Biology subjects

Novy, B.

Publications and source records attributed to Novy, B..

5 recordsLinked to original sources

bioRxiv2026

PHENOMS: Open-Source Software for Rust-Accelerated Hydrogen-Bond Analysis in Molecular Dynamics Simulations

Hydrogen-deuterium exchange mass spectrometry (HDX-MS) provides powerful insight into protein structure and dynamics, but interpretation of protection patterns at atomic resolution often requires complementary computational modeling. We present PHENOMS, an open-source Python package that integrates molecular dynamics trajectories with HDX-MS data to analyze backbone hydrogen-bond networks by tracking how individual hydrogen bonds and residue-residue contacts form, break, and reorganize throughout the simulations. This residue-level analysis can reveal local structural changes that may be missed by conventional global trajectory metrics. PHENOMS employs a multithreaded, Rust-accelerated computational engine that achieved an average 16-fold speedup (up to 100-fold) over widely used Python-based MD analysis packages in our benchmarks, while retaining individual hydrogen-bond resolution in every trajectory frame. We demonstrate PHENOMS through multiple retrospective case studies using published and in-house datasets, showing that it can recapitulate HDX-MS protection patterns, identify key residues that drive coordinated structural changes, and benchmark the computational efficiency of the approach. With automated quality-control workflows, PHENOMS provides a framework for integrating hydrogen-bond analysis with HDX-MS data or serves as a standalone, high-throughput tool for analyzing MD trajectories for broader applications in protein engineering, drug discovery, and structural biology.

biophysics↗

bioRxiv2025

Conserved Filovirus Proteins as Targets of Broad-Spectrum Antivirals

Filoviruses are enveloped, non-segmented, negative-strand RNA viruses belonging to the Filoviridae family, which includes five genera: Ebolavirus, Marburgvirus, Cuevavirus, Striavirus, and Thamnovirus. Members of this family cause severe and, often, fatal hemorrhagic fevers in humans and non-human primates, with high mortality rates. To date, only two filoviruses, Ebola virus (EBOV) and Marburg virus (MARV), are known to infect humans and are listed as priority pathogens by the World Health Organization due to their potential for re-emergence and the current lack of effective vaccines and antiviral treatments. In this study, we identify and characterize conserved binding sites within key filoviral proteins to support the development of broad-spectrum, direct-acting antiviral agents. We validated the significance of these conserved regions for drug discovery using existing experimental data. Our analysis revealed notably high sequence similarity among proteins from filoviruses capable of infecting humans (EBOV, TAFV, BDBV, SUDV, MARV, and RAVV) compared to those from non-zoonotic species, with the highest conservation observed in the L and VP40 proteins--both critical for viral genome transcription and replication. Furthermore, we compiled and analyzed available experimental data on known antiviral compounds targeting these proteins, identifying several agents with cross-filovirus activity, including Galidesivir, Remdesivir, and Favipiravir. The integrated approach described here--combining sequence and structural conservation analysis with chemical structure and antiviral activity data--demonstrates a strategy that could be extended to the development of broad-spectrum therapeutics across multiple viral families. HIGHLIGHTSO_LIConserved filovirus sites targeted for broad-spectrum antivirals. C_LIO_LIStructural modeling identifies key antiviral binding sites. C_LIO_LIViral internal proteins are crucial targets for inhibition. C_LIO_LIRemdesivir validates conserved polymerase as a druggable target. C_LIO_LIStudy highlights need for pan-filovirus drug screening C_LI TOC GRAPHIC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/678902v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@4fd25eorg.highwire.dtl.DTLVardef@7c4076org.highwire.dtl.DTLVardef@16c0961org.highwire.dtl.DTLVardef@1dbd8a0_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

DNAJC13 localization to endosomes is opposed by its J domain and its disordered C-terminal tail

