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5017 Results

Showing 4271-4280 of 5017 results
Publications
01/01/25 | Structural dynamics and binding of Caenorhabditis elegans lifespan-extending lipid binding protein-3 to polyunsaturated fatty acids.
Cuevas AR, Tillman MC, Wang MC, Ortlund EA
Protein Sci. 2025 Jan 01;34(1):e5249. doi: 10.1002/pro.5249

Intracellular lipid binding proteins (iLBPs) play crucial roles in lipid transport and cellular metabolism across the animal kingdom. Recently, a fat-to-neuron axis was described in Caenorhabditis elegans, in which lysosomal activity in the fat liberates polyunsaturated fatty acids (PUFAs) that signal to neurons and extend lifespan with durable fecundity. In this study, we investigate the structure and binding mechanisms of a lifespan-extending lipid chaperone, lipid binding protein-3 (LBP-3), which shuttles dihomo-γ-linolenic (DGLA) acid from intestinal fat to neurons. We present the first high-resolution crystal structure of LBP-3, which reveals a classic iLBP fold with an unexpected and unique homodimeric arrangement via interstrand interactions that is incompatible with ligand binding. We identify key ionic interactions that mediate DGLA binding within the lipid binding pocket. Molecular dynamics simulations further elucidate LBP-3's preferential binding to DGLA due to its rotational freedom and access to favorable binding conformations compared to other 20-carbon PUFAs. We also propose that LBP-3 dimerization may be a unique regulatory mechanism for lipid chaperones.

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Publications
11/18/25 | Structural dynamics and neural representation of wing deformation.
Yarger AM, Maeda M, Siwanowicz I, Kajiyama H, Walker SM, Bomphrey RJ, Lin H
Proc Natl Acad Sci USA. 2025 Nov 18;122(46):e2518032122. doi: 10.1073/pnas.2518032122

Locomotor control is facilitated by mechanosensory inputs that report how the body interacts with a physical medium. Effective representation of compliant wing deformations is particularly challenging due to the many degrees of freedom. Structural configurations can constrain the stimulus space, and strategic placement of sensors can simplify computation. Here, we measured and modeled wing displacement fields and characterized spatiotemporal encoding of the wing mechanosensors. Our data show how dragonfly wing architecture prescribes deformation modes consistent across models and measurements. We found that the wing's state under normal flapping conditions is detected by the spike timing of few sensors, with additional sensors recruited under perturbation. The functional integration of wing biomechanics and sensor placement enables a straightforward solution for information transfer.

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Publications
11/25/24 | Structural dynamics of human ribosomes in situ reconstructed by exhaustive high-resolution template matching.
Rickgauer JP, Choi H, Moore AS, Denk W, Lippincott-Schwartz J
Mol Cell. 2024 Nov 25:. doi: 10.1016/j.molcel.2024.11.003

Protein synthesis is central to life and requires the ribosome, which catalyzes the stepwise addition of amino acids to a polypeptide chain by undergoing a sequence of structural transformations. Here, we employed high-resolution template matching (HRTM) on cryoelectron microscopy (cryo-EM) images of directly cryofixed living cells to obtain a set of ribosomal configurations covering the entire elongation cycle, with each configuration occurring at its native abundance. HRTM's position and orientation precision and ability to detect small targets (∼300 kDa) made it possible to order these configurations along the reaction coordinate and to reconstruct molecular features of any configuration along the elongation cycle. Visualizing the cycle's structural dynamics by combining a sequence of >40 reconstructions into a 3D movie readily revealed component and ligand movements, some of them surprising, such as spring-like intramolecular motion, providing clues about the molecular mechanisms involved in some still mysterious steps during chain elongation.

