A subgroup of light-driven sodium pumps with an additional Schiff base counterion

Light-driven sodium pumps (NaRs) are unique ion-transporting microbial rhodopsins. The major group of NaRs is characterized by an NDQ motif and has two aspartic acid residues in the central region essential for sodium transport. Here we identify a subgroup of the NDQ rhodopsins bearing an additional glutamic acid residue in the close vicinity to the retinal Schiff base. We thoroughly characterize a member of this subgroup, namely the protein ErNaR from Erythrobacter sp. HL-111 and show that the additional glutamic acid results in almost complete loss of pH sensitivity for sodium-pumping activity, which is in contrast to previously studied NaRs. ErNaR is capable of transporting sodium efficiently even at acidic pH levels. X-ray crystallography and single particle cryo-electron microscopy reveal that the additional glutamic acid residue mediates the connection between the other two Schiff base counterions and strongly interacts with the aspartic acid of the characteristic NDQ motif. Hence, it reduces its pKa. Our findings shed light on a subgroup of NaRs and might serve as a basis for their rational optimization for optogenetics.

Structural insights into light-driven anion pumping in cyanobacteria

Transmembrane ion transport is a key process in living cells. Active transport of ions is carried out by various ion transporters including microbial rhodopsins (MRs). MRs perform diverse functions such as active and passive ion transport, photo-sensing, and others. In particular, MRs can pump various monovalent ions like Na⁺, K⁺, Cl^-, I^-, NO₃^-. The only characterized MR proposed to pump sulfate in addition to halides belongs to the cyanobacterium Synechocystis sp. PCC 7509 and is named Synechocystis halorhodopsin (SyHR). The structural study of SyHR may help to understand what makes an MR pump divalent ions. Here we present the crystal structure of SyHR in the ground state, the structure of its sulfate-bound form as well as two photoreaction intermediates, the K and O states. These data reveal the molecular origin of the unique properties of the protein (exceptionally strong chloride binding and proposed pumping of divalent anions) and sheds light on the mechanism of anion release and uptake in cyanobacterial halorhodopsins. The unique properties of SyHR highlight its potential as an optogenetics tool and may help engineer different types of anion pumps with applications in optogenetics.

Na+-dependent gate dynamics and electrostatic attraction ensure substrate coupling in glutamate transporters

Excitatory amino acid transporters (EAATs) harness [Na⁺], [K⁺], and [H⁺] gradients for fast and efficient glutamate removal from the synaptic cleft. Since each glutamate is cotransported with three Na⁺ ions, [Na⁺] gradients are the predominant driving force for glutamate uptake. We combined all-atom molecular dynamics simulations, fluorescence spectroscopy, and x-ray crystallography to study Na⁺:substrate coupling in the EAAT homolog Glt_Ph A lipidic cubic phase x-ray crystal structure of wild-type, Na⁺-only bound Glt_Ph at 2.5-Å resolution revealed the fully open, outward-facing state primed for subsequent substrate binding. Simulations and kinetic experiments established that only the binding of two Na⁺ ions to the Na1 and Na3 sites ensures complete HP2 gate opening via a conformational selection-like mechanism and enables high-affinity substrate binding via electrostatic attraction. The combination of Na⁺-stabilized gate opening and electrostatic coupling of aspartate to Na⁺ binding provides a constant Na⁺:substrate transport stoichiometry over a broad range of neurotransmitter concentrations.

High-resolution structural insights into the heliorhodopsin family

Rhodopsins are the most abundant light-harvesting proteins. A new family of rhodopsins, heliorhodopsins (HeRs), has recently been discovered. Unlike in the known rhodopsins, in HeRs the N termini face the cytoplasm. The function of HeRs remains unknown. We present the structures of the bacterial HeR-48C12 in two states at the resolution of 1.5 Å, which highlight its remarkable difference from all known rhodopsins. The interior of HeR's extracellular part is completely hydrophobic, while the cytoplasmic part comprises a cavity (Schiff base cavity [SBC]) surrounded by charged amino acids and containing a cluster of water molecules, presumably being a primary proton acceptor from the Schiff base. At acidic pH, a planar triangular molecule (acetate) is present in the SBC. Structure-based bioinformatic analysis identified 10 subfamilies of HeRs, suggesting their diverse biological functions. The structures and available data suggest an enzymatic activity of HeR-48C12 subfamily and their possible involvement in fundamental redox biological processes.

New Insights on Signal Propagation by Sensory Rhodopsin II/Transducer Complex

The complex of two membrane proteins, sensory rhodopsin II (NpSRII) with its cognate transducer (NpHtrII), mediates negative phototaxis in halobacteria N. pharaonis. Upon light activation NpSRII triggers a signal transduction chain homologous to the two-component system in eubacterial chemotaxis. Here we report on crystal structures of the ground and active M-state of the complex in the space group I2₁2₁2₁. We demonstrate that the relative orientation of symmetrical parts of the dimer is parallel (“U”-shaped) contrary to the gusset-like (“V”-shaped) form of the previously reported structures of the NpSRII/NpHtrII complex in the space group P2₁2₁2, although the structures of the monomers taken individually are nearly the same. Computer modeling of the HAMP domain in the obtained “V”- and “U”-shaped structures revealed that only the “U”-shaped conformation allows for tight interactions of the receptor with the HAMP domain. This is in line with existing data and supports biological relevance of the “U” shape in the ground state. We suggest that the “V”-shaped structure may correspond to the active state of the complex and transition from the “U” to the “V”-shape of the receptor-transducer complex can be involved in signal transduction from the receptor to the signaling domain of NpHtrII.

