Proton uptake upon quinone reduction in bacterial reaction centers: IR signature and possible participation of a highly polarizable hydrogen bond network

The light-induced Q _A ^– /Q_A FTIR difference spectra of Rb. sphaeroides and Rp. viridis show very broad positive bands of small amplitude peaking around 2750 cm^–1. Upon ¹H/²H exchange these bands shift to about 2150 cm^–1. Similarly, the Q _B ^– /Q_B spectra exhibit broad continuum bands at 2600 and 2800 cm^–1 shifting to 2100 and 2200 cm^–1 in ²H₂O for Rb. sphaeroides and Rp. viridis, respectively. These continuum bands are tentatively interpreted in terms of highly polarizable hydrogen bonds in a large web of polar bonds involving cofactors, amino acid residues, and structured water molecules. As a working hypothesis, we propose that the protons participating in this web redistribute upon quinone reduction, increasing their concentration around the newly formed charged species, and leading to net proton uptake. Assuming that the precise localization of the mobile protons is dependent on the local electrostatic, this model can explain the apparent discrepancies between some results of FTIR experiments and of electrostatic calculations. Notably, it could help rationalize the observation that mobile protons tend to localize on Glu L212 upon Q_B reduction in Rb. sphaeroides, while for Q_B reduction in Rp. viridis and for Q_A reduction in both Rb. sphaeroides and Rp. viridis, proton uptake by a small number of carboxylic residues is not supported by the FTIR data.     

Probing heart cytochromec oxidase structure and function by infrared spectroscopy

IR spectra directly probe specific vibrators in bovine heart cytochromec oxidase, yielding quantitative as well as qualitative information on structures and reactions at these vibrators. C-O IR spectra reveal that CO binds to as two conformers each in isolated immobile environments sensitive to Fe _a and/or Cu_A oxidation state but remarkably insensitive to pH, medium, anesthetics, and other factors that affect activity. C-N IR spectra reveal that the one CN^– that binds to fully and partially oxidized enzyme can be in three different structures. These structures vary in relative amounts with redox level, thereby reflecting dynamic electron exchange among Fe _a , Cu_A, and Cu_B with associated changes in protein conformation of likely significance in O₂ reduction and H⁺-pumping. Azide IR spectra also reflect redox-dependent long-range effects. The amide I IR bands, due to C-O vibrators of peptide linkages and composed of multiple bands derived from different secondary structures, reveal high levels of -helix (60%) and subtle changes with redox level and exposure to anesthetics. N₂O IR spectra reveal that these anesthetic molecules at clinically relevant levels occupy three sites of different polarity within the enzyme as the enzyme is reversibly, but only partially, inhibited.     

Primary charge separation in the photosystem II core from Synechocystis: a comparison of femtosecond visible/midinfrared pump-probe spectra of wild-type and two P680 mutants

It is now quite well accepted that charge separation in PS2 reaction centers starts predominantly from the accessory chlorophyll B_A and not from the special pair P₆₈₀. To identify spectral signatures of B_A, and to further clarify the process of primary charge separation, we compared the femtosecond-infrared pump-probe spectra of the wild-type (WT) PS2 core complex from the cyanobacterium Synechocystis sp. PCC 6803 with those of two mutants in which the histidine residue axially coordinated to P_B (D2-His¹⁹⁷) has been changed to Ala or Gln. By analogy with the structure of purple bacterial reaction centers, the mutated histidine is proposed to be indirectly H-bonded to the C₉O carbonyl of the putative primary donor B_A through a water molecule. The constructed mutations are thus expected to perturb the vibrational properties of B_A by modifying the hydrogen bond strength, possibly by displacing the H-bonded water molecule, and to modify the electronic properties and the charge localization of the oxidized donor . Analysis of steady-state light-induced Fourier transform infrared difference spectra of the WT and the D2-His¹⁹⁷Ala mutant indeed shows that a modification of the axially coordinating ligand to P_B induces a charge redistribution of In addition, a comparison of the time-resolved visible/midinfrared spectra of the WT and mutants has allowed us to investigate the changes in the kinetics of primary charge separation induced by the mutations and to propose a band assignment identifying the characteristic vibrations of B_A.     

