Biology subjects

Greenwald, J.

Publications and source records attributed to Greenwald, J..

8 recordsLinked to original sources

bioRxiv2026

Cryo-EM structures of Alpha-Synuclein(31-100) amyloid fibrils reveal disease-like structural motifs without reproducing the Parkinson's Disease polymorph

The structural diversity of alpha-synuclein amyloid fibrils is closely linked to the pathogenesis of Parkinsons disease and related synucleinopathies. However, reproducing disease-associated fibril conformations from recombinant full-length protein in vitro has remained challenging. Inspired by successful truncation strategies developed for the Tau protein, we investigated whether removing the disordered terminal regions (< >) of alpha-synuclein could bias fibril assembly toward disease-relevant folds. We designed a truncated construct comprising residues 31-100, corresponding to the structured core of patient-derived Parkinsons disease fibrils, and systematically screened aggregation conditions across a broad range of pH values and ionic environments. Cryo-electron microscopy revealed four previously undescribed fibril structures, including new subtypes of the established type 1 and type 3 polymorphs and a novel fibril fold, termed type 10, which reproducibly formed under acidic conditions. Type 10 was observed as two distinct dimeric assemblies (10A and 10B) that share a common protofilament fold but differ in their inter-filament interfaces. Structural comparison with the patient-derived Parkinsons disease polymorph revealed local similarities, including conserved {beta}-strand organization and loop conformations within the fibril core, but remains structurally distinct overall. Our results demonstrate that rational construct design combined with systematic environmental screening reshapes the alpha-synuclein polymorphic landscape and promotes structural motifs characteristic of disease-associated fibrils.

biophysics↗

bioRxiv2026

On the Polymorph-Selection Determinants of α-Synuclein Amyloid Fibrils Studied at Atomic Resolution

Alpha-synuclein is an intensely studied intrinsically disordered protein whose aggregation into amyloid fibrils is connected to the progression of several neurodegenerative diseases, most commonly Parkinsons Disease. A remarkable feature that has emerged from this research is how easy it is to induce the protein to aggregate in vitro into a wide range of amyloid fibrils that appear to resemble the aggregates found in Lewy bodies in diseases like Parkinsons while at the same time how difficult it is to produce aggregates whose fold truly represents the disease-associated amyloids at the atomic level. In an effort to produce the disease-relevant fibrils in vitro we have analyzed over 60 independent samples by cryo-electron microscopy using helical reconstruction to obtain atomic resolution models for most of the samples. While not yet achieving our original goal, we have found that several overlooked parameters influence the structural outcomes of alpha-synuclein aggregation, in particular protein purity, preparation of the monomeric starting material and agitation method.

biophysics↗

bioRxiv2024

Prefrontal representations of retrospective spatial working memory in a rodent radial maze task

Working memory is the cognitive capacity for temporarily holding information in mind for processing or use. It has been theorized to depend upon executive and mnemonic subcomponents, although the contextual mapping of these subcomponents is not complete. Perturbations of prefrontal cortex (PFC) delay activity disrupt spatial working memory performance in rodent tasks. However, recordings of unperturbed PFC delay activity do not consistently contain mnemonic representations of spatial information in these tasks, calling into question the role that mnemonic PFC representations play in freely-moving spatial working memory. We hypothesized that increasing task complexity might increase the likelihood of mnemonic PFC representation emergence. We therefore used an automated eight-arm radial maze to implement a novel match-to-sample rodent spatial working memory task with seven options on each trial, and recorded calcium activity in PFC neurons during task performance. We found that the delay-phase activity of PFC neurons indeed contained mnemonic representations of spatial information at the population level. These representations were retrospective rather than prospective, and--surprisingly--were more evident on error trials. Together with previous results, these observations suggest that in freely-moving spatial working memory tasks, PFC mnemonic representations emerge to empower deviation from a routine behavioral strategy. Significance StatementPrefrontal cortex (PFC) activity is necessary for optimal performance of freely-moving spatial working memory tasks in rodents. Despite this, PFC representations of retrospective actions or stimuli--one quintessential working memory hallmark--are only variably observed during task delays, complicating our understanding of the PFCs role in spatial working memory. Here, we examine cellular-resolution PFC activity in a high-optionality match-to-sample radial maze task and find retrospective delay representations. Strikingly, these delay representations are more evident in error trials. This suggests that in the freely-moving context, explicit PFC representations of retrospective information support deviations from an entrained behavioral strategy, rather than equally supporting all spatial working memory-based behavior.

