Iron as a bound secondary electron donor in modified bacterial reaction centers.

The binding and oxidation of ferrous iron were studied in wild-type reaction centers and in mutants that have been modified to be both highly oxidizing and able to bind manganese [Thielges et al. (2005) Biochemistry 44, 7389-7394]. After illumination of wild-type reaction centers, steady-state optical spectroscopy showed that the oxidized bacteriochlorophyll dimer, P+, could oxidize iron but only as a second-order reaction at iron concentrations above 100 microM. In the modified reaction centers, P+ was reduced by iron in the presence of sodium bicarbonate with dissociation constants of approximately 1 microM for two mutants with different metal-binding sites. Transient optical spectroscopy showed that P+ was rapidly reduced with first-order rates of 170 and 275 s-1 for the two mutants. The dependence of the amplitude of this rate on the iron concentration yielded a dissociation constant of approximately 1 microM for both mutants, in agreement with the steady-state determination. The oxidation of bound iron by P+ was confirmed by the observation of a light-induced EPR signal centered at g values of 2.2 and 4.3 and attributed to high-spin Fe3+. Bicarbonate was required at pH 7 for low dissociation constants for both iron and manganese binding. The similarity between iron and manganese binding in these mutants provides insight into general properties of metal-binding sites in proteins.

Characterization of moisture-sensitive raw materials with simple spectroscopic techniques.

The quality of raw materials used in a synthetic process needs to be properly controlled in order to ensure optimal reaction conversion and desired quality of the resulting product. For air and water sensitive raw materials, quantitative analysis can be a challenging task. Spectroscopic techniques possess advantages of simple operation, fast analysis, low consumable costs and high sample throughput for the analysis of reactive raw materials. Three case studies utilizing spectroscopic analysis for air and water sensitive materials are discussed. First, FT-IR spectroscopy was utilized to determine the amount of residual acetic acid in acetic anhydride key raw material. Acetic anhydride was used in a methylenation reaction where the presence of residual acetic acid could quench a base used in the reaction, leading to incomplete conversion. A simple, one-frequency calibration method was developed to quantify acetic acid in acetic anhydride (2-35wt.%). Next, a novel near infrared reflectance spectroscopy (NIRS) method was used to determine the concentration of diisobutyl aluminum hydride (DIBAL-H) in toluene. DIBAL-H is a highly reactive and moisture-sensitive reagent used as a key raw material for the reduction of an active intermediate. A calibration method based on one-frequency was also developed to determine the concentration of DIBAL-H in toluene (0-1.5mole/L). Finally, a NIRS method based on partial least squares regression (PLS) was developed to quantify p-toluenesulfonic acid in p-toluenesulfonic anhydride, which is not amenable to chromatographic analysis.

Interpretation of the excess adsorption isotherms of organic eluent components on the surface of reversed-phase phenyl modified adsorbents.

The adsorption of three organic eluent components (acetonitrile, methanol, and tetrahydrofuran) from water were measured on four phenyl-type bonded phases using the minor disturbance method. The thicknesses of organic layer enriched above the phenyl-type bonded ligands were assessed and interpreted. Acetonitrile and tetrahydrofuran showed multilayer formation while methanol showed monomolecular adsorption. These results were compared to those obtained on alkyl bonded phases.

Characterization of phenyl-type HPLC adsorbents.

A set of different phenyl-modified HPLC adsorbents were characterized in terms of their surface area, pore volume, and bonded phase volume using low temperature nitrogen adsorption (LTNA). Adsorbents pore volume and interparticle volume were also measured using HPLC. Comparison of the pore volumes assessed with LTNA and HPLC suggests a compact molecular arrangement for all bonded phases studied. Simple and effective method for determination of the exact mass of adsorbent and total surface area in the column is suggested.

Reversed-phase high-performance liquid chromatography behavior of chaotropic counteranions.

The retention behavior of inorganic liophilic anions in reversed-phase HPLC columns was studied. Usually, the addition of these ions to the mobile phase influences the retention of protonated basic analytes similar to the effect of amphiphilic ions (ion-pairing agents). The nature of this influence is the subject of this paper. HPLC retention of perchlorate (ClO4-), tetrafluoroborate (BF4-), and hexafluorophosphate (PF6-) ions was studied on six columns with different bonded phases including alkyl, phenyl and perfluorophenyl phases. The effect of the mobile phase ionic strength on the retention of liophilic ions was investigated. The influence of the type of organic modifier, acetonitrile and methanol, on the retention of inorganic ions was also studied and interpreted on the basis of adsorption from solutions. Semi-empirical expression is suggested for the description of the retention profile of studied liophilic ions versus the eluent composition. Significant retention of these ions is observed in acetonitrile-water eluents. Multilayer-type adsorption of the acetonitrile on the reversed-phase surface and its strong dispersive (or pi-pi) interactions with liophilic ions are responsible for significant retention of these ions. This accumulation of liophilic ions in the adsorbed layer on the surface of reversed-phase material introduces an electrostatic component in the retention of protonated basic analytes.

