Halobacterium hubeiense sp. nov., a haloarchaeal species isolated from a bore core drilled in Hubei Province, PR China

Eight colonies of live microbes were isolated from an extensively surface-sterilized halite sample which had been retrieved from a depth of 2000 m from a salt mine in the Qianjiang Depression, Hubei Province, PR China. The eight colonies, obtained after 4 weeks of incubation, were named JI20-1T-JI20-8 and JI20-1T was selected as the type strain. The strains have been previously described, including a genomic analysis based on the complete genome for strain JI20-1T and draft genomes for the other strains. In that study, the name Halobacterium hubeiense was suggested, based on the location of the drilling site. Previous phylogenomic analysis showed that strain JI20-1T is most closely related to the Permian isolate Halobacterium noricense from Alpine rock salt. The orthologous average nucleotide identity (orthoANI) and digital DNA-DNA hybridization (dDDH) percentages between the eight strains are 100-99.6 % and 99.8-96.4 %, respectively. The orthoANI and dDDH values of these strains with respect to the type strains of species of the genus Halobacterium are 89.9-78.2 % and 37.3-21.6 %, respectively, supporting their placement in a novel extremely halophilic archaeal species. The phylogenomic tree based on the comparison of sequences of 632 core-orthologous proteins confirmed the novel species status for these haloarchaea. The polar lipid profile includes phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, and sulfated galactosyl mannosyl galactosyl glucosyl diether, a profile compatible with that of Halobacterium noricense. Based on genomic, phenotypic, and chemotaxonomic characterization, we propose strain JI20-1T (=DSM 114402T = HAMBI 3616T) as the type strain of a novel species in the genus Halobacterium, with the name Halobacterium hubeiense sp. nov.

X-ray absorption and molecular dynamics study of cation binding sites in the purple membrane

The present work describes the results of a study aimed at identifying candidate cation binding sites on the extracellular region of bacteriorhodopsin, including a site near the retinal pocket. The approach used is a combined effort involving computational chemistry methods (computation of cation affinity maps and molecular dynamics) together with the Extended X-Ray Absorption Fine Structure (EXAFS) technique to obtain relevant information about the local structure of the protein in the neighborhood of Mn(2+) ions in different affinity binding sites. The results permit the identification of a high-affinity binding site where the ion is coordinated simultaneously to Asp212(-) and Asp85(-). Comparison of EXAFS data of the wild type protein with the quadruple mutant E9Q/E74Q/E194Q/E204Q at pH 7.0 and 10.0 demonstrate that extracellular glutamic acid residues are involved in cation binding.

Transient movement of helix F revealed by photo-induced inactivation by reaction of a bulky SH-reagent to cysteine-introduced pharaonis phoborhodopsin (sensory rhodopsin II)

Pharaonis phoborhodopsin (ppR) is a photosensor of negative phototaxis in Natronomonas (Natronobacterium) pharaonis, an alkalophilic halophile. This protein has seven transmembrane helices into which a chromophore, all-trans retinal, binds to a specific lysine residue (located in helix G)via a protonated Schiff base. Various mutants were engineered to have a single cysteine in the F-helix. In the presence of a bulky fluorescent SH-reagent, MIANS, (2-(4'-maleimidylanilino)naphthalene-6-sulfonic acid, illumination decreased the photoreactivity or flash-yield (absorbance deflection immediately after the flash) of the L163C ppR mutant (in which Leu-163 was replaced with Cys) without changing the photocycling rate. The fluorescence of the isolated protein increased with increasing illumination. These observations suggest that during photocycling, the space around Cys-163 in the F-helix might open, permitting reaction with the relatively large molecule. This reaction occurred only at the M-state and not at the O-state. The implications are discussed.

Crystallization of membrane proteins from media composed of connected-bilayer gels

The use of hydrated-lipid gels in which the bilayer is an infinitely periodic (or at least continuous), three-dimensional structure offers a relatively new approach for the crystallization of membrane proteins. While excellent crystals of the Halobacterial rhodopsins have been obtained with such media, success remains poor in extending their use to other membrane proteins. Experience with crystallization of bacteriorhodopsin has led us to recognize a number of improvements that can be made in the use of such hydrated-gel media, which may now prove to be of general value for the crystallization of other membrane proteins.

Dynamics and orientation of transmembrane peptide from bacteriorhodopsin incorporated into lipid bilayer as revealed by solid state (31)P and (13)C NMR spectroscopy

13C and (31)P NMR spectra of a transmembrane peptide, [1-(13)C]Ala(14)-labeled A(6-34), of bacteriorhodopsin incorporated into dimyristoylphosphatidylcholine (DMPC) bilayer were recorded to clarify its dynamics and orientation in the lipid bilayer. This peptide is shown to take an alpha-helical form both in liquid crystalline and gel phases, as viewed from the conformation dependent (13)C chemical shifts. In addition, this peptide undergoes rapid rigid-body rotation about the helical axis at ambient temperature as viewed from the axially symmetric (13)C chemical shift anisotropy, whereas this symmetric anisotropy is changed to an asymmetric pattern at temperatures below 10 degrees C. We further incorporated the peptide into the spontaneously aligned DMPC bilayer to applied magnetic field, induced by dynorphin (dynorphin:DMPC =1:10), a heptadeca-opioid peptide with very high affinity to opioid receptor, in order to gain insight into its orientation in the bilayer. This magnetically aligned system turned out to be persistent even at 0 degrees C as viewed from (31)P NMR spectra of the lipid bilayer, after this peptide was incorporated into this system [A(6-34): dynorphin: DMPC = 4:10:100]. It was found from the (13)C NMR spectra of [1-(13)C]Ala(14) A(6-34) that the helical axis of A(6-34) is oriented parallel to the bilayer normal irrespective of the presence or absence of reorientation motion about the helical axis at a temperature above the lowered gel to liquid crystalline phase transition.

