Mechanism of Inward Proton Transport in an Antarctic Microbial Rhodopsin
Mechanism of Inward Proton Transport in an Antarctic Microbial Rhodopsin
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DOI：
10.1021/acs.jpcb.0c02767
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发表时间：
2020-06-18
影响因子：
3.3
通讯作者：
Brown, Leonid S.
中科院分区：
文献类型：
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作者：
Harris, Andrew;Lazaratos, Michalis;Brown, Leonid S.
虽然外向质子跨生物膜传输的研究和生物能量学的重要性是清楚的理解，内向光驱动的质子泵的微生物视紫红质一直是一个谜，无论是生理和机制。南极视紫红质是最近报道的一类新的视紫红质中的一个亚组，包括一个成员，表示为AntR，其被证明是适合于通过实验和计算进行广泛表征的。系统发育分析确定AntR作为不同的功能，作为外向离子泵的微生物视紫红质，和生物信息学序列分析揭示了氨基酸取代在保守的位点向外质子泵必不可少。AntR的建模和数值模拟，结合使用图论和社会科学中心性措施的高级分析，确定了氢键水分子和氨基酸残基的动态三维网络，这些网络在AntR中起着通信枢纽的作用。这个网络经历了重大的重排后，视网膜异构化，显示重要的变化，在连接的活性中心，视网膜席夫碱，相对侧的膜，质子运输所需的。通过光谱学和定点诱变对AntR的光化学循环进行了数值模拟和实验研究，使我们能够确定可以在与通常所知的外向泵相反的方向上传导质子的途径。
Although the outward-directed proton transport across biological membranes is well studied and its importance for bioenergetics is clearly understood, inward-directed light-driven proton pumping by microbial rhodopsins has remained a mystery both physiologically and mechanistically. A new family of Antarctic rhodopsins, which is a subgroup within a novel class of schizorhodopsins reported recently, includes a member, denoted as AntR, which proved amenable to extensive characterization with experiments and computation. Phylogenetic analyses identify AntR as distinct from the well-studied microbial rhodopsins that function as outward-directed ion pumps, and bioinformatics sequence analyses reveal amino acid substitutions at conserved sites essential for outward proton pumping. Modeling and numerical simulations of AntR, combined with advanced analyses using the graph theory and centrality measures from social sciences, identify the dynamic three-dimensional network of hydrogen-bonded water molecules and amino acid residues that function as communication hubs in AntR. This network undergoes major rearrangement upon retinal isomerization, showing important changes in the connectivity of the active center, retinal Schiff base, to the opposing sides of the membrane, as required for proton transport. Numerical simulations and experimental studies of the photochemical cycle of AntR by spectroscopy and sitedirected mutagenesis allowed us to identify pathways that could conduct protons in the direction opposite to that commonly known for outward-directed pumps.