Association between a photo-intermediate of a M-lacking mutant D75N of pharaonis phoborhodopsin and its cognate transducer

Pharaonis phoborhodopsin (ppR or pharaonis sensory rhodopsin II) is a receptor of the negative phototaxis of Natronobacterium pharaonis and forms a complex with its transducer pHtrII in membranes. Flash-photolyis of a D75N mutant did not yield the M-intermediate, but an O-like intermediate is observed in a ms time range. We examined the interaction between the D75N of ppR and t-Htr (truncated pHtrII). These formed a complex in the presence of 0.1% n-dodecyl-beta-maltoside, and the association accelerated the decay of the O of D75N from 15 to 56 s(-1). From the decay time constants under varying ratios of D75N and t-Htr, n, the molar ratio of D75N/t-Htr in the complex, and K(D), the dissociation constant, were estimated. The value of n was unity and K(D) was estimated to 146 nM. This K(D) value can be considered to be the association between the photo-intermediate and t-Htr, which is deduced by the method of estimation. Previously we (Photochem. Photobiol. 74 (2001) 489) reported a K(D) of 15 microM for the interaction between the wild-type and t-Htr by means of the change in M-decay rates. Therefore, this value should be the K(D) value for the interaction between M of the wild-type and t-Htr.     

Interaction of Natronobacterium pharaonis phoborhodopsin (sensory rhodopsin II) with its cognate transducer probed by increase in the thermal stability

Pharaonis phoborhodopsin (ppR, also called Natronobacterium pharaonis sensory rhodopsin II) and its transducer protein, pharaonis halobacterial transducer of ppR (pHtrII), form a signaling complex, and light signals are transmitted from the sensor to the transducer by the protein-protein interaction. A truncated pHtrII(1-159) consisting of intramembrane helices (expressing amino acid residues from the first to the 159th position) and ppR form the complex in a solution containing 0.1% n-dodecyl-beta-D-maltoside. At 75-85 degrees C, the time-dependent color loss of ppR was caused by denaturation. We found that pHtrII(1-159) retarded the denaturation rate of ppR. This increase in the thermal stability was used as a probe for the binding ability in the dark. Tyr199 of ppR and Asn74 of pHtrII(1-114) were proposed as amino acid residues interacting with each other through hydrogen bonding. Then,ppR and pHtrII(1-159) mutants at these positions were prepared to examine the effect on the binding in the dark. The wild-type and Y199F mutant can bind pHtrII(1-159), suggesting that the hydrogen bonding between these specific amino acid residues may not be the only cause of the binding, but the hydrophobic interaction via phenyl ring of ppR may contribute dominantly.     

Halorhodopsin from natronomonas pharaonis forms a trimer even in the presence of a detergent, dodecyl-beta-D-maltoside

Halorhodopsin (HR) is a transmembrane seven-helix retinal protein, and acts as an inward light-driven Cl⁻ pump. HR from Natronomonas pharaonis (NpHR) can be expressed in Escherichia coli inner membrane in large quantities. Here, we showed that NpHR forms the trimer structure even in the presence of 0.1% (2 m m ) to 1% (20 m m ) dodecyl-β- d -maltoside (DDM), whose concentrations are much higher than the critical micelle concentration (0.17 m m ). This conclusion was drawn from the following observations. (1) NpHR in the DDM solution showed an exciton-coupling circular dichroism (CD) spectrum. (2) From the elution volume of gel filtration, the molecular mass of the NpHR–DDM complex was estimated. After evaluation of the mass of the bound DDM molecules, the mass of NpHR calculated was approximately equal to that of the trimer. (3) The cross-linked NpHR by glutaraldehyde gave the SDS-PAGE corresponding to the trimer. Mass spectra of these samples also support the notion of the trimer. Using the membrane fractions expressing NpHR ( Escherichia coli and Halobacterium salinarum ), CD spectra showed exciton-coupling, which suggests strongly the trimer structure in the cell membrane.     

