Protein-cofactor interactions in bacterial reaction centers from Rhodobacter sphaeroides R-26: effect of hydrogen bonding on the electronic and geometric structure of the primary quinone. A density functional theory study

The effect of hydrogen bonding to the primary quinone (Q(A) and Q(*)(-)(A)) in bacterial reaction centers was studied using density functional theory (DFT) calculations. The charge neutral state Q(A) was investigated by optimizing the hydrogen atom positions of model systems extracted from 15 different X-ray structures. From this analysis, mean values of the H-bond lengths and directions were derived. It was found that the N(delta)-H of His M219 forms a shorter H-bond to Q(A) than the N-H of Ala M260. The H-bond of His M219 is linear and more twisted out of the quinone plane. The radical anion Q(*)(-)(A) in the protein environment was investigated by using a mixed quantum mechanics/molecular mechanics (QM/MM) approach. Two geometry optimizations with a different number of flexible atoms were performed. H-bond lengths were obtained and spectroscopic parameters calculated, i.e. the hyperfine and nuclear quadrupole couplings of magnetic nuclei coupled to the radical. Good agreement was found with the results provided by EPR/ENDOR spectroscopy. This implies that the calculated lengths and directions of the H-bonds to Q(*)(-)(A) are reliable values. From a comparison of the neutral and reduced state of Q(A) it was concluded that the H-bond distances are shortened by approximately 0.17 Angstroms (His M219) and approximately 0.13 Angstroms (Ala M260) upon single reduction of the quinone. It is shown that the point-dipole approximation can not be used for an estimation of H-bond lengths from measured hyperfine couplings in a system with out-of-plane H-bonding. In contrast, the evaluation of the nuclear quadrupole couplings of (2)H nuclei substituted in the hydrogen bonds yields H-bond lengths close to the values that were deduced from DFT geometry optimizations. The significance of hydrogen bonding to the quinone cofactors in biological systems is discussed.     

Variation of Ser-L223 hydrogen bonding with the QB redox state in reaction centers from Rhodobacter sphaeroides

Ser-L223 is close to ubiquinone (Q(B)) in the B-branch of the bacterial photosynthetic reaction center (bRC) from Rhodobacter (Rb) sphaeroides. Therefore, the presence of a hydrogen bond (H bond) between the two was naturally proposed from the crystal structure. The hydrogen bonding pattern of Q(B) from the light-exposed structure was studied by generating hydrogen atom coordinates based on the CHARMM force field. In the Q(B) neutral charge state (Q(B)(0)), no H bond was found between the oxygen of the OH group from Ser-L223 and the carbonyl oxygen of Q(B) that is distal to the non-heme iron. In the reduced state (Q(B)(-)), however, Ser-L213 was found to form an H bond with Q(B) only when Asp-L213 is protonated by more than 0.75 H(+). This indicates the significance of the protonation of Asp-L213 in forming an H bond between Ser-L223 and Q(B). We found that the driving force to form the H bond between Ser-L223 and Q(B) is enhanced by the positively charged Arg-L217. The calculated Q(B) redox potentials with or without this H bond discriminated two ET rates, which are close to the faster and slower time phases observed in UV-Vis and FTIR studies. Together with the calculated redox potential of the quinones, this H-bond formation could play a key role in conformational gating for the ET process from Q(A) to Q(B).     

Identification of the nitrogen donor hydrogen bonded with the semiquinone at the Q(H) site of the cytochrome bo3 from Escherichia coli

The selective (15)N isotope labeling was used for the identification of the nitrogen involved in a hydrogen bond formation with the semiquinone in the high-affinity Q(H) site in the cytochrome bo(3) ubiquinol oxidase. This nitrogen produces dominating contribution to X-Band (14)N ESEEM spectra. The 2D ESEEM (HYSCORE) experiments with the Q(H) site SQ in the series of selectively (15)N labeled bo(3) oxidase proteins have directly identified the N(epsilon) of R71 as an H-bond donor. In addition, selective (15)N labeling has allowed us for the first time to determine weak hyperfine couplings with the side-chain nitrogens from all residues around the SQ. Those are reflecting a distribution of the unpaired spin density over the protein in the SQ state of the quinone processing site.     

