Biology subjects

Hoffman, A. M.

Publications and source records attributed to Hoffman, A. M..

6 recordsLinked to original sources

bioRxiv2026

Partial agonists and heteromeric Kainate receptor desensitization

Kainate receptors (KARs) are glutamate-gated ion channels that mediate fast excitatory synaptic transmission in the central nervous system. KARs assemble as homo- or heterotetramers composed of five subunits (GluK1-5), with heteromeric assemblies representing the predominant native population. Although KARs share overall structures and basic functional properties with other ionotropic glutamate receptor subfamilies, they exhibit distinct gating kinetics, particularly with respect to desensitization. While earlier studies have demonstrated how agonist binding drives gate opening and subsequent desensitization, the mechanisms governing partial agonism and desensitization of KARs, especially in heteromeric KARs, remain incompletely understood. Here, we combine electrophysiology and microscale thermophoresis binding assays to elucidate how distinct KAR partial agonists control KAR desensitization and its recovery. While the onset rates of desensitization of homo- and heteromeric receptors activated by high/saturating concentrations of partial agonists are conserved between GluK2 and GluK2/GluK5 receptors, recovery from desensitization in heteromers is significantly slower than in homomers. Together with structural modeling and analysis of the GluK2 and GluK5 ligand binding domains (LBDs) in complex with orthosteric ligands, we show that agonist residence time and the extent of LBD bi-lobe closure across various agonists take precedence over subunit composition in governing KAR desensitization.

physiology↗

bioRxiv2025

Structural Basis of Inhibition and Desensitization in Heteromeric Kainate Receptors

Kainate receptors (KARs) mediate excitatory synaptic transmission and regulate neurotransmitter release. In the central nervous system, KARs predominantly exist as heterotetramers comprising low-affinity (GluK1-3) and high-affinity (GluK4-5) subunits, with GluK2/GluK5 being the most abundant. To elucidate their conformational transitions, we determined the cryo-electron microscopy (cryo-EM) structures of GluK2/GluK5 KARs in the apo and distinct ligand-bound states. The apo structure revealed compact packing with extensive inter-subunit interactions between the ligand-binding domains (LBDs) beyond the conserved D1-D1 upper-lobe contacts. The glutamate-bound structure exhibited enhanced packing that stabilized the desensitized conformation through increased intersubunit contacts relative to the homomeric KARs, indicating that the heterotetramers were conformationally less dynamic. To investigate subtype-specific antagonism, we engineered GluK2 and GluK5 mutants with altered affinities for the competitive antagonist UBP310. Structural analysis of these mutants revealed distinct UBP310 binding modes on the GluK2 versus the GluK5 subunits. Furthermore, we demonstrated that targeting GluK5 was more effective than targeting GluK2. Specifically, blocking GluK5 locked the receptor in a pore-occluded conformation, whereas antagonizing GluK2 retained structural flexibility above the pore. These findings provide a structural framework for understanding the distinct contributions of the GluK2 and GluK5 subunits to KAR function. TeaserCryo-EM structures of heteromeric kainate receptors reveal unique assembly and regulation mechanisms.

biophysics↗

bioRxiv2025

Insights into the Datasets, Tools, and Training Needs of the AnVIL Community: 2024

The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) provides a secure cloud-based environment where research and education communities can analyze genomic and biomedical data. The platform supports a wide range of data analysis as well as the ability to safely store and access data in compliance with NIH policies. Work on the AnVIL platform can be easily shared to promote reproducible science and collaboration. The purpose of this study is to better understand the current user base of the AnVIL platform. The AnVIL Community Poll aimed to collect baseline information, identify development opportunities, guide the prioritization of user support strategies, and succinctly but comprehensively describe the current AnVIL Community. The AnVIL Team disseminated the inaugural AnVIL Community Poll by sharing it broadly on social media and through AnVIL and related consortia mailing lists. We categorized respondents as either returning or potential users of the AnVIL platform (based on their provided usage description) and examined user experiences: specifically user backgrounds, technological comfort, research interests, computational needs, and preferences for training and support. Our sample of the AnVIL community found opportunities for platform adoption beyond the current user base and identified areas where training should be enhanced, training preferences, and user computational needs. Specifically, while most respondents were involved in human genomics research, there may be potential for growth in adoption of the platform by prioritizing materials to support clinical researchers. All respondents felt availability of specific tools or datasets was a key feature of the platform. The broader community may also benefit from further development or showcasing of resources to facilitate cost management, finding and incorporating analysis tools, and data import. Our sample greatly preferred virtual training opportunities and returning users of the platform foresaw needing large amounts of storage. This poll provided an insightful snapshot of the current state of the AnVIL and demonstrated areas where the AnVIL Team can take specific steps to address barriers related to platform adoption and further support the existing and varied AnVIL Community. This work can be built upon through user interviews, community discussion, and coordinating a recurring poll.

