Biology subjects

Bowers, A.

Publications and source records attributed to Bowers, A..

6 recordsLinked to original sources

bioRxiv2026

Macrocycle screening against the C-terminal region of CHD4 uncovers its role as an interaction hub in the formation of the nucleosome remodeling and deacetylase complex

The Nucleosome Remodeling and Deacetylase complex (NuRD) plays a key role in regulating hemoglobin expression in adult erythroid cells. Selectively disrupting this complex potently induces the expression of fetal hemoglobin, a proven therapeutic strategy for treating beta-hemoglobinopathies such as sickle cell anemia. In these studies, we have used mRNA display to identify small macrocyclic peptides that inhibit the interaction between two core components of NuRD, the SANT-SLIDE domain of CHD4 and the CR2 domain of GATAD2A. In addition, the screen suggested a second binding site on the CHD4 domain. Based on this observation, we hypothesized and confirmed that CDK2AP1 bound to this region of CHD4, leading us to purify and determine the structure of the ternary complex between CHD4, GATAD2A, and CDK2AP1. The results of our studies show that the SANT-SLIDE domain of CHD4 functions as a critical interaction hub in the formation of NuRD and suggest a strategy to block NuRD function for therapy.

biophysics↗

bioRxiv2026

Enhancing ML-based binder design with high-throughput screening: a comparison of mRNA and yeast display technologies

Recent advances in machine learning (ML)-based protein design methods have enabled the rapid in silico generation of large libraries of miniprotein binders with minimal manual input. While computational design capacity has scaled rapidly, experimental validation methods have lagged, creating a bottleneck in binder discovery pipelines. Here, we apply mRNA display to screen an ML-designed miniprotein binder library and directly compare its performance with the more widely used yeast surface display platform using a single shared DNA library. We screened 2,009 designs targeting the platelet receptor TLT-1 and 3,159 designs targeting the immune receptor B7-H3 across both platforms. While both selection methods reliably identified functional binders, we found that mRNA display preferentially enriched binders with slower dissociation rates. In addition, mRNA display achieved higher library coverage than yeast display, likely rescuing functional designs that are penalized in a cell-based expression system. Biophysical characterization of selected binders from both platforms revealed strong binding affinities and high thermal stabilities. These results showcase the power of integrating ML-based computational design tools with rapid in vitro selection technologies, providing a scalable framework for therapeutic miniprotein discovery. IMPORTANCEMiniprotein binders offer major advantages as next-generation therapeutics, including small size, high stability, and efficient production. In this work, we conduct a side-by-side comparison of mRNA and yeast display as platforms for high-throughput evaluation of de novo miniprotein binders. The binders generated here serve as starting points for therapeutics targeting TLT-1 or B7-H3, two clinically relevant molecules.

bioengineering↗

bioRxiv2025

Enhancing enzymatic bioconjugation efficiency via installation of a substrate recruitment domain

Enzyme mediated bioconjugation provides a method for easy and rapid formation of protein-protein and protein-small molecule conjugates under mild conditions. Promiscuous enzymes are of particular interest because they can catalyze conjugation reactions on a broad set of substrates. However, this promiscuity carries the risk of undesirable off-target modifications. To mitigate this effect, we used computational design to install a substrate recruitment domain (SRD) onto the promiscuous enzyme, tyrosinase. The redesigned tyrosinase, called D42, preferentially modifies tyrosine residues within the peptide core (core) linked to a 6-amino acid recognition motif/sequence (RS) specific for the SRD. Incorporation of the recognition sequence along with a neighboring tyrosine in peptides or proteins allows for rapid D42-mediated conversion of the tyrosine to an orthoquinone, which can be selectively modified with a variety of nucleophiles. We demonstrate the utility of our design system by rapidly installing cytotoxic molecules on a monoclonal antibody. For Table of Contents Only O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=72 SRC="FIGDIR/small/684804v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1a3b274org.highwire.dtl.DTLVardef@18eeedorg.highwire.dtl.DTLVardef@ee0aaeorg.highwire.dtl.DTLVardef@1ff3fa1_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Assessing substrate scope of the cyclodehydratase LynD by mRNA display-enabled machine learning models

