Biology subjects

Deans, E. E.

Publications and source records attributed to Deans, E. E..

3 recordsLinked to original sources

bioRxiv2025

Natural and patient-derived mutations in BK polyomavirus VP1 reveal structural determinants of BC-loop dependent antibody escape

BK polyomavirus (BKPyV) reactivation poses a serious threat to both renal and hematopoietic transplant outcomes, with no approved antiviral therapies. Neutralizing monoclonal antibodies targeting the viral capsid protein VP1 have recently advanced into clinical development, driven by promising in vitro potency. Since naturally elicited neutralizing antibodies arise following infection, we examined whether host immune pressure may have shaped the VP1 surface, with implications for therapeutic application. To probe the impact of VP1 coevolution on therapeutic engagement, we evaluated two neutralizing antibody formats: the clinical-stage monoclonal antibody 319C07 and nanobodies VHH16 and VHH17. Our X-ray crystallographic analysis of the VP1 pentameric core in complex with antibody fragments showed a convergent receptor- mimetic engagement of the sialic acid-binding cleft, mapping to a shared epitope centered around the VP1 BC-loop. Analysis of over 900 BKPyV VP1 sequences from public databases, combined with longitudinal VP1 sequence data from transplant recipients, highlighted widespread pre-existing diversity at the BC-loop contact sites, underscoring the evolutionary adaptability of BKPyV at this antigenic surface that may compromise therapeutic recognition. Through integrated mutagenesis and binding analyses, we show that circulating BC-loop mutations, including single amino acid substitutions, are sufficient to abrogate 319C07 binding and neutralization. Nanobodies VHH16 and VHH17, selected for their compact size and potential to access intrarenal sites of BKPyV replication, also exhibited complete loss of binding across multiple clinically observed VP1 variants. Our findings may offer a mechanistic framework to interpret the translational gap between in vitro neutralization and clinical efficacy of these biologics. As part of ongoing efforts to target VP1, we demonstrate, for the first time, small molecules with nanomolar to sub-nanomolar affinities against BKPyV VP1 variants including potent binding to JCPyV VP1. Our work paves a path towards a new class of antiviral strategies that could block replication at intracellular replication sites, provide a higher genetic barrier to resistance and the potential to address both viral reactivation and persistent, high- burden viremia in transplant settings.

microbiology↗

bioRxiv2021

Electrostatics cause the molecular chaperone BiP to preferentially bind oligomerized states of a client protein

Hsp70-family chaperones bind short monomeric peptides with a weak characteristic affinity in the low micromolar range, but can also bind some aggregates, fibrils, and amyloids, with low nanomolar affinity. While this differential affinity enables Hsp70 to preferentially target potentially toxic aggregates, it is unknown how Hsp70s differentiate between monomeric and oligomeric states of a target protein. Here we examine the interaction of BiP (the Hsp70 paralog in the endoplasmic reticulum) with proIGF2, the pro-protein form of IGF2 that includes a long and mostly disordered E-peptide region that promotes proIGF2 oligomerization. We discover that electrostatic attraction enables the negatively charged BiP to bind positively charged E-peptide oligomers with low nanomolar affinity. We identify the specific BiP binding sites on proIGF2, and although some are positively charged, as monomers they bind BiP with characteristically low affinity in the micromolar range. We conclude that electrostatics enable BiP to preferentially recognize oligomeric states of proIGF2. Electrostatic targeting of Hsp70 to aggregates may be broadly applicable, as all the currently-documented cases in which Hsp70 binds aggregates with high-affinity involve clients that are expected to be positively charged.

biochemistry↗

bioRxiv2019

Phenotypic size heterogeneity is a viral mechanism of persistence

Assembly of many enveloped animal viruses yields a mixture of particle morphologies, from small, essentially isometric forms to vastly longer, filamentous forms. Selective advantage of pleomorphic virus structure is apparent only in vivo, hindering functional characterization of distinct particle shapes. Here we sought to mimic the in vivo pressures on virus entry in cultured cells and in single-particle experiments of membrane fusion for influenza virus preparations enriched in spherical or filamentous particles. We show that filamentous shape confers functional advantage in the presence of neutralizing antibodies or fusion inhibitors and in cases of only limited fusion-protein activation. For very long particles, inactivation of >95% of associated fusion proteins still permits enough active-protein cooperation to induce membrane merger. Experiments with Ebola virus-like particles show that resistance to antibody pressure is a conserved feature of filamentous particles. Our results offer a strategy for averting drug resistance or immune evasion by targeting filamentous virus particles.

microbiology↗