Advanced theory of excitation energy transfer in dimers.

Previously, we developed a unified theory of the excitation energy transfer (EET) in dimers, which is applicable to all of the cases of excitonic coupling strength (Kimura, A.; Kakitani, T.; Yamato, T. J. Phys. Chem. B 2000, 104, 9276). This theory was formulated only for the forward reaction of the EET. In the present paper, we advanced this theory so that it might include the backward reaction of the EET as well as the forward reaction. This new theory is formulated on the basis of the generalized master equation (GME), without using physically unclear assumptions. Comparing the present result with the previous one, we find that the excitonic coupling strengths of criteria between exciton and partial exciton and between hot transfer and hopping (Förster) mechanisms are reduced by a factor of 2. The critical coherency eta c is also reduced significantly.

Spectral tuning of photoactive yellow protein.

We report a theoretical study on the optical properties of a small, water-soluble photosensory receptor, photoactive yellow protein (PYP). A hierarchical ab initio molecular orbital calculation accurately evaluated the optical absorption maximum of the wild-type, as well as the lambda(max) values of 12 mutants. Electronic excitation of the chromophore directly affects the electronic state of nearby atoms in the protein environment. This effect is explicitly considered in the present study. Furthermore, the spectral tuning mechanism of PYP was investigated at the atomic level. The static disorder of a protein molecule is intimately related to the complex nature of its energy landscape. By using molecular dynamics simulation and quantum mechanical structure optimization, we obtained multiple minimum energy conformations of PYP. The statistical distribution of electronic excitation energies of these minima was compared with the hole-burning experiment (Masciangioli, T. [2000] Photochem. Photobiol. 72, 639), a direct observation of the distribution of excitation energies.

Unique mechanisms of excitation energy transfer, electron transfer and photoisomerization in biological systems.

We discuss unique mechanisms typical in the elementary processes ofbiological functions. We focus on three topics. Excitation energytransfer in the light-harvesting antenna systems of photosyntheticbacteria is unique in its structure and the energy transfer mechanism. Inthe case of LH2 of Rhodopseudomonas acidophila, the B850 intra-ringenergy transfer and the inter-ring energy transfer between B800 and B850take place by the intermediate coupling mechanism of energy transfer. Theexcitonic coherent domain shows a wave-like movement along the ring, andthis property is expected to play a significant role in the inter-ringenergy transfer between LH2's. The electron transfer in biological systemsis mostly long-range electron transfer that occurs by the electrontunneling through the protein media. There is a long-standing problem thatwhich part of protein media is used for the electron tunneling root. As aresult of our detailed analysis, we found that the global electron tunnelingroot is a little winded with a width of a few angstrom, reflecting theproperty of tertiary and secondary structures of the protein and it isaffected by the thermal fluctuation of protein structure. Photoisomerizationof rhodopsin is very unique: The cis-transphotoisomerization ofrhodopsin occurs only around the C11 = C12 bond in the counterclockwisedirection. Its molecular mechanism is resolved by our MD simulation studyusing the structure of rhodopsin which was recently obtained by the X-raycrystallographic analysis.

Color tuning mechanism of human red and green visual pigments.

We investigated the molecular mechanism of a rather large red shift of 31 nm in a human red pigment compared with a human green pigment. In this analysis, we paid special attention to the phenomenon of nonadditivity of spectral shifts due to substitution of the key amino acids (OH-bearing amino acids) and the phenomenon of cooperativity by which the spectral shifts due to substitution of the key amino acids in the protein environment of red pigment are about 1.5 times larger than that in the protein environment of green pigment. The analysis was made by using a model of three active sites on which the key amino acids are located and four effective sites by which the effect of the key amino acids is modified. As a result, we found that the interaction between the active sites that occurs through the repolarization of the chromophore induced by the key amino acid is essential for the nonadditivity phenomenon. We also found that the interaction between the active site and the effective site plays a major role in the cooperativity phenomenon. More directly, we say that the highly polarizable property of the chromophore is the origin of the rather large red shift in red pigment. Based on these analyses, we conclude that the interaction between the polarizable chromophore and the protein moiety has the capability of producing a significant spectral shift, at least 1000 cm-1, even by substitution of moderate polar residues of the OH-bearing amino acids.