X-ray diffraction and neutron scattering studies of amphiphile-lipid bilayer organization

The lipid bilayer thickness d(L), the transbilayer distance of lipid phosphate groups d(pp/inf> and the lipid surface area A(L) of fluid hydrated bilayers of lamellar phases of egg phosphatidylcholine or dipalmitoylphosphatidylcholine containing N-alkyl-N,N-dimethylamine N-oxides (CnNO), 1,4-butanedi-ammonium-N,N'-dialkyl-N,N,N',N'-tetramethyl dibromides (GSn) or mono-hydrochlorides of [2-(alkyloxy)phenyl]-2-(1-piperidinyl)ethylesters of carbamic acid (CnA) were obtained by X-ray diffraction, and the bilayer thickness in extruded unilamellar dioleoylphosphatidylcholine vesicles containing C12NO was obtained by the neutron scattering. The values of d(L), d(pp/inf> and A(L) change linearly up to the 1:1 amphiphile:lipid molar ratio. The slopes of these dependencies increase for d(L) and d(pp/inf> and decrease for AL) with an increasing number of carbons n in the amphiphile long hydrocarbon substituent (18> or =n> or =8 for CnNO, 16> or =n> or =9 for GSn, 12> or =n> or =5 for CnA), while the opposite trends are observed for the short substituent (8> or =n>/=6 for CnNO, 9> or =n> or =7 for GSn, 5> or =n> or =3 for CnA). In case of long substituents, the effects on dL), dpp/inf> and AL) are caused by the decrease in the difference between the lipid and amphiphile hydrocarbon chain lengths and by the increase in their van der Waals attraction. The short substituent amphiphiles are mobile and exchange between multiple binding sites in the bilayer, minimizing the bilayer surface area.

Small-angle neutron scattering study of N-dodecyl-N,N-dimethylamine N-oxide induced solubilization of dioleoylphosphatidylcholine bilayers in liposomes

Mixtures of N-dodecyl-N,N-dimethylamine N-oxide (DDAO) and 1,2-dioleoylphosphatidyl choline (DOPC) in chloroform/methanol were evaporated, dried and hydrated in excess 2H2O. Aqueous dispersions thus prepared were extruded through polycarbonate filter with pores of diameter 500A. These samples were studied using small-angle neutron scattering. DDAO destabilizes the bilayer in unilamellar liposomes and solubilizes it into mixed micelles whose shape changes with the DDAO : DOPC molar ratio. Bilayers or/and bilayer fragments have been observed up to DDAO : DOPC = 1.5, rod-like particles (tubular, cylindric micelles) at 2.5 < DDAO : DOPC < 3.5, and transition to globular particles (spheroid micelles) at DDAO: DOPC > 4. In bilayers or/and bilayer fragments, DDAO modulates the thickness of the bilayer.

Small-angle neutron scattering study of the n-decane effect on the bilayer thickness in extruded unilamellar dioleoylphosphatidylcholine liposomes

Dioleoylphosphatidylcholine (DOPC) and n-decane were mixed and hydrated afterwards in an excess of heavy water at 1 wt.% of DOPC. From this dispersion, unilamellar liposomes were prepared by extrusion through polycarbonate filter with 500-A pores. Small-angle neutron scattering (SANS) was conducted on these liposomes. From the Kratky-Porod plot ln[I(Q)Q2] vs. Q2 of SANS intensity I(Q) in the range of scattering vectors Q corresponding to the interval 0.001 A(-2) < or = Q2 < or = 0.006 A(-2), the liposome bilayer radius of gyration Rg and the bilayer thickness parameter d(g) = 12(0.5)Rg were obtained. The values of d(g) indicated that the bilayer thickness is within the experimental error constant up to n-decane/DOPC approximately 0.5 molar ratio, and then increases by 2.4 +/- 1.3 A up to n-decane/DOPC = 1.2 molar ratio.

Effect of N-lauryl-N,N-dimethylamine N-oxide on dimyristoyl phosphatidylcholine bilayer thickness: a small-angle neutron scattering study

Small-angle neutron scattering on large extruded unilamellar dimyristoyl phosphatidylcholine (DMPC) liposomes was used to determine the DMPC bilayer thickness dL and its change in the presence of N-lauryl-N,N-dimethylamine N-oxide (LDAO). At 36 degrees C, the values of dL are dL = 3.44 +/- 0.10 nm and dL = 2.90 +/- 0.10 nm in pure DMPC bilayers and in bilayers at DMPC:LDAO = 2:1 molar ratio, respectively. Using the specific volumes of DMPC and LDAO and supposing that the molecular volumes and surface areas in the bilayer are additive, the surface areas of DMPC (ADMPC) and of LDAO (ALDAO) were found to be at 36 degrees C: ADMPC = 0.644 +/- 0.018 nm2 and ALDAO = 0.25 +/- 0.05 nm2.