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Exploring protein-membrane interactions through simulation and experiment

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Creative Commons 'BY' version 4.0 license

Protein/peptide interactions with cellular membranes are highly complex due to a myriad of membrane compositions and environmental variability. This research explores three protein-membrane systems. Bcl-xL, an anti-apoptotic protein that interacts with the mitochondrial outer membrane, is found to be regulated by both lipid composition and ionic conditions. A full-length Bcl-xL protein was built for simulation by combining two well-studied crystallographic structures, one of the soluble head and connective disordered loop, and another of the transmembrane helix which anchors the protein in the membrane. In conjunction with experimentalists, these simulations were able to illuminate the atomistic details of how Bcl-xL orients itself in the membrane and how different ionic conditions and protonation states of residues play a role in the conformation of Bcl-xL. In another study, pH Low Insertion Peptide, pHLIP, was prepared for simulation as a partially disordered structure in solution and as a transmembrane helix embedded in the membrane. These constructs explore changes in peptide conformation before insertion, and peptide orientation and interactions while inserted into the plasma membrane. The pHLIP peptide was shown to have stabilizing interactions between acidic residues and divalent cations in both scenarios. In particular, divalent cations played an important role in coordinating interactions between multiple negative charge centers. In a third study, Piezo1 membrane diffusion was explored by fluorescently tagging the ion channel and generating trajectories via total internal reflectance fluorescence microscopy, an experimental procedure carried out through collaboration with the Pathak Lab at UCI. Analysis of these single particle tracks via machine learning revealed consistent anomalous diffusion and heterogeneity within the subdiffusive mobile class and changes specific to drug-based perturbations of the ion-channel-membrane system. These works are part of the development of a clear picture of membrane-protein interactions and would advance our understanding of how these interactions regulate different cellular processes.

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This item is under embargo until January 10, 2025.