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Biology subjects

Martin-Perez, J.

Publications and source records attributed to Martin-Perez, J..

2 recordsLinked to original sources

Defining a Biofabrication Window for Visible-Light Photocrosslinkable Protein Bioinks in Extrusion Bioprinting

Extrusion bioprinting requires simultaneous control of material processability, rapid post-deposition stabilization, geometric fidelity, and cell compatibility. Here, we defined an experimental biofabrication window for three visible-light photocrosslinkable protein formulations based on silk fibroin (SF), gelatin methacryloyl (GelMA), and collagen methacryloyl (ColMA) using a extrusion-bioprinting workflow and ruthenium/sodium persulfate (Ru/SPS) photochemistry. Material-specific photocrosslinking conditions were first established under 430-nm irradiation and subsequently evaluated by ATR-FTIR spectroscopy, unconfined compression, short-term ARPE-19 cytocompatibility, and printing assays. Stable bulk hydrogels were obtained using 1-Ru/SPS, 45 mW, and 5 min for SF; 2.5- Ru/SPS, 45 mW, and 7 min for GelMA; and 2.5- Ru/SPS, 45 mW, and 6 min for ColMA. The selected formulations formed compliant hydrogels with initial compressive moduli of 0.60, 0.52, and 2.55 kPa for SF, GelMA, and ColMA, respectively, without significant differences among groups. Short-term XTT assays identified the unreacted Ru/SPS-containing precursor as a major biological constraint, whereas photoinitiator-free SF and GelMA maintained metabolic activity close to the culture-medium reference. GelMA and SF generated interconnected lattices with printability indices of 0.893 and 0.963, respectively. Detailed SF analysis showed high positional accuracy (96.9%) despite substantial post-deposition spreading, demonstrating that positioning accuracy and dimensional fidelity are distinct properties. Cell-laden printing was achieved with both SF and GelMA, and independent extrusion testing showed no statistically significant reduction in short-term ARPE-19 viability after SF bioprinting. Following the complete printing and photocrosslinking workflow, both formulations contained predominantly viable cells, but only SF retained the printed grid-associated cellular architecture under the tested conditions. These findings support the concept that biofabrication performance is an operational property arising from the intersection of photocrosslinking, cytocompatibility, extrusion compatibility, geometric fidelity, and post-fabrication structural stability.

bioengineering↗

Characterization of PROTACs by Ternary Complex Landscape Exploration using Monte Carlo simulations

PROTACs (Proteolysis-Targeting Chimeras) have emerged as a powerful modality for targeted protein degradation, yet their optimization still relies heavily on trial-and-error methods. A key factor in PROTAC degradation efficiency is the formation of the ternary complex (TC) between the PROTAC and its target proteins. However, due to their dynamic nature, PROTAC-mediated TCs can adopt multiple conformations, making their characterization challenging. Computational methods that account for this flexibility can provide more accurate predictions aligned with experimental results. Here, we explore the dynamic nature of TCs by analyzing their energy landscapes using protein-protein docking coupled with Monte Carlo sampling. This approach enables the identification of energetically relevant TC conformations, including those observed in experimental crystal structures, and allows estimation of thermodynamic and kinetic stability, as shown for a set of VHL-WDR5 PROTACs. Insights from these landscapes could support the screening and optimization of tens of similar PROTACs based on TC stability.

biophysics↗