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2. Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel

Author

Hu, Haidai, Ataka, Kenichi, Menny, Anaïs, Fourati, Zaineb, Sauguet, Ludovic, Corringer, Pierre-Jean, Koehl, Patrice, Heberle, Joachim, and Delarue, Marc

Subjects
Biochemistry and Cell Biology, Chemical Sciences, Biological Sciences, Bacterial Proteins, Cyanobacteria, Kinetics, Ligand-Gated Ion Channels, Models, Molecular, Protein Domains, Protons, Static Electricity, pentameric ligand-gated ion channel, pH activation, proton sensor, electrostatic networks, allosteric modulation
Abstract

The pentameric ligand-gated ion channel (pLGIC) from Gloeobacter violaceus (GLIC) has provided insightful structure-function views on the permeation process and the allosteric regulation of the pLGICs family. However, GLIC is activated by pH instead of a neurotransmitter and a clear picture for the gating transition driven by protons is still lacking. We used an electrostatics-based (finite difference Poisson-Boltzmann/Debye-Hückel) method to predict the acidities of all aspartic and glutamic residues in GLIC, both in its active and closed-channel states. Those residues with a predicted pKa close to the experimental pH50 were individually replaced by alanine and the resulting variant receptors were titrated by ATR/FTIR spectroscopy. E35, located in front of loop F far away from the orthosteric site, appears as the key proton sensor with a measured individual pKa at 5.8. In the GLIC open conformation, E35 is connected through a water-mediated hydrogen-bond network first to the highly conserved electrostatic triad R192-D122-D32 and then to Y197-Y119-K248, both located at the extracellular domain-transmembrane domain interface. The second triad controls a cluster of hydrophobic side chains from the M2-M3 loop that is remodeled during the gating transition. We solved 12 crystal structures of GLIC mutants, 6 of them being trapped in an agonist-bound but nonconductive conformation. Combined with previous data, this reveals two branches of a continuous network originating from E35 that reach, independently, the middle transmembrane region of two adjacent subunits. We conclude that GLIC's gating proceeds by making use of loop F, already known as an allosteric site in other pLGICs, instead of the classic orthosteric site.

Published
2018

6. Monitoring the Progression of Cell-Free Expression of Microbial Rhodopsins by Surface Enhanced IR Spectroscopy

Author

Ataka, Kenichi, Baumann, Axel, Chen, Jheng-Liang, Redlich, Aoife, Heberle, Joachim, and Schlesinger, Ramona

Subjects
sensory rhodopsin, co-translational folding, 500 Naturwissenschaften und Mathematik::530 Physik::530 Physik, cell-free expression, SEIRA (surface enhanced infrared absorption, FTIR—spectroscopy, 500 Naturwissenschaften und Mathematik::570 Biowissenschaften, Biologie::570 Biowissenschaften, Biologie, membrane protein folding, Biochemistry, Genetics and Molecular Biology (miscellaneous), Biochemistry, channelrhodopsin, Molecular Biology
Abstract

The translocon-unassisted folding process of transmembrane domains of the microbial rhodopsins sensory rhodopsin I (HsSRI) and II (HsSRII), channelrhodopsin II (CrChR2), and bacteriorhodopsin (HsBR) during cell-free expression has been investigated by Surface-Enhanced Infrared Absorption Spectroscopy (SEIRAS). Up to now, only a limited number of rhodopsins have been expressed and folded into the functional holoprotein in cell free expression systems, while other microbial rhodopsins fail to properly bind the chromophore all-trans retinal as indicated by the missing visible absorption. SEIRAS experiments suggest that all investigated rhodopsins lead to the production of polypeptides, which are co-translationally inserted into a solid-supported lipid bilayer during the first hour after the in-vitro expression is initiated. Secondary structure analysis of the IR spectra revealed that the polypeptides form a comparable amount of α-helical structure during the initial phase of insertion into the lipid bilayer. As the process progressed (>1 h), only HsBR exhibited a further increase and association of α-helices to form a compact tertiary structure, while the helical contents of the other rhodopsins stagnated. This result suggests that the molecular reason for the unsuccessful cell-free expression of the two sensory rhodopsins and of CrChR2 is not due to the translation process, but rather to the folding process during the post-translational period. Taking our previous observation into account that HsBR fails to form a tertiary structure in the absence of its retinal, we infer that the chromophore retinal is an integral component of the compaction of the polypeptide into its tertiary structure and the formation of a fully functional protein.

