JACS Au
● American Chemical Society (ACS)
Preprints posted in the last 90 days, ranked by how well they match JACS Au's content profile, based on 43 papers previously published here. The average preprint has a 0.03% match score for this journal, so anything above that is already an above-average fit.
Shah, T.; Heidari, S.; Rydzewski, J.; Torabifard, H.
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NSD2 is a histone methyltransferase that modifies lysine 36 in histone H3 (H3K36), playing a central role in chromatin organization and transcriptional regulation. Oncogenic mutations, such as E1099K and T1150A in NSD2, have been associated with hyperactive methylation, but the molecular mechanisms underlying this gain of function remain poorly understood. In this study, we performed all-atom molecular dynamics simulations on models of NSD2 bound to the nucleosome for the wild type (WT), E1099K, T1150A, and the E1099K/T1150A double mutant. Analysis of MD simulations reveals that the global dynamics of the enzymes remain unaltered upon mutations. The time-lagged independent component analysis (tICA) and Markov state modeling uncovered fundamental differences in free-energy landscapes among the variants. The WT NSD2 exhibited energetically and kinetically unfavorable transitions between the macrostates along with extended enzyme-substrate distances. On the other hand, the mutant systems demonstrate reduced SAM-H3K36 distances with modified energy landscapes that facilitate transitions or favor prolonged occupancy of catalytically competent states. Importantly, the mutations reorganize the network of intramolecular contacts around the catalytic site, SAM-binding pocket, and histone-binding interface, optimizing substance engagement geometry. These findings demonstrate that oncogenic mutations achieve hyperactivity through strategic reorganization of conformational dynamics rather than simple destabilization, balancing local flexibility with global stability to enhance catalytic efficiency. Our results provide mechanistic insights into NSD2 dysregulation in cancer and establish a framework to develop allosteric inhibitors that target the enzymes dynamic landscape.
Röntgen, A.; Fusco, G.; Breiter, J.; Beckwith, J. S.; Lachica, J.; Toomey, C. E.; Singh, J.; Klementieva, O.; Gandhi, S.; Lee, S.; De Simone, A.; Toprakcioglu, Z.; Vendruscolo, M.
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The aggregation of -synuclein (Syn) is a molecular hallmark of Parkinson's disease (PD) and other synucleinopathies. Understanding the molecular mechanisms that determine the aggregation of this protein may thus facilitate the development of disease-modifying therapies. While Syn is most commonly expressed as a 140-residue protein (Syn-140), recent evidence suggests an involvement of alternatively spliced Syn isoforms in disease onset and progression. Here, we report and characterise the interaction between Syn-140 and the aggregation-prone Syn-112 variant, one of the most abundant Syn splice isoforms. We found that amounts as low as 1% of Syn-112 accelerate the nucleation and aggregation of Syn-140. To further investigate this phenomenon, we employed MALDI-MS and NMR spectroscopy, confirming that Syn-140 and Syn-112 monomers interact strongly with one another. Furthermore, to assess the association of Syn-112 with disease pathology, we performed immunohistochemical staining combined with confocal microscopy on PD brain samples. Thereby, we found an increase in the number as well as the area of Syn-112 immunoreactive aggregates compared to healthy controls. These results illustrate how low-abundance Syn splice isoforms can modulate the aggregation landscape of Syn-140 and in turn contribute to the molecular heterogeneity of synucleinopathies.
Louet, A. A. B.; Stuke, J.; Pietrek, L.; Vendruscolo, M.; Hummer, G.
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Post-translational modifications (PTMs) of the tau protein are increasingly recognized as pivotal regulators in the onset and progression of tauopathies, such as Alzheimers disease (AD). To systematically evaluate the structural and functional consequences of specific PTMs, we generated and analyzed seven distinctly modified variants of the tau-K32 construct. These included phosphorylation at Ser202/Thr205, phosphorylation at Ser258/Ser262/Ser356, full phosphorylation at all reported Ser/Thr sites, acetylation at Lys274/Lys281, acetylation at Lys280, full acetylation at all sites, and an unmodified control. Selection of PTM sites was guided by prior experimental literature. By incorporating fully modified tau models, we assessed the global impact of widespread modifications on structural properties and aggregation behavior. Our findings establish a comparative framework for understanding how discrete and cumulative PTMs modulate tau aggregation and provide mechanistic insight into PTM-induced tau dysfunction relevant to neurodegenerative diseases.
