Biology subjects

Bicer, D.

Publications and source records attributed to Bicer, D..

4 recordsLinked to original sources

bioRxiv2026

EnZight: A Structure-Guided Algorithm to Identify and Prioritize Substitution Hotspots for Enzyme Engineering

Homologous protein structures contain valuable information about tolerated sequence variation. However, translating this information into practical enzyme design strategies remains challenging. Here we present EnZight, a user-friendly web server that integrates homologous structural alignment with intuitive visualization to identify substitution hotspots in protein cores. EnZight exploits structurally aligned homologs to identify positions where the surrounding structural environment is conserved while the residue at the position varies across homologs. This enables prediction of substitutions that preserve fold integrity while modulating function and thermostability. The approach further provides interactive structural outputs that allow users to inspect and prioritize substitutions manually. To validate the use of EnZight, we used a polyurethane-degrading amidase as a proof of concept. We constructed 34 variants, and 97% were successfully expressed, indicating high foldability of the predicted substitutions. Several substitutions improved both catalytic turnover and thermostability, and, importantly, beneficial substitutions combined additively, enabling stepwise accumulation of improvements. The best triple mutant variant exhibited a six-fold increase in catalytic turnover and 2{degrees}C increase in apparent melting temperature. Enhanced activity toward the pharmaceutical micropollutant flutamide further demonstrates EnZight's broad applicability in identifying substitutions that enable enzyme optimization across diverse substrates.

bioengineering↗

bioRxiv2026

Fragment Based Active Site Exploration of Urethane Hydrolases Reveals a Diversity of Urethane Binding Modes

Recent advances in the discovery, characterisation, and engineering of urethanases provide new opportunities for the sustainable biocatalytic degradation of polyurethane waste. A mechanistic understanding of enzyme-plastic interactions is essential for structure-based engineering to enhance urethanase activity. However, the extremely complex and hydrophobic nature of polyurethane makes it challenging to elucidate the structural basis of enzyme-plastic interactions. Here, we used a fragment-based approach to characterise the active sites of two novel urethanases with different catalytic scaffolds, employing both a crystallographic fragment-screening (FASE) campaign and soluble fragments of plastic-like analogues that mimic the substrate, transition state, or product. FASE identified new substrate-binding subpockets while interactions of plastic mimetics in the active site provided a mechanistic understanding of the recognition and binding of polyurethane fragments by these subpockets. These results highlight a diversity of binding modes among urethanases toward different polyurethane fragments. SynopsisFragment-based active site exploration of urethanases to elucidate polyurethane binding and cleavage

biochemistry↗

bioRxiv2025

Rare missense variants of the leukocyte common antigen related receptor (LAR) display reduced activity in transcellular adhesion and synapse formation

The leukocyte common antigen related receptor (LAR) is a member of the LAR receptor protein tyrosine phosphatase (RPTP) family of synaptic adhesion molecules that contribute to the proper alignment and specialization of synaptic connections in the mammalian brain. LAR-RPTP members have been genetically associated with neuropsychiatric disorders, but the molecular consequences of genetic perturbations of LAR remain unstudied. Using exome sequencing data from psychiatric patients and controls, we identify rare missense variants of LAR that render the extracellular domain (ECD) unstable and susceptible to proteolytic cleavage. Using recombinant and cellular systems, we describe three variants that cause disruption of the LAR:NGL-3 interaction, which results in loss of transcellular adhesion and synaptogenic effects. Furthermore, we show that overexpression of two of these variants elicit altered morphological phenotypes in an imaging-based morphological profiling assay compared to wild type LAR, suggesting that destabilization of the LAR ECD has broad effects on LAR function. In conclusion, our study identifies three rare, missense variants in LAR that could provide insights into LAR involvement with psychiatric pathobiology.

neuroscience↗

bioRxiv2024

Structural insights into Pseudomonas aeruginosa lysine-specific uptake mechanism for extremely low pH regulation

Under conditions of extremely low pH, in addition to transporting lysine, bacterial lysine-specific permease (LysP) interacts with the transcriptional regulator CadC to upregulate cadBA operon expression. cadBA encodes CadA, which decarboxylates lysine to cadaverine, and CadB, which exports cadaverine to the environment to reduce acidity. This process is crucial for survival of pathogenic bacteria in their hosts. Here, we report the inward-occluded (3.2 - 5.3 [A]) cryo-EM structure of Pseudomonas aeruginosa LysP bound to L-lysine and in complex with a nanobody. L-lysine is coordinated by hydrophobic stacking, cation-{pi} interactions and hydrogen bonding mostly with polar uncharged LysP residues. LysP reconstituted into liposomes showed robust and specific transport of L-lysine with the transport being inhibited by L-4-thialysine (S-2-aminoethyl-L-cysteine). These findings inform our understanding of the specific recognition, inhibition, and transport mechanism of L-lysine by LysP, which will have important ramifications for the design of antibiotics to target bacterial LysP.

biochemistry↗