Trapped tyrosyl radical populations in modified reaction centers from Rhodobacter sphaeroides.

The photosynthetic reaction center from the purple bacterium Rhodobacter sphaeroides has been modified such that the bacteriochlorophyll dimer, when it becomes oxidized after light excitation, is capable of oxidizing tyrosine residues. One factor in this ability is a high oxidation-reduction midpoint potential for the dimer, although the location and protein environment of the tyrosine residue appear to be critical as well. These factors were tested in a series of mutants, each of which contains changes, at residues L131, M160, M197, and M210, that give rise to a bacteriochlorophyll dimer with a midpoint potential of at least 800 mV. The protein environment was altered near tyrosine residues that are either present in the wild type or introduced by mutagenesis, focusing on residues that could act as acceptors for the phenolic proton of the tyrosine upon oxidation. These mutations include Ser M190 to His, which is near Tyr L162, the combination of His M193 to Tyr and Arg M164 to His, which adds a Tyr-His pair, and the combinations of Arg L135 to Tyr with Tyr L164 to His, Arg L135 to Tyr with Tyr L144 to Glu, and Arg L135 to Tyr with Tyr L164 to Phe. Radicals were produced in the mutants by using light to initiate electron transfer. The radicals were trapped by freezing the samples, and the relative populations of the oxidized dimer and tyrosyl radicals were determined by analysis of low-temperature electron paramagnetic resonance spectra. The mutants all showed evidence of tyrosyl radical formation at high pH, and the extent of radical formation at Tyr L135 with pH differed depending on the identity of L144 and L164. The results show that tyrosine residues within approximately 10 A of the dimer can become oxidized when provided with a suitable protein environment.

Dependence of tyrosine oxidation in highly oxidizing bacterial reaction centers on pH and free-energy difference.

The pH and temperature dependences of tyrosine oxidation were measured in reaction centers from mutants of Rhodobacter sphaeroides containing a tyrosine residue near a highly oxidizing bacteriochlorophyll dimer. Under continuous illumination, a rapid increase in the absorption change at 420 nm was observed because of the formation of a charge-separated state involving the oxidized dimer and reduced primary quinone, followed by a slow absorption decrease attributed to tyrosine oxidation. Both the amplitude and rate of the slow absorption change showed a pH dependency, indicating that, at low pH, the rate of tyrosine oxidation is limited by the transfer of the phenolic proton to a nearby base. Below 17 degrees C, the rate of the slow absorption change had a strong exponential dependence on the temperature, indicating a high activation energy. At higher pH and temperature, the overall rate of tyrosyl formation appears to be limited by a proposed conformational change in the reaction center that is also observed in reaction centers that do not undergo tyrosine oxidation. The yield of tyrosyl formation measured using electron paramagnetic resonance spectroscopy decreased significantly at 4 degrees C compared to 20 degrees C and was lower at both temperatures in mutants expected to have a slightly smaller driving force for tyrosyl formation.

Correlation of proton release and electrochromic shifts of the optical spectrum due to oxidation of tyrosine in reaction centers from Rhodobacter sphaeroides.

Reaction centers from the Y(L167) mutant of Rhodobacter sphaeroides, containing a highly oxidizing bacteriochlorophyll dimer and a tyrosine residue substituted at Phe L167, were compared to reaction centers from the Y(M) mutant, with a tyrosine at M164, and a quadruple mutant containing a highly oxidizing dimer but no nearby tyrosine residue. Distinctive features in the light-induced optical and EPR spectra showed that the oxidized bacteriochlorophyll dimer was reduced by Tyr L167 in the Y(L167) mutant, resulting in a tyrosyl radical, as has been found for Tyr M164 in the Y(M) mutant. In the Y(L167) mutant, the net proton uptake after formation of the tyrosyl radical and the reduced primary quinone ranged from +0.1 to +0.3 H(+)/reaction center between pH 6 and pH 10, with a dependence that is similar to the quadruple mutant but different than the large proton release observed in the Y(M) mutant. In the light-induced absorption spectrum in the 700-1000 nm region, the Y(L167) mutant exhibited unique changes that can be assigned as arising primarily from an approximately 30 nm blue shift of the dimer absorption band. The optical signals in the Y(L167) mutant were pH dependent, with a pK(a) value of approximately 8.7, indicating that the tyrosyl radical is stabilized at high pH. The results are modeled by assuming that the phenolic proton of Tyr L167 is trapped in the protein after oxidation of the tyrosine, resulting in electrostatic interactions with the tetrapyrroles and nearby residues.