Many of the biosynthetic pathways for ribosomal synthesized and post-translationally modified peptide (RiPP) natural products make use of multi-domain enzymes with separate recruitment and catalysis domains that separately bind and modify peptide substrates. This "division of labor" allows RiPP enzymes to use relatively open and promiscuous active sites to perform chemistry at multiple residues within a peptide substrate seemingly regardless of the surrounding context. Defining, measuring, and predicting the seemingly broad substrate promiscuity of RiPPs necessitates high throughput assays, capable of assessing activity against very large libraries of peptides. Using mRNA display, a high throughput peptide display technology, we examine the substrate promiscuity of the RiPP cyclodehydratase, LynD. The vast substrate profiling that can be done with mRNA display enables the construction of deep learning models for accurate prediction of substrate processing by LynD. These models further inform on epistatic interactions involved in enzymatic processing. This work will facilitate the further elucidation of other RiPP enzymes and enable their use in the modification of mRNA display libraries for selection of modified peptide-based inhibitors and therapeutics.

biochemistry↗

bioRxiv2019

Evaluation of Reproducibility in Urology Publications

Take Home MessageMany components of transparency and reproducibility are lacking in urology publications, making study replication, at best, difficult.\n\nIntroductionReproducibility is essential for the integrity of scientific research. Reproducibility is measured by the ability of investigators to replicate the outcomes of an original publication by using the same materials and procedures.\n\nMethodsWe sampled 300 publications in the field of urology for assessment of multiple indicators of reproducibility, including material availability, raw data availability, analysis script availability, pre-registration information, links to protocols, and whether the publication was freely available to the public. Publications were also assessed for statements about conflicts of interest and funding sources.\n\nResultsOf the 300 sample publications, 171 contained empirical data and could be analyzed for reproducibility. Of the analyzed articles, 0.58% (1/171) provided links to protocols, and none of the studies provided analysis scripts. Additionally, 95.91% (164/171) did not provide accessible raw data, 97.53% (158/162) did not provide accessible materials, and 95.32% (163/171) did not state they were pre-registered.\n\nConclusionCurrent urology research does not consistently provide the components needed to reproduce original studies. Collaborative efforts from investigators and journal editors are needed to improve research quality, while minimizing waste and patient risk.

scientific communication and education↗

bioRxiv2018

Hazard detection with monocular bioptic telescopes in a driving simulator

ABSTRACT\n\nPurpose: Recently we developed a driving simulator paradigm to evaluate detection of road hazards when using a bioptic telescope and conducted an initial study using normally-sighted observers with simulated vision loss. We now extend our investigation to quantifying the extent to which visually impaired bioptic users are able to use their fellow (non-telescope) eye to compensate for the ring scotoma of a monocular bioptic telescope. We tested the hypothesis that detection rates would be higher in binocular viewing (fellow eye could potentially compensate) than monocular viewing (fellow eye patched so it could not compensate) for pedestrian hazards present in the scene only while the telescope was being used.\n\nMethods: Sixteen bioptic telescope users (17-80 y) completed six test drives, including three with binocular viewing interleaved between three with monocular viewing. While driving, they used their own monocular bioptic telescopes to read information on highway road signs (n = 71) and pressed the horn when they saw a pedestrian hazard (n = 50). Twenty-six of the pedestrians were programed to appear, run on the road ahead of the driver for 1s within the ring scotoma and then disappear, within the period when participants were reading signs through the bioptic. The timing of the head movement to look into and out of the bioptic was determined and events were then categorized by whether or not the pedestrian hazard was present in the scene only while using the bioptic.\n\nResults: When pedestrian hazards were in the scene only while subjects were using the bioptic to read a sign, detection rates were significantly higher in binocular than monocular viewing (68% vs. 40%). However, when pedestrians when subjects had a brief view of the pedestrian either beforeor after looking through the bioptic, then detection rates did not differ in binocular and monocular viewing (78% vs. 79%). By comparison, when not using the bioptic detection rates were higher (> 90%) and reaction times were shorter (without 0.95 s vs. with 1.25 s)\n\nConclusions: Our results suggest that under binocular viewing conditions the fellow eye was able to compensate for the ring scotoma to a certain extent when subjects used a monocular telescope to read road signs; however, performance was not as good as without the bioptic.

neuroscience↗