Marcel Schmidt am Busch

The Eighth Bacteriochlorophyll Completes the Excitation Energy Funnel in the FMO Protein

The Fenna-Matthews-Olson (FMO) light-harvesting protein connects the outer antenna system (chlorosome/baseplate) with the reaction center complex in green sulfur bacteria. Since its first structure determination in the mid-70s, this pigment-protein complex has become an important model system to study excitation energy transfer. Recently, an additional bacteriochlorophyll a (the eighth) pigment was discovered in each subunit of this homotrimer. Our structure-based calculations of the optical properties of the FMO protein demonstrate that the eighth pigment is the linker to the baseplate, confirming recent suggestions from crystallographic studies.

Normal mode analysis of the spectral density of the Fenna-Matthews-Olson light-harvesting protein: how the protein dissipates the excess energy of excitons.

We report a method for the structure-based calculation of the spectral density of the pigment–protein coupling in light-harvesting complexes that combines normal-mode analysis with the charge density coupling (CDC) and transition charge from electrostatic potential (TrEsp) methods for the computation of site energies and excitonic couplings, respectively. The method is applied to the Fenna–Matthews–Olson (FMO) protein in order to investigate the influence of the different parts of the spectral density as well as correlations among these contributions on the energy transfer dynamics and on the temperature-dependent decay of coherences. The fluctuations and correlations in excitonic couplings as well as the correlations between coupling and site energy fluctuations are found to be 1 order of magnitude smaller in amplitude than the site energy fluctuations. Despite considerable amplitudes of that part of the spectral density which contains correlations in site energy fluctuations, the effect of these correlations on the exciton population dynamics and dephasing of coherences is negligible. The inhomogeneous charge distribution of the protein, which causes variations in local pigment–protein coupling constants of the normal modes, is responsible for this effect. It is seen thereby that the same building principle that is used by nature to create an excitation energy funnel in the FMO protein also allows for efficient dissipation of the excitons’ excess energy.

Structure-Based Calculations of Optical Spectra of Photosystem I Suggest an Asymmetric Light-Harvesting Process

Optical line shape theory is combined with a quantum-chemical/electrostatic calculation of the site energies of the 96 chlorophyll a pigments and their excitonic couplings to simulate optical spectra of photosystem I core complexes from Thermosynechococcus elongatus. The absorbance, linear dichroism and circular dichroism spectra, calculated on the basis of the 2.5 A crystal structure, match the experimental data semiquantitatively allowing for a detailed analysis of the pigment-protein interaction. The majority of site energies are determined by multiple interactions with a large number (>20) of amino acid residues, a result which demonstrates the importance of long-range electrostatic interactions. The low-energy exciton states of the antenna are found to be located at a nearest distance of about 25 A from the special pair of the reaction center. The intermediate pigments form a high-energy bridge, the site energies of which are stabilized by a particularly large number (>100) of amino acid residues. The concentration of low energy exciton states in the antenna is larger on the side of the A-branch of the reaction center, implying an asymmetric delivery of excitation energy to the latter. This asymmetry in light-harvesting may provide the key for understanding the asymmetric use of the two branches in primary electron transfer reactions. Experiments are suggested to check for this possibility.

Site-dependence of van der Waals interaction explains exciton spectra of double-walled tubular J-aggregates

The simulation of the optical properties of supramolecular aggregates requires the development of methods, which are able to treat a large number of coupled chromophores interacting with the environment. Since it is currently not possible to treat large systems by quantum chemistry, the Frenkel exciton model is a valuable alternative. In this work we show how the Frenkel exciton model can be extended in order to explain the excitonic spectra of a specific double-walled tubular dye aggregate explicitly taking into account dispersive energy shifts of ground and excited states due to van der Waals interaction with all surrounding molecules. The experimentally observed splitting is well explained by the site-dependent energy shift of molecules placed at the inner or outer side of the double-walled tube, respectively. Therefore we can conclude that inclusion of the site-dependent dispersive effect in the theoretical description of optical properties of nanoscaled dye aggregates is mandatory.

