Biology subjects

Aydin, D.

Publications and source records attributed to Aydin, D..

3 recordsLinked to original sources

bioRxiv2025

Molecular mechanism of exchange coupling in CLC chloride/proton antiporters

The ubiquitous CLC membrane transporters are unique in their ability to exchange anions for cations. Despite extensive study, there is no mechanistic model that fully explains their 2:1 Cl-/H+ stoichiometric exchange mechanism. Here, we provide such a model. Using differential hydrogen-deuterium exchange mass spectrometry, cryo-EM structure determination, and molecular dynamics simulations, we uncovered conformational dynamics in CLC-ec1, a bacterial CLC homolog that has served as a paradigm for this family of transporters. Simulations based on a cryo-EM structure at pH 3 revealed critical steps in the transport mechanism, including release of Cl- ions to the extracellular side, opening of the inner gate, and water wires that facilitate H+ transport. Surprisingly, these water wires occurred independently of Cl-binding, prompting us to reassess the relationship between Cl- binding and Cl-/H+ coupling. Using isothermal titration calorimetry and quantitative flux assays on mutants with reduced Cl- binding affinity, we conclude that, while Cl- binding is necessary for coupling, even weak binding can support Cl-/H+ coupling. By integrating our findings with existing literature, we establish a complete and efficient CLC 2:1 Cl-/H+ exchange mechanism.

biophysics↗

bioRxiv2021

Structural insights into distinct signaling profiles of the μOR activated by diverse agonists

Drugs targeting the G protein-coupled -opioid receptor (OR) are the most effective analgesics available but are also associated with fatal respiratory depression. While some partial opioid agonists appear to be safer than full agonists, the signaling pathways responsible for respiratory depression have yet to be elucidated. Here we investigated the structural and mechanistic basis of action of lofentanil (LFT) and mitragynine pseudoindoxyl (MP), two OR agonists with different safety profiles. LFT, one of the most potent and lethal opioids, and MP, a derivative from the kratom plant with reduced respiratory depression in animal studies at equianalgesic doses, exhibited markedly different signaling efficacy profiles for G protein subtype activation and recruitment of {beta}-arrestins. Cryo-EM structures of the OR-Gi1 complex with MP (2.5[A]) and LFT (3.2[A]) revealed that the two ligands engage distinct sub-pockets, and molecular dynamics (MD) simulations showed additional differences in the binding site that propagate to the intracellular side of the receptor where G proteins and {beta}-arrestins bind. While MP favors the precise G protein-bound active state observed in the cryo-EM structures, LFT favors a distinct active state. These results highlight how drugs engaging different parts of the OR orthosteric pocket can lead to distinct signaling outcomes.

biophysics↗

bioRxiv2017

Conserved lipid and small molecule modulation of COQ8 reveals regulation of the ancient UbiB family

Human COQ8A (ADCK3) and Saccharomyces cerevisiae Coq8p (collectively COQ8) are UbiB family proteins essential for mitochondrial coenzyme Q (CoQ) biosynthesis. However, the biochemical activity of COQ8 and its direct role in CoQ production remain unclear, in part due to lack of known endogenous regulators of COQ8 function and of effective small molecules for probing its activity in vivo. Here we demonstrate that COQ8 possesses evolutionarily conserved ATPase activity that is activated by binding to membranes containing cardiolipin and by phenolic compounds that resemble CoQ pathway intermediates. We further create an analog-sensitive version of Coq8p and reveal that acute chemical inhibition of its endogenous activity in yeast is sufficient to cause respiratory deficiency concomitant with CoQ depletion. Collectively, this work defines lipid and small molecule modulators of an ancient family of atypical kinase-like proteins and establishes a chemical genetic system for further exploring the mechanistic role of COQ8 in CoQ biosynthesis.

biochemistry↗