Effects of freezing out protein vibrational modes on electron transfer kinetics in bacterial reaction centers.

We propose a model that some vibrational modes of the protein in bacterial photosynthetic reaction centers may be frozen at low temperatures. The freezing of the protein-environmental motion can affect the electron transfer rate through changes in the reorganization energy and the free energy gap. We offer a qualitative explanation of the different kinetics of the ET processes in reaction centers which are cooled in the dark and cooled under illumination.

Fluorescence quantum yield of visual pigments: evidence for subpicosecond isomerization rates.

The fluorescence quantum yields (phi f) for bovine and squid rhodopsins are determined. Both pigments yield similar results, with an average value for phi f of 1.2 (+/- 0.5) X 10(-5). Since the estimated radiative lifetime of rhodopsin is 5 nsec, the rate constant of the process that competes with fluorescence must be on the order of 0.1 psec. Given the large quantum yield for isomerization of rhodopsin's retinal chromophore, this process is likely to correspond to the motion along retinal's C11-C12 torsional coordinate that leads to cis-trans isomerization. An empirical excited-state potential energy curve along this coordinate is derived. It is shown that subpicosecond torsional motion to highly twisted nonfluorescing regions of the potential is possible and, in fact, likely. Our results require the existence of a barrier-less excited-state potential energy curve and suggest that cis-trans isomerization occurs in less than 1 psec.

Squid retinochrome. Configurational changes of the retinal chromophore.

The configurations of the retinal chromophore in light and dark reactions of squid retinochrome were investigated by means of high-performance liquid chromatography. Orange light isomerized the chromophore of retinochrome, all-trans-retinal, mainly to the 11-cis configuration in metaretinochrome. Irradiation with shorter-wavelength lights not only accelerates the photoreversal of metaretinochrome to retinochrome but also leads to a slight production of isoretinochrome (13-cis-retinochrome), yielding a photoequilibrium mixture of three kinds of retinochrome. 13-cis- and 9-cis-retinochromes are photosensitive, and are converted into metaretinochrome upon irradiation with orange light. When steadily exposed to orange light in the presence of a trace of retinochrome-protein, all of the all-trans-, 13-cis-, and 9-cis-retinals are catalytically isomerized only to the 11-cis form, although the reaction rate is reduced in the order of the retinals listed above. In the dark, 9-cis-retinochrome, like retinochrome, remains unchanged, but both meta- and 13-cis-retinochromes slowly change to retinochrome. The chromophore of 13-cis-retinochrome changes directly to the all-trans form, whereas the 11-cis chromophore of metaretinochrome goes to all-trans mainly through the 13-cis form. The direct isomerization from 11-cis to all-trans hardly occurs at temperatures as low as 20 degrees C, and shows high values of the activation enthalpy and entropy changes. Based upon these findings, the role of retinochrome in the photoreception of the visual cells is discussed.

Theoretical studies of the electrochromic response of carotenoids in photosynthetic membranes.

Molecular orbital calculations are carried out on a number of carotenoids in the presence of an external charge and a constant electric field. The external charge is used to represent the strong permanent field that is believed to polarize carotenoids in photosynthetic membranes and thus to account for their linear response to the transmembrane potential. Our calculations show that the in vitro leads to in vivo spectral shifts of carotenoids (approximately 25 nm) can be produced by a charge in close proximity to the molecule. The interaction of the induced dipole moment with a constant field accounts for the observed magnitude of the electrochromic response in photosynthetic bacteria. The existence of a second pool of carotenoids that shows a significant (approximately 20 nm) wavelength shift but no electrochromic response can be explained by an external charge positioned near the center of the molecule that affects its absorption maximum while inducing essentially no dipole moment. The spectral shift for this pool is due to the induction of higher multipoles. These also account for discrepancies that arise when one attempts to account quantitatively for available experimental results on carotenoid band shifts in terms of classical electrochromic theory.