Wu, Q.; Ciftci, D.; Canul Tec, J.; Reyes, N.; Gregorio, G.; Huang, Y.; Boudker, O.
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Membrane transporters move polar solutes across lipid bilayers to regulate cellular metabolism, signaling, and drug distribution. These proteins operate via an alternating-access mechanism, cycling between extracellular-, intermediate-, and intracellular-facing conformations. The human excitatory amino acid transporter 1 (EAAT1) protects neurons from excitotoxic damage by mediating the uptake of glutamate and aspartate into glial cells. Defects in EAAT1 function result in numerous pathologies, including epilepsy and ataxia, suggesting that positive modulation of these transporters might ameliorate glutamate neurotoxicity. However, developing EAAT1 activators requires understanding the timing of conformational changes, which remain largely unexplored. Here, we establish an experimental platform that combines single-molecule Forster resonance energy transfer (smFRET) to monitor real-time conformational dynamics, single-transporter activity assays to correlate dynamics with function, and cryogenic electron microscopy (cryoEM) to visualize discrete conformations at high resolution. This platform enables detection of [A]ngstrom-scale movements of single transporter molecules in real time, revealing that EAAT1 intersperses rapid conformational dynamics with long pauses. Slow and fast dynamics can be modulated by substrates, membrane composition, and mutations, and are correlated with the enrichment of specific structural states. We leverage this platform to investigate an EAAT1 mutation associated with severe episodic ataxia and show that it inhibits transport by stabilizing a paused cytoplasm-facing conformation. These results identify multimodal dynamics as an intrinsic, regulatable feature of EAAT1 function and, therefore, a potential therapeutic target. Henceforth, our integrated platform will facilitate investigations of other regulatory factors, including the effects of small-molecule and lipid modulators on the transport cycle.
Nag, N.; Roychowdhury, S.; Yadav, A. J.; Padhi, A.; Chattopadhyay, K.; Tripathi, T.
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The dysfunction of nucleocytoplasmic transport (NCT) and tau aggregation are emerging as interconnected hallmarks of neurodegenerative tauopathies. However, the molecular basis by which components of the nuclear pore complex and tau interact remains unclear. Here, we combine experimental and computational approaches to elucidate the mechanism of heterotypic phase separation between the FG-repeat domain of nucleoporin Nup98 (FG-Nup98) and tau. In vitro assays revealed that FG-Nup98 and tau undergo coacervation, forming dynamic condensates whose morphology and dynamics depend on stoichiometry, macromolecular crowding, and ionic strength. FRAP indicated reduced tau mobility within FG-Nup98-rich condensates, supporting a scaffold-client model. Complementary computational analyses revealed hierarchical binding energetics: FG-Nup98 self-association is strongest, followed by FG-Nup98-tau and tau-tau interactions. While FG-Nup98 forms stable homotypic networks, tau-tau contacts are transient but energetically favorable, which suggests that elevated tau concentrations may trigger a transition from droplets to tau aggregates. Together, these results establish that multivalent FG-Nup98-tau interactions drive condensate formation that could potentially perturb the permeability barrier of the nuclear pore. This study elucidates the coordinated behaviors of FG-Nup98-tau condensates and provides a framework for understanding NCT defects in tauopathies.
Feito, A.; Tejedor, A. R.; Ocana, A.; Teran, A.; Merlino, A.; Marasco, D.; Herrero, S.; R. Espinosa, J.
