Comments on the optical lineshape function: Application to transient hole-burned spectra of bacterial reaction centers

Citation: Reppert, M., Kell, A., Pruitt, T., & Jankowiak, R. (2015). Comments on the optical lineshape function: Application to transient hole-burned spectra of bacterial reaction centers. Journal of Chemical Physics, 142(9), 7. doi:10.1063/1.4913685The vibrational spectral density is an important physical parameter needed to describe both linear and non-linear spectra of multi-chromophore systems such as photosynthetic complexes. Low-temperature techniques such as hole burning (HB) and fluorescence line narrowing are commonly used to extract the spectral density for a given electronic transition from experimental data. We report here that the lineshape function formula reported by Hayes et al. [J. Phys. Chem. 98, 7337 (1994)] in the mean-phonon approximation and frequently applied to analyzing HB data contains inconsistencies in notation, leading to essentially incorrect expressions in cases of moderate and strong electron-phonon (el-ph) coupling strengths. A corrected lineshape function L(omega) is given that retains the computational and intuitive advantages of the expression of Hayes et al. [J. Phys. Chem. 98, 7337 (1994)]. Although the corrected lineshape function could be used in modeling studies of various optical spectra, we suggest that it is better to calculate the lineshape function numerically, without introducing the mean-phonon approximation. New theoretical fits of the P870 and P960 absorption bands and frequency-dependent resonant HB spectra of Rb. sphaeroides and Rps. viridis reaction centers are provided as examples to demonstrate the importance of correct lineshape expressions. Comparison with the previously determined el-ph coupling parameters [Johnson et al., J. Phys. Chem. 94, 5849 (1990); Lyle et al., ibid. 97, 6924 (1993); Reddy et al., ibid. 97, 6934 (1993)] is also provided. The new fits lead to modified el-ph coupling strengths and different frequencies of the special pair marker mode, omega(sp), for Rb. sphaeroides that could be used in the future for more advanced calculations of absorption and HB spectra obtained for various bacterial reaction centers. (c) 2015 AIP Publishing LLC

Site Energies of Active and Inactive Pheophytins in the Reaction Center of Photosystem II from Chlamydomonas Reinhardtii

31 Pags. The definitive version is available at: http://pubs.acs.org/journal/jpcbfkIt is widely accepted that the primary electron acceptor in various Photosystem II (PSII) reaction centers (RCs) is pheophytin a (Pheo a) within the D1 protein (PheoD1), while PheoD2 (within the D2 protein) is photochemically inactive. The Pheo site energies, however, have remained elusive, due to inherent spectral congestion. While most researchers over the last two decades assigned the Qy-states of PheoD1 and PheoD2 bands near 678–684 nm and 668–672 nm, respectively, recent modeling [Raszewski et al. Biophys. J. 2005, 88, 986–998; Cox et al. J. Phys. Chem. B 2009, 113, 12364–12374] of the electronic structure of the PSII RC reversed the location of the active and inactive Pheos, suggesting that the mean site energy of PheoD1 is near 672 nm, whereas PheoD2 (~677.5 nm) and ChlD1 (~680 nm) have the lowest energies (i.e., the PheoD2-dominated exciton is the lowest excited state). In contrast, chemical pigment exchange experiments on isolated RCs suggested that both pheophytins have their Qy absorption maxima at 676–680 nm [Germano et al. Biochem. 2001, 40, 11472–11482; Germano et al. Biophys. J. 2004, 86, 1664–1672]. To provide more insight into the site energies of both PheoD1 and PheoD2 (including the corresponding Qx transitions, which are often claimed to be degenerate at 543 nm) and to attest that the above two assignments are most likely incorrect, we studied a large number of isolated RC preparations from spinach and wild-type Chlamydomonas reinhardtii (at different levels of intactness) as well as the Chlamydomonas reinhardtii mutant (D2-L209H), in which the active branch PheoD1 is genetically replaced with chlorophyll a (Chl a). We show that the Qx-/Qy-region site-energies of PheoD1 and PheoD2 are ~545/680 nm and ~541.5/670 nm, respectively, in good agreement with our previous assignment [Jankowiak et al. J. Phys. Chem. B 2002, 106, 8803–8814]. The latter values should be used to model excitonic structure and excitation energy transfer dynamics of the PSII RCs.Partial support to B.N. (involved in calculations) was provided by the NSF EPSCoR Grant. V.Z. (involved in writing the manuscript) acknowledges support by NSERC. R.T.S., R.P., and M.S. were involved in the design and preparation of D2-mutant and RCs. They acknowledge support from USDOE, Photosynthetic Antennae Research Center (R.T.S.), MICIN (Grant AGL2008-00377) in Spain (R.P.), and the U.S. Department of Energy’s Photosynthetic Systems Program within the Chemical Sciences, Geosciences, and Biosciences Division of the Office of Basic Energy Sciences under NREL Contract #DE-AC36-08-GO28308 (M.S.).Peer reviewe