Oceanobacillus iheyensis gen. nov., sp. nov., a deep-sea extremely halotolerant and alkaliphilic species isolated from a depth of 1050 m on the Iheya Ridge

An extremely halotolerant and alkaliphilic bacterium was isolated previously from deep-sea sediment collected at a depth of 1050 m on the Iheya Ridge. The strain, designated HTE831 (JCM 11309, DSM 14371), was Gram-positive, strictly aerobic, rod-shaped, motile by peritrichous flagella, and spore-forming. Strain HTE831 grew at salinities of 0-21% (w/v) NaCl at pH 7.5 and 0-18% at pH 9.5. The optimum concentration of NaCl for growth was 3% at both pH 7.5 and 9.5. The G+C content of its DNA was 35.8%. Low level (12-30%) of DNA-DNA relatedness between strain HTE831 and the species of these genera was found, indicating that HTE831 could not be classified as a member of a new species belonging to known genera. Based on phylogenetic analysis using 16S rDNA sequencing, chemotaxonomy, and the physiology of strain HTE831, it is proposed that this organism is a member of a new species in a new genus, for which the name Oceanobacillus iheyensis is proposed.

The voltage-dependent proton pumping in bacteriorhodopsin is characterized by optoelectric behavior

The light-driven proton pump bacteriorhodopsin (bR) was functionally expressed in Xenopus laevis oocytes and in HEK-293 cells. The latter expression system allowed high time resolution of light-induced current signals. A detailed voltage clamp and patch clamp study was performed to investigate the DeltapH versus Deltapsi dependence of the pump current. The following results were obtained. The current voltage behavior of bR is linear in the measurable range between -160 mV and +60 mV. The pH dependence is less than expected from thermodynamic principles, i.e., one DeltapH unit produces a shift of the apparent reversal potential of 34 mV (and not 58 mV). The M(2)-BR decay shows a significant voltage dependence with time constants changing from 20 ms at +60 mV to 80 ms at -160 mV. The linear I-V curve can be reconstructed by this behavior. However, the slope of the decay rate shows a weaker voltage dependence than the stationary photocurrent, indicating that an additional process must be involved in the voltage dependence of the pump. A slowly decaying M intermediate (decay time > 100 ms) could already be detected at zero voltage by electrical and spectroscopic means. In effect, bR shows optoelectric behavior. The long-lived M can be transferred into the active photocycle by depolarizing voltage pulses. This is experimentally demonstrated by a distinct charge displacement. From the results we conclude that the transport cycle of bR branches via a long-lived M(1)* in a voltage-dependent manner into a nontransporting cycle, where the proton release and uptake occur on the extracellular side.

New photointermediates in the two photon signaling pathway of sensory rhodopsin-I

Sensory rhodopsin-I (SRI) functions as a color discriminating receptor in halobacterial phototaxis. SRI exists in the membrane as a molecular complex with a signal transducer protein. Excitation of its thermally stable form, SRI(587), generates a long-lived photointermediate of its photocycle, S(373), and an attractant phototactic response. S(373) decays thermally in a few seconds into SRI(587.) However, when S(373) is excited by UV-blue light, it photoconverts into SRI(587) in less than a second, generating a repellent phototactic response. Only one intermediate of this back-photoreaction, S(b)(510), is known. We studied the back-photoreaction in both native SRI and its transducer free form fSRI by measuring laser flash induced absorption changes of S(373) photoproducts from 100 ns to 1 s in the 350-750 nm range. Using global exponential fitting, we determined the spectra and kinetics of the photointermediates. S(373) and fS(373) when pumped with 355 nm laser light generate in less than 100 ns two intermediate species: a previously undetected species that absorbs maximally at about 410 nm, S(b)(410), and the previously described S(b)(510). These two intermediates appear to be in a rapid equilibrium, which probably entails protonation change of the Schiff base chromophore. At pH 6 this system relaxes to SRI(587) via another intermediate absorbing maximally around 550 nm, which thermally decays back to the ground state. The same intermediates are seen in the presence and absence of transducer; however, the kinetics are affected by binding of the transducer.

Atomic force microscopy of native purple membrane

Atomic force microscopy (AFM) allows the observation of surface structures of purple membrane (PM) in buffer solution with subnanometer resolution. This offers the possibility to classify the major conformations of the native bacteriorhodopsin (BR) surfaces and to map the variability of individual polypeptide loops connecting transmembrane alpha-helices of BR. The position, the variability and the flexibility of these loops depend on the packing arrangement of BR molecules in the lipid bilayer with significant differences observed between the trigonal and orthorhombic crystal forms. Cleavage of the Schiff base bond leads to a disassembly of the trigonal PM crystal, which is restored by regenerating the bleached PM. The combination of single molecule AFM imaging and single molecule force-spectroscopy provides an unique insight into the interactions between individual BR molecules and the PM, and between secondary structure elements within BR.

Structural determinants of purple membrane assembly

The purple membrane is a two-dimensional crystalline lattice formed by bacteriorhodopsin and lipid molecules in the cytoplasmic membrane of Halobacterium salinarum. High-resolution structural studies, in conjunction with detailed knowledge of the lipid composition, make the purple membrane one of the best models for elucidating the forces that are responsible for the assembly and stability of integral membrane protein complexes. In this review, recent mutational efforts to identify the structural features of bacteriorhodopsin that determine its assembly in the purple membrane are discussed in the context of structural, calorimetric and reconstitution studies. Quantitative evidence is presented that interactions between transmembrane helices of neighboring bacteriorhodopsin molecules contribute to purple membrane assembly. However, other specific interactions, particularly between bacteriorhodopsin and lipid molecules, may provide the major driving force for assembly. Elucidating the molecular basis of protein-protein and protein-lipid interactions in the purple membrane may provide insights into the formation of integral membrane protein complexes in other systems.

Refinement of the geometry of the retinal binding pocket in dark-adapted bacteriorhodopsin by heteronuclear solid-state NMR distance measurements

The bacterial proton pump bacteriorhodopsin (BR) is a 26.5 kDa seven-transmembrane helical protein. Several structural models have been published at > or =1.55 A resolution. The initial cis-trans isomerization of the retinal moiety involves structural changes within <1 A. To understand the chromophore-protein interactions that are important for light-driven proton transport, very accurate measurements of the protein geometry are required. To reveal more structural details at the site of the retinal, we have, therefore, selectively labeled the tryptophan side chains of BR with (15)N and metabolically incorporated retinal, (13)C-labeled at position 14 or 15. Using these samples, heteronuclear distances were measured with high accuracy using SFAM REDOR magic angle spinning solid-state NMR spectroscopy in dark-adapted bacteriorhodopsin. This NMR technique is applied for the first time to a high-molecular mass protein. Two retinal conformers are distinguished by their different isotropic 14-(13)C chemical shifts. Whereas the C14 position of 13-cis-15-syn-retinal is 4.2 A from [indole-(15)N]Trp86, this distance is 3.9 A in the all-trans-15-anti conformer. This latter distance allows us to check on the details of the active center of BR in the various published models derived from X-ray and electron diffraction data. The experimental approach and the results reported in this paper enforce the notion that distances between residues of a membrane protein binding pocket and a bound ligand can be determined at subangstrom resolution.

