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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 switch-like operation of CL/K/D proton shuttle is pH-dependent.(A) The Lys251NH3+ forms a salt bridge with the Asp252COO−, when SQ is bound at the Qi-site. The rotation is extensive, if compared to the structure with peripheral cardiolipin (CL)9 or the initial pose22. If the inward pose of Lys251NH3+ is compared to the Lys251NH2 pose, it shows that the neutral lysine turns outwards. See Fig. 1 for further details. (B) The empirical pKa calculations indicate that the Asp252 side chain would be neutral, when the Lys251 side chain is out of the Qi-site (pKa value from 1SQP; Table S7). The Lys251NH3+ keeps the outward pose, when the Asp252 side chain is neutral, i.e. the switching does not happen, when the Qi-site is acidic. (C) The CL/K/D switching is triggered by the deprotonation of Asp252 side chain. The Lys251NH3+ rotates inwards and forms a salt bridge with the Asp252COO−. The empricial pKa calculations indicate that Lys251 and Asp252 are charged when forming a salt bridge (pKa value from 2FYN, G chain; Table S7). After a direct H+ proton transfer (*) from the Lys251NH3+ to the Asp252COO−, the neutral lysine rotates out to accept another H+ from the CL (*). The Asp252COOH donates the newly acquired H+ to the solvent, if the pH rises at the Qi-site. This back-and-forth rotation of Lys251 would happen as long as the Qi-site was basic; ensuring also continuous protonation of His217.
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f4: The switch-like operation of CL/K/D proton shuttle is pH-dependent.(A) The Lys251NH3+ forms a salt bridge with the Asp252COO−, when SQ is bound at the Qi-site. The rotation is extensive, if compared to the structure with peripheral cardiolipin (CL)9 or the initial pose22. If the inward pose of Lys251NH3+ is compared to the Lys251NH2 pose, it shows that the neutral lysine turns outwards. See Fig. 1 for further details. (B) The empirical pKa calculations indicate that the Asp252 side chain would be neutral, when the Lys251 side chain is out of the Qi-site (pKa value from 1SQP; Table S7). The Lys251NH3+ keeps the outward pose, when the Asp252 side chain is neutral, i.e. the switching does not happen, when the Qi-site is acidic. (C) The CL/K/D switching is triggered by the deprotonation of Asp252 side chain. The Lys251NH3+ rotates inwards and forms a salt bridge with the Asp252COO−. The empricial pKa calculations indicate that Lys251 and Asp252 are charged when forming a salt bridge (pKa value from 2FYN, G chain; Table S7). After a direct H+ proton transfer (*) from the Lys251NH3+ to the Asp252COO−, the neutral lysine rotates out to accept another H+ from the CL (*). The Asp252COOH donates the newly acquired H+ to the solvent, if the pH rises at the Qi-site. This back-and-forth rotation of Lys251 would happen as long as the Qi-site was basic; ensuring also continuous protonation of His217.

Mentions: The Lys251NH3+ can rotate directly into the Qi-site, form a salt bridge with the Asp252COO− (Figs 3A,B and 4A and S3; Table S2), and participate in the half-protonated SQ binding either directly (Fig. 2B) or via a water bridge (Fig. 2A).


Atomistic determinants of co-enzyme Q reduction at the Q i -site of the cytochrome bc 1 complex
The switch-like operation of CL/K/D proton shuttle is pH-dependent.(A) The Lys251NH3+ forms a salt bridge with the Asp252COO−, when SQ is bound at the Qi-site. The rotation is extensive, if compared to the structure with peripheral cardiolipin (CL)9 or the initial pose22. If the inward pose of Lys251NH3+ is compared to the Lys251NH2 pose, it shows that the neutral lysine turns outwards. See Fig. 1 for further details. (B) The empirical pKa calculations indicate that the Asp252 side chain would be neutral, when the Lys251 side chain is out of the Qi-site (pKa value from 1SQP; Table S7). The Lys251NH3+ keeps the outward pose, when the Asp252 side chain is neutral, i.e. the switching does not happen, when the Qi-site is acidic. (C) The CL/K/D switching is triggered by the deprotonation of Asp252 side chain. The Lys251NH3+ rotates inwards and forms a salt bridge with the Asp252COO−. The empricial pKa calculations indicate that Lys251 and Asp252 are charged when forming a salt bridge (pKa value from 2FYN, G chain; Table S7). After a direct H+ proton transfer (*) from the Lys251NH3+ to the Asp252COO−, the neutral lysine rotates out to accept another H+ from the CL (*). The Asp252COOH donates the newly acquired H+ to the solvent, if the pH rises at the Qi-site. This back-and-forth rotation of Lys251 would happen as long as the Qi-site was basic; ensuring also continuous protonation of His217.
© Copyright Policy - open-access
Related In: Results  -  Collection

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f4: The switch-like operation of CL/K/D proton shuttle is pH-dependent.(A) The Lys251NH3+ forms a salt bridge with the Asp252COO−, when SQ is bound at the Qi-site. The rotation is extensive, if compared to the structure with peripheral cardiolipin (CL)9 or the initial pose22. If the inward pose of Lys251NH3+ is compared to the Lys251NH2 pose, it shows that the neutral lysine turns outwards. See Fig. 1 for further details. (B) The empirical pKa calculations indicate that the Asp252 side chain would be neutral, when the Lys251 side chain is out of the Qi-site (pKa value from 1SQP; Table S7). The Lys251NH3+ keeps the outward pose, when the Asp252 side chain is neutral, i.e. the switching does not happen, when the Qi-site is acidic. (C) The CL/K/D switching is triggered by the deprotonation of Asp252 side chain. The Lys251NH3+ rotates inwards and forms a salt bridge with the Asp252COO−. The empricial pKa calculations indicate that Lys251 and Asp252 are charged when forming a salt bridge (pKa value from 2FYN, G chain; Table S7). After a direct H+ proton transfer (*) from the Lys251NH3+ to the Asp252COO−, the neutral lysine rotates out to accept another H+ from the CL (*). The Asp252COOH donates the newly acquired H+ to the solvent, if the pH rises at the Qi-site. This back-and-forth rotation of Lys251 would happen as long as the Qi-site was basic; ensuring also continuous protonation of His217.
Mentions: The Lys251NH3+ can rotate directly into the Qi-site, form a salt bridge with the Asp252COO− (Figs 3A,B and 4A and S3; Table S2), and participate in the half-protonated SQ binding either directly (Fig. 2B) or via a water bridge (Fig. 2A).

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.