High and low potential forms of the QA quinone electron acceptor in Photosystem II of Thermosynechococcus elongatus and spinach

The redox potential of Q(A) in Photosystem II (PSII) from Thermosynechococcus elongatus was titrated monitoring chlorophyll fluorescence. A high potential form (E(m)=+60 ± 25 mV) was found in the absence of Mn(4)Ca, the active site for water oxidation. The low potential form (E(m)=-60 ± 48 mV), which is difficult to measure in conventional titration experiments, could be "locked in" by cross-linking the active enzyme. This indicates that the presence of Mn(4)Ca is relayed to the quinone site by significant structural changes in the protein. The presence of high and low potential forms agrees with what has been seen in plants, algae from our lab and in T. elongatus (Shibamoto et al., Biochemistry 48 (2009) 10682-10684). In the latter work, the potentials of Q(A) were shifted to lower potentials compared to other measurements. The redox potential of Q(A) in Mn-depleted PSII from spinach was titrated in the presence of redox mediators and the midpoint potential was shifted by 80 mV towards a more negative value compared to titrations without mediators. The lower values of the midpoint potential of the (Q(A)/Q(A)(-)) redox couple in the literature could be due to a perturbation due to a specific mediator.     

Pseudo Jahn-Teller origin of cis-trans and other conformational changes. The role of double bonds

Based on the pseudo Jahn-Teller effect (PJTE) theory, an approach is developed to rationalize and predict the conformations and conformational changes in molecular systems with a common pattern, a double bond. It is shown that starting with the high-symmetry geometry of the environment (in many cases D(2d)), the double bond descends from an e(2) electronic configuration (e is a twofold degenerate MO) which produces a variety of PJT distortions, the main of which is the rotational (b(1)) transformation D(2d) → D(2h) accompanied by the formation of the double bond. Further PJT interactions with higher energy E-states may trigger additional distortions which in D(2h) symmetry are classified as in-plane (e(i)) cis and trans, and out-of-plane (e(o)) chair and boat. The realization of these conformations depends on the positions of the excited E-states and the PJTE parameter values. The two emerging PJTE problems, ((3)A(2) + (3)E(1) + (3)E(2)) ? (e(i) + e(o)) and ((1)A(1) + (1)B(1) + (1)B(2) + (1)E(1) + (1)E(2)) ? (b(1) + e(i) + e(o)), are formulated in the matrix form and provide a general picture of the ground and excited adiabatic potential energy surfaces. Following this scheme in combination with ab initio calculations, the possible conformations and conformational transitions are analyzed for several specific systems including (in increasing complexity) N(2)H(2), C(2)H(4), N(2)(NH(2))(2) and N(2)(C(6)H(5))(2) (azobenzene). The family of molecular systems with a double bond is vast, but the importance of the PJT approach developed here is also in its general validity as it can be applied to any other systems.     

Molecular structure of substituted phenylamine alpha-OMe- and alpha-OH-p-benzoquinone derivatives. Synthesis and correlation of spectroscopic, electrochemical, and theoretical parameters.

