X-ray structures of carbonmonoxymyoglobin (MbCO) are available for different pH values. We used conventional electrostatic continuum methods to calculate the titration behavior of MbCO in the pH range from 3 to 7. For our calculations, we considered five different x-ray structures determined at pH values of 4, 5, and 6. We developed a Monte Carlo method to sample protonation states and conformations at the same time so that we could calculate the population of the considered MbCO structures at different pH values and the titration behavior of MbCO for an ensemble of conformers. To increase the sampling efficiency, we introduced parallel tempering in our Monte Carlo method. The calculated population probabilities show, as expected, that the x-ray structures determined at pH 4 are most populated at low pH, whereas the x-ray structure determined at pH 6 is most populated at high pH, and the population of the x-ray structures determined at pH 5 possesses a maximum at intermediate pH. The calculated titration behavior is in better agreement with experimental results compared to calculations using only a single conformation. The most striking feature of pH-dependent conformational changes in MbCO-the rotation of His-64 out of the CO binding pocket-is reproduced by our calculations and is correlated with a protonation of His-64, as proposed earlier.

The electron-transfer reactions involving the quinones in the bacterial photosynthetic reaction center (bRC) are coupled to a proton uptake by the bRC. In this study, we calculated the energies of the different states of the bRC occurring during these electron-transfer and protonation reactions by an electrostatic model. We considered the possibility that titratable groups of the bRC can change their protonation during these reactions. The protonation probabilities of titratable groups were obtained by a Monte Carlo calculation. In contrast to earlier studies by other groups, we used atomic partial charges derived from quantum-chemical calculations. Our calculated reaction energies are in agreement with experiments. We found that the proton uptake by the bRC is coupled more strongly to changes of the redox state of the quinones than to changes of their protonation state. Thus, the proton uptake by the bRC occurs predominantly before the protonation of QB. According to our computations, the reduction of QB* - to the doubly negative state QB2- is energetically even more unfavorable in the bRC than in solution. Therefore, we suggest that the second electron transfer from QA to QB occurs after QB has received its first proton. We found that the QA. -QB. - state is more populated at pH 7.5 than the QA. -QB.H state. The low population of the QA. -QB.H state may be the reason why the singly protonated QB could not be detected spectroscopically. Our calculations imply that the first protonation of QB. - is a prerequisite for the second electron transfer between QA and QB. Therefore, a pH dependence of the equilibrium between the states QA. -QB. - and QA. -QB. H can also explain the experimentally observed pH dependence of the rate for the second electron-transfer step. On the basis of our calculated reaction energies, we propose the following sequence for the electron-transfer and protonation reactions: (1) first electron transfer from QA to QB, (2) first protonation of QB (at the distal oxygen close to Ser L223), (3) second electron transfer from QA to QB, and (4) second protonation of QB (at the proximal oxygen close to His L190).

The electron transfer between the two quinones Q(A) and Q(B) in the bacterial photosynthetic reaction center (bRC) is coupled to a conformational rearrangement. Recently, the X-ray structures of the dark-adapted and light-exposed bRC from Rhodobacter sphaeroides were solved, and the conformational changes were characterized structurally. We computed the reaction free energy for the electron transfer from to Q(B) in the X-ray structures of the dark-adapted and light-exposed bRC from Rb. sphaeroides. The computation was done by applying an electrostatic model using the Poisson-Boltzmann equation and Monte Carlo sampling. We accounted for possible protonation changes of titratable groups upon electron transfer. According to our calculations, the reaction energy of the electron transfer from to Q(B) is +157 meV for the dark-adapted and -56 meV for the light-exposed X-ray structure; i.e., the electron transfer is energetically uphill for the dark-adapted structure and downhill for the light-exposed structure. A common interpretation of experimental results is that the electron transfer between and Q(B) is either gated or at least influenced by a conformational rearrangement: A conformation in which the electron transfer from to Q(B) is inactive, identified with the dark-adapted X-ray structure, changes into an electron-transfer active conformation, identified with the light-exposed X-ray structure. This interpretation agrees with our computational results if one assumes that the positive reaction energy for the dark-adapted X-ray structure effectively prevents the electron transfer. We found that the strongly coupled pair of titratable groups Glu-L212 and Asp-L213 binds about one proton in the dark-adapted X-ray structure, where the electron is mainly localized at Q(A), and about two protons in the light-exposed structure, where the electron is mainly localized at Q(B). This finding agrees with recent experimental and theoretical studies. We compare the present results for the bRC from Rb. sphaeroides to our recent studies on the bRC from Rhodopseudomonas viridis. We discuss possible mechanisms for the gated electron transfer from to Q(B) and relate them to theoretical and experimental results.

In photosynthesis, light is captured by antenna proteins. These proteins transfer the excitation energy with almost 100% quantum efficiency to the reaction centers, where charge separation takes place. The time scale and pathways of this transfer are controlled by the protein scaffold, which holds the pigments at optimal geometry and tunes their excitation energies (site energies). The detailed understanding of the tuning of site energies by the protein has been an unsolved problem since the first high-resolution crystal structure of a light-harvesting antenna appeared >30 years ago [Fenna RE, Matthews BW (1975) Nature 258:573-577].Here, we present a combined quantum chemical/electrostatic approach to compute site energies that considers the whole protein in atomic detail and provides the missing link between crystallography and spectroscopy. The calculation of site energies of the Fenna-Matthews-Olson protein results in optical spectra that are in quantitative agreement with experiment and reveals an unexpectedly strong influence of the backbone of two ␣-helices. The electric field from the latter defines the direction of excitation energy flow in the Fenna-Matthews-Olson protein, whereas the effects of amino acid side chains, hitherto thought to be crucial, largely compensate each other. This result challenges the current view of how energy flow is regulated in pigment-protein complexes and demonstrates that attention has to be paid to the backbone architecture.energy transfer ͉ light-harvesting ͉ optical spectra ͉ photosynthesis ͉ structure-based simulation P hotosynthesis is the fundamental biological process in which solar energy is converted into biomass. The first step is the capture of light by arrays of protein-bound dye molecules (pigments). These pigment-protein complexes (PPCs) are therefore termed light-harvesting complexes or antenna proteins (1). They transfer the excitation energy with high quantum yield to specialized PPCs, the reaction centers, where the energy is used to trigger the chemical modification of substrates. To guide the excitation energy flow in a certain direction there has to be an energy sink, that is, the pigments in the target region are required to absorb at lower energies than the initially excited chromophores. A complication of this simple picture arises from long-range electrostatic interactions between the local excitations (excitonic couplings), which are a prerequisite for energy transfer. These couplings cause the excited states of the PPC (exciton states) to be delocalized, that is, their electronic wave functions contain contributions of several pigments in the complex. Directed energy transport results from energetic relaxation transferring population between exciton states of different spatial extents. The latter depend crucially on excitonic couplings and site energies, so that the elucidation of energy-transfer mechanisms on the basis of spectroscopic data (2-4) and crystal structures (5-7) requires knowledge of both these quantities (8, 9), which are not direct...

No abstract