Relocation of internal bound water in bacteriorhodopsin during the photoreaction of M at low temperatures: an FTIR study

Changes in the FTIR difference spectra upon photoconversion of the M intermediate to its photoproduct(s) M' were studied in wild-type bacteriorhodopsin and several mutants at low temperatures. The studies aimed at examining whether internally bound water molecules interact with the chromophore and the key residues Asp85 and Asp96 in M, and whether these water molecules participate in the reprotonation of the Schiff base. We have found that three water molecules are perturbed by the isomerization of the chromophore in the M --> M' transition at 80 K. The perturbation of one water molecule, detected as a bilobe at 3567(+)/3550(-) cm(-)(1), relaxed in parallel with the relaxation of an Asp85 perturbation upon increasing temperature from 80 to 100 and 133 K (before the reprotonation of the Schiff base). Two water bands of M at 3588 and 3570 cm(-)(1) shift to 3640 cm(-)(1) upon photoconversion at 173 K. These bands were attributed to water molecules which are located in the vicinity of the Schiff base and Asp85 (Wat85). In the M to M' transition at 80 and 100 K, where the Schiff base remained unprotonated, the Wat85 pair stayed in similar states to those in M. The reprotonation of the Schiff base at 133 K occurred without the restoration of the Wat85 band around 3640 cm(-)(1). This band was restored at higher temperatures. Two water molecules in the region surrounded by Thr46, Asp96, and Phe219 (Wat219) were perturbed in the M to M' transition at 80 K and relaxed in parallel with the relaxation of the perturbation of Asp96 upon increasing the temperature. Mutant studies show that upon photoisomerization of the chromophore at 80 K one of the Wat219 water molecules moves closer to Val49 (located near the lysine side chain attached to retinal, and close to the Schiff base). These data along with our previous results indicate that the water molecules in the cytoplasmic domain participate in the connection of Asp96 with the Schiff base and undergo displacement during photoconversions, presumably shuttling between the Schiff base and a site close to Asp96 in the L to M to N transitions.

Ordered membrane insertion of an archaeal opsin in vivo

The prevailing model of polytopic membrane protein insertion is based largely on the in vitro analysis of polypeptide chains trapped during insertion by arresting translation. To test this model under conditions of active translation in vivo, we have used a kinetic assay to determine the order and timing with which transmembrane segments of bacterioopsin (BO) are inserted into the membrane of the archaeon Halobacterium salinarum. BO is the apoprotein of bacteriorhodopsin, a structurally well characterized protein containing seven transmembrane alpha-helices (A-G) with an N-out, C-in topology. H. salinarum strains were constructed that express mutant BO containing a C-terminal His-tag and a single cysteine in one of the four extracellular domains of the protein. Cysteine translocation during BO translation was monitored by pulse-chase radiolabeling and rapid derivatization with a membrane-impermeant, sulfhydryl-specific gel-shift reagent. The results show that the N-terminal domain, the BC loop, and the FG loop are translocated in order from the N terminus to the C terminus. Translocation of the DE loop could not be examined because cysteine mutants in this region did not yield a gel shift. The translocation order was confirmed by applying the assay to mutant proteins containing two cysteines in separate extracellular domains. Comparison of the translocation results with in vivo measurements of BO elongation indicated that the N-terminal domain and the BC loop are translocated cotranslationally, whereas the FG loop is translocated posttranslationally. Together, these results support a sequential, cotranslational model of archaeal polytopic membrane protein insertion in vivo.

Irreversible conformational change of bacterio-opsin induced by binding of retinal during its reconstitution to bacteriorhodopsin, as studied by (13)C NMR

We compared (13)C NMR spectra of [3-(13)C]Ala- and [1-(13)C]Val-labeled bacterio-opsin (bO), produced either by bleaching bR with hydroxylamine or from a retinal-deficient strain, with those of bacteriorhodopsin (bR), in order to gain insight into the conformational changes of the protein backbone that lead to correct folding after retinal is added to bO. The observed (13)C NMR spectrum of bO produced by bleaching is not greatly different from that of bR, except for the presence of suppressed or decreased peak-intensities. From careful evaluation of the intensity differences between cross polarization magic angle spinning (CP-MAS) and dipolar decoupled-magic angle spinning (DD-MAS) spectra, it appears that the reduced peak-intensities arise from reduced efficiency of cross polarization or interference of internal motions with proton decoupling frequencies. In particular, the E-F and F-G loops and some transmembrane helices of the bleached bO have acquired internal motions whose frequencies interfere with proton decoupling frequencies. In contrast, the protein backbone of the bO from the retinal-negative cells is incompletely folded. Although it contains mainly a-helices, its very broad (13)C NMR signals indicate that its tertiary structure is different from bR. Importantly, this changed structure is identical in form to that of bleached bO from wild-type bR after it was regenerated with retinal in vitro, and bleached with hydroxylamine. We conclude that the binding of retinal is essential for the correct folding of bR after it is inserted in vitro into the lipid bilayer, and the final folded state does not revert to the partially folded form upon removal of the retinal.

High-field EPR studies of the structure and conformational changes of site-directed spin labeled bacteriorhodopsin

Cw and pulsed high-field EPR (95 GHz, 3.4 T) are performed on site-directed spin labeled bacteriorhodopsin (BR) mutants. The enhanced Zeeman splitting leads to spectra with resolved g-tensor components of the nitroxide spin label. The g(xx) component shift determined for 10 spin labels located in the cytoplasmic loop region and in the protein interior along the BR proton channel reveals a maximum close to position 46 between the proton donor D96 and the retinal. A plot of g(xx) versus A(zz) of the nitrogen discloses grouping of 12 spin labeled sites in protic and aprotic sites. Spin labels at positions 46, 167 and 171 show the aprotic character of the cytoplasmic moiety of the proton channel whereas nitroxides at positions 53, 194 and 129 reveal the protic environment in the extracellular channel. The enhanced sensitivity of high-field EPR with respect to anisotropic reorientational motion of nitroxides allows the characterization of different motional modes for spin labels bound to positions 167 and 170. The motional restriction of the nitroxide at position 167 of the double mutant V167C/D96N is decreased in the M(N) photo-intermediate. An outward shift of the cytoplasmic moiety of helix F in the M(N) intermediate would account for the high-field EPR results and is in agreement with diffraction and recent X-band EPR data.