Protein-protein interaction of a Pharaonis halorhodopsin mutant forming a complex with Pharaonis halobacterial transducer protein II detected by Fourier-transform infrared spectroscopy

Pharaonis halorhodopsin (pHR) functions as a light-driven inward chloride ion pump in Natoronomonas pharaonis, while pharaonis phoborhodopsin (ppR; also called pharaonis sensory rhodopsin II, pSRII), is a light sensor for negative phototaxis. ppR forms a 2:2 complex with its cognate transducer protein (pHtrII) through intramembranous hydrogen bonds: Tyr199(ppR)-Asn74(pHtrII) and Thr189(ppR)-Glu43 (pHtrII), Ser62(pHtrII). It was reported that a pHR mutant (P240T/F250Y), which possesses the hydrogen-bonding sites, impairs its pumping activity upon complexation with pHtrII. In this study, effect of the complexation with pHtrII on the structural changes upon formation of the K, L(1) and L(2) intermediates of pHR was investigated by use of Fourier-transform infrared spectroscopy. The vibrational changes of Tyr250(pHR) and Asn74(pHtrII) were detected for the L(1) and L(2) intermediates, supporting that Tyr250(pHR) forms a hydrogen bond with Asn74(pHtrII) as similarly to Tyr199(ppR). The conformational changes of the retinal chromophore were never affected by complexation with pHtrII, but amide-I vibrations were clearly different in the absence and presence of pHtrII. The molecular environment around Asp156(pHR) in helix D is also slightly affected. These additional structural changes are probably related to blocking of translocation of a chloride ion from the extracellular to the cytoplasmic side during the photocycle.     

Participation of the surface structure of Pharaonis phoborhodopsin, ppR and its A149S and A149V mutants, consisting of the C-terminal alpha-helix and E-F loop, in the complex-formation with the cognate transducer pHtrII, as revealed by site-directed 13C solid-state NMR

We have recorded 13C solid state NMR spectra of [3-13C]Ala-labeled pharaonis phoborhodopsin (ppR) and its mutants, A149S and A149V, complexed with the cognate transducer pharaonis halobacterial transducer II protein (pHtrII) (1-159), to gain insight into a possible role of their cytoplasmic surface structure including the C-terminal alpha-helix and E-F loop for stabilization of the 2:2 complex, by both cross-polarization magic angle spinning (CP-MAS) and dipolar decoupled (DD)-MAS NMR techniques. We found that 13C CP-MAS NMR spectra of [3-13C]Ala-ppR, A149S and A149V complexed with the transducer pHtrII are very similar, reflecting their conformation and dynamics changes caused by mutual interactions through the transmembrane alpha-helical surfaces. In contrast, their DD-MAS NMR spectral features are quite different between [3-13C]Ala-A149S and A149V in the complexes with pHtrII: 13C DD-MAS NMR spectrum of [3-13C]Ala-A149S complex is rather similar to that of the uncomplexed form, while the corresponding spectral feature of A149V complex is similar to that of ppR complex in the C-terminal tip region. This is because more flexible surface structure detected by the DD-MAS NMR spectra are more directly influenced by the dynamics changes than the CP-MAS NMR. It turned out, therefore, that an altered surface structure of A149S resulted in destabilized complex as viewed from the 13C NMR spectrum of the surface areas, probably because of modified conformation at the corner of the helix E in addition to the change of hydropathy. It is, therefore, concluded that the surface structure of ppR including the C-terminal alpha-helix and the E-F loops is directly involved in the stabilization of the complex through conformational stability of the helix E.     

Tryptophan 171 in Pharaonis phoborhodopsin (sensory rhodopsin II) interacts with the chromophore retinal and its substitution with alanine or threonine slowed down the decay of M- and O-intermediate

Pharaonis phoborhodopsin (ppR), also called pharaonis sensory rhodopsin II, NpSRII, is a photoreceptor for the photophobic response of Natronomonas pharaonis. Tryptophan 182 (W182) of bacteriorhodopsin (bR) is near the chromophore retinal and has been suggested to interact with retinal during the photoreaction and also to be involved in the hydrogen-bonding network around the retinal. W182 of bR is conserved in ppR as tryptophan 171 (W171). To elucidate whether W171 of ppR interacts with retinal during the photoreaction and/or is involved in the hydrogen-bonding network as in bR, we formed W171-substituted mutants of ppR, W171A and W171T. Our low-temperature spectroscopic study has revealed that the substitution of W171 to Ala or Thr resulted in the stabilization of M- and O-intermediates. The stability of M and absorption spectral changes during the M-decay were different depending on the substituted residue. These findings suggest that W171 in ppR interacts with retinal and the degree of the interaction depends on the substituted residues, which might be rate determining in the M-decay. In addition, the involvement of W171 in the hydrogen-bonding network is suggested by the O-decay. We also found that glycerol slowed the decay of M and not of O.     