Published
2022
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11. Orientational control of the physiological reaction of cytochrome c oxidase tethered to a gold electrode

Author

Ataka, Kenichi, Richter, Bjorn, and Heberle, Joachim

Subjects
Cytochrome c -- Research, Monomolecular films -- Chemical properties, Histidine -- Chemical properties, Histidine -- Research, Chemicals, plastics and rubber industries
Abstract

The functionality of a lipid-reconstituted recombinant cytochrome c oxidase (CcO) monolayer that is specifically bound through histidine tags (His-tags) to a nickel chelating nitrilotriacetic acid (Ni-NTA)-modified gold electrode is described. The method has shown that the orientation of the membrane protein can be controlled depending on the position of the affinity tag.

Published
2006

17. Tailor-Made Modification of a Gold Surface for the Chemical Binding of a High-Activity [FeFe] Hydrogenase

Author

Krassen, Henning, Stripp, Sven T., Boehm, Nadine, Berkessel, Albrecht, Happe, Thomas, Ataka, Kenichi, Heberle, Joachim, Krassen, Henning, Stripp, Sven T., Boehm, Nadine, Berkessel, Albrecht, Happe, Thomas, Ataka, Kenichi, and Heberle, Joachim

Abstract

Hydrogenases are iron-sulfur proteins that catalyze hydrogen turnover in a wide range of microorganisms. Three different classes have been described, and among these [FeFe] hydrogenases are the most active in H-2 evolution. Hydrogenases are redox enzymes that have been shown to exchange electrons with graphite and modified noble metal electrodes. Making use of the latter, diffusible electron carriers are required to enable redox catalysis, as proteins do not specifically bind to the electrode surface. Diffusion-limited electron transfer can be replaced by electron injection into immobilized hydrogenase by binding the redox mediator to the electrode surface. Here, we present the synthesis and spectroelectrochemical characterization of 1-( 10-mercaptodecyl)-1'-benzyl-4,4'-bipyridinium dibromide (MBBP), which is used as redox-active linker. CrHydA1, the high-activity [FeFe] hydrogenase from Chlamydomonas reinhardtii, is immobilized on the linker-modified gold electrode. Each surface modification step is controlled in situ by surface-enhanced infrared absorption spectroscopy (SEIRAS). Functionality of the electrode-protein hybrid is demonstrated by recording the linker-supported current. The specific catalytic rate of hydrogen evolution by CrHydA1 (2.9 mu molH(2)min(-1)mg(-1) hydrogenase) promises a valuable approach for further optimization of this novel bioelectrical interface.

Published
2011
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18. Scanning near-field IR microscopy of proteins in lipid bilayers

Author

Ballout, Fouad, Krassen, Henning, Kopf, Ilona, Ataka, Kenichi, Bruendermann, Erik, Heberle, Joachim, Havenith, Martina, Ballout, Fouad, Krassen, Henning, Kopf, Ilona, Ataka, Kenichi, Bruendermann, Erik, Heberle, Joachim, and Havenith, Martina

Abstract

We use infrared near-field microscopy to chemically map the morphology of biological matrices. The investigated sample is built up from surface-tethered membrane proteins (cytochrome c oxidase) reconstituted in a lipid bilayer. We have carried out infrared near-field measurements in the frequency range between 1600 and 1800 cm(-1). By simultaneously recording the topography and chemical fingerprint of the protein-tethered lipid bilayer with a lateral resolution of 80 nm x 80 nm, we were able to probe locally the chemical signature of this membrane and to provide a local map of its surface morphology.

Published
2011
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21. Diversifying Metal-Ligand Cooperative Catalysis in Semi-Synthetic [Mn]-Hydrogenases

Author

Pan, Hui-Jie, Huang, Gangfeng, Wodrich, Matthew D., Tirani, Farzaneh Fadaei, Ataka, Kenichi, Shima, Seigo, and Hu, Xile

Subjects
metal&#8211, manganese, ligand cooperation, biomimetics, hydrogenase, hydrogen activation
Abstract

The reconstitution of [Mn]-hydrogenases using a series of Mn-I complexes is described. These complexes are designed to have an internal base or pro-base that may participate in metal-ligand cooperative catalysis or have no internal base or pro-base. Only Mn-I complexes with an internal base or pro-base are active for H-2 activation; only [Mn]-hydrogenases incorporating such complexes are active for hydrogenase reactions. These results confirm the essential role of metal-ligand cooperation for H-2 activation by the Mn-I complexes alone and by [Mn]-hydrogenases. Owing to the nature and position of the internal base or pro-base, the mode of metal-ligand cooperation in two active [Mn]-hydrogenases is different from that of the native [Fe]-hydrogenase. One [Mn]-hydrogenase has the highest specific activity of semi-synthetic [Mn]- and [Fe]-hydrogenases. This work demonstrates reconstitution of active artificial hydrogenases using synthetic complexes differing greatly from the native active site.

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