Membrane insertion kinetics of a protein domain in vivo. The bacterioopsin n terminus inserts co-translationally

The pathway by which segments of a polytopic membrane protein are inserted into the membrane has not been resolved in vivo. We have developed an in vivo kinetic assay to examine the insertion pathway of the polytopic protein bacterioopsin, the apoprotein of Halobacterium salinarum bacteriorhodopsin. Strains were constructed that express the bacteriorhodopsin mutants I4C:H(6) and T5C:H(6), which carry a unique Cys in the N-terminal extracellular domain and a polyhistidine tag at the C terminus. Translocation of the N-terminal domain was detected using a membrane-impermeant gel shift reagent to derivatize the Cys residue of nascent radiolabeled molecules. Derivatization was assessed by gel electrophoresis of the fully elongated radiolabeled population. The time required to translocate and fully derivatize the Cys residues of I4C:H(6) and T5C:H(6) is 46 +/- 9 and 61 +/- 6 s, respectively. This is significantly shorter than the elongation times of the proteins, which are 114 +/- 26 and 169 +/- 16 s, respectively. These results establish that translocation of the bacterioopsin N terminus and insertion of the first transmembrane segment occur co-translationally and confirm the use of the assay to monitor the kinetics of polytopic membrane protein insertion in vivo.

Binding of volatile anesthetics to purple membranes studied by X-ray diffraction

Volatile anesthetics, diiodomethane and trifluoroethyl iodide, acted on the purple membrane of Halobacterium halobium in two different modes depending on the concentration. At low concentration, the absorption maximum of bacteriorhodopsin shifted from 561 to 558 nm (BR558) and the M-intermediate of the photocycle decayed faster than the native one. Higher concentration induced a species absorbing maximally at 480 nm (BR480) and the long-lived M-intermediates. The X-ray study suggested that anesthetics bound specifically to the protein-lipid interfacial region within a trimer near the surface of membrane in BR558 and entered into the hydrophobic domain of the membrane in BR480.

Towards a bacteriorhodopsin-silicon neuromorphic photosensor

We describe our efforts towards constructing a hybrid protein-silicon neuromorphic photosensor based on the photo-active protein bacteriohodopsin. This protein displays an differential photosensitivity similar to the response of the receptive field of an X-type retinal ganglion cell. Similar bacteriohodopsin photoelectrode arrays display inherent edge detection and motion enhancement. We discuss challenges associated with constructing and understanding the protein-silicon interface and possible chemical solutions for our experimental device.

Ultraviolet resonance Raman spectra of Trp-182 and Trp-189 in bacteriorhodopsin: novel information on the structure of Trp-182 and its steric interaction with retinal

Ultraviolet (244 nm) resonance Raman spectra of Trp-182 and Trp-189 in bacteriorhodopsin were obtained by subtracting the spectrum of the mutants, Trp-182-->Phe or Trp-189-->Phe, from that of the wild-type. Analysis of the spectra shows that the chi2,1 torsion angle about the Cbeta-C3 bond is +/-93 degrees for Trp-182 and +/-100 degrees for Trp-189. Both Trp residues are moderately hydrogen bonded to proton acceptors at their indolyl nitrogens in hydrophobic environments. The environmental hydrophobicity is particularly strong for Trp-182, as judged from the splitting of the W7 Raman band to a triplet. The Raman information on the structure and environment of Trp-189 is consistent with the molecular model from electron diffraction [Grigorieff et al. (1996) J. Mol. Biol. 259, 393-421]. On the other hand, the chi2,1 angle and the hydrogen-bonding state of Trp-182 found here differ from those in the model structure. Revision of the model to correspond to the Raman findings would require a 60 degrees rotation of the Trp-182 indole ring about the Cbeta-C3 bond toward the chromophore retinal and the presence of a water molecule that is hydrogen bonded to the indolyl nitrogen. The triplet feature of the W7 band of Trp-182 is attributable to unusually strong steric repulsion between the indole ring and the 9- and 13-methyl groups of the retinal. Resonance Raman spectra in the visible suggest that this steric conflict destabilizes the 13-cis isomeric state of the retinal.

Surface of bacteriorhodopsin revealed by high-resolution electron crystallography

Bacteriorhodopsin is a transmembrane protein that uses light energy, absorbed by its chromophore retinal, to pump protons from the cytoplasm of bacteria such as Halobacterium salinarium into the extracellular space. It is made up of seven alpha-helices, and in the bacterium forms natural, two-dimensional crystals called purple membranes. We have analysed these crystals by electron cryo-microscopy to obtain images of bacteriorhodopsin at 3.0 A resolution. The structure covers nearly all 248 amino acids, including loops outside the membrane, and reveals the distribution of charged residues on both sides of the membrane surface. In addition, analysis of the electron-potential map produced by this method allows the determination of the charge status of these residues. On the extracellular side, four glutamate residues surround the entrance to the proton channel, whereas on the cytoplasmic side, four aspartic acids occur in a plane at the boundary of the hydrophobic-hydrophilic interface. The negative charges produced by these aspartate residues is encircled by areas of positive charge that may facilitate accumulation and lateral movement of protons on this surface.

The height of biomolecules measured with the atomic force microscope depends on electrostatic interactions

In biological applications of atomic force microscopy, the different surface properties of the biological sample and its support become apparent. Observed height differences between the biomolecule and its supporting surface are thus not only of structural origin, but also depend on the different sample-tip and support-tip interactions. This can result in negative or positive contributions to the measured height, effects that are described by the DLVO (Derjaguin, Landau, Verwey, Overbeek) theory. Experimental verification shows that the electrostatic interactions between tip and sample can strongly influence the result obtained. To overcome this problem, pH and electrolyte concentration of the buffer solution have to be adjusted to screen out electrostatic forces. Under these conditions, the tip comes into direct contact with the surface of support and biological system, even when low forces required to prevent sample deformation are applied. In this case, the measured height can be related to the thickness of the native biological structure. The observed height dependence of the macromolecules on electrolyte concentration makes it possible to estimate surface charge densities.