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The inhibition of A{beta}42 ({beta}-amyloid) fibril formation is a key therapeutic strategy in Alzheimer's disease research. Paddlewheel diruthenium complexes have shown promising activity against A{beta}42 aggregation and preformed fibril disaggregation, yet their molecular mode of action remains poorly understood. In this work, we perform atomistic simulations to explore how charge modulation influences the interactions of three analogous paddlewheel diruthenium complexes, the parent neutral complex [Ru2Cl(D-p-FPhF)(O2CCH3)3], and its anionic [Ru2Cl2(D-p-FPhF)(O2CCH3)3]- and cationic [Ru2(D-p-FPhF)(O2CCH3)3]+ counterparts (D-p-FPhF- is the N,N' -bis(4-fluorophenyl)formamidinato ligand) with A{beta}42. Our results indicate that electrostatic tuning governs binding affinity and the extent of interaction across the A{beta}42 fibril surface. As the complexes' charge changes from -1 to +1, the interaction pattern shifts from localized contacts to widespread, multi-site engagement encompassing key charged, aromatic, and hydrophobic regions of A{beta}42. This enhanced binding correlates with longer-lived, thermodynamically stable interactions at the fibril interface, which effectively lower the free energy penalty for fibril disassembly. Overall, our findings propose a mechanism in which charge-dependent activation through ligand exchange enhances fibril recognition and promotes disruptive binding modes, demonstrating the potential of charge-tunable diruthenium complexes as therapeutic modulators of A{beta}42 fibril stability.
Perera, D.; Ajiboye, E.; Pitakatuwana, K.; Wier, S.; Duong, V.; Wu, H.
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Apolipoprotein E (APOE) and Triggering Receptor Expressed on Myeloid cells 2 (TREM2) are the two strongest genetic risk factors of late-onset Alzheimers disease. ApoE binds to the low-density lipoprotein receptor (LDLR) to facilitate the uptake of ApoE-lipoprotein particles. TREM2 is a cell surface receptor expressed on microglia in the brain. The activation of TREM2 is essential for microglia to carry out protective functions against AD pathology. Several studies have shown that TREM2 signaling is activated through direct interaction between TREM2 and ApoE. In addition to its important role in AD pathogenesis, the ApoE/TREM2 interaction has been shown to induce immunosuppression of neutrophils within the tumor microenvironment. Despite its clinical importance, a high-resolution molecular understanding of the complex remains elusive. Here, we carried out chemical cross-linking mass spectrometry (XL-MS) analysis of the ApoE3/TREM2ECD complex to identify intra- and inter-protein cross-links, which were used as restraints to guide integrative protein-protein docking. Our data support a binding model in which a helix-loop-helix motif within the ApoE3 hinge and C-terminal region forms a transient hydrophobic pocket that wraps around the hydrophobic tip of the TREM2 ectodomain. This model is further supported by de novo-designed mini-protein binders, which show the same binding mode as identified by our XL-MS experiment. These results establish a robust framework for developing mini-protein-based TREM2 agonists.
Abakah, B.; Shimogawa, M.; Miranda-Castrodad, P.; Rhoades, E.; Petersson, E. J.
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-Synuclein (S), a protein that plays a central role in Parkinsons disease and related synucleinopathies, is an intrinsically disordered protein (IDP) whose functional interactions and aggregation behavior can be strongly influenced by post-translational modifications (PTMs). Phosphorylation, acetylation, and other PTMs regulate Ss interactions with lipid membranes and binding partners, whereas their dysregulation is associated with aggregation and neuronal toxicity. Despite significant progress through chemical and semi-synthetic approaches, investigating the combinatorial effects of PTMs has remained challenging due to the lack of accessible, site-specific methods. Here, we present an integrated strategy combining genetic code expansion, enzymatic modification, and intein-mediated click chemistry to generate S variants bearing multiple defined PTMs and a C-terminal fluorescent label. The resulting constructs enable direct evaluation of how individual and combined PTMs influence S structure, lipid binding, and cellular internalization. Our approach expands the molecular toolkit for dissecting PTM crosstalk in S and other aggregation-prone IDPs, advancing mechanistic understanding and supporting the development of therapeutic strategies for neurodegenerative disease.
Liu, W.; Chanda, S.
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Ubiquitin (Ub) conjugating enzymes (E2s) are central to Ub signaling, yet their systematic activity-based profiling remains challenging due to the weak nucleophilicity and elevated pKa of their catalytic cysteines. Existing Ub probes primarily target deubiquitinases (DUBs) and the only reported E2-targeting probe requires E1-dependent activation to capture limited E2s. To profile E2s broadly, here Ub chloromethylketone (UbCMK) is reported as a standalone activity-based probe. Density functional theory calculations identified CMK as a highly electrophilic warhead with a low activation barrier for reaction with weakly nucleophilic thiolates. UbCMK was synthesized via activated cysteine-based protein ligation and irreversibly labeled multiple E2s and cysteine DUBs. Activity-based protein profiling and quantitative proteomics in HEK293T cell lysates revealed broad enrichment of E2 enzymes, including many previously inaccessible to other probes. UbCMK furthermore enables activity-dependent quantification of endogenous E2 mobilization across oxidative, proteotoxic, inflammatory, metabolic, lipid oxidative, and genotoxic stress conditions. In addition, UbCMK engages both E1s and DUBs as well, indicating its broad utility as a probe. Collectively, these results establish UbCMK as a powerful chemical tool that expands activity-based protein profiling coverage across the Ub-proteasome system and enables functional interrogation of E2 enzymes under physiological and pathological conditions.