Identification of metabolites from 2D 1H-13C HSQC NMR using peak correlation plots

Background

Identification of individual components in complex mixtures is an important and sometimes daunting task in several research areas like metabolomics and natural product studies. NMR spectroscopy is an excellent technique for analysis of mixtures of organic compounds and gives a detailed chemical fingerprint of most individual components above the detection limit. For the identification of individual metabolites in metabolomics, correlation or covariance between peaks in ¹H NMR spectra has previously been successfully employed. Similar correlation of 2D ¹H-¹³C Heteronuclear Single Quantum Correlation spectra was recently applied to investigate the structure of heparine. In this paper, we demonstrate how a similar approach can be used to identify metabolites in human biofluids (post-prostatic palpation urine).

Results

From 50 ¹H-¹³C Heteronuclear Single Quantum Correlation spectra, 23 correlation plots resembling pure metabolites were constructed. The identities of these metabolites were confirmed by comparing the correlation plots with reported NMR data, mostly from the Human Metabolome Database.

Conclusions

Correlation plots prepared by statistically correlating ¹H-¹³C Heteronuclear Single Quantum Correlation spectra from human biofluids provide unambiguous identification of metabolites. The correlation plots highlight cross-peaks belonging to each individual compound, not limited by long-range magnetization transfer as conventional NMR experiments.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0413-z) contains supplementary material, which is available to authorized users.     

Charge separation in Rhodobacter sphaeroides mutant reaction centers with increased midpoint potential of the primary electron donor

Primary charge separation dynamics in four mutant reaction centers (RCs) of the purple bacterium Rhodobacter sphaeroides with increased midpoint potential of the primary electron donor P (M160LH, L131LH, M197FH, and M160LH + L131LH + M197FH) have been studied by femtosecond transient absorption spectroscopy at room temperature. The decay of the excited singlet state in the wild-type and mutant RCs is complex and has two main exponential components, which indicates heterogeneity of electron transfer rates or the presence of reverse electron transfer reactions. The radical anion band of monomeric bacteriochlorophyll B_A at 1020 nm was first observed in transient absorbance difference spectra of single mutants. This band remains visible, although with somewhat reduced amplitude, even at delays up to tens of picoseconds when stimulated emission is absent and the reaction centers are in the P⁺H _A ^? state. The presence of this band in this time period indicates the existence of thermodynamic equilibrium between the P⁺B _A ^? H_A and P⁺B_AH _A ^? states. The data give grounds for assuming that the value of the energy difference between the states P*, P⁺B _A ^? H_A, and P⁺B_AH _A ^? at early times is of the same order of magnitude as the energy kT at room temperature. Besides, monomeric bacteriochlorophyll B_A is found to be an immediate electron acceptor in the single mutant RCs, where electron transfer is hampered due to increased energy of the P⁺B _A ^? state with respect to P*.     

Characterization of second site mutations show that fast proton transfer to QB − is restored in bacterial reaction centers of Rhodobacter sphaeroides containing the Asp-L213 → Asn lesion

The structural basis for proton coupled electron transfer to Q_B in bacterial reaction centers (RCs) was studied by investigating RCs containing second site suppressor mutations (Asn M44 Asp, Arg M233 Cys, Arg H177 His) that complement the effects of the deleterious Asp L213 Asn mutation [DN(L213)]. The suppressor RCs all showed an increased proton coupled electron transfer rate k _AB ⁽²⁾(Q_A ^–Q_B ^– + H⁺ Q_AQ_BH^–) by at least 10³ (pH 7.5) and a recombination rate k _BD (D⁺Q_AQ_B ^– DQ_AQ_B) 15–40 times larger than the value found in DN(L213) RCs. Proton transfer was studied by measuring the dependence of k _AB ⁽²⁾ on the free energy for electron transfer (G_et). k _AB ⁽²⁾ was independent of G_et in DN(L213) RCs, but dependent on G_et in native and all suppressor RCs. This shows that proton transfer limits the k _AB ⁽²⁾ reaction with a rate of 0.1s^–1 in DN(L213) RCs but is not rate limiting and at least 10⁸-fold faster in native and 10⁵-fold faster in the suppressor RCs. The increased rate of proton transfer by the suppressor mutations are proposed to be due to: (i) a reduction in the barrier to proton transfer by providing a more negative electrostatic potential near Q_B ^–; and/or (ii) structural changes that permit fast proton transfer through the network of protonatable residues and water molecules near Q_B.     