Manganese oxidation by modified reaction centers from Rhodobacter sphaeroides.

The transfer of an electron from exogenous manganese (II) ions to the bacteriochlorophyll dimer, P, of bacterial reaction centers was characterized for a series of mutants that have P/P(+) midpoint potentials ranging from 585 to 765 mV compared to 505 mV for wild type. Light-induced changes in optical and EPR spectra of the mutants were measured to monitor the disappearance of the oxidized dimer upon electron donation by manganese in the presence of bicarbonate. The extent of electron transfer was strongly dependent upon the P/P(+) midpoint potential. The midpoint potential of the Mn(2+)/Mn(3+) couple was calculated to decrease linearly from 751 to 623 mV as the pH was raised from 8 to 10, indicating the involvement of a proton. The electron donation had a second order rate constant of approximately 9 x 10(4) M(-1) s(-1), determined from the linear increase in rate for Mn(2+) concentrations up to 200 microM. Weak dissociation constants of 100-200 microM were found. Quantitative EPR analysis of the six-line free Mn(2+) signal revealed that up to seven manganese ions were associated with the reaction centers at a 1 mM concentration of manganese. The association and the electron transfer between manganese and the reaction centers could be inhibited by Ca(2+) and Na(+) ions. The ability of reaction centers with high potentials to oxidize manganese suggests that manganese oxidation could have preceded water oxidation in the evolutionary development of photosystem II.

Kinetic analysis and subambient temperature on-line on-column derivatization of an active aldehyde.

The chromatographic analysis of aldehydes under typical reversed-phase conditions may be a challenging task due to an equilibrium process leading to the formation of a gem diol species regardless of acidic or basic conditions. Initially, a reversed-phase HPLC gradient elution was developed to determine the amount of a n acetylenic aldehyde in a reaction mixture. Significant fronting was observed under acidic and basic conditions even at -5 degrees C. In order to circumvent this problem, a reversed-phase HPLC gradient method on a C18 column at subambient temperature was developed using diethylamine as a mobile phase additive for on-line on-column derivatization of the aldehyde moiety. The on-line on-column reaction rate for the derivatization of the aldehyde with diethylamine was determined as a function of column temperature. An Arrhenius plot was constructed and the activation energy was calculated. The chromatographic behavior of the derivatized acetylenic aldehyde and products formed in-situ in the chromatographic system were studied at various temperatures ranging from -10 to 60 degrees C. It was found that the reaction products could be controlled by adjusting the column temperature. Different reaction pathways were identified as a function of temperature. The products and the reaction pathways were characterized by NMR, LC-MS and UV spectra.

Influence of the protein environment on the properties of a tyrosyl radical in reaction centers from Rhodobacter sphaeroides.

The influence of the local environment on the formation of a tyrosyl radical was investigated in modified photosynthetic reaction centers from Rhodobacter sphaeroides. The reaction centers contain a tyrosine residue placed approximately 10 A from a highly oxidizing bacteriochlorophyll dimer. Measurements by both optical and electron paramagnetic resonance spectroscopy revealed spectral features that are assigned as arising primarily from an oxidized bacteriochlorophyll dimer at low pH values and from a tyrosyl radical at high pH values, with a well-defined transition that occurred with a pK(a) of 6.9. A model based on the wild-type structure indicated that the Tyr at M164 is likely to form a hydrogen bond with His M193 and to interact weakly with Glu M173. Substitution of Tyr or Glu for His at M193 increased the pK(a) for the transition from 6.9 to 8.9, while substitution of Gln for His M193 resulted in a higher pK(a) value. Substitution of Glu M173 with Gln resulted in loss of the partial formation of the tyrosyl that occurs in the other mutants at low pH values. The results are interpreted in terms of the ability of the residues to act as proton acceptors for the oxidized tyrosine, with the pK(a) values reflecting those of either the putative proton acceptor or the tyrosine, in accord with general models of amino acid radicals.

Mechanistic aspects of chiral discrimination on an amylose tris(3,5-dimethylphenyl)carbamate.

