Biology subjects

von Buelow, S.

Publications and source records attributed to von Buelow, S..

3 recordsLinked to original sources

bioRxiv2026

Proteome-wide identification and modeling of interactions between transactivation domains and arginine-glycine-rich regions

Transcription factors (TFs) and RNA-binding proteins (RBPs) coordinate gene expression across transcriptional and post-transcriptional layers, yet the principles that govern their direct physical coupling, especially through intrinsically disordered regions, remain unclear. Here we combine proteome-scale interaction mapping, disordered-region annotation, coarse-grained simulations and sequence-based prediction to dissect a prevalent TF-RBP interface mediated by acidic/hydrophobic transactivation domains (TADs) and arginine-glycine-rich (RG/RGG) regions. Network analysis reveals a global enrichment of RBP partners among TF interactions and identifies TF and RBP hubs that bridge transcriptional regulation with RNA-centered pathways. Using a sequence grammar enriched in acidic and aromatic residues, we define 230 RG/RGG-binding TAD-like segments across 190 TFs and we map 1,008 compact RG/RGG regions across 823 RBPs based on proteome-wide motif spacing. Coarse-grained simulations (CALVADOS) of representative TAD-RGG pairs quantify interaction propensities and indicate that association is primarily driven by electrostatic complementarity and charge patterning, with sequence "stickiness" modulating interaction strength. Using a hybrid machine-learning model we predicted simulated interaction strengths from a compact, interpretable set of features and extrapolate these rules to the full combinatorial space, enabling systematic prioritization of candidate TF-RBP couplings. To validate these predictions experimentally, we used NMR titration experiments on a subset of TAD-RGG pairs spanning the predicted affinity range, which showed agreement between predicted affinities and NMR-derived dissociation constants. Together, our results support a predominantly electrostatic mode of association and establish a quantitative framework for identifying and prioritising TF-RBP partnerships, revealing how complementary sequence grammars within disordered regions couple transcriptional regulation to RNA processing and transport.

biophysics↗

bioRxiv2024

Proteome-scale quantification of the interactions driving condensate formation of intrinsically disordered proteins

Intrinsically disordered protein regions facilitate cellular organization through phase separation into biomolecular condensates. However, the molecular interactions driving this process remain poorly understood because of experimental limitations. Here, we advance experimental throughput by several orders of magnitude by developing Condensate Partitioning by mRNA-Display (CPmD). The method allows analysis of partitioning of hundred thousand peptides derived from the disordered proteome into reconstituted condensates. Our results demonstrate that the amino acid content, rather than specific sequence, primarily determines partitioning behavior. Importantly, quantification of the partitioning energies of peptides allows us to decipher the molecular grammar of the relevant interactions, allowing accurate prediction of the formation of condensates of diverse full-length disordered protein regions. The results reveal how physicochemical properties of disordered regions encode biological functions through formation of biomolecular condensates.

biophysics↗

bioRxiv2018

Structure, dynamics and roX2-lncRNA binding of tandem double-stranded RNA binding domains dsRBD1,2 of Drosophila helicase Maleless

Maleless (MLE) is an evolutionary conserved member of the DExH family of helicases in Drosophila. Besides its function in RNA editing and presumably siRNA processing, MLE is best known for its role in remodelling non-coding roX RNA in the context of X chromosome dosage compensation in male flies. MLE and its human orthologue, DHX9 contain two tandem double-stranded RNA binding domains (dsRBDs) located at the N-terminal region. The two dsRBDs are essential for localization of MLE at the X-territory and it is presumed that this involves binding roX secondary structures. However, for dsRBD1 roX RNA binding has so far not been described. Here, we determined the solution NMR structure of dsRBD1 and dsRBD2 of MLE in tandem and investigated its role in double-stranded RNA (dsRNA) binding. Our NMR data show that both dsRBDs act as independent structural modules in solution and are canonical, non-sequence-specific dsRBDs featuring non-canonical KKxAK RNA binding motifs. NMR titrations combined with filter binding experiments document the contribution of dsRBD1 to dsRNA binding in vitro. Curiously, dsRBD1 mutants in which dsRNA binding in vitro is strongly compromised do not affect roX2 RNA binding and MLE localization in cells. These data suggest alternative functions for dsRBD1 in vivo.

biochemistry↗