Biology subjects

Wales, D. J.

Publications and source records attributed to Wales, D. J..

5 recordsLinked to original sources

bioRxiv2026

Decoding the Structural and Functional Impact of the Leukaemia-Associated A338V Mutation in GPR183

G protein-coupled receptors rely on dynamic conformational changes to coordinate G protein activation and recruitment of regulatory transducers such as G protein-coupled receptor kinases and {beta}-arrestins. The chemotactic receptor GPR183 has been implicated in a context-dependent role in hematological malignancies. Here, we investigated the impact of A338V mutation located within the C-terminal tail of GPR183. This mutation is associated with acute myeloid leukaemia. Using bioluminescence resonance energy transfer-based assays in HEK293A cells, we assessed receptor-proximal signaling events. The A338V variant displayed preserved agonist potency and comparable agonist-induced Gi activation relative to wild type, although constitutive activity towards Gi was modestly reduced. In contrast, recruitment of GRK2 and {beta}-arrestin2 was consistently impaired across multiple assay configurations. These differences were not attributable to altered receptor abundance, as the C-tail untagged mutant exhibited increased plasma membrane expression despite reduced regulatory transducer engagement. While intramolecular conformational biosensor measurements revealed subtle differences in global receptor conformation between WT and A338V, extensive molecular dynamics simulations supported the altered conformational sampling of the C-terminal tail in the A338V variant. Together, these data support a model in which the A338V substitution selectively alters C-terminal structural dynamics, impairing GRK2 and {beta}-arrestin2 recruitment while preserving G protein activation.

pharmacology and toxicology↗

bioRxiv2026

Exploring RNA conformational ensembles in silico: progress and challenges

RNA function is intrinsically linked to its structural polymorphism, with molecules exploring the heterogeneous conformational ensembles resulting from complex energy landscapes. These landscapes arise from competing interactions, small energetic separations between microstates, and strong coupling to the environment, posing significant challenges for both experimental characterization and molecular simulation. In this chapter, we review current computational strategies that aim to explore RNA conformational ensembles in silico, with a specific focus on energy landscape-based approaches and atomistic simulations. We discuss key limitations related to sampling efficiency, force-field accuracy, and ensemble analysis, and illustrate their impact through case studies on a self-cleaving ribozyme and an H-type pseudoknot. Finally, we highlight emerging directions, including closer integration with experimental data and the growing role of machine learning, which will probably reinforce the predictive power of in silico RNA energy landscape exploration.

molecular biology↗

bioRxiv2024

Parp7 generates an ADP-ribosyl degron that controls negative feedback of androgen signaling

AbstractThe androgen receptor (AR) tranduces the effects of circulating and tumor-derived androgens to the nucleus through ligand-induced changes in protein conformation, localization, and engagement with chromatin binding sites. Understanding these events and their integration with signal transduction is critical for defining how AR drives prostate cancer and unveiling pathway features that are amenable to therapeutic intervention. Here, we describe a novel post-transcriptional mechanism that controls AR protein levels on chromatin and associated gene output which is based on a highly selective, inducible degradation mechanism. We find that the mono-ADP-ribosyltransferase PARP7 generates an ADP-ribosyl degron on a single cysteine within the DNA binding domain of AR, which is then recognized by the ADP- ribose reader domain in the ubiquitin E3 ligase DTX2 and degraded by the proteasome. Mathematical modeling of the pathway suggested that PARP7 ADP-ribosylates chromatin-bound AR, a prediction that was validated in cells using an AR mutant that undergoes nuclear import but fails to bind DNA. Lysine- independent, non-conventional ubiquitin conjugation to ADP-ribosyl-cysteine and AR degradation by the proteasome forms the basis of a negative feedback loop that regulates specific modules of AR target genes. Our data expand the repertoire of mono-ADP-ribosyltransferase enzymes to include gene regulation based on highly selective protein degradation. One Sentence SummaryPARP7 mono-ADP-ribosylates the androgen receptor on Cys620 to mark the androgen receptor for ubiquitin conjugation by an E3 ligase with ADP-ribose reader function, resulting in in negative feedback of AR-dependent gene expression.

cancer biology↗

bioRxiv2023

Energy landscapes and heat capacity signatures for monomers and dimers of amyloid forming hexapeptides

Amyloid formation is a hallmark of various neurodegenerative disorders. In this contribution, energy landscapes are explored for various hexapeptides that are known to form amyloids. Heat capacity (CV) analysis at low temperature for these hexapeptides reveals that the low energy structures contributing to the first heat capacity feature above a threshold temperature exhibit a variety of backbone conformations for amyloid forming monomers. The corresponding control sequences do not exhibit such structural polymorphism, as diagnosed via end-to-end distance and a dihedral angle defined for the monomer. A similar heat capacity analysis for dimer conformations obtained using basin-hopping global optimisation, shows clear features in end-to-end distance versus dihedral correlation plots, where amyloid-forming sequences exhibit a preference for larger end-to-end distances and larger positive dihedrals. These results hold for sequences taken from tau, amylin, insulin A chain, a de-novo designed peptide, and various control sequences. While there is a little overall correlation between the aggregation propensity and the temperature at which the low-temperature CV feature occurs, further analysis suggests that the amyloid forming sequences exhibit the key CV feature at a lower temperature compared to control sequences derived from the same protein.

biophysics↗

bioRxiv2023

Energy landscapes and heat capacity signatures for peptides correlate with phase separation propensity

Phase separation plays an important role in the formation of membraneless compartments within the cell, and intrinsically disordered proteins with low-complexity sequences can drive this compartmentalisation. Various intermolecular forces, such as aromatic-aromatic and cation-aromatic interactions, promote phase separation. However, little is known about how the ability of proteins to phase separate under physiological conditions is encoded in their energy landscapes, and this is the focus of the present investigation. Our results provide a first glimpse into how the energy landscapes of minimal peptides that contain{pi} -{pi} and cation-{pi} interactions differ from the peptides that lack amino acids with such interactions. The peaks in the heat capacity (CV) as a function of temperature report on alternative low-lying conformations that differ significantly in terms of their enthalpic and entropic contributions. The CV analysis and subsequent quantification of frustration of the energy landscape suggest that the interactions that promote phase separation leads to features (peaks or inflection points) at low temperatures in CV, more features may occur for peptides containing residues with better phase separation propensity and the energy landscape is more frustrated for such peptides. Overall, this work links the features in the underlying single-molecule potential energy landscapes to their collective phase separation behaviour, and identifies quantities (CV and frustration metric) that can be utilised in soft material design.

biophysics↗