Biology subjects

Najafi, S.

Publications and source records attributed to Najafi, S..

4 recordsLinked to original sources

bioRxiv2026

A water-pinning hotspot drives templated tau aggregation

Tau assembles into fibrillar aggregates that are pathological hallmarks of a group of neurodegenerative diseases collectively called tauopathies. Templated aggregation of naive tau to seeding-competent fibrils that proceed from cell to cell is a key driver of prion-like progression of tauopathies. This study tests the hypothesis that tau, an intrinsically disordered protein (IDP), achieves in-register stacking to form seed-competent fibrils by a pinning action of tau to each other and/or the seed surface via a single dominant hotspot to avoid mismatch in tau stacking to fibrils. Structured solvation water has been proposed to be a signature of such hotspots at both the tau fibril-end surface and soluble tau monomers. Although jR2R3-P301L tau exhibits a heterogeneous hydration landscape in its intrinsically disordered state, with enhanced water structuring near the P301L mutation site, it is unclear whether a localized hotspot exists at the fibril end surface and surface water facilitates the initial contacts in templated aggregation. Using rapid 1H-15N SOFAST-HMQC NMR to track seed-induced aggregation of jR2R3-P301L in real time, complemented by molecular dynamics simulation of fibril surface hydration, we identify a residue-specific pinning hotspot that is prone to dewetting followed by sequential folding and incorporation of the remaining segment in a two-step dock-and-lock process. Site-specific spin labeling further demonstrates that blocking this pinning hotspot disrupts templated aggregation, leading to shorter fibrils. The identification of a dominant pinning site will facilitate the rational design of binders to effectively disrupt fibril extension or serve as diagnostic or therapeutic strategies.

biophysics↗

bioRxiv2026

Context-Aware Hydrophobicity Modeling: HydroMap and FastHydroMap

Hydrophobicity governs a vast range of phenomena, from protein-protein interactions to nanomaterial assembly, and can be rigorously quantified by the dewetting free energy (Fdewet) of a molecule or surface. However, hydrophobicity remains widely treated as an additive property of amino acid identity, obscuring the fact that waters response is a collective property of the surface, shaped by curvature, chemical patterning, and neighboring residues. Direct calculation of Fdewet via specialized molecular simulations captures this collective behavior but is prohibitively slow, leaving in place broadly-used, decades-old sequence-based hydropathy scales that neglect the physics of solvation. Here we show that residue-level Fdewet can be predicted from a compact set of local water features (water structural signatures and residue-water potential energy) extracted from a brief and inexpensive all-atom simulation. We embed this insight in two models: HydroMap, which predicts Fdewet directly from water features, and FastHydroMap, a computationally inexpensive graph neural network surrogate trained on HydroMap that requires no solvent simulation. HydroMap and FastHydroMap capture context-dependent hydrophobicity that classical, sequence-only hydropathy scales miss. We demonstrate this across three protein systems: on an -synuclein amyloid filament, strongly dewetting interfaces align with unassigned peptide densities, revealing hidden binding sites; in calmodulin, hydrophobicity redistributes upon Ca2+ binding; and for Protein G, time-resolved hydrophobicity changes track the folding trajectory. Together, these models make Fdewet a computationally inexpensive descriptor for proteins, membranes, and other surfaces, enabling rapid scoring for materials design and a time-resolved view of dynamic hydrophobic-mediated processes such as protein folding. Significance StatementHydrophobicity, the tendency of surfaces to expel water, drives how proteins fold and how molecules recognize one another. For decades, it has widely been treated as a fixed property of an amino acid or chemical group, but water actually responds to the collective shape and chemistry of a surface, such as that presented by a protein, not to its components in isolation. Measuring this collective response from molecular simulation is rigorous but prohibitively slow. We show that it can instead be inferred from a compact set of features describing water structure and interactions near a surface, and we use this insight to build models that predict hydrophobicity rapidly and at residue resolution, enabling practical, physically grounded design of hydrophobic-mediated interactions.

biophysics↗

bioRxiv2025

Rapid proteasomal degradation of mutant feline McDonough sarcoma-like tyrosine kinase-3 overcomes tyrosine kinase inhibitor resistance of acute myeloid leukemia cells

