Biology subjects

Ser, Z.

Publications and source records attributed to Ser, Z..

4 recordsLinked to original sources

bioRxiv2026

Ara h 2 and FcϵRIα binding elicit state-dependent allostery in IgE

Background: Peanuts are among the most prevalent food allergens responsible for anaphylaxis, particularly in children. Allergic responses may be mitigated by disrupting molecular interactions between immunoglobulin-E (IgE) and its binding partners: peanut allergen (Ara h 2) and IgE receptors (Fc{epsilon}RI). However, the structural dynamics of IgE upon engaging these factors are not yet fully elucidated. Objective: To characterize how Ara h 2 and/or Fc{epsilon}RI binding influence IgE flexibility and its interdomain communications. Methods: The structural dynamics of full-length IgE in various unbound and bound states were examined by combining molecular dynamics (MD) simulations with cross linking mass spectrometry (XLMS). Causal relationship between IgE domains were characterized to infer allosteric communication pathways, which were assessed through hydrogen-deuterium exchange mass spectrometry (HDX-MS). Results: Non canonical bent IgE conformations were identified. We demonstrate that Fc{epsilon}RI binding immobilizes IgE predominantly by stabilizing and restricting Fc flexibility, whereas Ara h 2 binding induces specific conformational changes within the Fc{epsilon}RI-binding region. Our results further suggest that the C{epsilon} domains retain sufficient freedom to enable causal dynamics by the Fabs in a binding-dependent manner, thereby modulating the receptor engagement potential of IgE. Notably, concurrent binding of Ara h 2 and Fc{varepsilon}RI to IgE shifts the allosteric communication between the Fabs and Fc regions from the C{epsilon}3 to C{epsilon}4 domain. Conclusion: Our findings provide new insights into the dynamic regulation of IgE and its role in allergic responses. This could serve as a structural framework for understanding IgE signaling in peanut allergy and suggest potential targets for therapeutic interventions

immunology↗

bioRxiv2023

Integrative proteogenomics using ProteomeGenerator2

Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation and transcription, enabling population-scale studies of human biology, disease, and diverse organisms. Likewise, advances in mass spectrometry proteomics now permit highly sensitive and accurate studies of protein expression at the whole proteome-scale. However, most proteomic studies rely on consensus databases to match spectra to peptide and proteins sequences, and thus remain limited to the analysis of canonical protein sequences. Here, we develop ProteomeGenerator2 (PG2), based on the scalable and modular ProteomeGenerator framework. PG2 integrates genome and transcriptome sequencing to incorporate protein variants containing amino acid substitutions, insertions, and deletions, as well as non-canonical reading frames, exons, and other variants caused by genomic and transcriptomic variation. We benchmarked PG2 using synthetic data and genomic, transcriptomic, and proteomic analysis of human leukemia cells. PG2 can be integrated with current and emerging sequencing technologies, assemblers, variant callers, and mass spectral analysis algorithms, and is available open-source from https://github.com/kentsisresearchgroup/ProteomeGenerator2.

bioinformatics↗

bioRxiv2021

Integrative analysis reveals unique features of the Smc5/6 complex

Structural maintenance of chromosomes (SMC) complexes are critical chromatin modulators. In eukaryotes, the cohesin and condensin SMC complexes organize chromatin, while the Smc5/6 complex directly regulates DNA replication and repair. The molecular basis for Smc5/6s distinct functions is currently poorly understood. Here, we report an integrative structural study of the budding yeast Smc5/6 complex using electron microscopy, cross-linking mass spectrometry, and computational modeling. We show that while the complex shares a similar overall organization with other SMC complexes, it possesses several unique features. In contrast to the reported folded-arm structures of cohesin and condensin, our data suggest that Smc5 and Smc6 arm regions do not fold back on themselves. Instead, these long filamentous regions interact with subunits uniquely acquired by the Smc5/6 complex, namely the Nse2 SUMO ligase and the Nse5-Nse6 subcomplex. Further, we show that Nse5-Nse6 subcomplex adopts a novel structure with an extensive dimerization interface and multiple domains contacting other subunits of the Smc5/6 complex. We also provide evidence that the Nse5-Nse6 module uses its SUMO-binding motifs to contribute to Nse2-mediated sumoylation. Collectively, our integrative multi-scale study identifies distinct structural features of the Smc5/6 complex and functional cooperation amongst its co-evolved unique subunits.

molecular biology↗

bioRxiv2018

Optimized cross-linking mass spectrometry for in situ interaction proteomics

Recent development of mass spectrometer cleavable protein cross-linkers and algorithms for their spectral identification now permits large-scale cross-linking mass spectrometry (XL-MS). Here, we optimized the use of cleavable disuccinimidyl sulfoxide (DSSO) cross-linker for labeling native protein complexes in live human cells. We applied a generalized linear mixture model to calibrate cross-link peptide-spectra matching (CSM) scores to control the sensitivity and specificity of large-scale XL-MS. Using specific CSM score thresholds to control the false discovery rate, we found that higher-energy collisional dissociation (HCD) and electron transfer dissociation (ETD) can both be effective for large-scale XL-MS protein interaction mapping. We found that the density and coverage of protein-protein interaction maps can be significantly improved through the use of multiple proteases. In addition, the use of sample-specific search databases can be used to improve the specificity of cross-linked peptide spectral matching. Application of this approach to human chromatin labeled in live cells recapitulated known and revealed new protein interactions of nucleosomes and other chromatin-associated complexes in situ. This optimized approach for mapping native protein interactions should be useful for a wide range of biological problems.

systems biology↗