Chloride and proton transport in bacteriorhodopsin mutant D85T: different modes of ion translocation in a retinal protein

Replacement of aspartate 85 (D85) in bacteriorhodopsin (BR) by threonine but not be asparagine creates at pH<7 an anion-binding site in the molecular similar to that in chloride pump halorhodopsin. Binding of various anions to BR-D85T causes a blue shift of the absorption maximum by maximally 57 nm. Connected to this color change is a change in the absorption difference spectrum of the initial state and the longest living photo intermediate from a positive difference maximum at 460 nm in the absence of transported anions to one at 630 nm in their presence. Increasing anion concentration cause decreasing decay times of this intermediate. At physiological pH, BR-D85T but not BR-D85N transports chloride ions inward in green light, protons outward in blue or green light and protons inward in white light (directions refer to the intact cell). The proton movements are observable also in BR-D85N. Thus, creation of an anion-binding site in BR is responsible for chloride transport and introduction of anion-dependent spectroscopic properties at physiological pH. The different transport modes are explained with the help of the recently proposed IST model, which states that after light-induced isomerization of the retinal an ion transfer step and an accessibility change of the active site follow. The latter two steps occur independently. In order to complete the cyclic event, the accessibility change, ion transfer and isomerization state have to be reversed. The relative rates of accessibility changes and ion transfer steps define ultimately the vectoriality of ion transfers. All transport modes described here for the same molecule can satisfactorily be described in the framework of this general concept.

Glutamate-194 to cysteine mutation inhibits fast light-induced proton release in bacteriorhodopsin

Substitution of glutamic acid-194, a residue on the extracellular surface of bacteriorhodopsin, with a cysteine inhibits the fast light-induced proton release that normally is coupled with the deprotonation of the Schiff base during the L to M transition. Proton release in this mutant occurs at the very end of the photocycle and coincides with deprotonation of the primary proton acceptor, Asp-85, during the O to bR transition. the E194C mutation also results in a slowing down of the photocycle by about 1 order of magnitude as compared to the wild type and produces a strong effect on the pH dependence of dark adaptation that is interpreted as a drastic reduction or elimination of the coupling between the primary proton acceptor Asp-85 and the proton release group. These data indicate that Glu-194 is a critical component of the proton release complex in bacteriorhodopsin.

Secondary structures comparison of aquaporin-1 and bacteriorhodopsin: a Fourier transform infrared spectroscopy study of two-dimensional membrane crystals

Aquaporins are integral membrane proteins found in diverse animal and plant tissues that mediate the permeability of plasma membranes to water molecules. Projection maps of two-dimensional crystals of aquaporin-1 (AQP1) reconstituted in lipid membranes suggested the presence of six to eight transmembrane helices in the protein. However, data from other sequence and spectroscopic analyses indicate that this protein may adopt a porin-like beta-barrel fold. In this paper, we use Fourier transform infrared spectroscopy to characterize the secondary structure of highly purified native and proteolyzed AQP1 reconstituted in membrane crystalline arrays and compare it to bacteriorhodopsin. For this analysis the fractional secondary structure contents have been determined by using several different algorithms. In addition, a neural network-based evaluation of the Fourier transform infrared spectra in terms of numbers of secondary structure segments and their interconnections [sij] has been performed. The following conclusions were reached: 1) AQP1 is a highly helical protein (42-48% alpha-helix) with little or no beta-sheet content. 2) The alpha-helices have a transmembrane orientation, but are more tilted (21 degrees or 27 degrees, depending on the considered refractive index) than the bacteriorhodopsin helices. 3) The helices in AQP1 undergo limited hydrogen/deuterium exchange and thus are not readily accessible to solvent. Our data support the AQP1 structural model derived from sequence prediction and epitope insertion experiments: AQP1 is a protein with at least six closely associated alpha-helices that span the lipid membrane.

Nanosecond retinal structure changes in K-590 during the room-temperature bacteriorhodopsin photocycle: picosecond time-resolved coherent anti-stokes Raman spectroscopy

Time-resolved vibrational spectra are used to elucidate the structural changes in the retinal chromophore within the K-590 intermediate that precedes the formation of the L-550 intermediate in the room-temperature (RT) bacteriorhodopsin (BR) photocycle. Measured by picosecond time-resolved coherent anti-Stokes Raman scattering (PTR/CARS), these vibrational data are recorded within the 750 cm-1 to 1720 cm-1 spectral region and with time delays of 50-260 ns after the RT/BR photocycle is optically initiated by pulsed (< 3 ps, 1.75 nJ) excitation. Although K-590 remains structurally unchanged throughout the 50-ps to 1-ns time interval, distinct structural changes do appear over the 1-ns to 260-ns period. Specifically, comparisons of the 50-ps PTR/CARS spectra with those recorded with time delays of 1 ns to 260 ns reveal 1) three types of changes in the hydrogen-out-of-plane (HOOP) region: the appearance of a strong, new feature at 984 cm-1; intensity decreases for the bands at 957 cm-1, 952 cm-1, and 939 cm-1; and small changes intensity and/or frequency of bands at 855 cm-1 and 805 cm-1; and 2) two types of changes in the C-C stretching region: the intensity increase in the band at 1196 cm-1 and small intensity changes and/or frequency shifts for bands at 1300 cm-1 and 1362 cm-1. No changes are observed in the C = C stretching region, and no bands assignable to the Schiff base stretching mode (C = NH+) mode are found in any of the PTR/CARS spectra assignable to K-590. These PTR/CARS data are used, together with vibrational mode assignments derived from previous work, to characterize the retinal structural changes in K-590 as it evolves from its 3.5-ps formation (ps/K-590) through the nanosecond time regime (ns/K-590) that precedes the formation of L-550. The PTR/CARS data suggest that changes in the torsional modes near the C14-C15 = N bonds are directly associated with the appearance of ns/K-590, and perhaps with the KL intermediate proposed in earlier studies. These vibrational data can be primarily interpreted in terms of the degree of twisting of the C14-C15 retinal bond. Such twisting may be accompanied by changes in the adjacent protein. Other smaller, but nonetheless clear, spectral changes indicate that alterations along the retinal polyene chain also occur. The changes in the retinal structure are preliminary to the deprotonation of the Schiff base nitrogen during the formation of M-412. The time constant for the ps/ns K-590 transformation is estimated from the amplitude change of four vibrational bands in the HOOP region to be 40-70 ns.