Thirteen C(6) para-substituted anilinebenzoquinones derived from perezone (PZ) (2-(1,5-dimethyl-4-hexenyl)-3-hydroxy-5-methyl-1,4-benzoquinone) were prepared to analyze the effect of the substituents on quinone electronic properties. The effect of a hydrogen bond between the alpha-hydroxy and carbonyl C(4)-O(4) groups was determined in perezone derivatives by substituting electron-donor and electron-acceptor groups such as -OMe, -Me, -Br, and -CN and comparing the -OH (APZs) and -OMe (APZms) derivatives. Reduction potentials of these compounds were measured using cyclic voltammetry in anhydrous acetonitrile. The typical behavior of quinones, with or without alpha-phenolic protons, in an aprotic medium was not observed for APZs due to the presence of coupled, self-protonation reactions. The self-protonation process gives rise to an initial wave, corresponding to the irreversible reduction reaction of quinone (HQ) to hydroquinone (HQH(2)), and to a second electron transfer, attributed to the reversible reduction of perezonate (Q(-)) formed during the self-protonation process. This reaction is favored by the acidity of the alpha-OH located at the quinone ring. To control the coupled chemical reaction, we considered both methylation of the -OH group (APZms) and addition of a strong base, tetramethylammonium phenolate (Me(4)N(+)C(6)H(5)O(-)), to completely deprotonate the APZs. Methylation led to recovery of reversible, bi-electronic behavior (Q/Q(*)(-) and Q(*)(-)/Q(2)(-)), indicating the nonacidic properties of the NH group. The addition of a strong base resulted in reduction of perezonate (Q(-)) obtained from the acid-base reaction of APZs with Me(4)N(+)C(6)H(5)O(-) to produce the dianion radical (Q(*)(2)(-)). Although the nitrogen atom interferes with direct conjugation between both rings by binding the quinone with the para-substituted ring, the UV-vis spectra of these compounds showed the existence of intramolecular electronic transfer from the respective aniline to the quinone moiety. (13)C NMR chemical shifts of the quinone atoms provided additional evidence for this electron transfer. These findings were also supported by linear variation in cathodic peak potentials (E(pc)) vs Hammett sigma(p) constants associated with the different electrochemical transformations: Q/Q(*)(-), Q(*)(-)/Q(2)(-) for APZms or HQ/HQH(2) and Q(-)/Q(*)(2)(-) for APZs. The electronic properties of model anilinebenzoquinones were determined at a B3LYP/6-31G(d,p) level of theory within the framework of the density functional theory. Our theoretical calculations predicted that all the compounds are floppy molecules with a low rotational C-N barrier, in which the degree of conjugation of the lone nitrogen pair with the quinone system depends on the magnitude of the electronic effect of the substituents of the aniline ring. Natural charges show that C(1) is more positive than C(4) although the LUMO orbital is located at C(4). Hence, if the natural charge distribution in the molecule controls the first electron addition, this should occur at carbon atom C(1). If the process is controlled by the LUMO orbitals, however, electron addition would first occur at C(4). For the APZms series susceptibility of the first reduction wave to the substitution effect (rho(pi) = 147 mV) is lower than that of the second reduction wave (rho(pi) = 156 mV). Thus, the first, one-electron transfer in the quinone system is controlled by the natural charge distribution of the molecule and therefore takes place at C(1).     

Inhibition of photosynthetic electron transport by UV-A radiation targets the photosystem II complex

We have studied the inhibition of photosynthetic electron transport by UV-A (320-400 nm) radiation in isolated spinach thylakoids. Measurements of Photosystem II (PSII) and Photosystem I activity by Clark-type oxygen electrode demonstrated that electron flow is impaired primarily in PSII. The site and mechanism of UV-A induced damage within PSII was assessed by flash-induced oxygen and thermoluminescence (TL) measurements. The flash pattern of oxygen evolution showed an increased amount of the S0 state in the dark, which indicate a direct effect of UV-A in the water-oxidizing complex. TL measurements revealed the UV-A induced loss of PSII centers in which charge recombination between the S2 state of the water oxidizing complex and the semireduced Q(A)- and Q(B)- quinone electron acceptors occur. Flash-induced oscillation of the B TL band, originating from the S2Q(B)- recombination, showed a decreased amplitude after the second flash relative to that after the first one, which is consistent with a decrease in the amount of Q(B)- relative to Q(B) in dark adapted samples. The efficiency of UV-A light in inhibiting PSII electron transport exceeds that of visible light 45-fold on the basis of equal energy and 60-fold on the basis of equal photon number, respectively. In conclusion, our data show that UV-A radiation is highly damaging for PSII, whose electron transport is affected both at the water oxidizing complex, and the binding site of the Q(B) quinone electron acceptor in a similar way to that caused by UV-B radiation.     

Distribution of the cationic state over the chlorophyll pair of the photosystem II reaction center