A possible new mechanism of temperature dependence of electron transfer in photosynthetic systems.

A new theory for the electron transfer by the non-adiabatic process is formulated taking into account the origin shift and the frequency change of the vibration. The resultant formulas are quite similar to those of Jortner (Jortner, J. (1976) J. Chem. Phys. 64, 4860-4867) except that the free energy gap delta G is used instead of the energy gap delta E. By applying this theory to the photosynthetic electron transfer, the role of the remarkable temperature dependence of the electron transfer from cytochrome to P+ in Chromatium vinosum and the experimental data were reproduced very well using a small value of the coupling strength in contrast with the previous theory. This implies that proteins play a role to exclude many of the solvent molecules from the region of the electron transfer reaction between the donor and acceptor molecules. The negative activation process in the back electron transfer from QA- to P+, the very slow back electron transfer from I- to P+ and the solvent isotope effect on the cytochrome oxidation are also successfully explained by this new theory. It is shown that even a qualitative conclusion as to the molecular parameters obtained from the temperature dependence of the electron transfer is different between the present theory and that of Jortner.

Molecular mechanism for the initial process of visual excitation. IV. Energy surfaces of visual pigments and photoisomerization mechanism.

Using the twisted conformations of the chromophores for visual pigments and intermediates which were theoretically determined in the previous paper, energy surfaces of the pigment at - 190 degrees C were obtained as functions of the torsional angles theta 9-10 and theta 11-12 or of the torsional angles theta 9-10 and theta 13-14. In these calculations, the existence of specific reaction paths between rhodopsin (R) and bathorhodopsin (B), between isorhodopsin I (I) and bathorhodopsin, and between isorhodopsin II (I') and bathorhodopsin were assumed. It was shown that the total energy surfaces of the excited states had minima C1 at theta 9-10 approximately -10 degrees and theta 11-12 approximately -80 degrees, C2 at theta 9-10 approximately -85 degrees and theta 11-12 approximately -5 degrees, and C3 at theta 9-10 approximately -0 degree and theta 13-14 approximately -90 degrees. These minima are considered to correspond to the thermally barrierless common states as denoted by Rosenfeld et al. Using the total energy surfaces in the ground and excited states, the molecular mechanism of the photoisomerization reaction was suggested. Quantum yields for the photoconversions among R, I, I' and B were related to the rates of vibrational relaxations, radiationless transitions and thermal excitations. Some discussion was made of the temperature effect on the quantum yield. Similar calculations of the energy surfaces were also made at other temperatures where lumirhodopsin or metarhodopsin I is stable. Relative energy levels of the pigments and the intermediates were discussed.

Molecular mechanism for the initial process of visual excitation. III. Theoretical studies of optical spectra and conformations of chromophores in visual pigments, their analogues and intermdiates based on the torsion model.

The torsion model with which we proposed to interpret the specific properties of the photoisomerization reaction of rhodopsin has been developed to apply to isorhodopsin I, isorhodopsin II and some intermediates. Based on this model, optical absorption wavelengths and oscillator strengths, as well as rotational strengths of visual pigments, analogues and intermediates at low temperatures are analyzed by varying twisted conformations of the chromophores. As a result, it was found that most of the optical data could be very well accounted for quantitatively by the torsion model. The twisting characters in the chromophore of rhodopsin are very similar to those of isorhodopsin. The obtained conformations of the chromophores are very similar in rhodopsin and its analogues, and in isorhodopsin and its analogues. Those of the chromophores of bathorhodopsin, lumirhodopsin and metarhodopsin I are similar to one another except that the conjugated chain of metarhodopsin I bends considerably when compared with the other intermediates.