The CP43 Proximal Antenna Complex of Higher Plant Photosystem II Revisited: Modeling and Hole Burning Study. I

The final version is available at: http://pubs.acs.org/journal/jpcbfkThe CP43 core antenna complex of photosystem II is known to possess two quasi-degenerate “red”-trap states (Jankowiak, R. et al. J. Phys. Chem. B 2000, 104, 11805). It has been suggested recently ( Zazubovich, V.; Jankowiak, R. J. Lumin. 2007, 127, 245) that the site distribution functions of the red states (A and B) are uncorrelated and that narrow holes are burned in the subpopulations of chlorophylls (Chls) from states A and B that are the lowest-energy Chl in their complex and previously thought not to transfer energy. This model of uncorrelated excitation energy transfer (EET) between the quasidegenerate bands is expanded by taking into account both electron−phonon and vibrational coupling. The model is applied to fit simultaneously absorption, emission, zero-phonon action, and transient hole burned (HB) spectra obtained for the CP43 complex with minimized contribution from aggregation. It is demonstrated that the above listed spectra can be well-fitted using the uncorrelated EET model, providing strong evidence for the existence of efficient energy transfer between the two lowest energy states, A and B (either from A to B or from B to A), in CP43. Possible candidate Chls for the low-energy A and B states are discussed, providing a link between CP43 structure and spectroscopy. Finally, we propose that persistent holes originate from regular NPHB accompanied by the redistribution of oscillator strength due to excitonic interactions, rather than photoconversion involving Chl−protein hydrogen bonding, as suggested before (Hughes J. L. et al. Biochemistry 2006, 45, 12345). In the accompanying paper ( Reppert, M.; Zazubovich, V.; Dang, N. C.; Seibert, M.; Jankowiak, R. J. Phys. Chem. B 2008, 9934), it is demonstrated that the model discussed in this manuscript is consistent with excitonic calculations, which also provide very good fits to both transient and persistent HB spectra obtained under non-line-narrowing conditions.This work was supported by the start-up funding at the Department of Chemistry, Kansas State University (RJ, NCD, MR and BN), and in part by the U.S. Department of Energy (DOE) EPSCoR grant (RJ), Energy Biosciences Program, Basic Energy Sciences, DOE (MS and NCD) and BFU2005-07422-CO2-01; Spain (RP). VZ acknowledges support by NSERC.Peer reviewe

Spectral and Conformational Analysis of Deoxyadenosine Adducts Derived from syn-and anti-Dibenzo[a,l]pyrene Diol Epoxides: Fluorescence Studies

Low-temperature fluorescence spectra and results of conformational studies with trans- syn-, cis-syn-, trans-anti-, and cis-anti-dibenzo[a,l]pyrene diol epoxide (DB[a,l]PDE)-derived deoxyadenosine (dA) adducts are presented and compared with those previously obtained for the stereoisomeric DB[a,l]P tetrols [Jankowiak, R., et al. (1997) Chem. Res. Toxicol. 10, 677-686]. In contrast to DB[a,l]P tetrols, for which only trans isomers exhibited two conformers, all stereoisomeric dA adducts adopt two different conformations with either half-chair or halfboat structures for the cyclohexenyl ring, and an "open"-or "folded"-type configuration between dA and the DB[a,l]P moiety. The major conformations observed for trans-syn-, cis-syn-, and cis-anti-DB [a,l]PDE-14-N 6 dA could be assigned on the basis of the previous calculations for the DB[a,l]P tetrols. The major conformers of the trans-syn-and cis-syn-DB [a,l]PDE-14-N 6 -dA adducts exist in conformations I and II, with their fluorescence origin bands at ∼382 and ∼389 nm, respectively. In conformation I, the cyclohexenyl ring adopts a half-boat structure with dA in a pseudoaxial position (an open configuration), whereas the cyclohexenyl ring in conformation II adopts a half-chair structure with dA in pseudoequatorial position (a folded configuration). The major conformation of cis-anti-DB[a,l]PDE-14-N 6 dA, with its origin band at ∼389 nm, was also assigned as a folded-type configuration with a half-chair structure in the cyclohexenyl ring. Molecular mechanics and dynamical simulations were performed for interpretation of the low-temperature fluorescence spectra and 1 H NMR coupling constants observed for the trans-anti-DB[a,l]PDE-14-N 6 dA adduct. The major conformer of this adduct has a half-chair structure in the cyclohexenyl ring, but a deviation from planarity in the fjord region different from that of conformer II of cis-anti-DB [a,l]PDE-N 6 dA. This new structure is labeled as conformer II′. Its (0,0) fluorescence band is at 388.1 and 388.3 nm in ethanol and glycerol/water glasses, respectively, consistent with the folded-type configuration revealed by the calculations. The fluorescence line-narrowed spectra reveal that the trans- dA adducts can be distinguished. Thus, their spectra should prove useful for identification of DB[a,l]P-DNA adducts formed at low levels in biological samples

