Quantum chemistry study of proteins in bacterial photosynthetic reaction center

Abstract

Quantum chemistry study on proteins L and M in the Rhodopseudomonas viridis (Rh. viridis) photosynthetic reaction center (PRC) are presented. The calculations were performed at ab initio level with Clementi minimal basis set by means of the overlapping‐dimer approximation (ODA)–extended negative factor counting (ENFC) method. Additional point charges were added to individual residues to simulated ionized aqueous environment of the proteins in the calculations. Meanwhile, the electronic structure of protein complex MH (protein M plus the α‐helix segment of protein H) was studied as well to examine the weak interaction between proteins M and H. As the first case of global quantum chemistry calculation for proteins in PRC, details of the electronic structure and the influence of proteins on the electron transfer process (ET) were studied. Moreover, new three‐dimensional structure plots of subunit L and M were given based on the distribution of the components of frontier orbitals in order to more clearly understand the structure–function relationship of the proteins in electron transfer reactions. Calculation results indicated that the components of frontier orbitals are extremely localized at individual residues. Amino acid residues, having contributed to the frontier orbitals of protein L, are located at the flexible random area of L, while those having contributed to the frontier orbitals of protein M are located at the rigid α‐helix area. This asymmetry of proteins L and M provides new understanding the ET reaction that takes place mainly along branch L in the PRC of Rh. viridis. Meanwhile, there is frontier orbital localized amino acid distribution around the V‐shaped pocket areas of protein L (M) that were expected to have an important interaction with QA (QB). All results indicate that protein provided a heterogeneous environment for pigment molecules and some important interaction between protein residues and pigment molecules are worthy of further investigation. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 30–40, 2001