换，表明互变异构平衡，因此D85发生了部分电离。我们提供了一个质子笼的证据，并检测了D85与质子穿梭R82之间的预制质子路径。D96和D85的质子与水交换，与从头算分子动力学模拟一致。我们提出，视网膜异构化使观察到的质子交换过程不可逆，并向细胞外释放位点传递质子。

更新日期：2020-01-04

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