Application of fluorescence resonance energy transfer (FRET) to investigation of light-induced conformational changes of the phoborhodopsin/transducer complex

The photoreceptor phoborhodopsin (ppR; also called sensory rhodopsin II) forms a complex with its cognate the Halobacterial transducer II (pHtrII) in the membrane, through which changes in the environmental light conditions are transmitted to the cytoplasm in Natronomonas pharaonis to evoke negative phototaxis. We have applied a fluorescence resonance energy transfer (FRET)-based method for investigation of the light-induced conformational changes of the ppR/pHtrII complex. Several far-red dyes were examined as possible fluorescence donors or acceptors because of the absence of the spectral overlap of these dyes with all the photointermediates of ppR. The flash-induced changes of distances between the donor and an acceptor linked to cysteine residues which were genetically introduced at given positions in pHtrII(1-159) and ppR were determined from FRET efficiency changes. The dye-labeled complex was studied as solubilized in 0.1% n-dodecyl-beta-D-maltoside (DDM). The FRET-derived changes in distances from V78 and A79 in pHtrII to V185 in ppR were consistent with the crystal structure data (Moukhametzianov, R. et al. [2006] Nature, 440, 115-119). The distance from D102 in pHtrII linker region to V185 in ppR increased by 0.33 angstroms upon the flash excitation. These changes arose within 70 ms (the dead time of instrument) and decayed with a rate of 1.1 +/- 0.2 s. Thus, sub-angstrom-scale distance changes in the ppR/pHtrII complex were detected with this FRET-based method using far-red fluorescent dyes; this method should be a valuable tool to investigate conformation changes in the transducer, in particular its dynamics.     

Influence of pH for the determination of serum albumin by a dye-binding method in the presence of a detergent

In the dye-binding method, the absorbance increase caused by a protein error of a pH indicator is observed only in a restricted pH range. However, this pH range in the presence of a detergent has not yet been examined. Thus, the author investigated the pH (pH(UL)) where the absorbance increase becomes zero by a calculation based on the chemical equilibrium of a protein error of a pH indicator, and by experiments using four sulfonephthalein dyes. The pH(UL) value changed only with the detergent concentration, but did not change at all due to the dye, buffer solution or protein concentrations. Although the pH(UL) value was different according to the kind of dye used, it correlated well with the pK(D) values (dissociation constant) of BPB, BCG, BCP and BTB. The characteristics of pH(UL) in the reactions of the four dyes indicated good agreement with that obtained by a calculation.     

Variants of cation arrangement in the 36 net of tantalates and niobates with 1:1 stoichiometry

We have analyzed and tabulated the variants of mutual ordered arrangements of cations of two types with 1∶1 stoichiometry in cation matrices having planar trigon 3⁶ nets. A net with two nodes in its unit cell has a sole variant, which occurs in the wolframite type structure. With four nodes in the cell, there are two variants: the scheelite type and the variant found in α-and β-LaTaO₄. With 6 nodes, there are six, and with 8 nodes, more than 20 variants. In the ABO₄ (A=REE, B=Ta Nb) structural type (M'-fergusonite, fluorite, α-LaTaO₄, β-LaTaO₄, and fergusonite) having a more or less distorted face-centered cubic cation subcell in common, we have the wolframite type of arrangement for M'-fergusonite and fluorite, the scheelite type for fergusonite, and the partly scheelite type for α-and β-LaTaO₄. We offer a system for representing the atomic arrangement by recording the alternation of atoms in linear rows of three directions. Institute of Inorganic Chemistry, Siberian Branch Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 35, No. 6, pp. 129–135, November–December, 1994 Translated by T. Yudanova     

Dynamics change of phoborhodopsin and transducer by activation: study using D75N mutant of the receptor by site-directed solid-state 13C NMR

Pharaonis phoborhodopsin (ppR or sensory rhodopsin II) is a negative phototaxis receptor of Natronomonas pharaonis, and forms a complex, which transmits the photosignal into cytoplasm, with its cognate transducer (pHtrII). We examined a possible local dynamics change of ppR and its D75N mutant complexed with pHtrII, using solid-state (13)C NMR of [3-(13)C]Ala- and [1-(13)C]Val-labeled preparations. We distinguished Ala C(beta) (13)C signals of relatively static stem (Ala221) in the C-terminus of the receptors from those of flexible tip (Ala228, 234, 236 and 238), utilizing a mutant with truncated C-terminus. The local fluctuation frequency at the C-terminal tip was appreciably decreased when ppR was bound to pHtrII, while it was increased when D75N, that mimics the signaling state because of disrupted salt bridge between C and G helices prerequisite for the signal transfer, was bound to pHtrII. This signal change may be considered with the larger dissociation constant of the complex between pHtrII and M-state of ppR. At the same time, it turned out that fluctuation frequency of cytoplasmic portion of pHtrII is lowered when ppR is replaced by D75N in the complex with pHtrII. This means that the C-terminal tip partly participates in binding with the linker region of pHtrII in the dark, but this portion might be released at the signaling state leading to mutual association of the two transducers in the cytoplasmic regions within the ppR/pHtrII complex.     