animal behavior and cognition↗

bioRxiv2024

Novel multiparametric bulk and single EV pipeline for adipose cell-specific biomarker discovery in paired human biospecimens

Obesity remains a growing and global public health burden across a broad spectrum of metabolic, systemic, and neurodegenerative diseases. Previously considered merely a fat storage depot, adipose tissue is now recognized as an active endocrine organ crucial for metabolic and systemic regulation of local and distant organs. A burgeoning line of investigation centers on adipose-derived extracellular vesicles (ADEVs) and their pivotal role in obesity-associated pathobiology. However, robust methodologies are lacking for specifically isolating and characterizing human ADEVs. To bridge this gap, we have developed a robust multiparametric framework incorporating bulk and single EV characterization, proteomics, and mRNA phenotyping. EVs from matched human visceral adipose tissue, mature adipocyte-conditioned media, and plasma collected from the same individual bariatric surgical patients were analyzed and subjected to bottom-up proteomics analysis. This framework integrates bulk EV proteomics for cell-specific marker identification and subsequent single EV interrogation with single-particle interferometric reflectance imaging (SP-IRIS) and total internal reflection fluorescence (TIRF) microscopy. Our proteomics analysis revealed 76 unique proteins from adipose tissue-derived EVs (ATEVs), 512 unique proteins from adipocyte EVs (aEVs), and 1003 shared proteins. Prominent pathways enriched in ATEVs included lipid metabolism, extracellular matrix organization, and immune modulation, while aEVs exhibited enhanced roles in chromatin remodeling, oxidative stress responses, and metabolic regulation. Notably, adipose tissue-specific proteins such as adiponectin and perilipin were highly enriched in ADEVs and confirmed in circulating plasma EVs. Colocalization of key EV and adipocyte markers, including CD63 and PPARG, were validated in circulating plasma EVs. In summary, our study paves the way toward a tissue and cell-specific, multiparametric framework for an adiposity EV signature in obesity-driven diseases.

molecular biology↗

bioRxiv2023

On the pH-dependence of α-synuclein amyloid polymorphism and the role of secondary nucleation in seeding experiments

The aggregation of the protein -synuclein is closely associated with several neurodegenerative disorders and as such the structures of the amyloid fibril aggregates have high scientific and medical significance. However, there are dozens of unique atomic-resolution structures of these aggregates, and such a highly polymorphic nature of the -synuclein fibrils hampers efforts in disease-relevant in vitro studies on -synuclein amyloid aggregation. In order to better understand the factors that affect polymorph selection, we studied the structures of -synuclein fibrils in vitro as a function of pH and buffer using cryo-EM helical reconstruction. We find that in the physiological range of pH 5.8-7.4 a pH- dependent selection between Types 1, 2 and 3 polymorphs occurs. Our results indicate that even in the presence of seeds, the polymorph selection during aggregation is highly dependent on the buffer conditions, attributed to the non-polymorph-specific nature of secondary nucleation. We also uncovered two new polymorphs that occur at pH 7.0 in phosphate-buffered saline. The first is a monofilament Type 1 fibril that highly resembles the structure of the juvenile-onset synucleinopathy polymorph found in patient-derived material. The second is a new Type 5 polymorph that resembles a polymorph that has been recently reported in a study that used diseased tissues to seed aggregation. Taken together, our results highlight the shallow amyloid energy hypersurface that can be altered by subtle changes in the environment, including the pH which is shown to play a major role in polymorph selection and in many cases appears to be the determining factor in seeded aggregation. The results also suggest the possibility of producing disease-relevant structure in vitro.

