Biology subjects

Lundstrom, S. L.

Publications and source records attributed to Lundstrom, S. L..

4 recordsLinked to original sources

bioRxiv2025

Proteome integral solubility alteration assay for monitoring antibody-antigen cell interactions

The Proteome Integral Solubility Alteration (PISA) assay is commonly used to identify and characterize interactions between small molecules and the cellular proteome. In this study, a modified PISA approach identified tumor necrosis factor alpha (TNF) as the antigen of the monoclonal antibody infliximab in activated monocytes - uniquely among [~]8,000 cellular proteins. These results highlight the potential of PISA-based analysis not only for monitoring antibody-antigen interactions in therapeutic development, but also for identifying new antigens and characterizing the initial effector functions of antibodies within complex proteome environments. TeaserModified PISA pinpointed TNF- as Infliximabs antigen among 8000 proteins, highlighting broad potential for therapeutic antigen studies.

molecular biology↗

bioRxiv2025

Towards a species search engine: KISSE offers a rigorous statistical framework for bone collagen tandem mass spectrometry data

DNA and bone collagen are two key sources of resilient molecular markers used to identify species from their remains. Collagen is more stable than DNA, and thus it is preferred for ancient and degraded samples. Current mass spectrometry-based collagen sequencing approaches are empirical and lack a rigorous statistical framework. Based on the well-developed approaches to protein identification in shotgun proteomics, we introduce a first approximation of the species search engine (SSE). Our SSE named KISSE is based on a species-specific library of collagenous peptides that uses both peptide sequences and their relative abundances. The developed statistical model can identify the species and the probability of correct identification, as well as determine the likelihood of the analyzed species not being in the library. We discuss the advantages and limitations of the proposed approach and the possibility of extending it to other tissues.

zoology↗

bioRxiv2024

Gel-Assisted Proteome Position Integral Shift (GAPPIS) Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Novel Caspase 3 Substrates

Here we present a high-throughput virtual top-down proteomics approach that restores the molecular weight (MW) information in shotgun proteomics, and demonstrate its utility in studying proteolytic events in programmed cell death. With Gel-Assisted Proteome Position Integral Shift (GAPPIS), we quantified over 7000 proteins in staurosporine-induced apoptotic HeLa cells and identified 84 proteins exhibiting in a statistically significant manner at least two of the following features: 1) a negative MW shift; 2) an elevated ratio in a pair of a semi-tryptic and tryptic peptide, 3) a negative shift in the standard deviation of MW estimated for different peptides, and 4) a negative shift in skewness of the same data. Of these proteins, 58 molecules were novel caspase 3 substrates. Further analysis identified the preferred cleavage sites consistent with the known caspase cleavages after the DXXD motif. As a powerful tool for high-throughput MW analysis simultaneously with the conventional expression analysis, GAPPIS assay can prove useful in studying a broad range of biological processes involving proteolytic events.

biochemistry↗

bioRxiv2022

Mapping the GALNT1 substrate landscape with versatile proteomics tools

O-GalNAc type glycosylation is a common post-translational modification (PTM) of proteins catalyzed by polypeptide GalNAc transferases, but the substrate specificity of these transferases is poorly understood. Here we develop a strategy based on integral thermal proteome solubility profiling to identify and prioritize the protein substrates of polypeptide N-acetylgalactosaminyltransferase 1 (GALNT1). Combined with glycoprotein enrichment followed by HCD and soft EThcD gas-phase fragmentation technique, we uncover hundreds of novel GALNT1 substrates in two model human cell lines. GALNT1-mediated O-glycosylation is more common on Thr than Ser residues, with a strong preference for Pro at positions +3 and +4 in respect to O-glycosylation. These results implicate GALNT1 in potentially regulating proteins in several diverse pathways, including some unexpected processes, such as TCA cycle and DNA transcription. This study depicts a roadmap for identification of functional substrates for glycosyltransferases, facilitating fundamental insight into the role of glycosylation in homeostasis and disease.

biochemistry↗