von Roten, V.; Ivanovic, M. T.; Gopi, S. R.; Holla, A.; Prestel, A.; Nüesch, M.; Tamburrini, K. C.; Nettels, D.; Kragelund, B. B.; Best, R.; Schuler, B.
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The free-energy surfaces that underlie the conformational distributions of intrinsically disordered proteins (IDPs) are shallow and lack the deep minima characteristic of stable, folded structures. However, even in the absence of secondary or tertiary structure, sequence patterning can lead to conformational preferences and changes in chain dimensions as a function of solution conditions. While patterning effects have received extensive attention from simulation and theory, there is little corresponding data from experiment. Here we investigate the impact of charge patterning on chain dimensions and dynamics in a set of specifically designed polyampholytic IDP variants across the natural range of charge segregation with single-molecule FRET, nanosecond fluorescence correlation, circular dichroism, and NMR spectroscopy. We find that the conformational ensembles and their cooperative response to salt concentration show prominent and systematic dependencies on charge patterning, and to some extent on residue type. In contrast, the chain dynamics remain in the tens-of-nanosecond range, consistent with the absence of pronounced free-energy barriers. In close combination with molecular simulations, we show how the concept of susceptibility can be used to quantify cooperativity in the absence of barriers and relate it to the shallow free-energy surfaces of IDPs.
Kleczko, K. M.; Gestaut, D.; Dobbins, S.; Abramovich, J.; Sitron, C. S.; Li, L.; Chan, R.; Wang, N.; Yang, X. W.; Hartl, F.-U.; Frydman, J.
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Accurate measurement of protein aggregation is essential for studying neurodegenerative diseases. The standard ThT assay reports on amyloid formation but is blind to early oligomers and is prone to interference. We describe Q-DOAS, a plate-reader assay that quantifies protein self-assembly in real time via proximity-quenching of a single, site-specifically conjugated dye (BODIPY-TMR). Using mutant Huntingtin-exon 1 (mHTT-Ex1) and -Synuclein A53T, we show Q-DOAS detects pre-amyloid oligomers, yielding quantitative kinetic data compatible with mechanistic analysis. We demonstrate its utility to dissect mutational effects, screen for protein and small-molecule inhibitors, and quantify amyloid seeding activity in cellular and mouse models of Huntingtons disease. Q-DOAS also detects seeds in cerebrospinal fluid from Parkinsons disease patients without amplification. Q-DOAS provides a sensitive, robust, and scalable tool for studying the earliest events in amyloid pathologies and for advancing therapeutic development.
Balaji, R.; Bhardwaj, S.; Baa, J.; Joshi, H.; Patel, B. K.
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Mechanistic elucidation and inhibition of the pathogenic aberrant mitochondrial localization of the RNA/DNA-binding protein, TDP-43, can help in the therapeutics of the neurodegenerative disease amyotrophic lateral sclerosis (ALS). A mitochondrial localization sequence of TDP-43, M1, is largely solvent inaccessible, therefore, how it interacts with the mitochondrial import machinery to facilitate TDP-43s transit to mitochondria is unclear. Towards this, we examined the unfolding TDP-43s N-terminal domain (NTD) that hosts M1, using equilibrium all-atom molecular dynamics (MD) simulations, and observed an early loss of the hydrogen-bonded interactions between {beta}4-{beta}5 bridge and the interactions involving residues Phe-35 and Gly-40 of M1, indicating structural lability of M1 to become solvent-accessible that may enhance its interaction with the mitochondrial receptor(s) for import. Furthermore, via virtual screening of 2,115 FDA-approved and 515,545 non-FDA-approved small molecules from ZINC15 database towards binding to M1 and inhibiting TDP-43s mitochondrial import, we identified a molecule, ZINC73240059, that was previously characterized as an inhibitor of MAP kinase-activating protein kinase 2 (MAPKAPK2). ZINC73240059 remains stably bound to M1 of NTD during MD simulations manifesting negative Gibbs free energy ({Delta}G) with significant contribution from Pro-36 of M1. Overall, ZINC73240059 can be a molecule of interest towards thwarting TDP-43s pathogenic mitochondrial localization in ALS.
