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1. Structural insights into perilipin 3 membrane association in response to diacylglycerol accumulation

   https://doi.org/10.1038/s41467-023-38725-w  

   Choi, Yong Mi; Ajjaji, Dalila; Fleming, Kaelin D.; Borbat, Peter P.; Jenkins, Meredith L.; Moeller, Brandon E.; Fernando, Shaveen; Bhatia, Surita R.; Freed, Jack H.; Burke, John E.; et al (June 2023, Nature Communications)

   Abstract Lipid droplets (LDs) are dynamic organelles that contain an oil core mainly composed of triglycerides (TAG) that is surrounded by a phospholipid monolayer and LD-associated proteins called perilipins (PLINs). During LD biogenesis, perilipin 3 (PLIN3) is recruited to nascent LDs as they emerge from the endoplasmic reticulum. Here, we analyze how lipid composition affects PLIN3 recruitment to membrane bilayers and LDs, and the structural changes that occur upon membrane binding. We find that the TAG precursors phosphatidic acid and diacylglycerol (DAG) recruit PLIN3 to membrane bilayers and define an expanded Perilipin-ADRP-Tip47 (PAT) domain that preferentially binds DAG-enriched membranes. Membrane binding induces a disorder to order transition of alpha helices within the PAT domain and 11-mer repeats, with intramolecular distance measurements consistent with the expanded PAT domain adopting a folded but dynamic structure upon membrane binding. In cells, PLIN3 is recruited to DAG-enriched ER membranes, and this requires both the PAT domain and 11-mer repeats. This provides molecular details of PLIN3 recruitment to nascent LDs and identifies a function of the PAT domain of PLIN3 in DAG binding. 

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2. Progress in Lipid Droplet Simulations: How Polarizability Shapes Triacylglycerol Behavior in Bulk and Interfacial Environments

   https://doi.org/10.1021/acs.jctc.5c00882  

   Braun, R Jay; Swanson, Jessica MJ (August 2025, Journal of Chemical Theory and Computation)

   Triacylglycerols (TG) are the primary neutral lipids in lipid droplets (LDs), organelles responsible for lipid storage, metabolism, and signaling. Molecular dynamics (MD) simulations have provided valuable insight into LD structure, but fixed-charge force fields struggle to capture TG behavior across both hydrophobic cores and polar interfaces. Here, we develop and evaluate a polarizable TG model using the Drude2023 lipid force field and benchmark its performance against experimental measurements of bulk density, TG−water interfacial tension, core hydration, and monolayer expansion. The Drude model accurately reproduces the experimental properties and captures key monolayer features such as surface-oriented TGs (SURF-TGs) and chemically distinct membrane packing defects. Compared to fixed-charge models such as C36-standard and C36-cutoff, the Drude polarizable model is the only force field able to capture the dual nature of TG at polar−nonpolar interfaces like the LD monolayer and more homogeneous hydrophobic environments, like the LD core. However, C36-standard is consistent with the Drude results for the LD monolayer, while C36-cutoff is consistent with the decreased hydration in the LD core. Even with large applied surface tensions, C36-cutoff does not produce Drude-like LD monolayer properties. These results highlight the importance of dynamic polarizability and establish Drude2023 as a more reliable framework for simulating TG in heterogeneous systems like LDs. 

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3. CHARMM‐GUI Nanodisc Builder for modeling and simulation of various nanodisc systems

   https://doi.org/10.1002/jcc.25773  

   Qi, Yifei; Lee, Jumin; Klauda, Jeffery B.; Im, Wonpil (January 2019, Journal of Computational Chemistry)

   Nanodiscs are discoidal protein–lipid complexes that have wide applications in membrane protein studies. Modeling and simulation of nanodiscs are challenging due to the absence of structures of many membrane scaffold proteins (MSPs) that wrap around the membrane bilayer. We have developed CHARMM‐GUINanodisc Builder(http://www.charmm-gui.org/input/nanodisc) to facilitate the setup of nanodisc simulation systems by modeling the MSPs with defined size and known structural features. A total of 11 different nanodiscs with a diameter from 80 to 180 Å are made available in both the all‐atom CHARMM and two coarse‐grained (PACE and Martini) force fields. The usage of theNanodisc Builderis demonstrated with various simulation systems. The structures and dynamics of proteins and lipids in these systems were analyzed, showing similar behaviors to those from previous all‐atom and coarse‐grained nanodisc simulations. We expect theNanodisc Builderto be a convenient and reliable tool for modeling and simulation of nanodisc systems. © 2019 Wiley Periodicals, Inc. 