Influence of C-5 substituted cytosine and related nucleoside analogs on the formation of benzo[a]pyrene diol epoxide-dG adducts at CG base pairs of DNA

Endogenous 5-methylcytosine (MeC) residues are found at all CG dinucleotides of the p53 tumor suppressor gene, including the mutational ‘hotspots' for smoking induced lung cancer. MeC enhances the reactivity of its base paired guanine towards carcinogenic diolepoxide metabolites of polycyclic aromatic hydrocarbons (PAH) present in cigarette smoke. In the present study, the structural basis for these effects was investigated using a series of unnatural nucleoside analogs and a representative PAH diolepoxide, benzo[a]pyrene diolepoxide (BPDE). Synthetic DNA duplexes derived from a frequently mutated region of the p53 gene (5′-CCCGGCACCC GC[15N3,13C1-G]TCCGCG-3′, + strand) were prepared containing [15N3, 13C1]-guanine opposite unsubstituted cytosine, MeC, abasic site, or unnatural nucleobase analogs. Following BPDE treatment and hydrolysis of the modified DNA to 2′-deoxynucleosides, N2-BPDE-dG adducts formed at the [15N3, 13C1]-labeled guanine and elsewhere in the sequence were quantified by mass spectrometry. We found that C-5 alkylcytosines and related structural analogs specifically enhance the reactivity of the base paired guanine towards BPDE and modify the diastereomeric composition of N2-BPDE-dG adducts. Fluorescence and molecular docking studies revealed that 5-alkylcytosines and unnatural nucleobase analogs with extended aromatic systems facilitate the formation of intercalative BPDE-DNA complexes, placing BPDE in a favorable orientation for nucleophilic attack by the N2 position of guanin

Conformations of depurinating adducts from dibenzo[a,l]pyrene diolepoxide

The extremely potent carcinogen dibenzo[a,l]pyrene (DB[a,l]P) is known to form a multitude of stable and unstable (depurinating) adducts, the latter via both the one-electron oxidation and the monooxygenation pathway. Laser induced fluorescence spectra of the depurinating adducts from DB[a,l]P diolepoxide show either a blueshift or a redshift, and in some solvent systems a double origin band is observed. These effects are believed to be due to subtle conformational equilibria and were further investigated for syn-DB[a,l]PDE-N7Gua, syn-DB[a,l]PDE-N7Ade, and syn-DB[a,l]PDE-N3Ade. Using molecular mechanics, molecular dynamics, and semi-empirical quantum mechanical calculations we found that these adducts may indeed exist in two conformations: one in which the saturated ring adopts a half-chair conformation (allowing for π-π stacking), and one in which a boat conformation is preferred. In the case of synDB[a,l]PDE-N7Ade the calculations predict, in agreement with experimental results, a strong preference for the latter conformation. This unusual conformation explains the experimentally observed 1H NMR coupling constants for the protons of the saturated ring

Site Energies of Active and Inactive Pheophytins in the Reaction Center of Photosystem II from Chlamydomonas Reinhardtii

