Understanding Microbial Rhodopsins by linking Solid-State NMR with computational Approaches
Final Report Abstract
Rhodopsins are found in all phyla of life and they probably represent the most abundant phototrophic system covering a wide range of functions from sensing, ion pumping to channel gating. They represent a rather versatile family of proteins while retaining the structural scaffold of seven transmembrane helices (TMHs) with a retinal chromophore bound to a conserved lysine. By far the most abundant microbial rhodopsin family members belong to the proteorhodopsins (PRs), which represented the first evidence for a bacterial retinal-based photoreceptor. Their prevalent occurrence in microbial communities in the ocean’s photic zone and their ability to act as light-driven proton pumps which creates a transmembrane electrochemical gradient, makes retinal-based phototrophy a very important bioenergetic factor in marine ecosystems during nutrient deficient periods. Their discovery revealed a high degree of evolutionary adaptation to ambient light, resulting in blue- and green-absorbing variants that correlate with a conserved glutamine/leucine at position 105. Based on an integrated approach combining solid-state NMR spectroscopy with dynamic nuclear polarization and linear-scaling QM/MM methods, this single residue is shown to be responsible for a variety of synergistically coupled structural and electrostatic changes along the retinal polyene chain, ionone ring, and within the binding pocket. They collectively explain the observed color shift. Furthermore, analysis of the differences in chemical shifts between nuclei within the same residues in green and blue proteorhodopsins also reveals a correlation with the respective degree of conservation. Our data show that the highly conserved color change mainly affects other highly conserved residues, illustrating a high degree of robustness of the color phenotype to sequence variation. Besides of novel insight into the color adaptation of PRs, our study also highlights the strengths of the combination of advanced solid-state NMR spectroscopy including DNP with novel QM/MM methods.
Publications
-
Automated Fragmentation Quantum Mechanical Calculation of 15N and 13C Chemical Shifts in a Membrane Protein. Journal of Chemical Theory and Computation, 19(20), 7405-7422.
Zhang, Jinhuan; Kriebel, Clara Nassrin; Wan, Zheng; Shi, Man; Glaubitz, Clemens & He, Xiao
-
Structural and functional consequences oftheH180A mutation of the light-driven sodium pump KR2. Biophysical Journal, 122(6), 1003-1017.
Kriebel, Clara Nassrin; Asido, Marvin; Kaur, Jagdeep; Orth, Jennifer; Braun, Philipp; Becker-Baldus, Johanna; Wachtveitl, Josef & Glaubitz, Clemens
-
Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins. Science Advances, 10(4).
Mao, Jiafei; Jin, Xinsheng; Shi, Man; Heidenreich, David; Brown, Lynda J.; Brown, Richard C. D.; Lelli, Moreno; He, Xiao & Glaubitz, Clemens
