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

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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 Lys251-Asp252 salt bridge formation in the simulations.(A) The Lys251NH3+-Asp252COO− salt bridge is formed on both A (blue line) and (B) B (red line) dimer sides in the conf1 (Table 1) simulation with neutral SQ bound at the Qi-site. (C) On the B side, Lys251 side chain assumes a clearly outward rotamer pose during the conf3 (Table 1) simulation with bound Q, although the side chain is initially forming a salt bridge with Asp252COO− after the equilibration time. (D) On the A side, the neutral Lys251 and Asp252 side chains are not within bonding distance from the very beginning of the conf4 (Table 1) simulation with bound Q at the Qi-site. The H-bonding distance of 3.4 Å is indicated with a black line. For clarity, the results are shown as 10-point moving averages. The trajectory data shown in the A–D panels correspond to the substrate binding mode snapshots shown in Fig. 2A–D, where the salt bridge forming residues are shown.
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f3: The Lys251-Asp252 salt bridge formation in the simulations.(A) The Lys251NH3+-Asp252COO− salt bridge is formed on both A (blue line) and (B) B (red line) dimer sides in the conf1 (Table 1) simulation with neutral SQ bound at the Qi-site. (C) On the B side, Lys251 side chain assumes a clearly outward rotamer pose during the conf3 (Table 1) simulation with bound Q, although the side chain is initially forming a salt bridge with Asp252COO− after the equilibration time. (D) On the A side, the neutral Lys251 and Asp252 side chains are not within bonding distance from the very beginning of the conf4 (Table 1) simulation with bound Q at the Qi-site. The H-bonding distance of 3.4 Å is indicated with a black line. For clarity, the results are shown as 10-point moving averages. The trajectory data shown in the A–D panels correspond to the substrate binding mode snapshots shown in Fig. 2A–D, where the salt bridge forming residues are shown.

Mentions: (3) If the C1-group is reduced first (to produce neutral/half-protonated SQ), Lys251 side chain can rotate inward to form a lasting salt bridge with the Asp252COO− (Figs 3A,B and S3; Table S2) and participate in the substrate binding (Fig. 2A,B and S3; Table S2). The Lys251NH3+ at the Qi-site helps to orient the quinone ring to assure H-bonding between the C4-carbonyl and the epsilon protonated His217 side chain. Accordingly, the neutral Lys251 points out of the Qi-site similarly as would happen with stably binding Q (Figs 2C,D and 3C,D).


Atomistic determinants of co-enzyme Q reduction at the Q i -site of the cytochrome bc 1 complex
The Lys251-Asp252 salt bridge formation in the simulations.(A) The Lys251NH3+-Asp252COO− salt bridge is formed on both A (blue line) and (B) B (red line) dimer sides in the conf1 (Table 1) simulation with neutral SQ bound at the Qi-site. (C) On the B side, Lys251 side chain assumes a clearly outward rotamer pose during the conf3 (Table 1) simulation with bound Q, although the side chain is initially forming a salt bridge with Asp252COO− after the equilibration time. (D) On the A side, the neutral Lys251 and Asp252 side chains are not within bonding distance from the very beginning of the conf4 (Table 1) simulation with bound Q at the Qi-site. The H-bonding distance of 3.4 Å is indicated with a black line. For clarity, the results are shown as 10-point moving averages. The trajectory data shown in the A–D panels correspond to the substrate binding mode snapshots shown in Fig. 2A–D, where the salt bridge forming residues are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: The Lys251-Asp252 salt bridge formation in the simulations.(A) The Lys251NH3+-Asp252COO− salt bridge is formed on both A (blue line) and (B) B (red line) dimer sides in the conf1 (Table 1) simulation with neutral SQ bound at the Qi-site. (C) On the B side, Lys251 side chain assumes a clearly outward rotamer pose during the conf3 (Table 1) simulation with bound Q, although the side chain is initially forming a salt bridge with Asp252COO− after the equilibration time. (D) On the A side, the neutral Lys251 and Asp252 side chains are not within bonding distance from the very beginning of the conf4 (Table 1) simulation with bound Q at the Qi-site. The H-bonding distance of 3.4 Å is indicated with a black line. For clarity, the results are shown as 10-point moving averages. The trajectory data shown in the A–D panels correspond to the substrate binding mode snapshots shown in Fig. 2A–D, where the salt bridge forming residues are shown.
Mentions: (3) If the C1-group is reduced first (to produce neutral/half-protonated SQ), Lys251 side chain can rotate inward to form a lasting salt bridge with the Asp252COO− (Figs 3A,B and S3; Table S2) and participate in the substrate binding (Fig. 2A,B and S3; Table S2). The Lys251NH3+ at the Qi-site helps to orient the quinone ring to assure H-bonding between the C4-carbonyl and the epsilon protonated His217 side chain. Accordingly, the neutral Lys251 points out of the Qi-site similarly as would happen with stably binding Q (Figs 2C,D and 3C,D).

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.