Biology subjects

Craik, C.

Publications and source records attributed to Craik, C..

6 recordsLinked to original sources

bioRxiv2026

Structure-guided design of a targeted autoantibody degrader for neurologic disease

Despite rapid progress in the diagnosis of autoantibody-mediated neurologic diseases, standard-of-care therapeutic options remain limited to nonspecific immunosuppression. Here, we report an alternative therapeutic strategy using targeted protein degradation to eliminate pathogenic autoantibodies while leaving the rest of the immune system intact. We previously discovered autoimmune vitamin B12 central deficiency (ABCD), a neurologic condition in which autoantibodies targeting the transcobalamin receptor (CD320) impair the transport of cobalamin (B12) from the blood into the central nervous system (CNS). Combining scanning alanine mutagenesis by phage display, cryo-electron microscopy, and computational modeling, we elucidated a highly conserved anti-CD320 epitope and defined the structural determinants of antigen-autoantibody binding. Next, we synthesized a lysosome-targeting chimera (LYTAC) comprising the lysosome targeting glycan, triGalNAc, fused to the antigenic epitope of CD320 as autoantibody bait. In vitro, this LYTAC promoted the specific lysosomal internalization and extracellular clearance of anti-CD320, restoring homeostatic cellular uptake of B12. In a passive transfer mouse model of ABCD, LYTAC treatment rapidly cleared anti-CD320 from circulation and prevented penetration of anti-CD320 into the CNS. These findings uncover the mechanism of autoantibody-antigen binding in ABCD and demonstrate targeted autoantibody degradation as a therapeutic strategy that may be generalizable to other autoimmune neurologic diseases.

neuroscience↗

bioRxiv2025

Antibody Reveals Conformational Latch Controlling Herpesvirus Proteases

Human herpesviruses (HHVs) are widespread pathogens that cause severe disease. Their replication depends on the HHV protease (HHV Pr), an enzyme essential for capsid maturation. Because HHV Pr must dimerize to become catalytically active, disrupting dimer formation is a promising strategy for antiviral therapeutic development. We isolated a conformationally selective antibody inhibitor, Fab5, from a fully human naive Fab-phage library that recognizes monomeric human cytomegalovirus protease (HCMV Pr). A 2.6 [A] cryoelectron microscopy (cryo-EM) structure of the Fab5-HCMV Pr complex revealed that Fab5 binds a flexible loop distal from the active site and dimer interface which we call the latch loop. In HCMV Pr dimers, this loop secures the C-terminal tail to the protein core. Structure-guided mutagenesis confirmed that the latch loop is essential for HCMV Pr dimerization and activity. This loop is structurally conserved across all HHV Prs, and we show its functional role in Kaposis Sarcoma-associated herpesvirus (KSHV) Pr as well. The latch loop plays a mechanistic role in the conformational transition required for HHV Pr activity, and it forms a cryptic site that presents a new avenue for future allosteric inhibitor development.

biochemistry↗

bioRxiv2024

Leucine Aminopeptidase LyLAP enables lysosomal degradation of membrane proteins

Proteolysis of hydrophobic helices is required for complete breakdown of every transmembrane protein trafficked to the lysosome and sustains high rates of endocytosis. However, the lysosomal mechanisms for degrading hydrophobic domains remain unknown. Combining lysosomal proteomics with functional genomic data mining, we identify Lysosomal Leucine Aminopeptidase (LyLAP; formerly Phospholipase B Domain-Containing 1) as the hydrolase most tightly associated with elevated endocytic activity. Untargeted metabolomics and biochemical reconstitution demonstrate that LyLAP is not a phospholipase, but a processive monoaminopeptidase with strong preference for N-terminal leucine - an activity necessary and sufficient for breakdown of hydrophobic transmembrane domains. LyLAP is upregulated in pancreatic ductal adenocarcinoma (PDA), which relies on macropinocytosis for nutrient uptake, and its ablation led to buildup of undigested hydrophobic peptides, which compromised lysosomal membrane integrity and inhibited PDA cell growth. Thus, LyLAP enables lysosomal degradation of membrane proteins, and may represent a vulnerability in highly endocytic cancer cells. One sentence summaryLyLAP degrades transmembrane proteins to sustain high endocytosis and lysosomal membrane stability in pancreatic cancer.

