An Asp to Asn mutation is a toxic trigger in beta-2 microglobulin: structure and biophysics

Beta-2 microglobulin (β2m) is part of the Major Histocompatibility Complex Class I (MHC I) and when monomeric becomes an aggregation prone protein that is responsible for a human disorder known as dialysis-related amyloidosis. In 2012 Valleix et al. described a new familial systemic amyloidosis: an unreported β2m mutant (D76N) is the etiological agent of such disease. Main symptoms were chronic diarrhea, loss of weight and polyneuropathy: large amyloid deposits were found in internal organs. From the biophysical point of view, the D76N β2m is much less stable and more amyloidogenic than wt β2m; however, its crystal structure reveals very minor conformational changes compared with the wt protei

Direct interaction between the PRDM3 and PRDM16 tumor suppressors and the NuRD chromatin remodeling complex

Aberrant isoform expression of chromatin-associated proteins can induce epigenetic programs related to disease. The MDS1 and EVI1 complex locus (MECOM) encodes PRDM3, a protein with an N-terminal PR-SET domain, as well as a shorter isoform, EVI1, lacking the N-terminus containing the PR-SET domain (ΔPR). Imbalanced expression of MECOM isoforms is observed in multiple malignancies, implicating EVI1 as an oncogene, while PRDM3 has been suggested to function as a tumor suppressor through an unknown mechanism. To elucidate functional characteristics of these N-terminal residues, we compared the protein interactomes of the full-length and ΔPR isoforms of PRDM3 and its closely related paralog, PRDM16. Unlike the ΔPR isoforms, both full-length isoforms exhibited a significantly enriched association with components of the NuRD chromatin remodeling complex, especially RBBP4. Typically, RBBP4 facilitates chromatin association of the NuRD complex by binding to histone H3 tails. We show that RBBP4 binds to the N-terminal amino acid residues of PRDM3 and PRDM16, with a dissociation constant of 3.0 μM, as measured by isothermal titration calorimetry. Furthermore, high-resolution X-ray crystal structures of PRDM3 and PRDM16 N-terminal peptides in complex with RBBP4 revealed binding to RBBP4 within the conserved histone H3-binding groove. These data support a mechanism of isoform-specific interaction of PRDM3 and PRDM16 with the NuRD chromatin remodeling complex

A ligand discovery toolbox for the WWE domain family of human E3 ligases

The WWE domain is a relatively under-researched domain found in twelve human proteins and characterized by a conserved tryptophan-tryptophan-glutamate (WWE) sequence motif. Six of these WWE domain-containing proteins also contain domains with E3 ubiquitin ligase activity. The general recognition of poly-ADP-ribosylated substrates by WWE domains suggests a potential avenue for development of Proteolysis-Targeting Chimeras (PROTACs). Here, we present novel crystal structures of the HUWE1, TRIP12, and DTX1 WWE domains in complex with PAR building blocks and their analogs, thus enabling a comprehensive analysis of the PAR binding site structural diversity. Furthermore, we introduce a versatile toolbox of biophysical and biochemical assays for the discovery and characterization of novel WWE domain binders, including fluorescence polarization-based PAR binding and displacement assays, 15N-NMR-based binding affinity assays and 19F-NMR-based competition assays. Through these assays, we have characterized the binding of monomeric iso-ADP-ribose (iso-ADPr) and its nucleotide analogs with the aforementioned WWE proteins. Finally, we have utilized the assay toolbox to screen a small molecule fragment library leading to the successful discovery of novel ligands targeting the HUWE1 WWE domain

Class I major histocompatibility complex, the trojan horse for secretion of amyloidogenic β2-microglobulin

To form extracellular aggregates, amyloidogenic proteins bypass the intracellular quality control, which normally targets unfolded/aggregated polypeptides. Human D76N \u3b22-microglobulin (\u3b22m) variant is the prototype of unstable and amyloidogenic protein that forms abundant extracellular fibrillar deposits. Here we focus on the role of the class I major histocompatibility complex (MHCI) in the intracellular stabilization of D76N \u3b22m. Using biophysical and structural approaches, we show that the MHCI containing D76N \u3b22m (MHCI76) displays stability, dissociation patterns, and crystal structure comparable with those of the MHCI with wild type \u3b22m. Conversely, limited proteolysis experiments show a reduced protease susceptibility for D76N \u3b22m within the MHCI76 as compared with the free variant, suggesting that the MHCI has a chaperone-like activity in preventing D76N \u3b22m degradation within the cell. Accordingly, D76N \u3b22m is normally assembled in the MHCI and circulates as free plasma species in a transgenic mouse model

Enabling Open Machine Learning of Deoxyribonucleic Acid-Encoded Library Selections to Accelerate the Discovery of Small Molecule Protein Binders

Machine learning (ML) is increasingly used in DNA-encoded library (DEL) screening for ligand discovery, but its success depends on access to suitable data sets, which are often proprietary and costly. To overcome this, we present the first fully open, automated DEL-ML framework using public DEL data sets and chemical fingerprints to enable reproducible, accessible drug discovery. Our workflow─from model training to virtual screening and compound selection─requires no human intervention. As a proof of concept, we identified binders for WDR91 by training ML models on the HitGen OpenDEL library (3B molecules) and screening the Enamine REAL Space library (37B molecules), yielding 50 candidates. Experimental testing confirmed seven novel binders with dissociation constants between 2.7-21 μM. Our open-source approach matches the performance of proprietary methods, demonstrating that public DEL data can support robust ML-driven ligand discovery and fostering transparency and broader community participation in drug development