The reaction center chlorophylls a (Chla) of photosystem II (PSII) are composed of six Chla molecules including the special pair Chla P(D1)/P(D2) harbored by the D1/D2 heterodimer. They serve as the ultimate electron abstractors for water oxidation in the oxygen-evolving Mn(4)CaO(5) cluster. Using the PSII crystal structure analyzed at 1.9 ? resolution, the redox potentials of P(D1)/P(D2) for one-electron oxidation (E(m)) were calculated by considering all PSII subunits and the protonation pattern of all titratable residues. The E(m)(Chla) values were calculated to be 1015-1132 mV for P(D1) and 1141-1201 mV for P(D2), depending on the protonation state of the Mn(4)CaO(5) cluster. The results showed that E(m)(P(D1)) was lower than E(m)(P(D2)), favoring localization of the charge of the cationic state more on P(D1). The P(D1)(?+)/P(D2)(?+) charge ratio determined by the large-scale QM/MM calculations with the explicit PSII protein environment yielded a P(D1)(?+)/P(D2)(?+) ratio of ~80/~20, which was found to be due to the asymmetry in electrostatic characters of several conserved D1/D2 residue pairs that cause the E(m)(P(D1))/E(m)(P(D2)) difference, e.g., D1-Asn181/D2-Arg180, D1-Asn298/D2-Arg294, D1-Asp61/D2-His61, D1-Glu189/D2-Phe188, and D1-Asp170/D2-Phe169. The larger P(D1)(?+) population than P(D2)(?+) appears to be an inevitable fate of the intact PSII that possesses water oxidation activity.     

Proton transfer reactions and dynamics of sulfonic acid group in Nafion®

Proton transfer reactions and dynamics of the hydrophilic group (-SO(3)H) in Nafion? were studied at low hydration levels using the complexes formed from CF(3)SO(3)H, H(3)O(+) and nH(2)O, 1 ≤n≤ 3, as model systems. The equilibrium structures obtained from DFT calculations suggested at least two structural diffusion pathways at the -SO(3)H group namely, the "pass-through" and "pass-by" mechanisms. The former involves the protonation and deprotonation at the -SO(3)H group, whereas the latter the proton transfer in the adjacent Zundel complex. Analyses of the asymmetric O-H stretching frequencies (ν(OH)) of the hydrogen bond (H-bond) protons showed the threshold frequencies (ν(OH*)) of proton transfer in the range of 1700 to 2200 cm(-1). Born-Oppenheimer Molecular Dynamics (BOMD) simulations at 350 K anticipated slightly lower threshold frequencies (ν(A)(OH*,MD)), with two characteristic asymmetric O-H stretching frequencies being the spectral signatures of proton transfer in the H-bond complexes. The lower frequency (ν(A)(OH,MD))) is associated with the oscillatory shuttling motion and the higher frequency (ν(B)(OH,MD))) the structural diffusion motion. Comparison of the present results with BOMD simulations on protonated water clusters indicated that the -SO(3)H group facilitates proton transfer by reducing the vibrational energy for the interconversion between the two dynamic states (Δν), resulting in a higher population of the H-bonds with the structural diffusion motion. One could therefore conclude that the -SO(3)H groups in Nafion? act as active binding sites which provide appropriate structural, energetic and dynamic conditions for effective structural diffusion processes in a proton exchange membrane fuel cell (PEMFC). The present results suggested for the first time a possibility to discuss the tendency of proton transfer in H-bond using Δν(BA)(OH,MD)) and provided theoretical bases and guidelines for the investigations of proton transfer reactions in theory and experiment.     

Water Activity Regulates the Q(A)(-) to Q(B) electron transfer in photosynthetic reaction centers from Rhodobacter sphaeroides

We report on the effects of water activity and surrounding viscosity on electron transfer reactions taking place within a membrane protein: the reaction center (RC) from the photosynthetic bacterium Rhodobacter sphaeroides. We measured the kinetics of charge recombination between the primary photoxidized donor (P(+)) and the reduced quinone acceptors. Water activity (aW) and viscosity (eta) have been tuned by changing the concentration of cosolutes (trehalose, sucrose, glucose, and glycerol) and the temperature. The temperature dependence of the rate of charge recombination between the reduced primary quinone, Q(A)(-), and P(+) was found to be unaffected by the presence of cosolutes. At variance, the kinetics of charge recombination between the reduced secondary quinone (Q(B)(-)) and P(+) was found to be severely influenced by the presence of cosolutes and by the temperature. Results collected over a wide eta-range (2 orders of magnitude) demonstrate that the rate of P(+)Q(B)(-) recombination is uncorrelated to the solution viscosity. The kinetics of P(+)Q(B)(-) recombination depends on the P(+)Q(A)(-)Q(B) <--> P(+)Q(A)Q(B)(-) equilibrium constant. Accordingly, the dependence of the interquinone electron transfer equilibrium constant on T and aW has been explained by assuming that the transfer of one electron from Q(A)(-) to Q(B) is associated with the release of about three water molecules by the RC. This implies that the interquinone electron transfer involves at least two RC substates differing in the stoichiometry of interacting water molecules.     

