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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 cytochrome bc1 complex, proton/electron transfers of the Q-cycle, and the CL/K proton transfer pathway.(A) The dimer complex includes the cyt b (red/blue), cyt c1 (yellow/orange), and iron sulfur protein (ISP; cyan/magenta) subunits (PDB: 1ZRT)22. The Qo-site is located between the 2-iron 2-sulfur (Fe2S2) cluster and the low potential heme (bL). The Qi-site is adjacent to the high potential heme (bH). The arrows indicate the routes of the e− (orange) and H+ transfers (green). (B) The arrows indicate the direction of the H+/e− transfers during oxidation/reduction of the non-protonated Q, the half-protonated radical SQ and the fully protonated QH2 at the Qo- or Qi- sites, respectively. (C) In the CL/K pathway, lysine acquires a H+ from a cardiolipin (CL) molecule (PDB: 3CX5)9 and (D) passes it via a string of interconnected water molecules into the Qi-site to reduce the substrate (PDB: 1PP9)20. The H-bonds (≤3.4 Å) and possible bonds (≤3.6 Å) are shown with magenta and orange dotted lines, respectively. The CL-Lys251 interactions taking place at the membrane-protein periphery were considered in a previous MD simulation study8. The amino acid residues are shown as black sticks, substrate as yellow ball-and-stick representation and the heme bH group is shown as a CPK model.
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f1: The cytochrome bc1 complex, proton/electron transfers of the Q-cycle, and the CL/K proton transfer pathway.(A) The dimer complex includes the cyt b (red/blue), cyt c1 (yellow/orange), and iron sulfur protein (ISP; cyan/magenta) subunits (PDB: 1ZRT)22. The Qo-site is located between the 2-iron 2-sulfur (Fe2S2) cluster and the low potential heme (bL). The Qi-site is adjacent to the high potential heme (bH). The arrows indicate the routes of the e− (orange) and H+ transfers (green). (B) The arrows indicate the direction of the H+/e− transfers during oxidation/reduction of the non-protonated Q, the half-protonated radical SQ and the fully protonated QH2 at the Qo- or Qi- sites, respectively. (C) In the CL/K pathway, lysine acquires a H+ from a cardiolipin (CL) molecule (PDB: 3CX5)9 and (D) passes it via a string of interconnected water molecules into the Qi-site to reduce the substrate (PDB: 1PP9)20. The H-bonds (≤3.4 Å) and possible bonds (≤3.6 Å) are shown with magenta and orange dotted lines, respectively. The CL-Lys251 interactions taking place at the membrane-protein periphery were considered in a previous MD simulation study8. The amino acid residues are shown as black sticks, substrate as yellow ball-and-stick representation and the heme bH group is shown as a CPK model.

Mentions: To maintain diverse and complex cellular functions such as reproduction, growth or movement, all living organisms rely on constant supply of energy. The fundamentals of this life-sustaining energy metabolism or bioenergetics are known to a large extent, but the mechanistic details of relevant enzymatic reactions are still being actively studied and debated on. The membrane-embedded cytochrome (cyt) bc1 complex (or complex III; Fig. 1A) is a crucial component of the respiratory and photosynthetic electron transfer chains sustaining the energy requirements of both eukaryotes and bacteria.


Atomistic determinants of co-enzyme Q reduction at the Q i -site of the cytochrome bc 1 complex
The cytochrome bc1 complex, proton/electron transfers of the Q-cycle, and the CL/K proton transfer pathway.(A) The dimer complex includes the cyt b (red/blue), cyt c1 (yellow/orange), and iron sulfur protein (ISP; cyan/magenta) subunits (PDB: 1ZRT)22. The Qo-site is located between the 2-iron 2-sulfur (Fe2S2) cluster and the low potential heme (bL). The Qi-site is adjacent to the high potential heme (bH). The arrows indicate the routes of the e− (orange) and H+ transfers (green). (B) The arrows indicate the direction of the H+/e− transfers during oxidation/reduction of the non-protonated Q, the half-protonated radical SQ and the fully protonated QH2 at the Qo- or Qi- sites, respectively. (C) In the CL/K pathway, lysine acquires a H+ from a cardiolipin (CL) molecule (PDB: 3CX5)9 and (D) passes it via a string of interconnected water molecules into the Qi-site to reduce the substrate (PDB: 1PP9)20. The H-bonds (≤3.4 Å) and possible bonds (≤3.6 Å) are shown with magenta and orange dotted lines, respectively. The CL-Lys251 interactions taking place at the membrane-protein periphery were considered in a previous MD simulation study8. The amino acid residues are shown as black sticks, substrate as yellow ball-and-stick representation and the heme bH group is shown as a CPK model.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5035994&req=5

f1: The cytochrome bc1 complex, proton/electron transfers of the Q-cycle, and the CL/K proton transfer pathway.(A) The dimer complex includes the cyt b (red/blue), cyt c1 (yellow/orange), and iron sulfur protein (ISP; cyan/magenta) subunits (PDB: 1ZRT)22. The Qo-site is located between the 2-iron 2-sulfur (Fe2S2) cluster and the low potential heme (bL). The Qi-site is adjacent to the high potential heme (bH). The arrows indicate the routes of the e− (orange) and H+ transfers (green). (B) The arrows indicate the direction of the H+/e− transfers during oxidation/reduction of the non-protonated Q, the half-protonated radical SQ and the fully protonated QH2 at the Qo- or Qi- sites, respectively. (C) In the CL/K pathway, lysine acquires a H+ from a cardiolipin (CL) molecule (PDB: 3CX5)9 and (D) passes it via a string of interconnected water molecules into the Qi-site to reduce the substrate (PDB: 1PP9)20. The H-bonds (≤3.4 Å) and possible bonds (≤3.6 Å) are shown with magenta and orange dotted lines, respectively. The CL-Lys251 interactions taking place at the membrane-protein periphery were considered in a previous MD simulation study8. The amino acid residues are shown as black sticks, substrate as yellow ball-and-stick representation and the heme bH group is shown as a CPK model.
Mentions: To maintain diverse and complex cellular functions such as reproduction, growth or movement, all living organisms rely on constant supply of energy. The fundamentals of this life-sustaining energy metabolism or bioenergetics are known to a large extent, but the mechanistic details of relevant enzymatic reactions are still being actively studied and debated on. The membrane-embedded cytochrome (cyt) bc1 complex (or complex III; Fig. 1A) is a crucial component of the respiratory and photosynthetic electron transfer chains sustaining the energy requirements of both eukaryotes and bacteria.

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.