6-Halogenopyridin-2-olato complexes with the diruthenium(2+) core: Equilibria between head-to-head and head-to-tail structures

The dinuclear bis(6-X-pyridin-2-olato) ruthenium complexes [Ru₂(μ-XpyO)₂(CO)₄(PPh₃)₂] (X = Cl (4B) and Br (5B)), [Ru₂(μ-XpyO)₂(CO)₄(CH₃CN)₂] (X = Cl (6B), Br (7B) and F (8B)) and [Ru₂(μ-ClpyO)₂(CO)₄(PhCN)₂] (9B) were prepared from the corresponding tetranuclear coordination dimers [Ru₂(μ-XpyO)₂(CO)₄]₂ (1: X = Cl; 2: X = Br) and [Ru₂(μ-FpyO)₂(CO)₆]₂ (3) by treatment with an excess of triphenylphosphane, acetonitrile and benzonitrile, respectively. In the solid state, complexes 4B-9B all have a head-to-tail arrangement of the two pyridonate ligands, as evidenced by X-ray crystal structure analyses of 4B, 6B and 9B, in contrast to the head-to-head arrangement in the precursors 1-3. A temperature- and solvent-dependent equilibrium between the yellow head-to-tail complexes and the red head-to-head complexes 4A-7A and 9A, bearing an axial ligand only at the O,O-substituted ruthenium atom, exists in solution and was studied by NMR spectroscopy. Full ¹H and ¹³C NMR assignments were made in each case. Treatment of 1 and 2 with the N-heterocyclic carbene (NHC) 1-butyl-3-methylimidazolin-2-ylidene provided the complexes [Ru₂(μ-XpyO)₂(CO)₄(NHC)], X = Cl (11A) or Br (12A). An XRD analysis revealed the head-to-head arrangement of the pyridonate ligands and axial coordination of the carbene ligand at the O,O-substituted ruthenium atom. The conversion of 11A and 12A into the corresponding head-to-tail complexes was not possible.     

1H and 15N NMR resonance assignments and solution secondary structure of oxidized Desulfovibrio desulfuricans flavodoxin

Summary Sequence-specific ¹H and ¹⁵N resonance assignments have been made for 137 of the 146 nonprolyl residues in oxidized Desulfovibrio desulfuricans [Essex 6] flavodoxin. Assignments were obtained by a concerted analysis of the heteronuclear three-dimensional ¹H-¹⁵N NOESY-HMQC and TOCSY-HMQC data sets, recorded on uniformly ¹⁵N-enriched protein at 300 K. Numerous side-chain resonances have been partially or fully assigned. Residues with overlapping ¹H^N chemical shifts were resolved by a three-dimensional ¹H-¹⁵N HMQC-NOESY-HMQC spectrum. Medium-and long-range NOEs, ³J_NH coupling constants, and ¹H^N exchange data indicate a secondary structure consisting of five parallel -strands and four -helices with a topology similar to that of Desulfovibrio vulgaris [Hidenborough] flavodoxin. Prolines at positions 106 and 134, which are not conserved in D. vulgaris flavodoxin, contort the two C-terminal -helices.Abbreviations CSI chemical shift index - DQF-COSY double-quantum-filtered correlation spectroscopy - DIPSI decoupling in the presence of scalar interactions - FMN flavin mononucleotide - GARP globally optimized alternating phase rectangular pulse - HMQC heteronuclear multiple-quantum coherence - HSQC heteronuclear single-quantum coherence - NOE nuclear Overhauser effect - NOESY nuclear Overhauser enhancement spectroscopy - TOCSY total correlation spectroscopy - TPPI time-proportional phase increments - TSP 3-(trimethylsilyl)propionic-2,2,3,3-d ₄ acid, sodium salt     

