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Item type:Publication, De Novo Design of Zearalenone Binding Proteins: A Comparison of Tamarind Bio and CARPdock-NISE-Boltz-2 Pipelines for Biosensor Applications(2026-01-06)Zearalenone is a mycotoxin frequently found in cereals and pseudocereals, which has shown male reproductive toxicity and synergistic effects with other mycotoxins. Current detection methods for zearalenone are largely based on chromatography or antibody-based assays, and no de novo designed protein receptors are available as recognition elements for biosensors. In this work, de novo zearalenone-binding proteins have been designed using two competing computational pipelines: (i) Tamarind Bio's all-atom RFdiffusion-ProteinMPNN-RoseTTAFold workflow and (ii) a NISE-CARPdock pipeline combining scaffold generation, LaserMPNN design, and Boltz-2 folding. Three top candidates (RFdiff-ZB1, NC-ZB1, NC-ZB2) exhibited high structural confidence with global average pLDDT values between 0.97-0.98, docking analysis using GNINA produced docking scores of -5.99 to -9.70. Molecular-dynamics-based minimization yielded affinities of -10.48 to -10.92 kcal/mol with minimized pose RMSDs of 0.26-0.68 Å and CNNscores up to 0.80. These results are comparable to in silico benchmarks from natural zearalenone-binding proteins and mutants. This study presents the first comparison between Tamarind Bio and CARPdock-Boltz-2 workflows for de novo mycotoxin binder design and delivers three high-confidence candidates suitable for biosensing. Future work will include extended MD trajectories, experimental binding validation, and integration into impedance-based or other electrical transduction platforms for real-sample detection. - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Chitosan Eco-Friendly Approach to Oil Spill Cleanup: A Combined 2D TD-NMR Relaxation and Computational Modeling Study(Springer Science+Business Media, 2026-01-01)This work investigates the molecular interaction between chitosan, an effective and eco-friendly biopolymer, and crude oil components within petroleum emulsions. This mechanistic investigation combines 2D TD-NMR relaxation and computational modeling to understand chitosan’s role as an adsorbent and demulsifier for applications in environmental remediation. We applied a medium molecular mass chitosan to a series of six petroleum emulsions, spanning a representative range of medium and heavy crude oils (viscosities from 32.52 to 182.07 mm2.s-1 at 20 °C). The 2D D-T2 correlation maps were generated using the PFG-CPMG (Pulsed Field Gradient-Carr-Purcell-Meiboom-Gill) sequence to resolve the changes in oil and water mobility following chitosan addition. The key result is the observation of a characteristic shift in the diffusion coefficient (D) and transverse relaxation time (T2) of the oil component upon chitosan introduction. This shift provides direct evidence of the molecular interaction and the disruption of the emulsion stabilizing film. Furthermore, molecular modeling confirms strong water binding, complementing the TD-NMR findings. Overall, the study successfully demonstrates the utility of TD-NMR and molecular dynamics for mechanistic assessment, providing crucial, direct insight into the demulsification role of chitosan within petroleum emulsions.