The separation of [2R-[2alpha(R*),3alpha]]-5-[[2-[1-[3,5-bis-(trifluoromethyl)phenyl]ethoxy]-3(S)-4-fluorophenyl)4-morpholinyl]-methyl]-N,N-dimethyl-1H-1,2,3-triazole-4-methanamine hydrochloride from its enantiomer was achieved on an amylose tris-3,5-dimethylphenyl carbamate stationary phase. The retention of the enantiomers is dominated by weak hydrogen bonds while the enantioselectivity is governed by other kinds of interactions, e.g., inclusion in the amylose carbamate chains. Van't Hoffplots of 1nalpha vs. reciprocal temperature were non-linear and could be divided into two linear regions. One region at low temperature (5 degrees C- approximately 20 degrees C) and another one between 25 degrees C-70 degrees C with the change in slope occurring between 16 degrees C and 20 degrees C. DSC experiments suggested that the behavior can be attributed to breakage of H-bonds triggering a conformational change. Molecular simulation indicated a correlation between the interaction energies and the elution order obtained experimentally. The most retained enantiomer (R,R,S-enantiomer) interacts with the stationary phase through a hydrogen bond between the triazole proton and the C=O groups of the stationary phase, as well as through an inclusion in the cleft of the stationary phase. The other enantiomer exhibits a bifurcated H-bond between the triazolic proton and the C=O groups of the stationary phase leading to a less stable complex.

Effect of counter-anion concentration on retention in high-performance liquid chromatography of protonated basic analytes.

The influence of acid and salt concentration in the mobile phase on the retention of basic analytes has been studied. An increase in the retention of fully protonated analytes with increasing the concentration of inorganic additives was found. The addition of salt, such as perchlorate, trifluoroacetate, and phosphate, leads to the increase of retention for fully protonated analytes while mobile phase pH remains constant. The observed effect was attributed to the interaction of protonated analytes with the counter-anion of acid or salt, which leads to the disruption of the analyte solvation shell and the increase of its hydrophobicity and corresponding increase of retention. A mathematical model for the description of the influence of counter-anion concentration on analyte retention is proposed.

Effect of the eluent pH and acidic modifiers in high-performance liquid chromatography retention of basic analytes.

The retention of ionogenic bases in liquid chromatography is strongly dependent upon the pH of the mobile phase. Chromatographic behavior of a series of substituted aniline and pyridine basic compounds has been studied on C18 bonded silica using acetonitrile-water (10:90) as the eluent with different pHs and at various concentrations of the acidic modifier counter anions. The effect of different acidic modifiers on solute retention over a pH range from 1.3 to 8.6 was studied. Ionized basic compounds showed increased retention with a decrease of the mobile phase pH. This increase in retention was attributed to the interaction with counter anions of the acidic modifiers. The increase in retention is dependent on the nature of the counter anion and its concentration in the mobile phase. It was shown that altering the concentration of counter anion of the acidic modifier allows the optimization of the selectivity between basic compounds as well as for neutral and acidic compounds.

Geometry of chemically modified silica.

The effect of alkyl chain length on adsorbent pore volume and void volume of HPLC columns is described. The results provide evidence that alkyl chains attached on silica surface are densely packed. A correlation of a decrease of pore volume with an increase of the alkyl modifier chain length was found. Effective molecular volume of bonded chains was found to be similar to the molecular volume of corresponding liquid alkanes. An absence of noticeable penetration of acetonitrile, methanol, or tetrahydrofuran molecules between bonded chains at any water-organic eluent composition was found.

Interpretation of the excess adsorption isotherms of organic eluent components on the surface of reversed-phase adsorbents. Effect on the analyte retention.

The excess adsorption isotherms of acetonitrile, methanol and tetrahydrofuran from water on reversed-phase packings were studied, using 10 different columns packed with C1-C6, C8, C10, C12, and C18 monomeric phases, bonded on the same type of silica. The interpretation of isotherms on the basis of the theory of excess adsorption shows significant accumulation of the organic eluent component on the adsorbent surface on the top of "collapsed" bonded layer. The accumulated amount was shown to be practically independent of the length of alkyl chains bonded to the silica surface. A model that describes analyte retention on a reversed-phase column from a binary mobile phase is developed. The retention mechanism involves a combination of analyte distribution between the eluent and organic adsorbed layer, followed by analyte adsorption on the surface of the bonded phase. A general retention equation for the model is derived and methods for independent measurements of the involved parameters are suggested. The theory was tested by direct measurement of analyte retention from the eluents of varied composition and comparison of the values obtained with those theoretically calculated values. Experimental and theoretically calculated values are in good agreement.