Effect of temperature and surface potential on the electrogenic proton uptake in the QB site of the Rhodobacter sphaeroides photosynthetic reaction center: QA −. B −. → QAQBH2 transition

Direct electrometry was used to study the light-induced voltage changes in the Rhodobacter sphaeroides chromatophores adsorbed to a phospholipid-impregnated nitrocellulose film. After the second laser flash, a fast increase in the voltage associated with charge separation was followed by a slower increase attributed to the proton uptake in the Q_B site of the photosynthetic reaction centers. Kinetics and relative amplitudes of these voltage changes attributed to the Q_A ^–. _B ^–. Q_AQ_BH₂ transition, were measured as a function of pH and temperature between +4 and +40 °C. The kinetics can be approximated by a single exponent above +23 °C (100 µs at +25 °C, pH 7.2), whereas below this temperature, it was a good fit of two exponential approximation (65 µs and 360 µs with similar contributions at +10 °C, pH 7.2). The faster component diminished with an apparent pK 8.5, whereas the slower one was maintained at a constant level until pH 9.5 and then decreased. The calculated activation energy from the temperature dependence of the slower component (55 – 65 kJ/mol) was much higher than that of the faster component (< 10 kJ/mol). The two voltage components can be attributed to the transfer of the first (faster component) and the second (slower component) proton from the reaction center surface to Q_B. We suggested that higher activation energy of the slower component was due to a conformational change in the reaction center kinetically coupled to the second proton transfer to Q_BH^–.The faster component diminished in the presence of 1 M KCl, with an apparent pK 7.5. To explain this observation, we assume that: (i) the midpoint potential of the Q_A/Q_A ^–. redox pair was higher in 1 M KCl because of the reduced surface potential of chromatophores; (ii) the midpoint potential of the Q_B ^–./Q_BH^–. redox pair was insensitive to the surface potential change; (iii) the equilibrium constant of the reaction Q_A ^–.Q_B ^–. Q_AQ_BH^– decreased at high ionic strength.     

Membrane adenosine triphosphatase of Micrococcus lysodeikticus. Isolation of two forms of the enzyme complex and correlation between enzymatic stability,latency and activity.

Summary Two new forms of the plasma membrane ATP-ase ofMicrococcus lysodeikticus NCTC 2665 were isolated from a sub-strain of the microorganism by polyacrylamide gel electrophoresis. One of them had a mol.wt of 368,000 and a very low specific activity (0.80 µ mol.min^–1.mg protein^–1) that could not be stimulated by trypsin. This form has been called B^I (strain B, inactive). If the electrophoresis was carried out in the presence of reducing agents (i.e., dithiothreitol) and the pH of the effluent maintained at a value of 8.5 another form of the enzyme was obtained. This had a mol.wt of 385,000 and a specific activity of 2.5–5.0 µ mol.min^–1.mg protein^–1 that could be stimulated by trypsin to 5–10 µ mol.min^–1.mg protein^–1. This preparation of the ATPase has been called form B_A (strain B, enzyme active). The subunit composition of both forms has been studied by sodium dodecyl sulphate and urea gel electrophoresis and compared to that of the enzyme previously purified from the original strain (form A). The three forms of the enzyme had similar and subunits, with mol.wt of about 50,000 and 30,000 dalton, respectively. They also had in common the component(s) of relative mobility 1.0, whose status as true subunit(s) of the enzyme remains yet to be established. However, subunit, that had a mol.wt of about a 52,500 in form A (Andreu et al. Eur. J. Biochem. (1973) 37, 505–515), had a mol.wt similar to in form B_I and about 60,000 in form B_A. Furthermore B_A usually showed two types of this subunit ( and) and an additional peptide chain () with a mol.wt of about 25,000 dalton. This latter subunit seemed to account for the stimulation by trypsin of form B_A.Forms B_A could be converted to B_I by storage and freezing and thawing. Conventional protease activity could not be detected in any of the purified ATPase forms and addition of protease inhibitors to form B_A failed to prevent its conversion to form B_I. The low activity form (B_I) was more stable than the active forms of the enzyme and also differed in its circular dichroism. These results show thatM. lysodeikticus ATPase can be isolated in several forms. Although these variations may be artifacts caused by the purification procedures, they provide model systems for understanding the structural and functional relationships of the enzyme and for drawing some speculations about its functionin vivo.     