Three-dimensional model of sensory rhodopsin I reveals important restraints between the protein and the chromophore

A structural model is constructed for the integral membrane protein, sensory rhodopsin I (SRI), the phototaxis receptor of the archaeon Halobacterium salinarium. The model is built on the template of the homologous bacteriorhodopsin (BR). The modeling procedure includes sequence alignment, a side chain rotamer search and simulated annealing by restricted molecular dynamics. The structure is in general agreement with previous results from mutagenesis experiments, chromophore substitution and room and cryogenic temperature spectroscopy. In particular, a residue near the beta-ionone ring of the retinylidene chromophore is found to be critical in maintaining the proper isomeric conformation of the chromophore; a layer of residues lying on the cytoplasmic side of the chromophore pocket is found to modulate the restraints around the C13 region of the chromophore, affecting the isomerizations around its 13 = 14 bond that are important to the protein's activity. The restraints in these regions are more stringent in SRI than in BR. The tightened restraints are chiefly due to van der Waals interactions, where the attractive and repulsive components play separable roles. Aromatic residues account for a majority of the restrictive interactions. It is hypothesized that the enhanced barriers due to these restrictions regulate the progress of SRI's photocycle, so that it can couple with the phototaxis reaction chain in the bacterium. A possibility is also suggested that conformational changes of the protein provide the signal recognized by the transducer.

PROPERTIES OF A PURIFIED HALOPHILIC MALIC DEHYDROGENASE

Holmes, P. K. (University of Illinois, Urbana), and H. Orin Halvorson. Properties of a purified halophilic malic dehydrogenase. J. Bacteriol. 90:316-326. 1965.-The malic dehydrogenase (MDH) from Halobacterium salinarium required high concentrations of monovalent ions for stability and activity. Studies of inactivation rates at different salt concentrations suggested that approximately 25% NaCl (w/v) is required to stabilize MDH. From 50 to 100% reactivation, depending on the salt concentration present during inactivation, could occur in 2.5 to 5 m NaCl or KCl. The optimal salt concentration for activity of MDH was a function of the pH, and ranged from 1 to 3 m NaCl or KCl. The effect of salt concentration on the pH-activity curves occurred chiefly below pH 7.0. Inactivation of MDH with heat or thiol reagents showed that the enzyme was more labile in the state induced by absence of salt. The activation of MDH by salts was attributed to a decreased rate of dissociation of MDH and reduced nicotinamide adenine dinucleotide (NADH(2)). The inactivation of the enzyme in the absence of salt could be largely prevented by the presence of NADH(2). The S(20.w) of MDH decreased threefold at low salt concentrations. The enzyme was assumed to be in its native compact configuration only in the presence of a high concentration of salt.

PURIFICATION OF A SALT-REQUIRING ENZYME FROM AN OBLIGATELY HALOPHILIC BACTERIUM

Holmes, P. K. (University of Illinois, Urbana), and H. O. Halvorson. Purification of a salt-requiring enzyme from an obligately halophilic bacterium. J. Bacteriol. 90: 312-315. 1965.-The discovery that some halophilic enzymes may be reactivated from the salt-free and inactive state has facilitated the purification of nicotinamide adenine dinucleotide-linked malic acid dehydrogenase from crude extracts of Halobacterium salinarium. In the absence of large amounts of salt, the enzyme was totally inactive; yet, in this salt-free state, it could be purified by conventional techniques. The highly purified halophilic enzyme was shown to require a high concentration of salt for activity.

Electrospray ionization mass spectrometry of genetically and chemically modified bacteriorhodopsins

A simple method for the preparation of bacterio-rhodopsin for mass spectrometry is described, consisting of precipitation of the sample, removal of lipids by washing the sample, and dissolving it in an acidic mixture of organic solvents. Examples demonstrate the method's suitability for the analysis of genetically and chemically modified bacteriorhodopsins. The observed molecular masses are within 0.01% in accordance with the theoretical masses of the wild-type protein and modification products. This allows the detection of modifications accompanied by a mass change greater than 2 Da. Thus, only 9 of 380 possible binary amino acid exchanges are not amenable to analysis. Also chemical modifications of bacteriorhodopsin can be followed since it is possible to characterize reaction products and to approximate yields. However, secondary reactions like hydrolysis in the reaction medium or in the acid solvent used for sample preparation must be considered.

THE CELL ENVELOPES OF TWO EXTREMELY HALOPHILIC BACTERIA

The cell envelope of Halobacterium halobium was seen in thin sections of permanganate-fixed cells to consist of one membrane. This membrane appeared mostly as a unit membrane but in a few preparations it resembled a 5-layered compound membrane. The cell envelope of Halobacterium salinarium at high resolution was always seen as a 5-layered structure different in appearance from the apparent compound membrane of H. halobium. The "envelopes" which were isolated in 12.5 per cent NaCl from each organism were indistinguishable from each other in the electron microscope and comprised, in each case, a single unit membrane with an over-all thickness of about 110 A. Some chemical analyses were made of isolated membranes after freeing them from salt by precipitating and washing with trichloroacetic acid. Such precipitated membranes consisted predominantly of protein, with little carbohydrate and no peptido-aminopolysaccharide (mucopeptide). Sectioned whole cells of H. halobium contained intracellular electron-opaque structures of unknown function.

Internal molecular motions of bacteriorhodopsin: hydration-induced flexibility studied by quasielastic incoherent neutron scattering using oriented purple membranes

Quasielastic incoherent neutron scattering from hydrogen atoms, which are distributed nearly homogeneously in biological molecules, allows the investigation of diffusive motions occurring on the pico- to nanosecond time scale. A quasielastic incoherent neutron scattering study was performed on the integral membrane protein bacteriorhodopsin (BR), which is a light-driven proton pump in Halobacterium salinarium. BR is embedded in lipids, forming patches in the cell membrane of the organism, which are the so called purple membranes (PMs). Measurements were carried out at room temperature on oriented PM-stacks hydrated at two different levels (low hydration, h = 0.03 g of D2O per g of PM; high hydration, h = 0.28 g of D2O per g of PM) using time-of-flight spectrometers. From the measured spectra, different diffusive components were identified and analyzed with respect to the influence of hydration. This study supports the idea that a decrease in hydration results in an appreciable decrease in internal molecular flexibility of the protein structure. Because it is known from studies on the function of BR that the pump activity is reduced if the hydration level of the protein is insufficient, we conclude that the observed diffusive motions are essential for the function of this protein. A detailed analysis and classification of the different kinds of diffusive motions, predominantly occurring in PMs under physiological conditions, is presented.

