Abstract
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.