Reaction center light harvesting B875 complexes from Rhodocyclus gelatinosus: characterization and identification of quinones

Reaction center-B875 pigment-protein complexes were purified from Rhodocyclus gelatinosus. The proteic components consist of 7–8 polypeptides among which some were identified by their apparent molecular weights: the light harvesting B875 polypeptides and of 8 and 6 kDa, reaction center L (23 kDa), M (28 kDa) and H (34 kDa), cytochrome c (43 kDa). Four c-type hemes were found per reaction center. Flash-induced absorbance changes showed the presence of both Q_A and Q_B in the complex. Charge recombination times were determined to be: 1.16±0.2 (n=30) for P⁺Q_AQ_B ^- and 7–10 ms for P⁺Q_A ^- in presence of herbicides. From quinone analysis on one hand and kinetics of charge recombination on the other hand, we proposed that in the reaction center of Rhodocyclus gelatinosus Q_A is menaquinone 8 and Q_B is ubiquinone 8.     

Endothelin-1 Binding to Endothelin Receptors in the Rat Anterior Pituitary Gland: Interaction in the Recognition of Endothelin-1 Between ETA and ETB Receptors

1. ¹²⁵I-Endothelin (ET)-1 binding to the rat anterior pituitary gland was saturable and single, with a K _d of 71 pM and a B _max of 120 fmol/mg.2. When 1.0 M BQ-123 (ET_A antagonist) was added to the incubation buffer, the binding parameters were 8.3 pM and 8.0 fmol/mg, whereas 10 nM sarafotoxin S6c (ET_Bagonist) exerted little change in these binding parameters (K _d,72pM;B _max, 110 fmol/mg).3. ET_B receptor-related compounds such as sarafotoxin S6c, ET-3, IRL1620, and BQ-788 competitively inhibited ¹²⁵I-ET-1 binding, only when 1.0 M BQ-123 was present in the incubation buffer.4. Thus, the ET_B receptor is capable of binding ET-1 when the ET_A receptor is being occupied by BQ-123. A collaboration mechanism between the ET_A and the ET_B receptor may function in the recognition of ET-1, a typical bivalent ligand.     

Allosteric modulators of human A2B adenosine receptor

Background

Among adenosine receptors (ARs) the A_2B subtype exhibits low affinity for the endogenous agonist compared with the A₁, A_2A, and A₃ subtypes and is therefore activated when concentrations of adenosine increase to a large extent following tissue damages (e.g. ischemia, inflammation). For this reason, A_2B AR represents an important pharmacological target.

Methods

We evaluated seven 1-benzyl-3-ketoindole derivatives (7–9) for their ability to act as positive or negative allosteric modulators of human A_2B AR through binding and functional assays using CHO cells expressing human A₁, A_2A, A_2B, and A₃ ARs.

Results

The investigated compounds behaved as specific positive or negative allosteric modulators of human A_2B AR depending on small differences in their structures. The positive allosteric modulators 7a,b and 8a increased agonist efficacy without any effect on agonist potency. The negative allosteric modulators 8b,c and 9a,b reduced agonist potency and efficacy.

Conclusions

A number of 1-benzyl-3-ketoindole derivatives were pharmacologically characterized as selective positive (7a,b) or negative (8c, 9a,b) allosteric modulators of human A_2B AR.

General significance

The 1-benzyl-3-ketoindole derivatives 7–9 acting as positive or negative allosteric modulators of human A_2B AR represent new pharmacological tools useful for the development of therapeutic agents to treat pathological conditions related to an altered functionality of A_2B AR.     