Reorientations in the bacteriorhodopsin photoscycle are pH dependent

Chromophore reorientations during the bacteriorhodopsin photocycle in the purple membrane of Halobacterium salinarium have been detected by time-resolved linear dichroism measurements of the optical anisotropy over the pH range from 4 to 10 and at ionic strengths from 10 mM to 1 M. The results show that reorientations in the L and M states of bacteriorhodopsin are pH dependent, reaching their largest amplitude when the membrane is at pH 6-8. Reorientations on the millisecond time scale of unexcited spectator proteins in the native purple membrane also depend on pH, consistent with the suggestion that spectator reorientations are triggered by reorientation of the photoexcited protein. The results imply that a group with a PK(a) of 5 to 6 enables reorientations, and that the deprotonation of a site at pH values above 9 restricts reorientational motion. This suggests that reorientations in M may be correlated with proton release.

Correlation between surfactant/micelle structure and the stability of bacteriorhodopsin in solution

The rate of solubilization and isothermal bleaching of bacteriorhodopsin (bR) in a series of nine alkylammonium surfactants is studied by using time-resolved optical spectroscopy. The surfactant series RN(+)R'(3) covers a range in tail length (R = C(12)H(25), C(14)H(29), or C(16)H(33)) and headgroup size and hydrophobicity (R' = CH(3); C(2)H(5), or C(3)H(7)). The rate of bleaching increases initially with increasing surfactant concentration but decreases at higher concentrations. Possible explanations for this behavior are discussed. The kinetic data are consistent with the penetration of the surfactant into the protein interior. Interaction of the surfactants with the protein is a complicated, multistep process, and the rate curves are a function of at least four variables: 1) the micellar environment, 2) the length of the surfactant tail, 3) the size of the headgroup, and 4) the hydrophobicity of the headgroup. Our data provide new insights into the molecular characteristics that help define the performance of surfactants in the solubilization and denaturation of membrane-bound proteins.

Effect of transmembrane helix packing on tryptophan and tyrosine environments in detergent-solubilized bacterio-opsin

Bacterio-opsin (bO) is folded in a nearly native conformation in mixed micelles of dimyristoyl phosphatidyl choline (DMPC) and 3-[(3-cholamidopropyl)-dimehtylamonio]-1-propane sulfonic acid (CHAPS), but bO is partially unfolded in sodium dodecyl sulfate (SDS). UV difference spectroscopy was used to study the changes in environment of bO aromatic amino acid side chains that occur upon partial unfolding. The UV difference spectra of peptides in CHAPS/DMPC minus peptides in SDS were measured for bO and the following subfragments of bO: C1 (residues 72-248), C2 (1-71), V1 (1-166), V2 (167-248), CB7 (119-145), CB9 (164-209), and CB10 (72-118). The spectra show that, in partially unfolded bO in SDS, the Tyr and Trp absorbance is blue-shifted. The difference spectra were compared to solvent perturbation difference spectra of N-acetyl-L-tyrosine ethyl ester and N-acetyl-L-tryptophanamide. The exposure change calculated from the difference spectra was found to correlate with the change in the number of van der Waals contacting atoms upon partial unfolding, and also with the number of transmembrane helical segments. This result suggests a simple experimental method of testing helix packing arrangements derived from hydropathy plots and model building.

Interaction of tryptophan-182 with the retinal 9-methyl group in the L intermediate of bacteriorhodopsin

An intense indole N-H stretching vibrational band at 3486 cm-1 in the difference Fourier transform infrared spectrum is one of the characteristic features of the L intermediate of bacteriorhodopsin [Maeda, Sasaki, Ohkita, Simpson, & Herzfeld (1992) Biochemistry 31, 12543]. This band is now assigned to tryptophan-182. The Trp182-->Phe (W182F) protein shows specific features in the difference spectrum in the visible region upon L formation, and exhibits great delay in the L-M conversion. Fourier transform infrared difference spectra further indicate that while the intensity of the C-methyl in-plane bending vibration at 1009 cm-1 is lost in the L intermediate of the wild type, its intensity remains high in the W182F protein. The intensity of the N-H stretching vibration upon L formation is diminished considerably in an artificial bacteriorhodopsin containing 9-desmethylretinal. It also exhibits delayed M formation. These results suggest that Trp182 interacts with the retinal side chain through the 9-methyl group, and thereby affects the L-to-M conversion.

On the heterogeneity of the M population in the photocycle of bacteriorhodopsin

The M stage in the photocycle of bacteriorhodopsin (bR), a key step in its light-induced proton pump mechanism, is studied in water/glycerol suspensions over the temperature range between 20 and -60 degrees C. The biexponential decay of M is analyzed for wild-type (WT) bR and for its D96N, Y185F, and D115N mutants, at various pH values, according to the scheme: bR-->(hv) L-->M<-->(k1, k-1) N-->(k2) bR. The analysis leads to the conclusion that the N state is generated, with analogous rate parameters, in all cases, including the D96N mutant. Another approach involves probing the M state, generated by steady-state illumination at -60 degrees C, by fast cooling to -180 degrees C. Subsequent irradiation with blue light, followed by gradual warming up, induces the M-->(hv) M'-->bR'-->bR sequence of reactions. On the basis of characteristic difference spectra and transition temperatures observed for the M'-->bR' process, it is concluded that the initially observed M state at -60 degrees C, denoted as (M)a, is composed of three (or four) equilibrated substrates, MI, MII, MIII, and MIV. During the M-->N equilibration, which corresponds to the fast phase of the M decay, (M)a transforms into a second state, (M)b, in which MIII has been replaced by a fifth M substate, denoted as MV. MV is identified as the protein state in which an appropriate structural change allows reprotonation of the Schiff base, generating the N state. The low-temperature heterogeneity in M is discussed in terms of the two M states (M1 and M2) previously postulated [Váró, G., & Lanyi, J. K. (1990) Biochemistry 29, 2241] for the room temperature photocycle. The following conclusions are derived for both low and room temperature photocycles: (a) The M population is highly heterogeneous and pH dependent. (b) At least three transitions are observed between the initially formed M state and the M state that is equilibrated with N. These are assigned to protein conformational changes and to water molecule rearrangements. (c) In an aqueous suspension of WT bR at room temperature, the Schiff base reprotonation is controlled by D96. However, our results show that the formation and stability of the N state do not require the D96 residue. Moreover, at low temperatures, the (M)a-->(M)b protein structural transformation, which has not yet been resolved at room temperature, becomes the rate-determining step in the protonation of the Schiff base.

