The cytochrome bc1 complex (cyt bc1) is a key component in mitochondrial respiration and functions by catalyzing electron transfer (ET) coupled to the generation of a proton gradient that drives ATP synthesis. ET inhibitors of bacterial cyt bc1 that replace the natural ubiquinone/ubiquinol ligands are antibiotics and inhibitors of fungal cyt bc1 are fungicides. It is hypothesized that protein-ligand interactions, as well as ET chemistry, are mediated by amino acid side chain protonation equilibria. This contribution describes the use of constant pH molecular dynamics and free energy perturbation simulations to predict the protonation equilibria of ionizable amino acid side chains near ligand binding sites in cyt bc1, as well as their implications for the proposed protein-ligand interactions. We focus on the His161 side chain proposed to function in proton-coupled electron transfer.

Calculated pK<sub>a</sub> values for amino acid side chains near the ubiquinone and ubiquinol binding sites of cytochrome bc<sub>1</sub>

245th National Meeting (2013)

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Calculated pKa values for amino acid side chains near the ubiquinone and ubiquinol binding sites of cytochrome bc1

Calculated pK_a values for amino acid side chains near the ubiquinone and ubiquinol binding sites of cytochrome bc₁