Biology subjects

Rasche, R.

Publications and source records attributed to Rasche, R..

3 recordsLinked to original sources

bioRxiv2026

De novo design of light-controlled conformational protein switches

Light-responsive proteins offer the ability to control biology at an unmatched resolution. Yet, optogenetics is limited to a relatively small number of natural and engineered photoreceptors. The design of light-responsive proteins with native-like complexity is challenging as they must incorporate a light-responsive chromophore, couple chemical changes in the chromophore to structural changes in the protein, and ultimately propagate these changes to downstream effectors. Here, we present the computational design of new light-responsive proteins entirely from the bottom-up. We design de novo proteins that accurately bind a retinal chromophore and further design a protein conformational switching motion linked to retinal isomerisation. This switch unlocks a new protein-peptide interaction, creating light-activated heterodimers with an over 30-fold increase in binding upon illumination. Moreover, we show that the designed heterodimers are customisable, with tuneable wavelengths, sensitivities, and specificities. Further, we use the designed heterodimers to control biological function, regulating intracellular protein-protein interactions and cell-signalling receptors. Finally, we use real-time light-activated NMR to demonstrate that they undergo a defined light-activated conformational change. Overall, we computationally design a new class of light-responsive proteins that may open a new optogenetics toolbox with applications in biology.

biochemistry↗

bioRxiv2025

Structural Basis for a Scaffolding Role of the COM Domain in Nonribosomal Peptide Synthetases

Nonribosomal peptide synthetases (NRPSs) are multi-domain enzymes that catalyze the biosynthesis of therapeutically relevant natural products. Efficient peptide synthesis relies on intricate domain interactions, whose underlying principles remain poorly understood. The communication-mediating (COM) domains facilitate interactions between separate NRPS subunits like other docking domains, however, exhibit distinctive features that are unusual within this family: COM domains co-occur with epimerization (E) domains, are partially embedded within the adjacent condensation (C) domain and can also be found as an internal cis-COM domain with unknown function. We present the first crystal structure of a cis-COM domain within an E-COM-C domain arrangement from modules 4 and 5 of bacitracin synthetase 3 (BacC). The structure reveals a compactly folded COM domain sandwiched between E and C domains, suggesting a role in orienting these domains for efficient peptidyl carrier protein (PCP) shuttling. Through mutational analyses, dipeptide formation assays, and proximity-dependent photo-crosslinking experiments, we investigated both cis- and trans-COM domains and provide evidence supporting a principal role of COM domains as scaffolds of NRPS architecture. Their function as docking domains may be a secondary consequence of their division into separate donor and acceptor parts.

biochemistry↗

bioRxiv2024

Structure and mechanism of the RalGAP tumor suppressor complex

The RalGAP (GTPase activating protein) complexes are negative regulators of the Ral GTPases and thus crucial components that counteract (oncogenic) Ras signaling. However, no structural information on the architecture of this tumor suppressor complex is available hampering a mechanistic understanding of its functionality. Here, we present a cryo-EM structure of RalGAP that reveals an extended 58 nm tetrameric architecture comprising two heterodimers of the RalGAP and RalGAP{beta} subunits. We show that the catalytic domain of RalGAP requires stabilization by a unique domain of RalGAP{beta}, providing the molecular basis for why RalGAP complexes are obligatory heterodimers. Formation of RalGAP tetramers is not required for activity in vitro, but essential for function of the complex in vivo. Structural analysis of RalGAP subunit variants reported in cancer patients suggests effects on complex formation and thus functional relevance in tumor development, emphasizing the significance of the obtained structural information for medical research.

biochemistry↗