Biology subjects

McMurray, M.

Publications and source records attributed to McMurray, M..

4 recordsLinked to original sources

bioRxiv2026

The Synthetic Epitope Atlas: High-Throughput Design and Validation of De Novo Antibody-Antigen Complexes

AO_SCPLOWBSTRACTC_SCPLOWDe novo antibody design models lack sufficient training data to reliably generalize. We demonstrate scalable generation of structural training data for machine learning-driven antibody design by linking in silico designs of antibody-antigen complexes to high-throughput experimental binding validation. Using AlphaSeq, a yeast-based platform for measuring protein binding affinities, we measure the affinity and specificity of thousands of de novo "synthetic epitope proteins" (SEPs) designed to bind to VHHs. The resulting Synthetic Epitope Atlas (SEPIA) pairs over 26 million on- and off-target affinity measurements with computationally designed VHH-SEP "pseudo-structures." We validate strong, specific binding for 1,161 pseudo-structures and >75,000 VHH and SEP mutational variants. We show that these pseudo-structures complement existing structural databases and enable ML models to outperform confidence metrics commonly used to rank de novo antibody designs. Taken together, SEPIA establishes a scalable framework for improving de novo antibody design by augmenting sparse structural data with large-scale experimental binding data.

synthetic biology↗

bioRxiv2026

Coiled-coil homo-oligomerization and disaggregase Hsp104 act in parallel to stabilize orphan septins

Multiple septin family proteins co-assemble with strict subunit stoichiometry into hetero-oligomers. In the absence of native septin partners, purified septins aggregate in vitro, and "orphan" septins are found in pathological aggregates associated with neurodegenerative diseases. Cytosolic chaperones bind the septin GTPase domain to promote on-pathway septin folding but it was unclear how cells manage orphan septins to maintain septin subunit stoichiometry. Most septins have C-terminal domains (CTDs) that form heteromeric coiled coils within or between septin complexes. Here we present evidence that orphan yeast septins are protected from proteasomal degradation by forming transient coiled-coil homodimers and trimers and, in parallel, by the disaggregase chaperone Hsp104. Septins unable to undergo CTD-mediated homo-oligomerization require Hsp104 to accumulate to super-stoichiometric levels. We show that the number of septin-encoding mRNAs per yeast cell is low and variable, creating opportunities for transient subunit imbalances. These findings reveal a novel role for coiled coils and the cellular proteostasis machinery in the fidelity of higher-order septin assembly.

molecular biology↗

bioRxiv2024

Roles for the canonical polarity machinery in the de novo establishment of polarity in budding yeast spores

The yeast Saccharomyces cerevisiae buds at sites pre-determined by cortical landmarks deposited during prior budding. During mating between haploid cells in the lab, external pheromone cues override the cortical landmarks to drive polarization and cell fusion. By contrast, in haploid gametes (called spores) produced by meiosis, a pre-determined polarity site drives initial polarized morphogenesis independent of mating partner location. Spore membranes are made de novo so existing cortical landmarks were unknown, as were the mechanisms by which the spore polarity site is made and how it works. We find that the landmark canonically required for distal budding, Bud8, stably marks the spore polarity site along with Bud5, a GEF for the GTPase Rsr1 that canonically links cortical landmarks to the conserved Cdc42 polarity machinery. Cdc42 and other GTPase regulators arrive at the site during its biogenesis, after spore membrane closure but apparently at the site where membrane synthesis began, and then these factors leave, pointing to the presence of discrete phases of maturation. Filamentous actin may be required for initial establishment of the site, but thereafter Bud8 accumulates independent of actin filaments. These results suggest a distinct polarization mechanism that may provide insights into gamete polarization in other organisms. SIGNIFICANCE STATEMENTO_LIDormant budding yeast spores possess a single, stable cortical site that marks the location where polarized growth occurs upon dormancy exit. It was not known how the site forms or which molecules comprise it. C_LIO_LIUsing fluorescently tagged proteins in living cells undergoing sporulation, the authors found proteins canonically involved in polarization of non-spore cells arriving at the polarity site in a choreographed manner and required for site function. C_LIO_LIThese findings point to a distinct polarity mechanism from non-spore cells and raise new questions about polarity protein interactions with membranes that may be applicable to gametogenesis in other organisms. C_LI

cell biology↗

bioRxiv2022

Chaperone Requirements for De Novo Folding of Saccharomyces cerevisiae Septins

Polymers of septin protein complexes play cytoskeletal roles in eukaryotic cells. The specific subunit composition within complexes controls functions and higher-order structural properties. All septins have globular GTPase domains. The other eukaryotic cytoskeletal NTPases strictly require assistance from molecular chaperones of the cytosol, particularly the cage-like chaperonins, to fold into oligomerization-competent conformations. We previously identified cytosolic chaperones that bind septins and influence the oligomerization ability of septins carrying mutations linked to human disease, but it was unknown to what extent wild-type septins require chaperone assistance for their native folding. Here we use a combination of in vivo and in vitro approaches to demonstrate chaperone requirements for de novo folding and complex assembly by budding yeast septins. Individually purified septins adopted non-native conformations and formed non-native homodimers. In chaperonin- or Hsp70-deficient cells, septins folded slower and were unable to assemble post-translationally into native complexes. One septin, Cdc12, was so dependent on co-translational chaperonin assistance that translation failed without it. Our findings point to distinct translation elongation rates for different septins as a possible mechanism to direct a stepwise, co-translational assembly pathway in which general cytosolic chaperones act as key intermediaries.

molecular biology↗