Endosomes are a central sorting hub for membrane cargos. DNAJC13/RME-8 plays a critical role in endosomal trafficking by regulating the endosomal recycling or degradative pathways. DNAJC13 localizes to endosomes through its N-terminal Plekstrin Homology (PH)-like domain, which directly binds endosomal phosphoinositol-3-phosphate (PI(3)P). However, little is known about how DNAJC13 localization is regulated. Here, we show that two regions within DNAJC13, its J domain and disordered C-terminal tail, act as negative regulators of its PH-like domain. Using a structure-function approach combined with quantitative proteomics, we mapped these control points to a conserved YLT motif in the C-terminal tail as well as the catalytic HPD triad in its J domain. Mutation of either motif enhanced DNAJC13 endosomal localization in cells and increased binding to PI(3)P in vitro. Further, these effects required the N-terminal PH-like domain. We show that, similar to other PI(3)P binding domains, the N-terminal PH-like domain binds PI(3)P weakly in isolation and requires oligomerization for efficient PI(3)P binding and endosomal localization. Together, these results demonstrate that interaction between DNAJC13 and PI(3)P serves as a molecular control point for regulating DNAJC13 localization to endosomes. Significance StatementO_LIDNAJC13 controls endosomal sorting by regulating proteins which mediate the endosomal recycling and degradative subdomains. C_LIO_LIHere we show that subcellular localization of DNAJC13 is regulated through the coordinated action of three of its domains: the PH-like domain which has low affinity for PI(3)P, the J domain, and a YLT motif in its disordered C-terminus. C_LIO_LIThis study defines a novel mechanism by which DNAJC13 function is regulated. C_LI

cell biology↗

bioRxiv2024

Retromer Opposes Opioid-Induced Downregulation of the Mu Opioid Receptor

The mu opioid receptor (MOR) is protected from opioid-induced trafficking to lysosomes and proteolytic downregulation by its ability to access the endosomal recycling pathway through its C-terminal recycling motif, LENL. MOR sorting towards the lysosome results in downregulation of opioid signaling while recycling of MOR to the plasma membrane preserves signaling function. However, the mechanisms by which LENL promotes MOR recycling are unknown, and this sequence does not match any known consensus recycling motif. Here we took a functional genomics approach with a comparative genome-wide screen design to identify genes which control opioid receptor expression and downregulation. We identified 146 hits including all three subunits of the endosomal Retromer complex. We show that the LENL motif in MOR is a novel Retromer recycling motif and that LENL is a necessary, sufficient, and conserved mechanism to give MOR access to the Retromer recycling pathway and protect MOR from agonist-induced downregulation to multiple clinically relevant opioids including fentanyl and methadone.

cell biology↗

bioRxiv2022

A genome-wide CRISPR interference screen using an engineered trafficking biosensor reveals a role for RME-8 in opioid receptor regulation

G protein-coupled receptors (GPCRs) are the largest family of membrane-bound signaling molecules. Activity of these receptors is critically regulated by their trafficking through the endo-lysosomal pathway. Identifying the genes involved in GPCR trafficking is challenging due the complexity of sorting operations and low affinity protein-protein interactions. Here we present a chemical biology fluorescence-based technique to interrogate GPCR trafficking. We show that the engineered enzyme APEX2 is a highly sensitive biosensor for GPCR trafficking to the lysosome, and this trafficking can be monitored through APEX-based activation of fluorogenic substrates such as Amplex UltraRed (AUR). We used this approach to perform a genome-wide CRISPR interference screen focused on the delta type opioid receptor (DOR), a GPCR which modulates anxiety, depression, and pain. The screen identified 492 genes including known- and novel-regulators of DOR expression and trafficking. We demonstrate that one of the novel genes, RME-8, localizes to early endosomes and plays a critical role in regulating DOR trafficking to the lysosome. Together, our data demonstrate that GPCR-APEX2/AUR is a flexible and highly sensitive chemical biology platform for genetic interrogation of receptor trafficking.

cell biology↗