A novel experiment for the quantitative measurement of CSA(1HN)/CSA(15N) cross-correlated relaxation in 15N-labeled proteins*

An experiment is presented which allows for the quantitative measurement of the relaxation interference between the ¹H_N CSA and ¹⁵N CSA interactions in ¹⁵N labeled proteins. A constant-time buildup scheme is used to measure the differential relaxation rate, , between double-quantum (DQ) and zero-quantum (ZQ) ¹H_N-¹⁵N coherences. The CSA/CSA experiment was recorded at three different B_o field strengths. The CSA(¹H_N)/CSA(¹⁵N) cross-correlation rate was obtained from the linear fit of the measured rate, , versus B_o ² for 77 residues of the EH2 domain from mouse Eps15.     

Study of the oxidation of alkanes in their mixtures with oxygen and air under the action of a pulsed volume nanosecond discharge

The slow oxidation of alkanes (from methane to hexane) in their stoichiometric mixtures with oxygen or air under the action of nanosecond pulsed discharges was investigated. The discharges were excited in a tube of diameter 5 cm and length of 20 cm by 25-ns voltage pulses with an amplitude of 10 kV and a repetition rate of 40 Hz. The initial pressure in the mixture was varied in the range 0.76–10.1 torr. The current, the electric field strength, and the power deposited in a discharge were measured with a nanosecond time resolution. In time-resolved and time-integrated measurements, the intensities of the following bands were determined: CO ₂ ⁺ (B²Σ → X²Π, δv=0), CH(A²Δ, v′=0 → X²Π, v″=0), OH(A²Σ, v′=0 → X²Π, v″=0), CO(B¹Σ, v′=0 → A¹Π, v″=2), NO(A²Σ → X²Π, δv=3), N₂(C³Π, v′=1 → B³Π, v″=7), N₂(B³Π, v′=6 → A³Σ, v″=3), and N ₂ ⁺ (B²Σ, v′=0 → X²Σ, v″=2). The methane concentration was measured from the absorption of He-Ne laser radiation. Based on the results of optical measurements, the times of the complete oxidation of hydrocarbons were determined.     

Models of the bis-histidine-coordinated ferricytochromes: Mössbauer and EPR spectroscopic studies of low-spin iron(III) tetrapyrroles of various electronic ground states and axial ligand orientations

