Paper Citing NAMD - Abstract
Mukhopadhyay, B. P.; Ghosh, B.; Bairagya, H. R.; Nandi, T. K.; Chakrabarti, B.; Bera, A. K.
Molecular modeling of the ternary complex of rusticyanin-cytochrome c(4)-cytochrome oxidase: An insight to possible H-bond mediated recognition and electron transfer reaction in T. ferrooxidans
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 25:543-551, APR 2008
The metabolism of Thiobacillus ferrooxidans involves electron transfer from the Fe+2 ions in the extracellular environment to the terminal oxygen in the bacterial cytoplasm through a series of periplasmic proteins like Rusticyanin (RCy), Cytochrome (Cyt c(4)), and Cytochrome oxidase (CcO). The energy minimization and MD studies reveal the stabilization of the three redox proteins in their ternary complex through the direct and water mediated H-bonds and electrostatic interaction. The surface exposed polar residues of the three proteins, i.e., RCy (His 143, Thr 146, Lys 8 1, Glu 20), Cyt c(4) (Asp 5, 15, 52, Set 14, Glu 61), and CcO (Asp 135, Glu 126, 140, 142, Thr 177) formed the intermolecular hydrogen bonds and stabilized the ternary complex. The oxygen (O-epsilon 1) of Glu 126, 140, and 142 on subunit II of the CcO interact to the exposed side-chain and O-b atoms of the Asp 52 of Cyt c(4) and Glu 20 and Leu 12 of RCy. The Asp 135 of subunit II also forms H-bond with the N-epsilon atom of Lys 81 of RCy. The O-epsilon 1 of Glu 61 of Cyt c(4) is also H-bonded to O-gamma atom of Thr 177 of CcO. Solvation followed by MD studies of the ternary protein complex revealed the presence of seven water molecules in the interfacial region of the interacting proteins. Three of the seven water molecules (W 79, W 437, and W 606) bridged the three proteins by forming the hydrogen bonded network (with the distances similar to 2.10-2.95 angstrom) between the Lys 81 (RCy), Glu 61 (Cyt c(4)), and Asp 135 (CcO). Another water molecule W 603 was H-bonded to Tyr 122 (CcO) and interconnected the Lys 81 (RCy) and Asp 135 (CcO) through the water molecules W 606 and W 437. The other two water molecules (W 21 and W 455) bridged the RCy to Cyt c(4) through H-bonds, whereas the remaining W 76 interconnected the His 53 (Cytc(4)) to Glu 126 (CcO) with distances similar to 2.95-3.0 angstrom.