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4. Mechanistic Insights into the Selective Targeting of MLX to Triacylglycerol-Rich Lipid Droplets

   https://doi.org/10.1101/2024.07.15.603605  

   Braun, R Jay; Swanson, Jessica_M J (September 2025, bioRxiv)

   The activation of transcription factor Max-Like Protein x (MLX) is modulated by competition between active dimerization and inactive association with cytosolic lipid droplets (LDs). However, LD association has been shown to depend on the neutral lipid composition. This work explores the mechanism by which MLX specifically targets LDs rich in triacylglycerol (TG) over those with abundant sterol esters (SE). We compare the association ensembles for a potential minimal targeting sequence, an amphipathic helix-loop-helix hairpin, and the full dimerization and cytoplasmic localization domain (DCD), finding the latter requires larger packing defects and quantifiably alters LD membrane properties. Surprisingly, direct interactions with TG neutral lipids are not observed for either sequence. Instead, targeting to SE-rich LDs is blocked for both sequences by insufficient packing defects. We additionally explore the full mechanism of hairpin association, aiming to understand sequence-specific features that enable strong membrane association. We find that there are multiple association pathways, but that each involves a catch, dive, snorkeling, and embedding phase. The combination of multiple catch and dive residues placed on opposing ends of amphipathic helices lengthens the catch phase, greatly enhancing association in a manner that resembles kinetic selection. Once bound, locking interhelical interactions block dissociation. Collectively, our findings suggest that in addition to relative binding affinities, both kinetics and altered surface properties due to protein association could influence competition within the LD proteome. SignificanceThe transcription factor Max-Like Protein x (MLX plays) a central role in metabolic regulation by responding to nutrient status and, simultaneously, neutral lipid composition. This work reveals how MLX selectively targets triacylglycerol-rich lipid droplets (LDs) through sequence-specific interactions with packing defects. We show that LD surface modulates MLX binding and that MLX in turn alters monolayer properties, highlighting a dynamic interplay between protein association and membrane properties. These findings provide new insight into how protein localization and function may be regulated at LD surfaces, with implications for nutrient sensing and, more broadly, transcriptional control relevant to metabolic and disease states. 

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5. Quantitative assessment of morphological changes in lipid droplets and lipid–mito interactions with aging in brown adipose

   https://doi.org/10.1002/jcp.31340  

   Crabtree, Amber; Neikirk, Kit; Pinette, Julia A; Whiteside, Aaron; Shao, Bryanna; Bedenbaugh, Jessica; Vue, Zer; Vang, Larry; Le, Han; Demirci, Mert; et al (September 2024, Journal of Cellular Physiology)

   Abstract The physical characteristics of brown adipose tissue (BAT) are defined by the presence of multilocular lipid droplets (LDs) within the brown adipocytes and a high abundance of iron‐containing mitochondria, which give it its characteristic color. Normal mitochondrial function is, in part, regulated by organelle‐to‐organelle contacts. For example, the contact sites that mediate mitochondria–LD interactions are thought to have various physiological roles, such as the synthesis and metabolism of lipids. Aging is associated with mitochondrial dysfunction, and previous studies show that there are changes in mitochondrial structure and the proteins that modulate organelle contact sites. However, how mitochondria–LD interactions change with aging has yet to be fully clarified. Therefore, we sought to define age‐related changes in LD morphology and mitochondria–lipid interactions in BAT. We examined the three‐dimensional morphology of mitochondria and LDs in young (3‐month) and aged (2‐year) murine BAT using serial block face‐scanning electron microscopy and the Amira program for segmentation, analysis, and quantification. Our analyses showed reductions in LD volume, area, and perimeter in aged samples in comparison to young samples. Additionally, we observed changes in LD appearance and type in aged samples compared to young samples. Notably, we found differences in mitochondrial interactions with LDs, which could implicate that these contacts may be important for energetics in aging. Upon further investigation, we also found changes in mitochondrial and cristae structure for the mitochondria interacting with LDs. Overall, these data define the nature of LD morphology and organelle–organelle contacts during aging and provide insight into LD contact site changes that interconnect biogerontology with mitochondrial function, metabolism, and bioactivity in aged BAT. 

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