Enhanced macrocyclizing activity of the thioesterase from tyrocidine synthetase in presence of nonionic detergent

Macrocyclization carried out by thioesterase domains of multimodular nonribosomal peptide synthetases (NRPSs) is a key step in the biosynthesis of many biologically active peptides. The thioesterase excised from tyrocidine synthetase is a versatile macrocyclization catalyst and a useful tool for chemoenzymatic synthesis of diverse cyclic peptides. However, its utility is limited by its short lifetime of catalytic activity as well as significant flux of the acyl-enzyme intermediate to hydrolysis. The addition of Brij 58, a nonionic detergent, above the critical micelle concentration, has dramatic effects on enzyme activity: catalytic activity is extended to >60 min and the rate of cyclization (but not hydrolysis) increases 6-fold, resulting in a net 150- to 300-fold increase in cyclic product yields. This enhanced activity allowed enzymatic macrocyclization of a solid phase library of tyrocidine decapeptides to identify acceptable substitutions at the Orn9 position which had previously been inaccessible for diversification.     

Influence of the lead carboxylate on the molecular composition of its solutions with zirconium and titanium isopropoxides or n-butoxides: 2-ethylhexanoate vs acetate, a way to stabilize the first Pb-Zr carboxylatoalkoxides of 1:1 stoichiometry

The reactions between titanium or zirconium alkoxides namely Ti(OR)₄ (R = ⁱ Pr, ⁿ Bu) or Zr₂(O ⁱ Pr)₈(HO ⁱ Pr)₂, Zr(O ⁿ Bu)₄ respectively and lead 2-ethylhexanoate Pb(O₂CC₇H₁₅)₂ were investigated at room temperature (rt) and by heating. The various compounds were characterized by elemental analysis, FT-IR, ¹H and ²⁰⁷Pb NMR. The mixed-metal species obtained at rt were adducts Pb₄Zr₄(μ-O₂CR′)₈(OR)₁₆(OHR)₂ 1 and Pb₂Ti₄(μ-O₂CR′)₄(OR)₁₆ 2 (R′=CHCHEt(CH₂)₂Me, R = ⁱ Pr) independently of the stoichiometry used. The structures of 1 and 2 are based on triangular M₂Pb cores (M = Zr, Ti). with 6-coordinate transition metals -as required for perovskites- and 6- or 7-coordinate lead atoms. Similar observations were made with n-butoxides. Thermal and hydrolytic condensation reactions were investigated. Thermal condensation was more difficult for the n-butoxide derivatives than for the isopropoxide ones. Powders derived from the hydrolysis of the Single Source Precursor 1 in various conditions were characterized by TGA, XRD and SEM for the PZ ceramic.     

The chemistry of the phosphates of barium and tetravalent cations in the 1:1 stoichiometry

The chemistry of phosphates of barium and tetravalent cations [BaM^IV(PO₄)₂] is reviewed. Such phosphates crystallise in the C2/m space group for M^IV=Ti, Zr, Hf, Ge, Sn, and Mo, and in the P2₁/n space group for BaTh(PO₄)₂. The existence of BaM^IV(PO₄)₂ in which M^IV=Pb, Ce, and U is further evaluated. Several aspects, such as phase transitions in the compounds with yavapaiite structure, solid solutions of BaM^IV(PO₄)₂ compounds and practical applications are briefly discussed.     

Interaction of the halobacterial transducer to a halorhodopsin mutant engineered so as to bind the transducer: Cl- circulation within the extracellular channel

An alkali-halophilic archaeum, Natronomonas pharaonis, contains two rhodopsins that are halorhodopsin (phR), a light-driven inward Cl- pump and phoborhodopsin (ppR), the receptor of negative phototaxis functioning by forming a signaling complex with a transducer, pHtrII (Sudo Y. et al., J. Mol. Biol. 357 [2006] 1274). Previously, we reported that the phR double mutant, P240T/F250Y(phR), can bind with pHtrII. This mutant itself can transport Cl-, while the net transport was stopped upon formation of the complex. The flash-photolysis data were analyzed by a scheme in which phR --> 4 P1 --> P2 --> 4 P3 --> P4 --> phR. The P3 of the wild-type and the double mutant contained two components, X- and O-intermediates. After the complex formation, however, the P3 of the double mutant lacked the X-intermediate. These observations imply that the X-intermediate (probably the N-intermediate) is the state having Cl- in the cytoplasmic binding site and that the complex undergoes an extracellular Cl- circulation because of the inhibition of formation of the X-intermediate.     