The EPR and magnetic Mössbauer spectra of a series of axial ligand complexes of tetrakis(2,6-dimethoxyphenyl)porphyrinatoiron(III), [(2,6-(OMe)₂)₄TPPFeL₂]⁺, where L=N-methylimidazole, 2-methylimidazole, or 4-(dimethylamino)pyridine, of one axial ligand complex of tetraphenylporphyrin, the bis(4-cyanopyridine) complex [TPPFe(4-CNPy)₂]⁺, and of one axial ligand complex of tetraphenylchlorin, [TPCFe(ImH)₂]⁺, where ImH=imidazole, have been investigated and compared to those of low-spin Fe(III) porphyrinates and ferriheme proteins reported in the literature. On the basis of this and previous complementary spectroscopic investigations, three types of complexes have been identified: those having (d_xy)²(d_xz,d_yz)³ electronic ground states with axial ligands aligned in perpendicular planes (Type I), those having (d_xy)²(d_xz,d_yz)³ electronic ground states with axial ligands aligned in parallel planes (Type II), and those having the novel (d_xz,d_yz)⁴(d_xy)¹ electronic ground state (Type III). A subset of the latter type, with planar axial ligands aligned parallel to each other or strong macrocycle asymmetry that yield rhombic EPR spectra, cannot be created using the porphyrinate ligand. Type I centers are characterized by "large g_max" EPR spectra with g>3.2 and well-resolved, widely spread magnetic Mössbauer spectra having A_zz/g_NN>680 kG, with A_xx negative in sign but much smaller in magnitude than A_zz, while Type II centers have well-resolved rhombic EPR spectra with g_zz=2.4–3.1 and also less-resolved magnetic Mössbauer spectra, and usually have A_zz/g_NN in the range of 440–660 kG (but in certain cases as small as 180 kG) and A_xx again negative in sign but only somewhat smaller (but occasionally larger in magnitude) than A_zz, and Type III centers have axial EPR spectra with g_┴2.6 or smaller and g_║<1.0–1.95, but often not resolved, and less-resolved magnetic Mössbauer spectra having A_zz/g_NN in the range of 270–400 kG, and A_xx again negative in sign but much smaller in magnitude than A_zz. An exception to this rule is [TPPFe(4-CNPy)₂]⁺, which has A_xx/g_NN=–565 kG, A_yy/g_NN=629 kG, and A_zz/g_NN=4 kG. A subset of Type II complexes (Type II) have rhombicities (V/) much greater than 0.67 and A_zz/g_NN ranging from 320 to 170 kG, with A_xx also negative but with the magnitude of A_xx significantly larger than that of A_zz. These classifications are also observed for a variety of ferriheme proteins, and they lead to linear correlations between A_zz and either A_xx, g_zz, or V/ for Types I and II (but not for A_zz versus V/ for Type II). Not enough data are yet available on Type III complexes to determine what, if any, correlations may be observed.Abbreviations CCP cytochrome c peroxidase - 4-CNPy 4-cyanopyridine - cyt cytochrome - EFG electric field gradient - ESEEM electron spin echo envelope modulation - ImH imidazole - Mb myoglobin - MCD magnetic circular dichroism - 2-MeImH 2-methylimidazole - N-MeIm N-methylimidazole - 3NH₂PzH 3-aminopyrazole - 4-NMe₂Py 4-(dimethylamino)pyridine - [2,6-(OMe)₂]₄TPP dianion of tetrakis(meso-2,6-dimethoxyphenyl)porphyrin - OEiBC dianion of octaethylisobacteriochlorin - OEP dianion of octaethylporphyrin - PPIX dianion of protoporphyrin IX - Py pyridine - TMP dianion of meso-tetramesitylporphyrin - TPC dianion of meso-tetraphenylchlorin - TPP dianion of meso-tetraphenylporphyrin - 2,6-XylylNC 2,6-xylyl isocyanide     

Sequence-specific resonance assignment and secondary structure of (1–71) bacterioopsin

Summary The conformation of chymotryptic fragment C2 of bacteriorhodopsin (residues 1–71) was studied by 2D¹H NMR. The fragment was solubilized in a mixture of chloroform/methanol (11), 0.1 M LiClO₄. Most of the resonances in¹H NMR spectra of fragment C2 were assigned using phase-sensitive DQF-COSY, TOCSY, and NOESY techniques. To simplify the assignment procedure for overlapping regions of NMR spectra, an analog of fragment C2 with leucines deuterated in -positions was used. Deuterium exchange rates for amide protons were measured in a series of TOCSY spectra. Two right-handed -helical regions Pro⁸-Lys³⁰ and Lys⁴¹-Leu⁶² were identified on the basis of NOE connectivities and deuterium exchange rates. The N-terminal part of the fragment (Ala.²-Gly⁶) adopts the helical conformation stabilized by 3 hydrogen bonds.     

Subchronic Treatment with Methamphetamine and Phencyclidine Differentially Alters the Adenosine A1 and A2A Receptors in the Prefrontal Cortex,Hippocampus, and Striatum of the Rat

Subchronic treatment with MAP (4.6 mg/kg, i.p., once daily for 11 days) significantly decreased the K_d, but not B_max, values of [³H]1,3-dipropyl-8-cyclopentylxanthine ([³H]DPCPX) binding to adenosine A₁ receptors in the prefrontal cortex and hippocampus, but not striatum, of rat brain. However, subchronic treatment with PCP (10 mg/kg, i.p., once daily for 11 days) did not alter the K_d and B_max values of [³H]DPCPX binding to adenosine A₁ receptors in these three regions. Subchronic treatment with MAP or PCP did not alter the B_max and K_d values of [³H]2-p-(2-carboxyehyl)phenethylamino-5-N-ethylcarboxyamidoadenosine ([³H]CGS21680) binding to adenosine A_2A receptors in the striatum. Furthermore, subchronic treatment with MAP or PCP significantly decreased the specific binding of [³H]CGS21680 to adenosine A_2A receptors in the hippocampus, but not in the prefrontal cortex. Thus, these results suggest that MAP and PCP may produce differential effects on the adenosine A_2A receptors, but not adenosine A₁ receptors in rat brain.     