Increasing stability of the fullerenes with the number of carbon atoms: the experimental evidence

The values of the molar standard enthalpies of formation, Delta(f)H(o)(m)(C(76), cr) = (2705.6 +/- 37.7) kJ x mol(-1), Delta(f)H(o)(m)(C(78), cr) = (2766.5 +/- 36.7) kJ x mol(-1), and Delta(f)H(o)(m)(C(84), cr) = (2826.6 +/- 42.6) kJ x mol(-1), were determined from the energies of combustion, measured by microcombustion calorimetry on a high-purity sample of the D(2) isomer of fullerene C(76), as well as on a mixture of the two most abundant constitutional isomers of C(78) (C(2nu)-C(78) and D(3)-C(78)) and C(84) (D(2)-C(84), and D(2d)-C(84). These values, combined with the published data on the enthalpies of sublimation of each cluster, lead to the gas-phase enthalpies of formation, Delta(f)H(o)(m)(C(76), g) = (2911.6 +/- 37.9) kJ x mol(-1); Delta(f)H(o)(m)(C(78), g) = (2979.3 +/- 37.2) kJ x mol(-1), and Delta(f)H(o)(m)(C(84), (g)) = (3051.6 +/- 43.0) kJ x mol(-1), results that were found to compare well with those reported from density functional theory calculations. Values of enthalpies of atomization, strain energies, and the average C-C bond energy were also derived for each fullerene. A decreasing trend in the gas-phase enthalpy of formation and strain energy per carbon atom as the size of the cluster increases is found. This is the first experimental evidence that these fullerenes become more stable as they become larger. The derived experimental average C-C bond energy E(C-C) = 461.04 kJ x mol(-1) for fullerenes is close to the average bond energy E(C-C) = 462.8 kJ x mol(-1) for polycyclic aromatic hydrocarbons (PAHs).     

Dynamics of photodissociation of 3,3,3-d(3)-propene at 157 nm: site effect and hydrogen migration

In a preceding paper [Lee et al., J. Chem. Phys. 119, 827 (2003)], we measured the kinetic-energy distributions P(E(t)) and branching ratios of products from photolysis of propene at 157 nm using time-of-flight spectroscopy combined with photoionization. In the present work, hydrogen migration before fragmentation and a site effect on P(E(t)) and branching ratios were revealed from the photodissociation of CD(3)CHCH(2). Labeling of the methyl group with deuterium enabled us to differentiate between elimination of atomic and molecular hydrogen from the vinyl moiety and from the methyl moiety; the P(E(t)) and relative yields for the formation of H, D, H(2), HD, and D(2) were measured. Deuterium labeling allowed us to also differentiate the fragmentation after hydrogen transfer from that before hydrogen migration. The observation of isotopic variants of CD(3) and C(2)H(3) radicals in the C-C bond cleavage provides evidence for hydrogen transfer of propene because of site specificity. The fraction of fragmentation after hydrogen transfer is estimated to be 25%. The isotope-specific branching ratios for five dissociation pathways of CD(3)CHCH(2) were evaluated.     

Redox-active tyrosine residues: role for the peptide bond in electron transfer

Photosystem II (PSII) catalyzes the light-driven oxidation of water and reduction of plastoquinone. In PSII, redox-active tyrosine Z conducts electrons between the primary chlorophyll donor and the manganese cluster, which is the catalytic site. In this report, difference FT-IR spectroscopy is used to show that oxidation of redox-active tyrosine Z causes perturbations of the peptide bond. PSII data were acquired on control samples, as well as samples in which tyrosine was 2H4 (ring)-labeled. Comparison to model compound data, acquired both from tyrosinate and its 2H4 isotopomer, was performed. The PSII FT-IR spectrum exhibited vibrational bands that are assignable to imide and amide vibrational modes. In previous work, we have shown that oxidation of tyrosinate perturbs the terminal amino group of tyrosinate (Ayala, I.; Range, K.; York, D.; Barry, B. A. J. Am. Chem. Soc. 2002, 124, 5496-5505). Density functional calculations on tyrosinate supported the interpretation that the perturbation is due to spin delocalization onto the amino group. In tyrosine-containing dipeptides, perturbations of the peptide bond were observed. Therefore, the imide and amide perturbations observed here are attributed to spin delocalization into the peptide bond in PSII. Migration of the electron hole in PSII may be consistent with peptide bond involvement in tyrosyl radical-based electron-transfer reactions.     

