Biology subjects

Lin, H.-J. L.

Publications and source records attributed to Lin, H.-J. L..

4 recordsLinked to original sources

bioRxiv2025

The ten dollar proteome: low-cost, deep and quantitative proteome profiling of limited sample amounts using the Orbitrap Astral and timsTOF Ultra 2 mass spectrometers

Mass spectrometry (MS)-based proteomics remains technically demanding and prohibitively expensive for many large-scale or routine applications, with per-sample costs of hundreds of dollars or more. To democratize access to proteomics and facilitate its integration into more high-throughput multi-omic studies, we present a robust analytical framework for achieving in-depth, quantitative proteome profiling at a cost of approximately $10 per sample, termed the "$10 proteome." Using the Thermo Fisher Orbitrap Astral and Bruker timsTOF Ultra 2 mass spectrometers, we evaluated performance across sample inputs ranging from 200 pg to 100 ng and active gradient lengths from 5 to 60 minutes. Proteome coverage saturated within the low-nanogram input range, with [~]8000 protein groups quantified from as little as 10 ng of input and nearly 6000 protein groups from 200 pg. With already demonstrated low-cost one-pot sample preparation workflows that are appropriate for this sample input range, standardized MS acquisition settings, and high-throughput nanoLC operated at [~]10 min per sample, the $10 proteome becomes feasible. This study establishes a practical, scalable, and cost-effective foundation for global proteome profiling, paving the way for routine, large-scale applications in systems biology, clinical research and beyond.

systems biology↗

bioRxiv2025

CMG2 interaction with actin is required for growth factor-induced chemotaxis in endothelial cells.

Capillary morphogenesis gene 2 (CMG2/ANTXR2) is a cell surface receptor that contributes to corneal angiogenesis and is essential for orienting endothelial cell chemotaxis in growth factor gradients. However, the mechanism by which CMG2 transmits signals to orient endothelial cells is unknown. Here, we use affinity proteomics to identify proteins that interact with CMG2. This led us to investigate CMG2 interaction with F-actin in the context of serum and individual growth factors (bFGF/PDGF/VEGF) in both primary and immortalized endothelial cells. We also measured different matrix-protein-mediated changes in chemotaxis. We find that CMG2 function is matrix dependent, and that CMG2-actin interaction is required for serum- and growth-factor-induced chemotaxis. Inhibiting chemotaxis with CMG2 antagonists (collagen 6, penta-galloyl-glucose, or anthrax toxin protective antigen; PA) leads to the release of actin cytoskeleton from CMG2. Furthermore, CMG2 co-localizes with actin at the leading edge during live migration. This colocalization is disrupted by PA, which also disrupts directional movement. Finally, we demonstrate that the conserved actin binding domain of CMG2 directly binds to F-actin in vitro where it bundles F-actin, suggesting a mechanism by which it enables directional migration.

molecular biology↗

bioRxiv2023

Visualization of the Cdc48 AAA+ ATPase protein unfolding pathway

The Cdc48 AAA+ ATPase is an abundant and essential enzyme that unfolds substrates in multiple protein quality control pathways. The enzyme includes two conserved AAA+ ATPase cassettes, D1 and D2, that assemble as hexameric rings with D1 stacked above D2. Here, we report an ensemble of structures of Cdc48 affinity purified from lysate in complex with the adaptor Shp1 in the act of unfolding substrate. Our analysis reveals a continuum of structural snapshots that spans the entire translocation cycle. These data reveal new elements of Shp1-Cdc48 binding and support a "hand-over-hand" mechanism in which the sequential movement of individual subunits is closely coordinated. D1 hydrolyzes ATP and disengages from substrate prior to D2, while D2 rebinds ATP and re-engages with substrate prior to D1, thereby explaining the dominant role played by D2 in substrate translocation/unfolding.

biochemistry↗

bioRxiv2022

Structural stability of Human serum albumin is modified in rheumatoid arthritis

Differential scanning calorimetry (DSC) can interrogate changes in structure and/or concentration of the most abundant proteins in a biological sample via heat denaturation curves (HDCs). In blood serum for example, HDC changes are a result of either concentration or altered thermal stabilities for 7-10 proteins and has previously been shown capable of differentiating between sick and healthy human subjects. Here, we compare HDCs and proteomic profiles of 50 patients experiencing joint-inflammatory symptoms, 27 of which were clinically diagnosed with rheumatoid arthritis (RA). The HDC of all 50 subjects appeared significantly different from expected healthy curves, but comparison of additional differences between the RA the non-RA subjects allowed more specific understanding of RA samples. We used mass spectrometry (MS) to investigate the reasons behind the additional HDC changes in RA patients. The HDC differences do not appear to be directly related to differences in the concentrations of abundant serum proteins. Rather, the differences can be attributed to modified thermal stability of the most abundant protein, human serum albumin (HSA). By quantifying differences in the frequency of artificially induced post translational modifications (PTMs), we found that HSA in RA subjects had a much lower surface accessibility, indicating potential ligand or protein binding partners in certain regions that could explain the shift in HSA melting temperature in the RA HDCs. Several low abundance proteins were found to have significant changes in concentration in RA subjects and could be involved in or related to binding of HSA. Certain amino acid sites clusters were found to be less accessible in RA subjects, suggesting changes in HSA structure that may be related to changes in protein-protein interactions. These results all support a change in behavior of HSA which may give insight into mechanisms of RA pathology.

biochemistry↗