Journal
JOURNAL OF PHYSICAL CHEMISTRY B
Volume 124, Issue 24, Pages 4851-4872Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jpcb.0c02767
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Funding
- Canada Foundation for Innovation/Ontario Innovation Trust
- Natural Sciences and Engineering Research Council of Canada (NSERC) [RGPIN-2018-04397]
- University of Guelph
- Excellence Initiative via the Freie Universitat Berlin
- JSPS KAKENHI [19H05784]
- CREST [JPMJCR17N5]
- German Research Foundation via Collaborative Research Center [SFB 1078]
- NSERC Postgraduate Doctoral Scholarship
- DAAD Research Scholarship
- MITACS Globalink Scholarship
- Graduate Tuition Scholarship from the University of Guelph
- NSERC undergraduate summer research award (USRA)
- International Max Planck Research School on Multiscale Bio-Systems
- Grants-in-Aid for Scientific Research [19H05784] Funding Source: KAKEN
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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.
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