Structure-based modeling of energy transfer in photosynthesis

We provide a minimal model for a structure-based simulation of excitation energy transfer in pigment–protein complexes (PPCs). In our treatment, the PPC is assembled from its building blocks. The latter are defined such that electron exchange occurs only within, but not between these units. The variational principle is applied to investigate how the Coulomb interaction between building blocks changes the character of the electronic states of the PPC. In this way, the standard exciton Hamiltonian is obtained from first principles and a hierarchy of calculation schemes for the parameters of this Hamiltonian arises. Possible extensions of this approach are discussed concerning (i) the inclusion of dispersive site energy shifts and (ii) the inclusion of electron exchange between pigments. First results on electron exchange within the special pair of photosystem II of cyanobacteria and higher plants are presented and compared with earlier results on purple bacteria. In the last part of this mini-review, the coupling of electronic and nuclear degrees of freedom is considered. First, the standard exciton–vibrational Hamiltonian is parameterized with the help of a normal mode analysis of the PPC. Second, dynamical theories are discussed that exploit this Hamiltonian in the study of dissipative exciton motion.

Revealing the functional states in the active site of BLUF photoreceptors from electrochromic shift calculations.

Photoexcitation with blue light of the flavin chromophore in BLUF photoreceptors induces a switch into a metastable signaling state that is characterized by a red-shifted absorption maximum. The red shift is due to a rearrangement in the hydrogen bond pattern around Gln63 located in the immediate proximity of the isoalloxazine ring system of the chromophore. There is a long-lasting controversy between two structural models, named Q63A and Q63J in the literature, on the local conformation of the residues Gln63 and Tyr21 in the dark state of the photoreceptor. As regards the mechanistic details of the light-activation mechanism, rotation of Gln63 is opposed by tautomerism in the Q63A and Q63J models, respectively. We provide a structure-based simulation of electrochromic shifts of the flavin chromophore in the wild type and in various site-directed mutants. The excellent overall agreement between experimental and computed data allows us to evaluate the two structural models. Compelling evidence is obtained that the Q63A model is incorrect, whereas the Q63J is fully consistent with the present computations. Finally, we confirm independently that a keto–enol tautomerization of the glutamine at position 63, which was proposed as molecular mechanism for the transition between the dark and the light-adapted state, explains the measured 10 to 15 nm red shift in flavin absorption between these two states of the protein. We believe that the accurateness of our results provides evidence that the BLUF photoreceptors absorption is fine-tuned through electrostatic interactions between the chromophore and the protein matrix, and finally that the simplicity of our theoretical model is advantageous as regards easy reproducibility and further extensions.

The quest for energy traps in the CP43 antenna of photosystem II

To identify energy traps in CP43, a subcomplex of the photosystem II antenna system, site energies and excitonic couplings of the QY transitions of chlorophyll (Chl) a pigments bound to CP43 are computed using electrostatic models of pigment-protein and pigment-pigment interactions. The computations are based on recent crystal structures of the photosystem II core complex with resolutions of 1.9 and 2.1Å and compared to earlier results obtained at 2.9Å resolution. Linear optical spectra (i.e., absorption, linear dichroism, circular dichroism, and fluorescence) are simulated using the computed excitonic couplings, a refinement fit for the site energies, and a dynamical theory of optical lineshapes. A comparison of the obtained root mean square deviation of about 100 cm(-1) between directly calculated and refined site energies with the maximum range of about 350 cm(-1) of directly calculated site energies shows that the combined quantum chemical/electrostatic approach provides a semi-quantitative agreement with experiment. Possible reasons for the deviations are discussed, including limits of the electrostatic models and the lineshape theory as well as structural alterations of CP43 upon detachment from the core complex. Based on the simulations, an assignment of the two low-energy exciton states A and B of CP43, that where observed earlier in hole burning studies, is suggested. State A is assigned to a localized exciton state on Chl 37 in the lumenal layer of pigments. State B is assigned to an exciton state that is delocalized over several pigments in the cytoplasmic layer. The delocalization explains the smaller inhomogeneous width of state B compared to state A observed in hole burning spectra, which is proposed to be due to exchange narrowing. The assignment of states A and B largely confirms our earlier suggestion that was based on a fit of linear optical spectra and electrostatic calculations using the 2.9Å resolution structure. Interestingly, for the latter structure, the site energy of Chl 37 is obtained closer to the refined value than for 1.9 and 2.1Å resolution. This is explained by a variation of the site energy due to the influence of lipids that might be different in the core complex and isolated CP43. To remove remaining uncertainties in the assignment of states A and B, target sites for mutagenesis experiments are proposed based on the electrostatic computations. In particular, it is suggested to mutate Trp C63 close to Chl 37 to probe the identity of state A and to mutate Arg C41 close to Chl 47 to probe state B.