Electron transfer kinetics in photosynthetic reaction centers embedded in polyvinyl alcohol films

The coupling between electron transfer and protein dynamics has been studied at room temperature in isolated reaction centers (RCs) from the photosynthetic bacterium Rhodobacter sphaeroides by incorporating the protein in polyvinyl alcohol (PVA) films of different water/RC ratios. The kinetic analysis of charge recombination shows that dehydration of RC-containing PVA films causes reversible, inhomogeneous inhibition of electron transfer from the reduced primary quinone acceptor (Q(A)(-)) to the secondary quinone Q(B). A more extensive dehydration of solid PVA matrices accelerates electron transfer from Q(A)(-) to the primary photooxidized electron donor P(+). These effects indicate that incorporation of RCs into dehydrated PVA films hinders the conformational dynamics gating Q(A)(-) to Q(B) electron transfer at room temperature and slows down protein relaxation which stabilizes the primary charge-separated state P(+)Q(A)(-). A comparison with analogous effects observed in trehalose-coated RCs suggests that protein motions are less severely reduced in PVA films than in trehalose matrices at comparable water/RC ratios.     

Proton uptake of rhodobacter capsulatus reaction center mutants modified in the primary quinone environment

Flash-induced absorbance spectroscopy was used to analyze the proton uptake and electron transfer properties of photosynthetic reaction centers (RC) of Rhodobacter capsulatus that have been genetically modified near the primary quinone electron acceptor (Q(A)). M246Ala and M247Ala, which are symmetry-related to the positions of two acidic groups, L212Glu and L213Asp, in the secondary quinone electron acceptor (QB) protein environment, have been mutated to Glu and Asp, respectively. The pH dependence of the stoichiometry of proton uptake upon formation of the P+Q(A)- (H+/P+Q(A)-) and PQ(A) (H+/Q(A)-) (P is the primary electron donor, a noncovalently linked bacteriochlorophyll dimer) states have been measured in the M246Ala --> Glu and the M247Ala --> Asp mutant RC, in the M246Ala-M247Ala --> Glu-Asp double mutant and in the wild type (WT). Our results show that the introduction of an acidic group (Glu or Asp) in the QA protein region induces notable additional proton uptake over a large pH region (approximately 6-9), which reflects a delocalized response of the protein to the formation of Q(A)-. This may indicate the existence of a widely spread proton reservoir in the cytoplasmic region of the protein. Interestingly, the pH titration curves of the proton release caused by the formation of P+ (H+/P+: difference between H+/P+Q(A)- and H+/PQ(A)- curves) are nearly superimposable in the WT and the M246Ala --> Glu mutant RC, but substantial additional proton release is detected between pH 7 and 9 in the M247Ala --> Asp mutant RC. This effect can be accounted for by an increased proton release by the P+ environment in the M247Ala --> Asp mutant. The M247Ala --> Asp mutation reveals the existence of an energetic and conformational coupling between donor and acceptor sides of the RC at a distance of nearly 30A.     

An alternate proton acceptor for excited-state proton transfer in green fluorescent protein: rewiring GFP