scientific communication and education↗

bioRxiv2022

Metabolic strategies shared by basement residents of the Lost City hydrothermal field

Alkaline fluids venting from chimneys of the Lost City hydrothermal field flow from a potentially vast microbial habitat within the seafloor where energy and organic molecules are released by chemical reactions within rocks uplifted from Earths mantle. In this study, we investigated hydrothermal fluids venting from Lost City chimneys as windows into subseafloor environments where the products of geochemical reactions, such as hydrogen (H2), formate, and methane, may be the only available sources of energy for biological activity. Our deep sequencing of metagenomes and metatranscriptomes from these hydrothermal fluids revealed a few key species of archaea and bacteria that are likely to play critical roles in the subseafloor microbial ecosystem. We identified a population of Thermodesulfovibrionales (belonging to phylum Nitrospirae) as a prevalent sulfate-reducing bacterium that may be responsible for much of the consumption of H2 and sulfate in Lost City fluids. Metagenome-assembled genomes (MAGs) classified as Methanosarcinaceae and Candidatus Bipolaricaulota were also recovered from venting fluids and represent potential methanogenic and acetogenic members of the subseafloor ecosystem. These genomes share novel hydrogenases and formate dehydrogenase-like sequences that may be unique to hydrothermal and subsurface alkaline environments where hydrogen and formate are much more abundant than carbon dioxide. The results of this study include multiple examples of metabolic strategies that appear to be advantageous in hydrothermal and subsurface environments where energy and carbon are provided by geochemical reactions. IMPORTANCEThe Lost City hydrothermal field is an iconic example of a microbial ecosystem fueled by energy and carbon from Earths mantle. Uplift of mantle rocks into the seafloor can trigger a process known as serpentinization that releases hydrogen and creates unusual environmental conditions where simple organic carbon molecules are more stable than dissolved inorganic carbon. This study provides an initial glimpse into the kinds of microbes that live deep within the seafloor where serpentinization takes place, by sampling hydrothermal fluids exiting from the Lost City chimneys. The metabolic strategies that these microbes appear to be using are also shared by microbes that inhabit other sites of serpentinization, including continental subsurface environments and natural springs. Therefore, the results of this study contribute to a broader, interdisciplinary effort to understand the general principles and mechanisms by which serpentinization-associated processes can support life on Earth and perhaps other worlds.

microbiology↗

bioRxiv2020

Quantitative proteomics links the LRRC59 interactome to mRNA translation on the ER membrane

Protein synthesis on the endoplasmic reticulum (ER) requires the dynamic coordination of resident membrane proteins and cytoplasmic translation factors. While ER membrane proteins functioning in ribosome association, mRNA anchoring, and protein translocation, have been identified, little is known regarding the higher order organization of ER-localized translation. Here we utilized proximity proteomics to identify neighboring protein networks for the ribosome interactors SEC61{beta}, RPN1, SEC62, and LRRC59. Whereas the SEC61{beta} and RPN1 BioID reporters revealed translocon-associated networks, the SEC62 and LRRC59 reporters identified divergent interactome networks of previously unexplored functions. Notably, the SEC62 interactome is enriched in redox-linked proteins and ER luminal chaperones, whereas the LRRC59 interactome is enriched in SRP pathway components, translation factors, and ER-localized RNA-binding proteins. Analysis of the LRRC59 interactome by native immunoprecipitation identified similar protein and functional enrichments. Combined, these data reveal a functional domain organization for the ER and suggest a key role for LRRC59 in the organization of mRNA translation on the ER. SummaryHannigan et al. characterize the protein interactomes of four ER ribosome-binding proteins, providing evidence that ER-bound ribosomes reside in distinct molecular environments. Their data link SEC62 to ER redox regulation and chaperone trafficking, and suggest a role for LRRC59 in SRP-coupled protein synthesis.

cell biology↗

bioRxiv2018

Meta-organization of Translation Centers Revealed by Proximity Mapping of Endoplasmic Reticulum Ribosome Interactors

The endoplasmic reticulum (ER) is a nexus for mRNA localization and translation; the molecular organization of these processes remains however largely undefined. To gain insight into mechanisms supporting a diverse ER translational landscape, we utilized BioID labeling to study the protein neighborhoods of the Sec61 translocon, specifically Sec61{beta}, an established ribosome interactor, and ER proteins (Ribophorin I, LRRC59, and Sec62) previously implicated in ribosome association. Divergent protein interactomes enriched for distinct GO functions were identified for the four reporters, within a cohort of shared interactors. Efficient BioID tagging of ribosomes was only observed for the Sec61{beta} and LRRC59 reporters. RNA-seq analyses of the Sec61{beta}- and LRRC59-labeled ribosomes revealed divergent enrichments in mRNAs and identified a transcriptome-wide role for the ER in proteome expression. These data provide evidence for a mesoscale organization of the ER and suggest that such organization provides a mechanism for the diversity of translation on the ER.

cell biology↗