Biology subjects

Tully, M.

Publications and source records attributed to Tully, M..

5 recordsLinked to original sources

bioRxiv2026

DNA binding drives phase separation of the Gcn4 bZIP domain and reveals its conformational ensemble in the diluted and condensate phases

Liquid-liquid phase separation is widely invoked in transcriptional regulation, yet prevailing models attribute condensate formation primarily to intrinsically disordered activation domains rather than structured DNA-binding motifs. Here, we overturn this view by demonstrating that the isolated basic leucine zipper (bZIP) domain of the yeast transcription factor Gcn4 undergoes robust DNA-induced phase separation in the complete absence of its activation domain. Using small-angle X-ray scattering in combination with all-atom molecular dynamics simulations and ensemble optimization, we directly resolve the conformational landscape of the Gcn4 bZIP-DNA complex across coexisting dilute and condensed phases. Beyond the canonical uninterrupted helical conformation captured in crystal structures, we identify a previously unrecognized minor population featuring a pronounced helical kink at the basic region-leucine zipper junction. These findings establish DNA binding as a sufficient physical driver of bZIP phase separation and demonstrate that small-angle scattering can quantitatively interrogate protein conformational ensembles within biomolecular condensates, opening new avenues for the structural chemistry of phase-separated systems.

biophysics↗

bioRxiv2022

Architecture of the MKK6-p38α complex defines the basis of MAPK specificity and activation

The MAP kinase p38 is a central component of signalling in inflammation and the immune response and is, therefore, an important drug target. Little is known about the molecular mechanism of its activation by double-phosphorylation from MAP2Ks, due to the challenge of trapping a transient and dynamic hetero-kinase complex. Here, we applied a multidisciplinary approach to generate the first structure of p38 in complex with its MAP2K MKK6 and understand the activation mechanism. Integrating cryo-EM with MD simulations, HDX-MS and in cellulo experiments, we demonstrate a dynamic, multi-step, phosphorylation mechanism, reveal new catalytically relevant interactions, and show that MAP2K disordered N-termini determine pathway specificity. Our work captures, for the first time, a fundamental step of cell signalling: a kinase phosphorylating its downstream target kinase. One-Sentence SummaryIntegrative Cryo-EM and MD analysis of an active hetero-kinase complex reveals details of cellular signal transmission

biophysics↗

bioRxiv2020

A COVID-19 vaccine candidate using SpyCatcher multimerization of the SARS-CoV-2 spike protein receptor-binding domain induces potent neutralising antibody responses

There is dire need for an effective and affordable vaccine against SARS-CoV-2 to tackle the ongoing pandemic. In this study, we describe a modular virus-like particle vaccine candidate displaying the SARS-CoV-2 spike glycoprotein receptor-binding domain (RBD) using SpyTag/SpyCatcher technology (RBD-SpyVLP). Low doses of RBD-SpyVLP in a prime-boost regimen induced a strong neutralising antibody response in mice and pigs that was superior to convalescent human sera. We evaluated antibody quality using ACE2 blocking and neutralisation of cell infection by pseudovirus or wild-type SARS-CoV-2. Using competition assays with a monoclonal antibody panel, we showed that RBD-SpyVLP induced a polyclonal antibody response that recognised all key epitopes on the RBD, reducing the likelihood of selecting neutralisation-escape mutants. The induction of potent and polyclonal antibody responses by RBD-SpyVLP provides strong potential to address clinical and logistic challenges of the COVID-19 pandemic. Moreover, RBD-SpyVLP is highly resilient, thermostable and can be lyophilised without losing immunogenicity, to facilitate global distribution and reduce cold-chain dependence.

immunology↗

bioRxiv2019

KAP1 is an antiparallel dimer with a natively functional asymmetry

KAP1 (KRAB-domain associated protein 1) plays a fundamental role in regulating gene expression in mammalian cells by recruiting different transcription factors and altering the chromatin state. In doing so, KAP1 acts both as a platform for macromolecular interactions and as an E3 SUMO ligase. This work sheds light on the overall organization of the full-length protein combining solution scattering diffraction data, integrative modeling and single-molecule experiments. We show that KAP1 is an elongated antiparallel dimer with a native asymmetry at the C-terminal domain. This conformation supports our finding that the RING domain contributes to KAP1 auto-SUMOylation. Importantly, this intrinsic asymmetry has key functional implications for the KAP1 network of interactions, as the heterochromatin protein 1 (HP1) occupies only one of the two putative HP1 binding sites on the KAP1 dimer, resulting in an unexpected stoichiometry, even in the context of chromatin fibers.

biophysics↗

bioRxiv2018

Evidence of reduced viremia, pathogenicity and vector competence in a re-emerging European strain of bluetongue virus serotype 8 in sheep

The outbreak of bluetongue virus (BTV) serotype 8 (BTV-8) during 2006-2009 in Europe was the most costly epidemic of the virus in recorded history. In 2015, a BTV-8 strain re-emerged in France which has continued to circulate since then. To examine anecdotal reports of reduced pathogenicity and transmission efficiency, we investigated the infection kinetics of a 2007 UK BTV-8 strain alongside the re-emerging BTV-8 strain isolated from France in 2017. Two groups of eight BTV-naive British mule sheep were inoculated with 5.75 log10TCID50 ml-1 of either BTV-8 strain. BTV RNA was detected by 2 dpi in both groups with peak viremia occurring between 5-9 dpi. A significantly greater amount of BTV RNA was detected in sheep infected with the 2007 strain (6.0-8.8 log10 genome copies mL-1) than the re-emerging BTV-8 strain (2.9-7.9 log10 genome copies mL-1). All infected sheep developed BTV-specific antibodies by 9 dpi. BTV was isolated from 2 dpi to 12 dpi for 2007 BTV-8-inoculated sheep and from 5 to 10 dpi for sheep inoculated with the remerging BTV-8. In Culicoides sonorensis feeding on the sheep over the period 7-12 dpi, vector competence was significantly higher for the 2007 strain than the re-emerging strain. Both the proportion of animals showing moderate (as opposed to mild or no) clinical disease (6/8 vs 1/8) and the overall clinical scores (median 5.25 vs 3) were significantly higher in sheep infected with the 2007 strain, compared to those infected with the re-emerging strain. However, one sheep infected with the re-emerging strain was euthanized at 16 dpi having developed severe lameness. This highlights the potential of the re-emerging BTV-8 to still cause illness in naive ruminants with concurrent costs to the livestock industry.\n\nSummaryThe re-emerging Bluetongue virus serotype 8 still presents a threat to naive ruminants in Europe despite reduced virulence

epidemiology↗