de Alcantara Ferreira, J.; Walsh, D. J.; Turnbaugh, E.; Mills, J. H.; Supattapone, S.
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The pathogenic conversion of the cellular prion protein (PrPC) into the {beta}-sheet-rich isoform PrPSc is the pivotal pathogenic event in prion disease, yet the molecular steps that govern this structural transition remain elusive. In this study, we introduce a new approach to monitor site-specific conformational transitions that occur during infectious prion formation. The method relies on genetically encoded substitution of a fluorescent, environmentally sensitive non-canonical amino acid, L-(7-hydroxycoumarin-4-yl)ethylglycine (7-HCAA), into recombinant PrP substate molecules, allowing real-time monitoring of structural changes in high-efficiency in vitro PrPSc conversion reactions. As proof of principle, we show that the W99 7-HCAA recPrP substate efficiently propagates two different PrPSc conformers (infectious cofactor PrPSc and non-infectious protein-only PrPSc). Bioassays in knock-in mice expressing bank vole (BV) PrP confirm that W99 7-HCAA cofactor PrPSc produced by serial propagation is infectious, causing scrapie with an incubation period and neuropathological profile like those induced by wild-type cofactor PrPSc. Marked differences in fluorescence intensity were observed between native, misfolded, and denatured states of W99 7-HCAA PrP, confirming that 7-HCAA reports on local changes in PrP conformation. Together, these findings establish 7-HCAA as a site-specific and sensitive probe of local PrP conformation. Moreover, the results suggest a new and broadly applicable strategy for studying conformational dynamics in amyloid-forming proteins.
Carlstrom, G.; Hofurthner, T.; Akke, M.
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Chemical exchange saturation transfer (CEST) has become an indispensable NMR method to characterize slow exchange affecting biomacromolecules, especially for cases involving exchange between a major state and a minor state, the latter of which is often invisible in the spectrum. The CEST method is based on successive irradiation of selective regions of the NMR spectrum using a weak radiofrequency field, B1, while observing the effect on the visible major state when the B1 field saturates the invisible minor state. The need for selective saturation of narrow spectral regions has to date required acquisition of many tens of two-dimensional CEST spectra to sample the entire spectrum with sufficient resolution. Here we present the ACCEST method which measures an entire CEST profile from a single two-dimensional accordion-CEST spectrum plus a reference spectrum. ACCEST is based on the concept of accordion spectroscopy, where in the present implementation the carrier frequency of the weak saturating B1 field is stepped in synchrony with the dwell-time incrementation in the indirect dimension of the two-dimensional spectrum. We benchmarked ACCEST against conventional CEST, resulting in excellent agreement for both backbone 15N and methyl 13C CEST profiles. ACCEST offers substantial time savings that scale linearly with the number of spectra required in the corresponding conventional CEST experiment. Thus, ACCEST can dramatically speed up lengthy serial experiments, such as ligand titrations or temperature-dependent studies, and enable studies of non-equilibrium systems or samples with limited lifetimes.
Adkins, B. J.; Sidlowski, P. F. W.; Jennings, C. E.; Morrison, E. A.
