Cytochrome c Can Form a Well-Defined Binding Pocket for Hydrocarbons

Abstract

Cytochrome c can acquire peroxidase when it binds to cardiolipin in mitochondrial membranes. The resulting oxygenation of cardiolipin by cytochrome c provides an early signal for the onset of apoptosis. The structure of this enzyme-substrate complex is a matter of considerable debate. We present three structures at 1.7 – 2.0 Å resolution of a domain-swapped dimer of yeast iso-1-cytochrome c with the detergents, CYMAL-5, CYMAL-6 and ω-undecylenyl-β-D-maltopyranoside bound in a channel that places the hydrocarbon moieties of these detergents next to the heme. The heme is poised for peroxidase activity with water bound in place of Met80, which serves as the axial heme ligand when cytochrome c functions as an electron carrier. The hydroxyl group of Tyr67 sits 3.6 – 4.0 Å from the nearest carbon of the detergents, positioned to act as a relay in radical abstraction during peroxidase activity. Docking studies with linoleic acid, the most common fatty acid component of cardiolipin, show that C11 of linoleic acid can sit adjacent to Tyr67 and the heme, consistent with the oxygenation pattern observed in lipidomics studies. The well-defined hydrocarbon binding pocket provides atomic resolution evidence for the extended lipid anchorage model for cytochrome c/cardiolipin binding. Dimer dissociation/association kinetics for yeast versus equine cytochrome c indicate that formation of mammalian cytochrome c dimers in vivo would require catalysis. However, the dimer structure shows that only a modest deformation of monomeric cytochrome c would suffice to form the hydrocarbon binding site occupied by these detergents.

An approach for the identification of exemplar sites for scaling up targeted field observations of benthic biogeochemistry in heterogeneous environments

“…The full results of the survey will be reported in detail elsewhere (e.g. McCelland et al 2016;Silburn et al in prep), and confirmed that the targeted area contained a range of sediment types from sandy muds, through to gravelly sands, reflecting the wider shelf region (For full details, see Online Resource 3). In summary, coarser sediments dominate the central region, and the percentage of fine sediments (median grain size \ 63 lm), which ranges between 1.73 and 86.61% across the entire area, increases towards the Northeast and Southwest corners (Fig.…”

“…Sediment versus habitat type While the terms are often used interchangeably, they are commonly closely related (LaFrance et al 2014;Heip et al 1985), and the faunal analysis performed herein shows that sediment size is generally a good predictor of macrobenthic community structure (McCelland et al 2016). It should be noted that considerable overlap occurs in species occurrence between closely related sediment types.…”

Metalloprotein entatic control of ligand-metal bonds quantified by ultrafast x-ray spectroscopy

“…On a molecular level, the extended-lipid anchorage model (34) is typically proposed, in which CL binds to cyt c through electrostatic and hydrogen bonding interactions. Recent crystal structures of yeast iso-1–cyt c show that docked linoleic acid interacts with Asn52 and sits adjacent to the Tyr67 and heme (35). Thus, the linoleic acid can interrupt the internal hydrogen bonding network by interactions with either of these residues.…”

Calixarene capture of partially unfolded cytochrome c

“…The displacement of Ω‐loop D (Gly77 specifically) is highlighted by an arrow while disordered Ω‐loop C is signified by a dashed line. (B) As per A, and including domain‐swapped cyt c (PDB 5klu, red) and Lys73‐ligated cyt c (PDB 4q5p , navy). Residues 83–103 of domain‐swapped cyt c are not shown.…”