biophysics↗

bioRxiv2020

Dopamine D2 receptors modulate the cholinergic pause and inhibitory learning

Cholinergic interneurons (CINs) in the striatum respond to salient stimuli with a multiphasic response, including a pause, in neuronal activity. Slice physiology experiments have shown the importance of dopamine D2 receptors (D2Rs) in regulating CIN pausing yet the behavioral significance of the CIN pause and its regulation by dopamine in vivo is still unclear. Here, we show that D2R upregulation in CINs of the nucleus accumbens (NAc) lengthens the pause in CIN activity ex vivo and enlarges a stimulus-evoked decrease in acetylcholine (ACh) levels during behavior. This enhanced dip in ACh levels is associated with a selective deficit in the learning to inhibit responding in a Go/No-Go task. Our data demonstrate, therefore, the importance of CIN D2Rs in modulating the CIN response induced by salient stimuli and points to a role of the pause in inhibitory learning. This work has important implications for brain disorders with altered striatal dopamine and ACh function, including schizophrenia and attention-deficit hyperactivity disorder (ADHD).

neuroscience↗

bioRxiv2020

Mass Photometry of Membrane Proteins

Integral membrane proteins (IMPs) are biologically highly significant but challenging to study because they require maintaining a cellular lipid-like environment. Here, we explore the application of mass photometry (MP) to IMPs and membrane mimetic systems at the single particle level. We apply MP to amphipathic vehicles, such as detergents and amphipols, as well as to lipid and native nanodiscs, characterising the particle size, sample purity and heterogeneity. Using methods established for cryogenic electron microscopy, we eliminate detergent background, enabling high-resolution studies of membrane protein structure and interactions. We find evidence that, when extracted from native membranes using native styrene-maleic acid nanodiscs, the potassium channel KcsA is present as a dimer of tetramers - in contrast to results obtained using detergent purification. Finally, using lipid nanodiscs, we show that MP can help distinguish between functional and non-functional nanodisc assemblies, as well as determine the critical factors for lipid nanodisc formation.

biophysics↗

bioRxiv2018

Cooperative induction of ordered peptide and fatty acid aggregates

Interactions between biological membranes and disease-associated amyloids are well documented and their prevalence suggests that an inherent affinity exists between these two distinct molecular assemblies. Within the framework of our research project on amyloids and the origins of life, we hypothesized here that such interactions could increase both the sequence and structure space of peptide amyloids in a heterogeneous system and that if cooperative in nature, the interaction could be advantageous to the propagation of these entities in a prebiotic context. Thus, we have investigated the interplay between vesicle-forming fatty acids and amyloidogenic peptides, the respective precursors of lipids and proteins. Individually they are able to form ordered structures under a limited range of conditions with the bilayer of fatty acid vesicles and the cross-{beta} core of amyloids both being repetitive structures that could in principle support a cooperative interaction. Here we report that an 8-residue basic peptide that can form an amphipathic {beta}-strand, that is soluble at neutral pH and that can form amyloids above its pI at pH 11, is also able to cooperatively form novel co-aggregates of diverse structure with and in the context of simple fatty acids at neutral pH. Below the critical vesicle concentration (CVC) the mixtures of fatty acid and peptide yield a flocculent precipitate with an underlying {beta}-structure. Above the CVC, the mixtures yield ribbon or tube-like structures that bear some of the hallmarks of amyloids yet have associated with them a significant amount of fatty acids, likely in a bilayer structure. In the context of the origin of cellular life these results expand the phase space of both peptides and fatty acids while providing a simple yet robust physical connection between two distinct biological entities relevant for life.

biophysics↗