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Nuclear organization is dynamic and originates from the fundamental subunit of chromatin, the nucleosome. Post-translational modification of nucleosomal histones, particularly within intrinsically disordered histone tail regions, provides a dynamic regulatory mechanism of accessibility for chromatin-templated processes. While the epigenomic impacts of lysine acetylation and serine phosphorylation in the histone H3 tail are well-known, how these charge-altering post-translational modifications (PTMs) alter nucleosomal tail conformational dynamics remains incompletely characterized. Given that the functional implications of these PTMs are, at least in part, a consequence of modified nucleosome conformation, systematically cataloging the impact of histone PTMs on nucleosome dynamics provides crucial insight into both baseline cellular activity and epigenetic dysregulation that occurs in disease. Previously, our lab demonstrated that arginine citrullination mimetics lead to regional increases in H3 tail dynamics within nucleosome core particles. Here, we performed nuclear magnetic resonance spin relaxation experiments to investigate the effects of lysine acetylation and serine phosphorylation on H3 tail picosecond-nanosecond (ps-ns) dynamics. Using lysine-to-glutamine and serine-to-glutamate mutations as acetyllysine and phosphoserine mimetics, respectively, we found that these PTMs increase ps-ns conformational dynamics regionally around the PTM site, with a position-dependent effect. Additionally, we show that the type of PTM influences the extent of these increases: in general, the effect of mimetics trends in the order of phosphorylation [≤] acetylation < citrullination, suggesting a tunable method for altering histone tail dynamics. Taken together, these results illustrate the role of nucleosome conformational dynamics in conveying the effects of epigenomic PTMs, elucidating a mechanism of the histone language.
Torii, K.; Gerasimaite, R.; Lukinavicius, G.
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Inorganic polyphosphate (polyP) is a ubiquitous phosphate biopolymer involved in diverse cellular processes. Despite its significance, selective detection of polyP remains challenging because of its simple and highly charged structure. Here, we report a near-infrared (NIR) fluorogenic turn-on chemosensor for selective polyP detection and imaging, SiX-DPA-Zn. The probe combines a silicon-xanthene (SiX) fluorophore with a zinc(II)-coordinated 2,2'-dipicolylamine (DPA-Zn2+) recognition unit and shows more than 100-fold selectivity for inorganic polyP over ADP and ATP. SiX-DPA-Zn enables quantitative detection of polyP at micromolar concentrations in microplate assays and stains a broad range of polyP species, starting from tripolyphosphate, in polyacrylamide gels. In HEK293 cells expressing Escherichia coli polyphosphate kinase 1, the probe visualizes intracellular polyP and enables quantitative analysis of polyP levels in relation to nuclear proteins for example fibrillarin and nucleolin. Stimulated emission depletion (STED) microscopy further revealed subdiffraction-sized polyP granules within polyP aggregates. SiX-DPA-Zn is the first near-infrared (NIR) fluorogenic chemosensor for polyP that is compatible with multiple detection platforms, including microplate assays, polyacrylamide gel staining, confocal and super-resolution STED microscopy.
Fonda, B. D.; Murray, D. T.
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The Tar-DNA Binding Protein-43 C-terminal region, TDP43LC, has been previously shown to form amyloid-like fibrils with distinct folds in ALS and FTD. In both diseases, proteinaceous inclusions contain TDP43 C-terminal protein fragments as well as phosphorylated TDP43. Here, we use solution NMR to show that soluble phosphomimetic TDP43LC, P-TDP43LC, is structurally similar to wild-type TDP43LC. Disperse P-TDP43LC, like wild-type protein, contains a central helical region flanked by long disordered regions. Despite this similarity, our turbidity measurements, imaging, and kinetic assays show that P-TDP43LC has different aggregation behavior than wild-type protein. Using solid state NMR measurements we find that that phosphomimetic mutations alter the wild-type fibril conformation. Electrostatic repulsion from negatively charged sidechains, despite having little effect on the soluble proteins structure, perturbs amyloid-like fibril formation and selects for a different conformation in vitro. These results shed light on the structural role of TDP43LC phosphorylation in fibril formation in disease. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/725298v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@1c63aforg.highwire.dtl.DTLVardef@1d48ed6org.highwire.dtl.DTLVardef@1ed8fd3org.highwire.dtl.DTLVardef@17d67a8_HPS_FORMAT_FIGEXP M_FIG C_FIG SynopsisPhosphomimetic mutations at ALS and FTD neurodegeneration-associated sites in an amyloid forming protein perturbs the aggregated structure compared to wild-type protein.
Sarkar, S.; Nagaiah, H. M.; Klein, M. L.; Carnevale, V.