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Janelia Archives
Structural Glass
Designed with both form and function in mind, Janelia’s structural glass reflects its philosophy of transparent, collaborative science.
Publications
09/30/20 | Structural insight into the ATP-driven exporter of virulent peptide toxins.
Zeytuni N, Dickey SW, Hu J, Chou HT, Worrall LJ, Alexander JA, Carlson ML, Nosella M, Duong F, Yu Z, Otto M, Strynadka NC
Science Advances. 2020 Sep 30;6(40):. doi: 10.1126/sciadv.abb8219

is a major human pathogen that has acquired alarming broad-spectrum antibiotic resistance. One group of secreted toxins with key roles during infection is the phenol-soluble modulins (PSMs). PSMs are amphipathic, membrane-destructive cytolytic peptides that are exported to the host-cell environment by a designated adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporter, the PSM transporter (PmtABCD). Here, we demonstrate that the minimal Pmt unit necessary for PSM export is PmtCD and provide its first atomic characterization by single-particle cryo-EM and x-ray crystallography. We have captured the transporter in the ATP-bound state at near atomic resolution, revealing a type II ABC exporter fold, with an additional cytosolic domain. Comparison to a lower-resolution nucleotide-free map displaying an "open" conformation and putative hydrophobic inner chamber of a size able to accommodate the binding of two PSM peptides provides mechanistic insight and sets the foundation for therapeutic design.

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Publications
04/10/18 | Structural mechanism of functional modulation by gene splicing in NMDA receptors.
Regan MC, Grant T, McDaniel MJ, Karakas E, Zhang J, Traynelis SF, Grigorieff N, Furukawa H
Neuron. 2018 Apr 10;98(3):521-9. doi: 10.1016/j.neuron.2018.03.034

Alternative gene splicing gives rise to N-methyl-D-aspartate (NMDA) receptor ion channels with defined functional properties and unique contributions to calcium signaling in a given chemical environment in the mammalian brain. Splice variants possessing the exon-5-encoded motif at the amino-terminal domain (ATD) of the GluN1 subunit are known to display robustly altered deactivation rates and pH sensitivity, but the underlying mechanism for this functional modification is largely unknown. Here, we show through cryoelectron microscopy (cryo-EM) that the presence of the exon 5 motif in GluN1 alters the local architecture of heterotetrameric GluN1-GluN2 NMDA receptors and creates contacts with the ligand-binding domains (LBDs) of the GluN1 and GluN2 subunits, which are absent in NMDA receptors lacking the exon 5 motif. The unique interactions established by the exon 5 motif are essential to the stability of the ATD/LBD and LBD/LBD interfaces that are critically involved in controlling proton sensitivity and deactivation.

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Conferences
Structural Plasticity in the Mammalian Brain
The goal of this meeting is to bring together people working on structural plasticity in vivo, with a focus on the recent longitudinal imaging approaches and related studies. We hope to identify...
Publications
04/07/10 | Structural plasticity underlies experience-dependent functional plasticity of cortical circuits.
Wilbrecht L, Holtmaat A, Wright N, Fox K, Svoboda K
The Journal of Neuroscience. 2010 Apr 7;30(14):4927-32. doi: 10.1523/JNEUROSCI.6403-09.2010

The stabilization of new spines in the barrel cortex is enhanced after whisker trimming, but its relationship to experience-dependent plasticity is unclear. Here we show that in wild-type mice, whisker potentiation and spine stabilization are most pronounced for layer 5 neurons at the border between spared and deprived barrel columns. In homozygote alphaCaMKII-T286A mice, which lack experience-dependent potentiation of responses to spared whiskers, there is no increase in new spine stabilization at the border between barrel columns after whisker trimming. Our data provide a causal link between new spine synapses and plasticity of adult cortical circuits and suggest that alphaCaMKII autophosphorylation plays a role in the stabilization but not formation of new spines.

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Publications
04/23/14 | Structural plasticity within the barrel cortex during initial phases of whisker-dependent learning.
Kuhlman SJ, O’Connor DH, Fox K, Svoboda K
The Journal of Neuroscience. 2014 Apr 23;34(17):6078-83. doi: 10.1523/JNEUROSCI.4919-12.2014

We report learning-related structural plasticity in layer 1 branches of pyramidal neurons in the barrel cortex, a known site of sensorimotor integration. In mice learning an active, whisker-dependent object localization task, layer 2/3 neurons showed enhanced spine growth during initial skill acquisition that both preceded and predicted expert performance. Preexisting spines were stabilized and new persistent spines were formed. These findings suggest rapid changes in connectivity between motor centers and sensory cortex guide subsequent sensorimotor learning.

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