Reconstitution of iron-sulfur center FB results in complete restoration of NADP+ photoreduction in Hg-treated Photosystem I complexes from Synechococcus sp. PCC 6301

The F_B iron-sulfur cluster is destroyed preferentially by treating Photosystem I complexes with HgCl₂(Kojima Y, Niinomi Y, Tsuboi S, Hiyama T and Sakurai H (1987) Bot Mag 100: 243–53). When F_B is 95% depleted but F_Ais quantitatively retained in cyanobacterial PS I complexes, the reduction potential of F_A remains highly electronegative (E_m=–530 mV, n=1), the EPR spectral and spin relaxation properties of F_A and F_Xremain unchanged, but NADP⁺ photoreduction rates decline from 552 to 72 mol mg Chl^–1 h^–1.When F_B is reconstituted with FeCl₃, Na₂S and -mercaptoethanol, NADP⁺photoreduction rates recover to 528 mol mg Chl^–1 h^–1. The correlation between the presence of F_Band NADP⁺ photoreduction provides direct experimental evidence that this iron-sulfur cluster is required for electron throughput from cytochromec ₆ to flavodoxin or ferredoxin in Photosystem I.Abbreviations Chl chlorophyll - DPIP dichlorophenolindophenol - PS I Photosystem I Published as Journal Series #11091 of the University of Nebraska Agricultural Research Division. This paper is dedicated to the memory of the late Professor Daniel Arnon, who is remembered for his gracious and generous encouragement of the senior author's early career.     

Accurate measurement of <Superscript>15</Superscript>N–<Superscript>13</Superscript>C residual dipolar couplings in nucleic acids

New 3D HCN quantitative J (QJ) pulse schemes are presented for the precise and accurate measurement of one-bond ¹⁵N_1/9–¹³C₁, ¹⁵N_1/9–¹³C_6/8, and ¹⁵N_1/9–¹³C_2/4 residual dipolar couplings (RDCs) in weakly aligned nucleic acids. The methods employ ¹H–¹³C multiple quantum (MQ) coherence or TROSY-type pulse sequences for optimal resolution and sensitivity. RDCs are obtained from the intensity ratio of H₁–C₁–N_1/9 (MQ-HCN-QJ) or H_6/8–C_6/8–N_1/9 (TROSY-HCN-QJ) correlations in two interleaved 3D NMR spectra, with dephasing intervals of zero (reference spectrum) and 1/(2J_NC) (attenuated spectrum). The different types of ¹⁵N–¹³C couplings can be obtained by using either the 3D MQ-HCN-QJ or TROSY-HCN-QJ pulse scheme, with the appropriate setting of the duration of the constant-time ¹⁵N evolution period and the offset of two frequency-selective ¹³C pulses. The methods are demonstrated for a uniformly ¹³C, ¹⁵N-enriched 24-nucleotide stem-loop RNA sequence, helix-35, aligned in the magnetic field using phage Pf1. For measurements of RDCs systematic errors are found to be negligible, and experiments performed on a 1.5 mM helix-35 sample result in an estimated precision of ca. 0.07 Hz for ¹D_NC, indicating the utility of the measured RDCs in structure validation and refinement. Indeed, for a complete set of ¹⁵N_1/9–¹³C₁, ¹⁵N_1/9–¹³C_6/8, and ¹⁵N_1/9–¹³C_2/4 dipolar couplings obtained for the stem nucleotides, the measured RDCs are in excellent agreement with those predicted for an NMR structure of helix-35, refined using independently measured observables, including ¹³C–¹H, ¹³C–¹³C and ¹H–¹H dipolar couplings.Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1007/s10858-005-0646-2.