Madhu Sudhan Bhusal1*, Kiran Pudasainee1 and Hari Prasad Lamichhane1,2
The Photochemical reaction center in purple bacteria is carried out in the pigments which are bound and arranged in specific way by the proteins. In this work, we construct the potential energy surface from the Q_A binding site at the periphery of 10 Å sphere, to make more visualize the structural arrangement of Q_A binding site. The ubiquinone (Q_A) molecule contains two carbonyl oxygen atoms in the benzoquinone ring. The O_1 and O_4 atoms of ubiquinone make hydrogen bonds with ALA260 N - O_1 (≈2.84 Å away) and HIS219 N - O_4 (≈2.78 Å away) respectively, which help to stabilize the ubiquinone. The rest of the molecule is surrounded by mostly hydrophobic residues making van der Waal’s contacts. These segments form the entrance of the Q_A binding pocket and membrane binding surface. In fact, the Q_A binding site is deeply buried in the protein complex, and the positively charged residues surrounded near the membrane involved in interacting with the ubiquinone head group to facilitate the electron transfer
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