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Atomistic determinants of co-enzyme Q reduction at the Q i -site of the cytochrome bc 1 complex

View Article: PubMed Central - PubMed

ABSTRACT

The cytochrome (cyt) bc1 complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme’s substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Qi-site of the cyt bc1 complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Qi-site to facilitate binding of half-protonated semiquinone – a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Qi-site.

No MeSH data available.


The binding modes of semiquinone and quinone at the Qi-site of cytochrome bc1 complex.(A) On the A side of the dimer, the C1-hydroxyl of neutral SQ (shown with yellow ball-and-stick representation) forms a water bridge with the Asp252COO−, while the C4-carbonyl H-bonds with the epsilon protonated His217. A Lys251NH3+-Asp252COO− salt bridge is formed (conf1 in Table 1). The Asn221NH2 stabilizes the His217 positioning by H-bonding. (B) On the B side, the C4-hydroxyl of SQ H-bonds with both Lys251 and Asp252 that are forming a salt bridge (conf1 in Table 1). Both His217 and Asn221 H-bond with the C4-carbonyl of SQ. (C) On the B side, Q forms a water bridge with the Asp252COO− and H-bonds with the His217 and Asn221 side chains that are also bonded to each other (conf3 in Table 1). The lysine assumes the outward rotamer pose. (D) On the B side, the C1-carbonyl of Q H-bonds with the Asp252COOH and the As221NH2 H-bonds with the C4-carbonyl (conf4 in Table 1). Neutral Lys251 and Asp252 side chains are not bonding. For clarity only the polar protons are shown (cyan color). For further details see Fig. 1.
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f2: The binding modes of semiquinone and quinone at the Qi-site of cytochrome bc1 complex.(A) On the A side of the dimer, the C1-hydroxyl of neutral SQ (shown with yellow ball-and-stick representation) forms a water bridge with the Asp252COO−, while the C4-carbonyl H-bonds with the epsilon protonated His217. A Lys251NH3+-Asp252COO− salt bridge is formed (conf1 in Table 1). The Asn221NH2 stabilizes the His217 positioning by H-bonding. (B) On the B side, the C4-hydroxyl of SQ H-bonds with both Lys251 and Asp252 that are forming a salt bridge (conf1 in Table 1). Both His217 and Asn221 H-bond with the C4-carbonyl of SQ. (C) On the B side, Q forms a water bridge with the Asp252COO− and H-bonds with the His217 and Asn221 side chains that are also bonded to each other (conf3 in Table 1). The lysine assumes the outward rotamer pose. (D) On the B side, the C1-carbonyl of Q H-bonds with the Asp252COOH and the As221NH2 H-bonds with the C4-carbonyl (conf4 in Table 1). Neutral Lys251 and Asp252 side chains are not bonding. For clarity only the polar protons are shown (cyan color). For further details see Fig. 1.

Mentions: The SQ/Q binding at the Qi-site is described thoroughly based on the MD simulations (Fig. 2) and X-ray crystallographic data in the SI (Fig. S1; Table S1); however, the binding requirements are summarized here:


Atomistic determinants of co-enzyme Q reduction at the Q i -site of the cytochrome bc 1 complex
The binding modes of semiquinone and quinone at the Qi-site of cytochrome bc1 complex.(A) On the A side of the dimer, the C1-hydroxyl of neutral SQ (shown with yellow ball-and-stick representation) forms a water bridge with the Asp252COO−, while the C4-carbonyl H-bonds with the epsilon protonated His217. A Lys251NH3+-Asp252COO− salt bridge is formed (conf1 in Table 1). The Asn221NH2 stabilizes the His217 positioning by H-bonding. (B) On the B side, the C4-hydroxyl of SQ H-bonds with both Lys251 and Asp252 that are forming a salt bridge (conf1 in Table 1). Both His217 and Asn221 H-bond with the C4-carbonyl of SQ. (C) On the B side, Q forms a water bridge with the Asp252COO− and H-bonds with the His217 and Asn221 side chains that are also bonded to each other (conf3 in Table 1). The lysine assumes the outward rotamer pose. (D) On the B side, the C1-carbonyl of Q H-bonds with the Asp252COOH and the As221NH2 H-bonds with the C4-carbonyl (conf4 in Table 1). Neutral Lys251 and Asp252 side chains are not bonding. For clarity only the polar protons are shown (cyan color). For further details see Fig. 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5035994&req=5

f2: The binding modes of semiquinone and quinone at the Qi-site of cytochrome bc1 complex.(A) On the A side of the dimer, the C1-hydroxyl of neutral SQ (shown with yellow ball-and-stick representation) forms a water bridge with the Asp252COO−, while the C4-carbonyl H-bonds with the epsilon protonated His217. A Lys251NH3+-Asp252COO− salt bridge is formed (conf1 in Table 1). The Asn221NH2 stabilizes the His217 positioning by H-bonding. (B) On the B side, the C4-hydroxyl of SQ H-bonds with both Lys251 and Asp252 that are forming a salt bridge (conf1 in Table 1). Both His217 and Asn221 H-bond with the C4-carbonyl of SQ. (C) On the B side, Q forms a water bridge with the Asp252COO− and H-bonds with the His217 and Asn221 side chains that are also bonded to each other (conf3 in Table 1). The lysine assumes the outward rotamer pose. (D) On the B side, the C1-carbonyl of Q H-bonds with the Asp252COOH and the As221NH2 H-bonds with the C4-carbonyl (conf4 in Table 1). Neutral Lys251 and Asp252 side chains are not bonding. For clarity only the polar protons are shown (cyan color). For further details see Fig. 1.
Mentions: The SQ/Q binding at the Qi-site is described thoroughly based on the MD simulations (Fig. 2) and X-ray crystallographic data in the SI (Fig. S1; Table S1); however, the binding requirements are summarized here:

View Article: PubMed Central - PubMed

ABSTRACT

The cytochrome (cyt) bc1 complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme’s substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Qi-site of the cyt bc1 complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Qi-site to facilitate binding of half-protonated semiquinone – a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Qi-site.

No MeSH data available.