Molecular Modeling of the Ternary Complex of Rusticyanin-Cytochrome c₄-Cytochrome Oxidase: An Insight to Possible H-Bond Mediated Recognition and Electron Transfer Reaction inT.ferrooxidans

Abstract

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 c4), 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 81, Glu 20), Cyt c4 (Asp 5, 15, 52, Ser 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 (Oepsilon1) of Glu 126, 140, and 142 on subunit II of the CcO interact to the exposed side-chain and Ob atoms of the Asp 52 of Cyt c4 and Glu 20 and Leu 12 of RCy. The Asp 135 of subunit II also forms H-bond with the Nepsilon atom of Lys 81 of RCy. The Oepsilon1 of Glu 61 of Cyt c4 is also H-bonded to Ogamma 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 approximately 2.10-2.95 A) between the Lys 81 (RCy), Glu 61 (Cyt c4), 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 c4 through H-bonds, whereas the remaining W 76 interconnected the His 53 (Cytc4) to Glu 126 (CcO) with distances approximately 2.95-3.0 A.

Cupredoxins—A study of how proteins may evolve to use metals for bioenergetic processes

“…54, 55 No crystal or NMR structure of the rusticyanin-cytochrome c 4 complex is available; however, modeling studies revealed possible hydrogen-bond mediated recognition sites that included several water molecules that could stabilize this complex. 56, 57…”

Computational Structure Prediction Provides a Plausible Mechanism for Electron Transfer by the Outer Membrane Protein Cyc2 fromAcidithiobacillus ferrooxidans

“…Large interatomic distances between H57 and the copper ion make it unlikely that all the histidines chelate the same copper ion. We hypothesize that H57 could instead play a role in the electron transfer pathway between Cyc2 and Rcy, and D58 may be involved in stabilizing the interface between Cyc2 and Rcy due to its hydrogen bonding ability (66). Therefore, this residue patch is thought to be most likely Cyc2-Rcy interface on Rcy.…”

“…1b). The periplasmic proteins Rcy and Cyc1 have previously been crystallized and characterized (87; 1), and the surface interactions at the interface between Rcy and Cyc1 have been determined (66). The Cyc2 protein (485 amino acids, MW 52.4 kDa, Fig.…”

Structural Analysis of Respirasomes in Electron Transfer Pathway of Acidithiobacillus ferrooxidans: A Computer-Aided Molecular Designing Study

“…This limitation is hindering postulation of a valid model for the specific binding surfaces of respirasomes. However, a working model of binding interaction between RcY and Cyc1 has been proposed by Mukhopadhyay et al, who showed that water molecules are implicated in transferring electrons from RcY to Cyc1 [17][18][19]. It is intriguing to note that, despite more than 40 years of research, the structural features of Cyc2 and its interactions with RcY are poorly understood.…”