Sensory rhodopsin I photocycle intermediate SRI380 contains 13-cis retinal bound via an unprotonated Schiff base

Sensory rhodopsin I (SRI), the mutated derivative SRI-D76N and the complex of SRI with its transducer HtrI were overexpressed in Halobacterium salinarium and analyzed by resonance Raman spectroscopy. In the initial state SRI contains all-trans retinal bound via a protonated Schiff base as confirmed by retinal extraction which yields 95 +/- 3% all-trans retinal. The photocycle intermediate absorbing maximally at 380 nm (SRI380) contains a Schiff base linkage between the protein and 13-cis retinal. Extraction of illuminated SRI yields up to 93% 13-cis retinal. Neither the mutation D76N nor HtrI changed the vibrational pattern of the chromophore.

Membrane-mediated control of the bacteriorhodopsin photocycle

The ability of actinic light to modify the proportion of fast and slow forms of the M intermediate (i.e., Mf and M(s)) in the bacteriorhodopsin (BR) photocycle is lost by exposure of the purple membrane (PM) to 0.05% Triton for 1-2 min. The decay path of Mf through the O intermediate is also lost, and new, much slower kinetic forms of M appear. In this brief exposure, the trimer structure for BR, as measured by circular dichroism (CD) exciton coupling and sedimentability, is unaffected. The optical properties of the treated PM are affected within seconds of exposure to the detergent as indicated by an increase in transmittance and a blue shift in the wavelength of maximum absorbance for the ground state. Different concentrations of Triton cause reproducibly different changes in the kinetics of the system. These observations support the view that the BR trimer-membrane interaction is important in controlling the BR photocycle.

Proton migration along the membrane surface and retarded surface to bulk transfer

Since the proposal of the chemiosmotic theory there has been a continuing debate about how protons that have been pumped across membranes reach another membrane protein that utilizes the established pH gradient. Evidence has been gathered in favour of a 'delocalized' theory, in which the pumped protons equilibrate with the aqueous bulk phase before being consumed, and a 'localized' one, in which protons move exclusively along the membrane surface. We report here that after proton release by an integral membrane protein, long-range proton transfer along the membrane surface is faster than proton exchange with the bulk water phase. The rate of lateral proton diffusion can be calculated by considering the buffer capacity of the membrane surface. Our results suggest that protons can efficiently diffuse along the membrane surface between a source and a sink (for example H(+)-ATP synthase) without dissipation losses into the aqueous bulk.

The Schiff base counterion of bacteriorhodopsin is protonated in sensory rhodopsin I: spectroscopic and functional characterization of the mutated proteins D76N and D76A

Both sensory rhodopsin I (SR-I), a phototaxis receptor, and bacteriorhodopsin (BR), a light-driven proton pump, share residues which have been identified as critical for BR functioning. This includes Asp76, which in the case of bacteriorhodopsin (Asp85) functions both as the Schiff base counterion and proton acceptor. We found that substituting an Asn for Asp76 (D76N) in SR-I has no effect on its visible absorption unlike the analogous mutation (D85N) in BR which shifts the absorption to longer wavelengths. The mutated proteins D76N and D76A are also fully functional as phototaxis receptors in contrast to BR, where the analogous substitutions block proton transport. D76N was also found to exhibit a spectrally normal SR587-->S373 transition. However, FTIR difference spectroscopy reveals that two bands in the SR587-->S373 difference spectrum at 1766/1749 cm-1 (negative/positive), assigned to the C=O stretch mode of a carboxylic acid, disappear in D76N, although no changes are observed in the carboxylate region. In addition, the kinetics and yield of this photoreaction are altered. On this basis, it is concluded that, unlike Asp85 in bacteriorhodopsin, Asp76 is protonated in SR-I and undergoes an increase in its hydrogen bonding during the SR587-->S373 transition. This model accounts for the difference in color of SR-I and BR and the finding that Asn can substitute for Asp76 without greatly altering the SR-I phenotype. Interestingly, parallels exist between this residue and Asp83 in the visual receptor rhodopsin which has recently been found to exist in a protonated form and to undergo an almost identical change in hydrogen bonding during rhodopsin activation.

In vivo and in vitro analysis of transcription of the L region from the Halobacterium salinarium phage phi H: definition of a repressor-enhancing gene

The 12-kb L region of the Halobacterium salinarium phage phi H is able to replicate as a plasmid, conferring a certain immunity to the host cell. We show here that the whole region is utilised for transcription at one stage or another in the phage life cycle. The DNA segment between the lytic transcripts T4 and T1 is shown to be constitutively transcribed. The effects of transcription on immunity were investigated using transformation experiments with H. salinarium. In this way, we show in vivo that the immune transcript T9, which on its own has no influence on phage growth or immunity, has a co-operative effect on the phi H repressor. The immunity effects analysed are sufficient to account for the degree of immunity conferred by the L region.

In vitro synthesis of bacterio-opsin: integration into microsomal membranes

The translation and membrane integration of bacterio-opsin from Halobacterium salinarium were investigated. Plasmids containing the bacterio-opsin-gene with or without its original presequence were transcribed with the T7-RNA-polymerase and translated in vitro in a wheat germ system. The integration of the expressed bacterio-opsin into dog pancreas microsomes was studied. Both precursor bacterio-opsin and mature bacterio-opsin integrate into the eukaryotic membrane.

Picosecond dynamics of bacteriorhodopsin, probed by time-resolved infrared spectroscopy

The photoinduced reaction cycle of bacteriorhodopsin (BR) has been studied by means of a recently developed picosecond infrared spectroscopic method at ambient temperature. BR - K difference spectra between 1560 and 1700 cm-1 have been recorded at delay times from 100 ps to 14 ns. The spectrum remains unchanged during this period. The negative difference OD band at 1660 cm-1 indicates the peptide backbone responds within 50 ps. A survey in the region of carboxylic side chain absorption around 1740 cm-1 reveals that perturbations of those groups, present in low-temperature FTIR spectra, are not observable within 10 ns, suggesting a slow conformational change.