The neutral form of the chromophore in wild-type green fluorescent protein (wtGFP) undergoes excited-state proton transfer (ESPT) upon excitation, resulting in characteristic green (508 nm) fluorescence. This ESPT reaction involves a proton relay from the phenol hydroxyl of the chromophore to the ionized side chain of E222, and results in formation of the anionic chromophore in a protein environment optimized for the neutral species (the I* state). Reorientation or replacement of E222, as occurs in the S65T and E222Q GFP mutants, disables the ESPT reaction and results in loss of green emission following excitation of the neutral chromophore. Previously, it has been shown that the introduction of a second mutation (H148D) into S65T GFP allows the recovery of green emission, implying that ESPT is again possible. A similar recovery of green fluorescence is also observed for the E222Q/H148D mutant, suggesting that D148 is the proton acceptor for the ESPT reaction in both double mutants. The mechanism of fluorescence emission following excitation of the neutral chromophore in S65T/H148D and E222Q/H148D has been explored through the use of steady state and ultrafast time-resolved fluorescence and vibrational spectroscopy. The data are contrasted with those of the single mutant S65T GFP. Time-resolved fluorescence studies indicate very rapid (< 1 ps) formation of I* in the double mutants, followed by vibrational cooling on the picosecond time scale. The time-resolved IR difference spectra are markedly different to those of wtGFP or its anionic mutants. In particular, no spectral signatures are apparent in the picosecond IR difference spectra that would correspond to alteration in the ionization state of D148, leading to the proposal that a low-barrier hydrogen bond (LBHB) is present between the phenol hydroxyl of the chromophore and the side chain of D148, with different potential energy surfaces for the ground and excited states. This model is consistent with recent high-resolution structural data in which the distance between the donor and acceptor oxygen atoms is < or = 2.4 A. Importantly, these studies indicate that the hydrogen-bond network in wtGFP can be replaced by a single residue, an observation which, when fully explored, will add to our understanding of the various requirements for proton-transfer reactions within proteins.     

Hydrogen bonding and spin density distribution in the Qb semiquinone of bacterial reaction centers and comparison with the Qa site

In the photosynthetic reaction center from Rhodobacter sphaeroides, the primary (Q(A)) and secondary (Q(B)) electron acceptors are both ubiquinone-10, but with very different properties and functions. To investigate the protein environment that imparts these functional differences, we have applied X-band HYSCORE, a 2D pulsed EPR technique, to characterize the exchangeable protons around the semiquinone (SQ) in the Q(A) and Q(B) sites, using samples of (15)N-labeled reaction centers, with the native high spin Fe(2+) exchanged for diamagnetic Zn(2+), prepared in (1)H(2)O and (2)H(2)O solvent. The powder HYSCORE method is first validated against the orientation-selected Q-band ENDOR study of the Q(A) SQ by Flores et al. (Biophys. J.2007, 92, 671-682), with good agreement for two exchangeable protons with anisotropic hyperfine tensor components, T, both in the range 4.6-5.4 MHz. HYSCORE was then applied to the Q(B) SQ where we found proton lines corresponding to T ≈ 5.2, 3.7 MHz and T ≈ 1.9 MHz. Density functional-based quantum mechanics/molecular mechanics (QM/MM) calculations, employing a model of the Q(B) site, were used to assign the observed couplings to specific hydrogen bonding interactions with the Q(B) SQ. These calculations allow us to assign the T = 5.2 MHz proton to the His-L190 N(δ)H···O(4) (carbonyl) hydrogen bonding interaction. The T = 3.7 MHz spectral feature most likely results from hydrogen bonding interactions of O1 (carbonyl) with both Gly-L225 peptide NH and Ser-L223 hydroxyl OH, which possess calculated couplings very close to this value. The smaller 1.9 MHz coupling is assigned to a weakly bound peptide NH proton of Ile-L224. The calculations performed with this structural model of the Q(B) site show less asymmetric distribution of unpaired spin density over the SQ than seen for the Q(A) site, consistent with available experimental data for (13)C and (17)O carbonyl hyperfine couplings. The implications of these interactions for Q(B) function and comparisons with the Q(A) site are discussed.     

Proton transfer of NH3-HCl catalyzed by only one molecule

The proton transfer in NH(3)-HCl by only one molecule of catalyst was studied by using the MP2 method with the large 6-311++G(2d,2p) basis set. The 18 structures are obtained for the smallest units, NH(3)-HCl-A trimers, for which the proton transfer maybe occurred. The final results show that the proton transfers have occurred in the 15 cyclic shape structures for A = H(2)SO(4), H(2)SO(3), HCOOH (a), HF, H(2)O(2), HNO(3), HNO(2) (a), CH(3)OH, HCl, HNC, H(2)O, HNO(2) (b), NH(3), HCOOH (b), and HCHO, and not occurred in another 3 trimer structures for A = HCN, H(2)S, and PH(3). These results show that the proton transfer occurs from HCl to NH(3) when catalyst molecule A (acidic, neutral, or basic) not only as a proton donor strongly donates the proton to the Cl atom but as an acceptor strongly accepts the proton from the NH(3) molecule in the cyclic H-bond structure. In this work, a proton circumfluence model is proposed to explain the mechanism of the proton transfer. We find that, for the trimer, when the sum of two hydrogen bond lengths (R = R(1) + R(2)) is shorter than 5.0 A, molecule A has the ability to catalyze the proton transfer. In addition, we also find that the interaction energy E(int) between NH(3)-HCl and A is nearly related to the extent (R(H1)(-)(Cl)) of proton transfer, that is, the interaction energy E(int) increases with the proton transfer.     

