Biology subjects

Liu, A. C. H.

Publications and source records attributed to Liu, A. C. H..

5 recordsLinked to original sources

bioRxiv2026

Structural Basis for Activation of HRI by the DELE1 C-terminal domain

Haem-Regulated Inhibitor (HRI, aka EIF2AK1) is one of four stress-sensing kinases that phosphorylate eIF2 as part of the integrated stress response (ISR). HRI was first characterized as a haem-sensing kinase where it is inhibited when bound to haem. Recent studies have revealed another role for HRI in sensing mitochondrial stress via the mitochondrial protein DELE1. Upon stress, DELE1 is cleaved, and its C-terminal fragment (DELE1CTD) is released from the mitochondria to the cytoplasm, where it interacts with HRI, to trigger the ISR. This pathway is critical for mitochondrial quality control and neuronal health. Here, we perform biophysical analysis to demonstrate that purified recombinant DELE1CTD binds with high affinity to the N-terminal region of HRI, competing with and displacing haem to activate HRI and pointing to a shared binding site. Using Hydrogen Deuterium Exchange Mass Spectrometry (HDX-MS), we map the binding footprint of DELE1CTD on HRI and confirm that it overlaps with the haem-binding site. These findings support a simple activation mechanism: DELE1CTD activates HRI by excluding inhibitory haem from its binding site.

biochemistry↗

bioRxiv2026

CD59 organizes the plasma membrane to sustain oncogenic Ras-MAPK signaling and is a targetable vulnerability in acute myeloid leukemia

Acute myeloid leukemia (AML) is a clinically heterogeneous disease. Although the genetic abnormalities associated with poor prognosis are well defined, how they drive unfavorable outcomes remains unclear. Using published gene-expression and dependency datasets, we searched for cell-surface protein-coding genes associated with poor survival and required for AML growth, prioritizing this class of proteins for its accessibility to biologics. This search identified CD59, a GPI-anchored protein with a canonical role in complement regulation, whose high mRNA expression correlates with adverse-risk genetics and stemness signatures. CD59 silencing impaired proliferation across genetically diverse AML cell lines, reduced leukemic burden, and extended survival in cell xenograft models. Moreover, CD59 expression was enriched on leukemic stem cells (LSCs), and its depletion impaired LSC self-renewal and primary AML engraftment in vivo while sparing normal hematopoiesis. Mechanistically, these effects reflected a non-canonical role for CD59 in sustaining Ras-MAPK signaling, whereby its loss depleted inner-leaflet phosphatidylserine and impaired Ras and c-Raf membrane recruitment and activation. rILYd4, a recombinant fragment of the bacterial toxin intermedilysin that binds and degrades CD59, recapitulated these effects and sensitized cells to venetoclax in vivo. These findings reveal CD59 as a critical regulator of Ras-MAPK signaling required for AML growth and nominate its rILYd4-mediated degradation as a therapeutic strategy.

cancer biology↗

bioRxiv2025

Generative Design of High-Affinity Peptides Using BindCraft

Discovering high-affinity ligands directly from protein structures remains a key challenge in drug discovery. We applied BindCraft, a structure-guided generative modeling platform, to de novo design of peptide ligands for protein interfaces. Originally developed for miniprotein binders, we evaluated its use for shorter peptides (10-20mers) as peptides hold greater synthetic accessibility and therapeutic potential. For the oncoprotein MDM2, BindCraft generated 70 unique peptides; 15 were synthesized, and 7 showed specific binding with nanomolar affinities (KD = 65-165 nM). Competition assays confirmed site-specific binding for the intended target site. For another oncology target, WDR5, peptides were designed for the MLL (WIN) and MYC (WBM) sites. Of the peptides tested for each site, no validated hits were found for the WIN site, but six candidates bound the WBM site with sub-micromolar affinity (KD = 219-650 nM). Based on Bindcrafts structural prediction of the binding interface, we designed a stapled variant of the best WDR5 binder, improving the potency by 6-fold to a KD of 39 nM. Overall, our findings establish BindCraft as a powerful and accessible platform for structure-based peptide discovery, with remaining limitations, but with a promising success rate even for challenging targets.

biochemistry↗

bioRxiv2024

Cryo-EM of AKAP350 reveals fibrillar clusters and a potential association with DNA

Protein kinase A (PKA) is a promiscuous serine/threonine kinase that phosphorylates a broad-spectrum of effectors involved in vital processes such as glucose, glycogen, and lipid metabolism. Its activity is thus tightly controlled by a family of eukaryotic scaffolding proteins known as the A-kinase anchoring proteins (AKAPs) that confine PKA signaling to specific compartments in the cell. AKAP350 (the protein encoded by AKAP9) is a massive scaffolding protein that anchors PKA to the Golgi apparatus and the centrosome where it nucleates macromolecular signaling hubs that control microtubule nucleation and dynamics. Here, we have expressed and purified full-length AKAP350 from HEK293F cells in a functional conformation. Electron cryo-microscopy (cryo-EM) of the purified protein revealed polydisperse particles forming fibrillar clusters around 50 nm in diameter, and long, thin filaments that reconstructed into double-stranded DNA. Tomographic reconstruction of a tilt series of the purified protein by electron cryo-tomography (cryo-ET) further elucidated these fibrillar clusters as 3D bundles of entangled filaments. Mass spectrometry and DNA sequencing confirmed the co-purification of DNA and DNA binding proteins such as nuclear factor 1 B (NFIB) and nucleolin (NCL). Pulldown of NFIB and NCL, but not of CEP290, CDK5RAP2, and CEP170 was diminished in the presence of DNase-I, suggesting that AKAP350 interaction with these two proteins is mediated by DNA. Overall, this study has achieved a quality purification of AKAP350 from which a previously uncharacterized interaction landscape with DNA and DNA binding proteins was discovered.

biochemistry↗

bioRxiv2022

SARS-CoV-2 impairs interferon production via NSP2-induced repression of mRNA translation

Viruses evade the innate immune response by suppressing the production or activity of cytokines such as type I interferons (IFNs). Here we report the discovery of a novel mechanism by which the SARS-CoV-2 virus co-opts an intrinsic cellular machinery to suppress the production of the key immunostimulatory cytokine IFN-{beta}. We reveal that the SARS-CoV-2 encoded Non-Structural Protein 2 (NSP2) directly interacts with the cellular GIGYF2 protein. This interaction enhances the binding of GIGYF2 to the mRNA cap-binding protein 4EHP, thereby repressing the translation of the Ifnb1 mRNA. Depletion of GIGYF2 or 4EHP significantly enhances IFN-{beta} production, leading to reduced viral infection. Our findings reveal a new target for rescuing the antiviral innate immune response to SARS-CoV-2 and other RNA viruses.

microbiology↗