New thermal source of dimethoxycarbene leading to zwitterionic intermediates and 2:1 stoichiometry in reaction with electrophilic alkenes

[reaction: see text] At 50 degrees C, dimethyl dicyanofumarate and maleate react with 2 equiv of dimethoxycarbene to generate the products shown.     

Cooperative C(60) binding to a porphyrin tetramer arranged around a p-terphenyl axis in 1:2 host-guest stoichiometry

[structure: see text] Porphyrin tetramer 1 was newly designed and synthesized to construct a novel cooperative [60]fullerene (C(60)) binding system. Compound 1 has a p-terphenyl axis, which is expected to act as a scaffold for a guest-binding information transducer. In toluene, 1 can bind 2 equiv of C(60) to produce a 1:2 1/C(60) complex with association constants of 5800 M(-1) (K(1)) and 2000 M(-1) (K(2)). These values are significantly greater than those for control porphyrin dimers such as 2 and 3.     

Cocrystals of the antimalarial drug 11‐azaartemisinin with three alkenoic acids of 1:1 or 2:1 stoichiometry

The stoichiometry, X‐ray structures and stability of four pharmaceutical cocrystals previously identified from liquid‐assisted grinding (LAG) of 11‐azaartemisinin (11‐Aza; systematic name: 1,5,9‐trimethyl‐14,15,16‐trioxa‐11‐azatetracyclo[10.3.1.0^4,13.0^8,13]hexadecan‐10‐one) with trans‐cinnamic (Cin), maleic (Mal) and fumaric (Fum) acids are herein reported. trans‐Cinnamic acid, a mono acid, forms 1:1 cocrystal 11‐Aza:Cin ( 1 , C₁₅H₂₃NO₄·C₉H₈O₂). Maleic acid forms both 1:1 cocrystal 11‐Aza:Mal ( 2 , C₁₅H₂₃NO₄·C₄H₄O₄), in which one COOH group is involved in self‐catenation, and 2:1 cocrystal 11‐Aza₂:Mal ( 3 , 2C₁₅H₂₃NO₄·C₄H₄O₄). Its isomer, fumaric acid, only affords 2:1 cocrystal 11‐Aza₂:Fum ( 4 ). All cocrystal formation appears driven by acid–lactam R₂²(8) heterosynthons with short O—H…O=C hydrogen bonds [O…O = 2.56 (2) Å], augmented by weaker C=O…H—N contacts. Despite a better packing efficiency, cocrystal 3 is metastable with respect to 2 , probably due to a higher conformational energy for the maleic acid molecule in its structure. In each case, the microcrystalline powders from LAG were useful in providing seeding for the single‐crystal growth.     

Binding of a truncated form of lecithin:retinol acyltransferase and its N- and C-terminal peptides to lipid monolayers

Lecithin:retinol acyltransferase (LRAT) is a 230 amino acid membrane-associated protein which catalyzes the esterification of all-trans-retinol into all-trans-retinyl ester. A truncated form of LRAT (tLRAT), which contains the residues required for catalysis but which is lacking the N- and C-terminal hydrophobic segments, was produced to study its membrane binding properties. Measurements of the maximum insertion pressure of tLRAT, which is higher than the estimated lateral pressure of membranes, and the positive synergy factor a argue in favor of a strong binding of tLRAT to phospholipid monolayers. Moreover, the binding, secondary structure and orientation of the peptides corresponding to its N- and C-terminal hydrophobic segments of LRAT have been studied by circular dichroism and polarization-modulation infrared reflection absorption spectroscopy in monolayers. The results show that these peptides spontaneously bind to lipid monolayers and adopt an α-helical secondary structure. On the basis of these data, a new membrane topology model of LRAT is proposed where its N- and C-terminal segments allow to anchor this protein to the lipid bilayer.     

STRAP binds to and promotes the repair of N1-methyldeoxyadenosine in DNA

N1-methyladenosine(m1A) is an important RNA modification that functions in various biological processes by interacting with cellular proteins. However, the binding proteins of N1-methyldeoxyadenosine(1mdA) in DNA remain largely unknown. Herein, we employed a quantitative proteomics strategy to identify the potential binding proteins of 1mdA in human cells. Our results revealed that serine–threonine kinase receptor-associated protein(STRAP) can bind to 1mdA-carrying DNA. We further demonstrated t...