Molecular dynamics of hydrogen bonds in protein-D2O: the solvent isotope effect

We suggest that the H-bond in proteins not only mirrors the motion of hydrogen in its own atomistic setting but also finds its origin in the collective environment of the hydrogen bond in a global lattice of surrounding H2O molecules. This water lattice is being perturbed in its optimal entropic configuration by the motion of the H-bond. Furthermore, bonding interaction with the lattice drop the H-bond energy from some 5 kcal/mol for the pure protein in the absence of H2O, to some 1.6 kcal/mol in the presence of the H2O medium. This low value here is determined in a computer experiment involving MD calculations and is a value close to the generally accepted value for biological systems. In accordance with these computer experiments under ambient conditions, the H-bond energy is seriously depressed, hence confirming the subtle effect of the H2O medium directly interacting with the H-bond and permitting a strong fluxional behavior. Furthermore, water produces a very large change in the entropy of activation due to the hydrogen bond breakage, which affects the rate by as much as 2 orders of magnitude. We also observe that there is an entire ensemble of H-bond structures, rather than a single transition state, all of which contribute to this H-bond. Here the model is tested by changing to D2O as the surrounding medium resulting in a substantial solvent isotope effect. This demonstrates the important influence of the environment on the individual hydrogen bond.     

How can a single second sphere amino acid substitution cause reduction midpoint potential changes of hundreds of millivolts?

The active site metal ion of superoxide dismutase (SOD) is reduced and reoxidized as it disproportionates superoxide to dioxygen and hydrogen peroxide. Thus, the reduction midpoint potential (Em) is a critical determinant of catalytic activity. In E. coli Fe-containing SOD (FeSOD), reduction of Fe3+ is accompanied by protonation of a coordinated OH-, to produce Fe2+ coordinated by H2O. The coordinated solvent's only contact with the protein beyond the active site is a conserved Gln residue. Mutation of this Gln to His or Glu resulted in elevation of the Em by 220 mV and more than 660 mV, respectively [Yikilmaz et al., Biochemistry 2006, 45, 1151-1161], despite the fact that overall protein structure was preserved, His is a chemically conservative replacement for Gln, and neutral Glu is isostructural and isoelectronic with Gln. Therefore, we have investigated several possible bases for the elevated Em's, including altered Fe electronic structure, altered active site electrostatics, altered H-bonding and altered redox-coupled proton transfer. Using EPR, MCD, and NMR spectroscopies, we find that the active site electronic structures of the two mutants resemble that of the WT enzyme, for both oxidation states, and Q69E-FeSOD's apparent deviation from WT-like Fe3+ coordination in the oxidized state can be explained by increased affinity for a small anion. Spontaneous coordination of an exogenous anion can only stabilize oxidized Q69E-Fe3+SOD and, therefore, cannot account for the increased Em of Q69E FeSOD. WT-like anion binding affinities and active site pK's indicate that His69 of Q69H-FeSOD is neutral in both oxidation states, like Gln69 of WT-FeSOD, whereas Glu69 appears to be neutral in the oxidized state but ionized in the reduced state of Q69E-FeSOD. A 1.1 A resolution crystal structure of Q69E-Fe2+SOD indicates that Glu69 accepts a strong H-bond from coordinated solvent in the reduced state, in contrast to the case in WT-FeSOD where Gln69 donates an H-bond. These data and DFT calculations lead to the proposal that the elevated Em of Q69E-FeSOD can be substantially explained by (1) relief from enforced H-bond donation in the reduced state, (2) Glu69's capacity to provide a proton for proton-coupled Fe3+ reduction, and (3) strong hydrogen bond acceptance in the reduced state, which stabilizes coordinated H2O. Our results thus support the hypothesis that the protein matrix can apply significant redox tuning via its influence over redox-coupled proton transfer and the energy associated with it.