Biology subjects

Kamalaldinezabadi, S. S.

Publications and source records attributed to Kamalaldinezabadi, S. S..

5 recordsLinked to original sources

bioRxiv2026

Stimulating microglial neuroinflammation with amyloid-beta oligomers compatible with solid-state NMR structural characterization

Soluble amyloid-{beta} (A{beta}) oligomers are considered the primary neurotoxic species in Alzheimer's disease, yet the relationship between oligomer structure and biological activity remains poorly understood. Oligomer sample preparations amenable to high-resolution structural characterization have not been tested in cell-based assays, mostly because detergents used to drive oligomer formation are toxic to cells. Here, we describe a detergent-free protocol in which size-exclusion chromatography-isolated A{beta}42 monomers spontaneously oligomerize at 37 {degrees}C in a concentration- and temperature-dependent manner. Biophysical characterization shows a {beta}-sheet structure by circular dichroism, a self-associating population above 100 kDa by silver-stained SDS-PAGE, and bead-like strings by negative-stain TEM resembling the previously characterized SDS-induced 150 kDa oligomer. Solid-state NMR spectroscopy of selectively 13C/15N-labeled 37 {degrees}C oligomers yields well-resolved spectra with {beta}-strand chemical shifts, and two-dimensional 13C-13C DARR and CHHC experiments provide initial inter-residue distance constraints that reveal both similarities to and differences from the 150 kDa oligomer. Treatment of mouse microglial cells (MMCs) with 50 nM 37 {degrees}C oligomers elicited a robust pro-inflammatory cytokine response that exceeded that of monomeric A{beta}42, as demonstrated by Luminex multiplex profiling and principal component analysis. hiPSC-derived microglia (iMGs) treated with 1 {micro}M oligomers also separated from vehicle, establishing activity in a human cellular model. Monomeric A{beta}42 was inactive in both systems, indicating that inflammatory activity depends on the assembly state of A{beta}42 rather than on the presence of peptide alone. These results establish a detergent-free A{beta}42 oligomer preparation that is simultaneously compatible with solid-state NMR structural characterization and biologically active in neuroinflammation assays, providing a platform for studying microglial immune responses to oligomers.

neuroscience↗

bioRxiv2026

Cryo-EM Reveals VP1/VP2 N-Terminal Conformations in Adeno-Associated Virus 2 Capsids.

The AAV2 capsid assembles from three viral proteins, VP1, VP2, and VP3, expressed from a single cap gene. In the assembled T=1 60-subunit icosahedral capsid, they have a canonical stoichiometry of 1:1:10. Relative to VP3, VP1 and VP2 have N-terminal extensions that are required for endosomal escape and nuclear trafficking; however, these regions remain poorly resolved due to low stoichiometry, symmetry mismatches, and conformational heterogeneity of their N-termini. Here, we generated empty AAV2 capsids using a baculovirus expression system with time-course harvests, yielding approximately 2:3:5 and 1:2:7. VP1:VP2:VP3 ratios on days 3 and 5 post-infection, respectively. Cryo-EM single-particle and subparticle reconstructions revealed distinct N-terminal configurations associated with these different VP stoichiometries. Day 3 capsids contained an internal density protruding from the twofold axis and lacked the ordered {beta}A preceding residue 237, whereas day 5 capsids lacked the twofold protrusion and instead showed density associated with the fivefold axis, with {beta}A ordered to approximately residues 219-221. Fivefold subparticle reconstruction of day 5 capsids further resolved a density plug occluding the pore and an underlying density ring. These findings link VP stoichiometry to distinct conformations of the VP1/VP2 N-termini and provide structural evidence for alternative organization of these regions within the AAV2 capsid, offering new insights into the conformational landscape of AAV capsid heterogeneity.

biophysics↗

bioRxiv2026

Structural Co-optation and Loss-of-function Underlie the Evolution of Regulatory Novelty in the Glucokinase Regulatory Protein