Structure Prediction of Self-Assembled Dye Aggregates from Cryogenic Transmission Electron Microscopy, Molecular Mechanics, and Theory of Optical Spectra

Cryogenic transmission electron microscopy (cryo-TEM) studies suggest that TTBC molecules self-assemble in aqueous solution to form single-walled tubes with a diameter of about 35 Å. In order to reveal the arrangement and mutual orientations of the individual molecules in the tube, we combine information from crystal structure data of this dye with a calculation of linear absorbance and linear dichroism spectra and molecular dynamics simulations. We start with wrapping crystal planes in different directions to obtain tubes of suitable diameter. This set of tube models is evaluated by comparing the resulting optical spectra with experimental data. The tubes that can explain the spectra are investigated further by molecular dynamics simulations, including explicit solvent molecules. From the trajectories of the most stable tube models, the short-range ordering of the dye molecules is extracted and the optimization of the structure is iteratively completed. The final structural model is a tube of rings with 6-fold rotational symmetry, where neighboring rings are rotated by 30° and the transition dipole moments of the chromophores form an angle of 74° with respect to the symmetry axis of the tube. This model is in agreement with cryo-TEM images and can explain the optical spectra, consisting of a sharp red-shifted J-band that is polarized parallel to to the symmetry axis of the tube and a broad blue-shifted H-band polarized perpendicular to this axis. The general structure of the homogeneous spectrum of this hybrid HJ-aggregate is described by an analytical model that explains the difference in redistribution of oscillator strength inside the vibrational manifolds of the J- and H-bands and the relative intensities and excitation energies of those bands. In addition to the particular system investigated here, the present methodology can be expected to aid the structure prediction for a wide range of self-assembled dye aggregates.

Theory of FRET “Spectroscopic Ruler” for Short Distances: Application to Polyproline

Förster resonance energy transfer (FRET) is an important mechanism for the estimation of intermolecular distances, e.g., in fluorescent labeled proteins. The interpretations of FRET experiments with standard Förster theory relies on the following approximations: (i) a point-dipole approximation (PDA) for the coupling between transition densities of the chromophores, (ii) a screening of this coupling by the inverse optical dielectric constant of the medium, and (iii) the assumption of fast isotropic sampling over the mutual orientations of the chromophores. These approximations become critical, in particular, at short intermolecular distances, where the PDA and the screening model become invalid and the variation of interchromophore distances, and not just orientations, has a critical influence on the excitation energy transfer. Here, we present a quantum chemical/electrostatic/molecular dynamics (MD) method that goes beyond all of the above approximations. The Poisson-TrEsp method for the ab initio/electrostatic calculation of excitonic couplings in a dielectric medium is combined with all-atom molecular dynamics (MD) simulations to calculate FRET efficiencies. The method is applied to analyze single-molecule experiments on a polyproline helix of variable length labeled with Alexa dyes. Our method provides a quantitative explanation of the overestimation of FRET efficiencies by the standard Förster theory for short interchromophore distances for this system. A detailed analysis of the different levels of approximation that connect the present Poisson-TrEsp/MD method with Förster theory reveals error compensation effects, between the PDA and the neglect of correlations in interchromophore distances and orientations on one hand and the neglect of static disorder in orientations and interchromophore distances on the other. Whereas the first two approximations are found to decrease the FRET efficiency, the latter two overcompensate this decrease and are responsible for the overestimation of the FRET efficiency by Förster theory.