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Neurodegenerative diseases are closely linked to aberrant protein aggregation arising from failures in cellular proteostasis, yet the physical determinants governing transitions between soluble states, liquid-liquid phase separation (LLPS), and aggregation remain incompletely understood. Here, we investigate how protein backbone topology influences phase behavior using ubiquitin C-terminal hydrolase L1 (UCH-L1), a highly neuron-enriched deubiquitinase in the ubiquitin-proteasome system harboring a rare, evolutionarily conserved knotted backbone topology, and its Parkinsons disease-associated I93M mutant. Through multiscale molecular dynamics (MD) simulations of single-chain and multichain systems, we show that knot integrity acts as a conformational constraint that limits access to expanded states, and suppresses LLPS propensity. Destabilization of the native knotted ensemble in I93M reshapes the conformational ensemble, enhancing intermolecular contacts, strengthening hydrophobic interaction, and reducing solvation penalties, thereby stabilizing protein-rich phases. Within condensates, these changes lead to persistent interchain contacts, increased topological entanglement, and slower relaxation dynamics, indicative of a transition toward viscoelastic assemblies, whereas intact topology maintains dynamic, liquid-like behavior. Our results identify topological integrity as a key physical determinant of protein phase behavior and establish a mechanistic link between topological stability and condensate material properties, with implications for aggregation-associated neurodegeneration.
Wang, C.; Ma, C.-T.; Crotty, C.; Zeng, F.-Y.; Bobkov, A.; Covel, J. A.; Keane Rivera, E.; Sergienko, E.; Kosik, K. S.; Olson, S. H.; Jackson, M. R.; Rauch, J. N.
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The cellular uptake and propagation of tau are central features of tauopathies, including Alzheimers disease, and are mediated by the endocytic receptor low-density lipoprotein receptor-related protein 1 (LRP1). While prior studies have implicated LRP1 in tau binding and internalization, the biochemical features of this interaction and its suitability for therapeutic targeting remain incompletely defined. Here, we establish a quantitative and scalable framework to interrogate the tau-LRP1 interaction and identify small-molecule modulators. We engineered and purified the LRP1 ligand-binding domain 4 (BD4), a key region mediating tau interaction, and developed multiple orthogonal assays, including fluorescence polarization, split luciferase complementation, and time-resolved FRET, to measure LRP1-BD4 interactions with tau and a known peptide ligand. Across assay formats, we observe consistent binding affinities in the nanomolar range and demonstrate competitive displacement by tau, receptor-associated protein (RAP), and a peptide ligand, supporting overlapping binding interfaces. Leveraging these platforms, we performed small molecule high-throughput screening and identified a set of candidate inhibitors of the LRP1-BD4-tau interaction. Selected compounds reduced tau uptake in a cellular assay, phenocopying competitive inhibition by tau and a peptide ligand. Together, these studies define the LRP1-BD4-tau interaction as a biochemically tractable and druggable interface and establish an integrated discovery pipeline linking mechanistic characterization to functional cellular outcomes. This work provides a foundation for the development of therapeutic strategies targeting LRP1-mediated tau uptake.
Gagliano, G.; Raterink, A.; Yang, X.; Bergo, M. O.; Gustavsson, A.-K.
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Hutchinson-Gilford Progeria Syndrome (HGPS) is a genetic disease characterized by the accumulation of progerin, a mutant form of lamin A, at the nuclear envelope. Progerin disrupts the stability of the nuclear lamina, leading to genome instability and accelerated aging phenotypes. While structural nuclear defects are well-documented, the impact of progerin on real-time chromatin dynamics and the ability of current therapeutics to rescue these dynamics remains poorly understood. In this work, we employ single-particle tracking to quantify telomere dynamics in HGPS patient fibroblasts. We demonstrate that HGPS cells exhibit significantly increased telomere dynamics, characterized by expanded scan areas, increased diffusion coefficients, and larger jump distances compared to healthy controls. We further evaluated the efficacy of two clinically relevant treatments, the farnesyltransferase inhibitor Lonafarnib and the ICMT inhibitor C75, to determine if emerging treatments can restore chromatin dynamics compared to healthy controls. Our results reveal that Lonafarnib partially rescues telomere dynamics, shifting chromatin motion back towards healthy control levels, and that C75 provides a complete rescue of the dynamics for all parameters quantified. These findings provide a quantitative framework for understanding how nuclear lamina mutations induce aberrant genome dynamics and the efficacy of HGPS therapies on restoring those dynamics.