Peptides in plants, prediction tools, and dipeptide survival: a three-paper research roundup

This study examines phytosulfokine (PSK) peptide signaling in tomato reproductive thermotolerance. The authors report that heat induces expression of PSK precursors in anthers and that exogenous PSK reduces heat‑induced pollen abortion in their experiments. Genetic loss of the PSK receptor PSKR1 or the NADPH oxidase RBOHB was associated with disrupted reactive oxygen species (ROS) homeostasis and reduced pollen thermotolerance, with notable yield impacts under both controlled and field heat‑stress conditions reported by the authors. Mechanistically, the paper describes PSKR1‑mediated phosphorylation of RBOHB at Threonine‑266 and Serine‑340 in pollen, triggering ROS bursts that engage the HSF/HSP heat shock pathway; genetic complementation with phospho‑mimic variants is presented as evidence that phosphorylation at these residues can restore protective responses. The report frames PSK–ROS as a signaling axis and points to genetic or peptide‑based targets for further investigation, while not making application claims beyond the experimental context.

The benchmarking paper provides a comparative evaluation of 17 HLA class I peptide‑binding prediction models using a curated dataset of over 290,000 peptides across 44 HLA‑I alleles. The authors assessed accuracy, robustness, and interpretability, applying explainability methods such as SHAP and LIME to probe model behaviors. They describe substantial performance variation among models, noting advantages for self‑attention architectures (explicitly naming STMHCpan and BigMHC) and robust results for a capsule network implementation (CapsNet‑MHC_AN). The study reports that models trained on eluted ligand datasets tended to outperform affinity‑trained models, and that ensemble or multi‑algorithm strategies improved reliability. The authors highlight data quality and model architecture as central limits and recommend integration of diverse datasets and structural predictors for future improvements.

In laboratory simulations, the third paper investigates the effects of ionizing radiation on films of linear and cyclic dipeptides and alanine deposited on ZnSe substrates. Using in situ infrared absorption measurements during irradiation at different temperatures, the authors observe film degradation driven by ion‑induced fragmentation and sputtering, with cyclic dipeptides showing higher radioresistance than linear species in their tests. Low‑temperature spectra indicate formation of new, lower‑mass products, and the authors note spectral similarities that they interpret as suggestive of ion‑induced peptide polymerization under the conditions studied. They propose that cyclic dipeptides might plausibly survive harsh astrophysical environments and contribute to pathways toward larger organic species, while also noting that these laboratory‑scale simulations do not reproduce the full complexity of astrochemical environments and so further work is needed to assess relevance to prebiotic chemistry.