The glucokinase regulatory protein (GKRP) derives from an ancestral etherase. Despite existing as a single locus in the metazoans, GKRP evolved multiple novel functions unrelated to etherase activity. In jawed vertebrates, a protein-protein interaction (PPI) emerged that inhibits glucokinase (GCK) activity in the liver. This PPI is critical to maintaining glucose homeostasis. In mammals, GKRP is allosterically regulated by carbohydrates, with 6-phospharylated sugars promoting inhibition of GCK by GKRP, while 1-phosphorylated sugars relieve inhibition. Here, we use a vertical evolutionary approach to identify the genetic, biochemical, and biophysical mechanisms underlying the emergence of small-molecule allostery in GKRP. We pinpointed a single leucine to valine substitution in the N-terminus of GKRP from the ancestor of the euarchontoglires that, when introduced into the non-regulated placental mammal GKRP ancestor, installed sensitivity to sorbitol-6-phosphate (S6P). Interestingly, GKRPs inhibitory activity in the absence of S6P was reduced but unchanged in its presence. The mutation enabled co-optation of the ancestral etherase active site, which also existed as an ambiguous phosphorylated carbohydrate binding site in unregulated GKRPs. This substitution likely introduced an alternative conformation of the N-terminus causing apo-GKRP to sample a binding incompetent state prior to GCK binding. Our results suggest a simple model of the evolution of protein functional novelty where a single mutation can cause a large functional shift via co-optation of pre-existing structural features. Importantly, in contrast to many models of protein evolution, ours does not require the addition of new genetic material to realize a novel function such as small-molecule allosteric regulation.

biochemistry↗

bioRxiv2026

Evolution of Protein Regulation in the Vertebrate Glucose Sensor

Protein regulation is essential for cellular function and mis-regulation commonly causes disease. Despite this fact, we know little about how new regulatory strategies first emerge and how they evolve to act in concert to control complex physiological processes. Glucokinase (GCK), the bodys glucose sensor, lies at the heart of vertebrate glucose homeostasis and its activity is tightly controlled by multiple regulatory mechanisms. In the pancreas and liver, GCK is regulated by a unique form of monomeric allostery originating from the unliganded enzymes conformational dynamics. In the liver, GCK and GKRP form an inhibitory protein-protein interaction that sequesters GCK within the hepatocyte nucleus. Using a vertical, evolutionary approach, we resurrected extinct GCKs and GKRPs along correlated evolutionary trajectories. Using enzyme kinetics, limited proteolysis, hydrogen-deuterium exchange, high resolution NMR, and X-ray crystallography we determined the historical and molecular origins of protein regulation. Prior to the emergence of jawed vertebrates, a non-regulated GCK ancestor underwent a conformational expansion leading to monomeric allostery. This novel conformation includes an intrinsically disordered substrate binding loop. Paradoxically, the emergence of disorder did not require sequence change in the loop. The new GCK conformation also exposed a hydrophobic cleft. In the jawed vertebrate GKRP ancestor, a de novo loop insertion enabled exaptation of the pre-existing hydrophobic patch in GCK. Our results demonstrate how multiple, distinct regulatory strategies can arise at a central homeostatic control point through evolutionary addition of novel conformations. Additionally, our results provide a general mechanism for the emergence of heteromeric protein-protein interactions. Significance StatementGlucose homeostasis was a key innovation in vertebrate evolution. Here, we uncover the evolutionary basis of regulation in two key homeostatic proteins, glucokinase (GCK) and glucokinase regulatory protein (GKRP). We find that the unique cooperativity of vertebrate GCK resulted from an expansion of this enzymes conformational landscape. This expansion included sampling a new state and the emergence of intrinsic disorder, which did not require substitutions in the disordered region itself. We also discover that the GCK-GKRP interaction emerged when a pre-existing hydrophobic surface -- a structural spandrel resulting from prior conformational expansion -- was co-opted by loop insertion in GKRP, facilitating a new, inhibitory heteromeric interaction. Our results demonstrate how multiple, mechanistically distinct regulatory strategies arise from an ability to sample new protein conformations.

biochemistry↗

bioRxiv2024

Aggregation Dynamics of a 150 kDa Aβ42 Oligomer: Insights from Cryo Electron Microscopy and Multimodal Analysis

I.Protein misfolding is a widespread phenomenon that can result in the formation of protein aggregates, which are markers of various disease states, including Alzheimers disease (AD). In AD, amyloid beta (A{beta}) peptides, particularly A{beta}40 and A{beta}42, are key players in the diseases progression, as they aggregate to form amyloid plaques and contribute to neuronal toxicity. Recent research has shifted attention from solely A{beta} fibrils to also include A{beta} protofibrils and oligomers as potentially critical pathogenic agents. Particularly, oligomers demonstrate greater toxicity compared to other A{beta} specie. Hence, there is an increased interest in studying the correlation between toxicity and their structure and aggregation pathway. The present study investigates the aggregation of a 150 kDa A{beta}42 oligomer that does not lead to fibril formation over time. Using negative stain transmission electron microscopy (TEM), size exclusion chromatography (SEC), dynamic light scattering (DLS), and cryo-electron microscopy (cryo-EM), we demonstrate that 150 kDa A{beta}42 oligomers form higher-order string-like assemblies over time. The strings are unique from the classical A{beta} fibril structures. The significance of our work lies in elucidating molecular behavior of a novel non-fibrillar form of A{beta}42 aggregate.

biophysics↗