BackgroundFeline McDonough sarcoma (FMS)-related receptor tyrosine kinase 3 with activating internal tandem duplications (FLT3-ITD) causes acute myeloid leukemia (AML). Targeted protein degraders for FLT3 have evolved as drugs against leukemia. MethodsWe synthesized and characterized MA191 as novel von Hippel-Lindau (VHL)-based proteolysis targeting chimera (PROTAC) for FLT3. We analyzed protein expression, protein degradation mechanisms, and posttranslational modifications by immunoblot. Selective proteasome modulation, an inactive stereoisomer of MA191, and siRNA confirmed the event-driven degradation of FLT3-ITD. Hematopoietic cell survival and differentiation were determined by flow cytometry using apoptosis and cell surface markers. As models, we used cultured and primary human AML cells, FLT3 inhibitor-resistant AML cells, mature blood cells, and hematopoietic stem cells. We scrutinized the databases DepMap, GEPIA2, Hemap, and HPA to assess FLT3 expression and patient survival. Experiments with Danio rerio larvae verified in vivo anti-leukemic activity of MA191. ANOVA and Bonferroni correction were used for statistics. ResultsMA191 is a rapid nanomolar apoptosis inducer in AML cells harboring FLT3-ITD (IC50=10.16-11.6 nM; EC50=0.015-0.883 {micro}M). A stereoisomer of MA191 that cannot recruit VHL demonstrates that elimination of FLT3-ITD is superior to its inhibition. MA191 abrogates FLT3 inhibitor resistance from rebound activation of mitogen-activated kinases. Rapid depletion of FLT3-ITD by MA191 (DC50=10 nM) requires VHL, neddylation, and the pro-apoptotic BH3-only protein BIM. Reduction of FLT3-ITD by MA191 precedes apoptosis. This reveals an apoptosis-independent function of BIM on protein stability. Leukemia cells express more FLT3 than healthy cells (n=3675/n=1249) and FLT3 expression is associated with worse AML patient survival (p=0.0099). MA191 does not harm blood cells and bone marrow progenitor cells and does not disturb myeloid blood cell differentiation. In Danio rerio, MA191 halts AML cell proliferation without significant toxicity. Anti-leukemic effects of MA191 are not susceptible to anti-apoptotic effects of human stromal cells and mutations in the tyrosine kinase of FLT3-ITD that confer resistance to selective FLT3 inhibitors. Conclusionsthese insights and the disclosure of the structure of MA191 provide a framework for an improved design of PROTACs that target mutant FLT3 and are not vulnerable to extrinsic and intrinsic resistance mechanisms. Degradation kinetics appear as determinant of such resistance breakers. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=188 SRC="FIGDIR/small/660791v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@17e5988org.highwire.dtl.DTLVardef@27fbc4org.highwire.dtl.DTLVardef@1023648org.highwire.dtl.DTLVardef@39bdcb_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2023

Tau P301L mutation promotes core 4R tauopathy fibril fold through near-surface water structuring and conformational rearrangement

Tau forms toxic fibrillar aggregates in a family of neurodegenerative diseases known as tauopathies. The faithful replication of tauopathy-specific fibril structures is a critical gap for developing diagnostic and therapeutic tools. This study debuts a strategy of identifying a critical segment of tau that forms a folding motif that is characteristic of a family of tauopathies and isolating it as a standalone peptide that form seeding-competent fibrils. The 19-residue jR2R3 peptide (295-313) spanning the R2/R3 splice junction of tau, in the presence of P301L, forms seeding-competent amyloid fibrils. This tau fragment contains the hydrophobic VQIVYK hexapeptide that is part of the core of every pathological tau fibril structure solved to-date and an intramolecular counter-strand that stabilizes the strand-loop-strand (SLS) motif observed in 4R tauopathy fibrils. This study shows that P301L exhibits a duality of effects: it lowers the barrier for the peptide to adopt aggregation-prone conformations and enhances the local structuring of water around the mutation site that facilitates site-specific dewetting and in-register stacking of tau to form cross {beta}-sheets. We solve a 3 [A] cryo-EM structure of jR2R3-P301L fibrils with a pseudo 21 screw symmetry in which each half of the fibrils cross-section contains two jR2R3-P301L peptides. One chain adopts a SLS fold found in 4R tauopathies that is stabilized by a second chain wrapping around the SLS fold, reminiscent of the 3-fold and 4-fold structures observed in 4R tauopathies. These jR2R3-P301L fibrils are able to template full length tau in a prion-like fashion. Significance StatementThis study presents a first step towards designing a tauopathy specific aggregation pathway by engineering a minimal tau prion building block, jR2R3, that can template and propagate distinct disease folds. We present the discovery that P301L--among the widest used mutations in cell and animal models of Alzheimers Disease--destabilizes an aggregation-prohibiting internal hairpin and enhances the local surface water structure that serves as an entropic hotspot to exert a hyper-localized effect in jR2R3. Our study suggests that P301L may be a more suitable mutation to include in modeling 4R tauopathies than for modelling Alzheimers Disease, and that mutations are powerful tools for the purpose of designing of tau prion models as therapeutic tools.

biophysics↗