Identification of the P-loop lysine as a metal ligand in the absence of nucleotide at catalytic site 3 of chloroplast F1-ATPase from Chlamydomonas reinhardtii.

Site-directed mutations were made to the phosphate-binding loop lysine in the beta-subunit of the chloroplast F(1)-ATPase in Chlamydomonas reinhardtii (betaK167) to investigate the participation of this residue in the binding of metal to catalytic site 3 in the absence of nucleotide. The cw-EPR spectra of VO(2+) bound to site 3 of CF(1)-ATPase from wild type and mutants revealed changes in metal ligation resulting from mutations to betaK167. The three-pulse ESEEM spectrum of the wild-type CF(1)-ATPase with VO(2+) bound to site 3 shows an equatorially coordinating (14)N from an amine. The ESEEM spectra of the mutants do not show evidence of an equatorially coordinating amine group. The results presented here show that, in the absence of nucleotide, betaK167 is a ligand to the metal bound at catalytic site 3, suggesting a regulatory role for the P-loop lysine in addition to its known role in catalysis.

Pyridoxal phosphate binding sites are similar in human heme-dependent and yeast heme-independent cystathionine beta-synthases. Evidence from 31P NMR and pulsed EPR spectroscopy that heme and PLP cofactors are not proximal in the human enzyme.

Two classes of cystathionine beta-synthases have been identified in eukaryotes, the heme-independent enzyme found in yeast and the heme-dependent form found in mammals. Both classes of enzymes catalyze a pyridoxal phosphate (PLP)-dependent condensation of serine and homocysteine to produce cystathionine. The role of the heme in the human enzyme and its location relative to the PLP in the active site are unknown. (31)P NMR spectroscopy revealed that spin-lattice relaxation rates of the phosphorus nucleus in PLP are similar in both the paramagnetic ferric (T(1) = 6.34 +/- 0.01 s) and the diamagnetic ferrous (T(1) = 5.04 +/- 0.06 s) enzyme, suggesting that the two cofactors are not proximal to each other. This is also supported by pulsed EPR studies that do not provide any evidence for strong or weak coupling between the phosphorus nucleus and the ferric iron. However, the (31)P signal in the reduced enzyme moved from 5.4 to 2.2 ppm, and the line width decreased from 73 to 16 Hz, providing the first structural evidence for transmission to the active site of an oxidation state change in the heme pocket. These results are consistent with a regulatory role for the heme as suggested by previous biochemical studies from our laboratory. The (31)P chemical shifts of the resting forms of the yeast and human enzymes are similar, suggesting that despite the difference in their heme content, the microenvironment of the PLP is similar in the two enzymes. The addition of the substrate, serine, resulted in an upfield shift of the phosphorus resonance in both enzymes, signaling formation of reaction intermediates. The resting enzyme spectra were recovered following addition of excess homocysteine, indicating that both enzymes retained catalytic activity during the course of the NMR experiment.

5'-Deoxyadenosine contacts the substrate radical intermediate in the active site of ethanolamine ammonia-lyase: 2H and 13C electron nuclear double resonance studies.

The mechanism of propagation of the radical center between the cofactor, substrate, and product in the adenosylcobalamin- (AdoCbl) dependent reaction of ethanolamine ammonia-lyase has been probed by pulsed electron nuclear double resonance (ENDOR) spectroscopy. The radical of S-2-aminopropanol, which appears in the steady state of the reaction, was used in ENDOR experiments to determine the nuclear spin transition frequencies of (2)H introduced from either deuterated substrate or deuterated coenzyme and of (13)C introduced into the ribosyl moiety of AdoCbl. A (2)H doublet (1.4 MHz splitting) was observed centered about the Larmor frequency of (2)H. Identical ENDOR frequencies were observed for (2)H irrespective of its mode of introduction into the complex. A (13)C doublet ENDOR signal was observed from samples prepared with [U-(13)C-ribosyl]-AdoCbl. The (13)C coupling tensor obtained from the ENDOR powder pattern shows that the (13)C has scalar as well as dipole-dipole coupling to the unpaired electron located at C1 of S-2-aminopropanol. The dipole-dipole coupling is consistent with a distance of 3.4+/-0.2 A between C1 of the radical and C5' of the labeled cofactor component. These results establish that the C5' carbon of the 5'-deoxyadenosyl radical moves approximately 7 A from its position as part of AdoCbl to a position where it is in contact with C1 of the substrate which lies approximately 12 A from the Co(2+) of cob(II)alamin. These findings are also consistent with the contention that 5'-deoxyadenosine is the sole mediator of hydrogen transfers in ethanolamine ammonia-lyase.