31 Pags. The definitive version is available at: http://pubs.acs.org/journal/jpcbfkIt is widely accepted that the primary electron acceptor in various Photosystem II (PSII) reaction centers (RCs) is pheophytin a (Pheo a) within the D1 protein (PheoD1), while PheoD2 (within the D2 protein) is photochemically inactive. The Pheo site energies, however, have remained elusive, due to inherent spectral congestion. While most researchers over the last two decades assigned the Qy-states of PheoD1 and PheoD2 bands near 678–684 nm and 668–672 nm, respectively, recent modeling [Raszewski et al. Biophys. J. 2005, 88, 986–998; Cox et al. J. Phys. Chem. B 2009, 113, 12364–12374] of the electronic structure of the PSII RC reversed the location of the active and inactive Pheos, suggesting that the mean site energy of PheoD1 is near 672 nm, whereas PheoD2 (~677.5 nm) and ChlD1 (~680 nm) have the lowest energies (i.e., the PheoD2-dominated exciton is the lowest excited state). In contrast, chemical pigment exchange experiments on isolated RCs suggested that both pheophytins have their Qy absorption maxima at 676–680 nm [Germano et al. Biochem. 2001, 40, 11472–11482; Germano et al. Biophys. J. 2004, 86, 1664–1672]. To provide more insight into the site energies of both PheoD1 and PheoD2 (including the corresponding Qx transitions, which are often claimed to be degenerate at 543 nm) and to attest that the above two assignments are most likely incorrect, we studied a large number of isolated RC preparations from spinach and wild-type Chlamydomonas reinhardtii (at different levels of intactness) as well as the Chlamydomonas reinhardtii mutant (D2-L209H), in which the active branch PheoD1 is genetically replaced with chlorophyll a (Chl a). We show that the Qx-/Qy-region site-energies of PheoD1 and PheoD2 are ~545/680 nm and ~541.5/670 nm, respectively, in good agreement with our previous assignment [Jankowiak et al. J. Phys. Chem. B 2002, 106, 8803–8814]. The latter values should be used to model excitonic structure and excitation energy transfer dynamics of the PSII RCs.Partial support to B.N. (involved in calculations) was provided by the NSF EPSCoR Grant. V.Z. (involved in writing the manuscript) acknowledges support by NSERC. R.T.S., R.P., and M.S. were involved in the design and preparation of D2-mutant and RCs. They acknowledge support from USDOE, Photosynthetic Antennae Research Center (R.T.S.), MICIN (Grant AGL2008-00377) in Spain (R.P.), and the U.S. Department of Energy’s Photosynthetic Systems Program within the Chemical Sciences, Geosciences, and Biosciences Division of the Office of Basic Energy Sciences under NREL Contract #DE-AC36-08-GO28308 (M.S.).Peer reviewe

On light-induced photoconversion of B800 bacteriochlorophylls in the LH2 antenna of the purple sulfur bacterium Allochromatium vinosum

The B800-850 LH2 antenna from the photosynthetic purple sulfur bacterium Allochromatium vinosum exhibits an unusual spectral splitting of the B800 absorption band; i.e., two bands are well-resolved at 5 K with maxima at 805 nm (B800R) and 792 nm (B800B). To provide more insight into the nature of the B800 bacteriochlorophyll (BChl) a molecules, high-resolution hole-burning (HB) spectroscopy is employed. Both white light illumination and selective laser excitations into B800R or B800B lead to B800R → B800B phototransformation. Selective excitation into B800B leads to uncorrelated excitation energy transfer (EET) to B800R and subsequent B800R → B800B phototransformation. The B800B → B800R EET time is 0.9 ± 0.1 ps. Excitation at 808.4 nm (into the low-energy side of B800R) shows that the lower limit of B800R → B850 EET is about 2 ps, as the B800R → B800B phototransformation process could contribute to the corresponding zero-phonon hole width. The phototransformation of B800R leads to a ∼ 200 cm–1 average blue-shift of transition energies, i.e., B800R changes into B800B. We argue that it is unlikely that B800-B850 excitonic interactions give rise to a splitting of the B800 band. We propose that the latter is caused by different protein conformations that can lead to both strong or weak hydrogen bond(s) between B800 pigments and the protein scaffolding. Temperature-dependent absorption spectra of B800, which revealed a well-defined isosbestic point, support a two-site model, likely with strongly and weakly hydrogen-bonded B800 BChls. Thus, BChls contributing to B800R and B800B could differ in the position of the proton in the BChl carbonyl-protein hydrogen bond, i.e., proton dynamics along the hydrogen bond may well be the major mechanism of this phototransformation. However, the effective tunneling mass is likely larger than the proton mass