biochemistry↗

bioRxiv2023

A soybean rust effector protease suppresses host immunity and cleaves a 3-deoxy-7-phosphoheptulonate synthase

The devastating soybean rust (SBR) pathogen, Phakopsora pachyrhizi, encodes many secreted proteins, but only two have been functionally characterized for their roles in rust virulence. Here, we demonstrate that transient expression of P. pachyrhizi effector candidate 15 (PpEC15), an aspartic protease, leads to enhanced bacterial growth in planta, suppression of callose deposition, reduced expression of plant defense-related marker genes and suppression of pathogen-associated molecular pattern (PAMP)-induced reactive oxygen species (ROS). Stable expression of PpEC15 in soybean suppresses PAMP-induced ROS production and enhances bacterial growth, indicating that, collectively, PpEC15 suppresses host and non-host innate immune responses. Yeast-two-hybrid and proximity labeling identified putative PpEC15 interacting partners including a peptide-chain release factor (PCRF), a NAC83 (NAM, ATAF, and CUC) transcription factor, and a DAHP (3-deoxy-7-phosphoheptulonate) synthase. We further show that PpEC15 can cleave DAHP but does not cleave PCRF or NAC83. Virus-induced gene silencing of NAC83, PCRF and DAHP altered PAMP-induced ROS production and salicylic acid production, indicating that these proteins may be involved in immune signaling. Collectively, our data show that PpEC15 is conserved across P. pachyrhizi isolates and other economically important rust species and is involved in the suppression of plant basal defense responses. Understanding the role of PpEC15 in P. pachyrhizi virulence will provide a foundation for designing targeted intervention strategies to generate rust-resistant crops.

plant biology↗

bioRxiv2022

Structural Basis of Prostaglandin Efflux by MRP4

MRP4 is unique among the C family of ATP-binding cassette transporters for its role in translocating prostanoids, an important group of signaling molecules derived from unsaturated fatty acids. Using a reconstituted system, we report that a pair of prostaglandins (PGs) and the sulfonated-sterol DHEA-S preferentially enhance the ATPase activity of MRP4 over other previously proposed physiological substrates such as cyclic nucleotides or leukotrienes. We determined the cryo-EM structures of nanodisc embedded bovine MRP4 in (i) a nucleotide- and substrate-free state, (ii) in complex with PGE1, (iii) PGE2, and (iv) DHEA-S, and (v) a catalytically dead mutant E1202Q bound to ATP-Mg2+. The substrate-bound structures suggest unique features of the MRP4 binding site that distinguish its specificity for prostanoids from that of the related leukotriene transporter MRP1. The ATP-bound structure is in an outward-occluded conformation, revealing a novel state in the proposed alternate-access mechanism of MRP transport. Our study provides insights into the endogenous function of this versatile efflux transporter.

biochemistry↗

bioRxiv2018

KH-type splicing regulatory protein controls colorectal cancer cell growth and modulates the tumor microenvironment

KH-type splicing regulatory protein (KHSRP) is a multifunctional nucleic acid binding protein implicated in key aspects of cancer cell biology: inflammation and cell-fate determination. However, the role KHSRP plays in colorectal cancer (CRC) tumorigenesis remains largely unknown. Using a combination of in silico analysis of large datasets, ex vivo analysis of protein expression in patients, and mechanistic studies using in vitro models of CRC, we investigated the oncogenic role of KHSRP. We demonstrated KHSRP expression in the epithelial and stromal compartments of both primary and metastatic tumors. Elevated expression was found in tumor versus matched normal tissue, and we validated these findings in larger independent cohorts in silico. KHSRP expression was a prognostic indicator of worse overall survival (HR=3.74, 95% CI = 1.43-22.97, p=0.0138). Mechanistic data in CRC cell line models supported a role of KHSRP in driving epithelial cell proliferation in both a primary and metastatic setting, through control of the G1/S transition. Additionally, KHSRP promoted a pro-angiogenic extracellular environment by regulating the secretion of oncogenic proteins involved in diverse cellular processes such as migration and response to cellular stress. Our study provides novel mechanistic insight into the tumor-promoting effects of KHSRP in CRC.

cancer biology↗