Abstract
The endoplasmic reticulum (ER) is the main site of protein synthesis in eukaryotic cells and requires a high concentration of luminal chaperones to function. During protein synthesis, ER luminal chaperones are swept along the secretory pathway and must be retrieved to maintain cell viability. ER protein retrieval is achieved by the KDEL receptor, which recognises a C-terminal Lys-Asp-Glu-Leu (KDEL) sequence. Recognition of ER proteins by the KDEL receptor is pH dependent, with binding occurring under acidic conditions in the Golgi and release under conditions of higher pH in the ER. Recent crystal structures of the KDEL receptor in the apo and peptide bound state suggested that peptide binding drives the formation of a short-hydrogen bond that locks the KDEL sequence in the receptor and activates the receptor for COPI binding in the cytoplasm. Using quantum mechanical calculations we demonstrate that the strength of this short hydrogen bond is reinforced following protonation of a nearby histidine, providing a conceptual link between receptor protonation and KDEL peptide binding. Protonation also controls the water networks adjacent to the peptide binding site, leading to a conformational change that ultimately allows the receptor-complex to be recognized by the COPI system.
Highlights
The endoplasmic reticulum (ER) is the main site of protein synthesis in eukaryotic cells and requires a high concentration of luminal chaperones to function
The structures revealed the conformational changes that occur upon signal peptide binding, which alter the electrostatic surface of the receptor on the cytoplasmic side of the membrane that likely mediates the interaction of the receptor with either COPI or COPII to allow for KDEL dependent recycling of the receptor within the secretory pathway
Using a combination of molecular dynamics (MD) and quantum mechanics (QM) calculations we explored the role of this conserved histidine side chain in pH sensing, and the influence this has on the physical properties of the short hydrogen bond located at the core of the receptor
Summary
The endoplasmic reticulum (ER) is the main site of protein synthesis in eukaryotic cells and requires a high concentration of luminal chaperones to function. The higher pH in the ER results in deprotonation of the receptor and release of the KDEL peptide and associated cargo protein, whereupon the receptor is cycled back to the Golgi via COPII vesicles[10,11] It was discovered over 2 decades ago, the molecular mechanism of pH-dependent binding by the KDELR remains stubbornly e lusive[12]. Due to the protonatable nature of this residue within the physiological range of the secretory pathway, it was proposed that this side chain may form the pH sensor for the KDEL retrieval system This histidine is located adjacent to an unusually short hydrogen bond formed between a conserved tyrosine (Y158) and glutamate (E127), which functions to lock the receptor in an active state following binding of the ERS. We show that the presence of the short hydrogen-bond appears to dictate whether a continuous water cavity can form, which our simulations suggest may play an important role in the structural changes that result in signaling the recruitment of either the COPI or COPII coatomer proteins
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