In silico modeling of Arp1 and Arp2 as targets of Photox ADP-ribosylation
Bibliographic record
Abstract
Photox has been identified as an ADP-ribosylating toxin, produced by Photorhabdus luminescens, which targets actin. Recent unpublished studies have suggested that Photox may also target actin-related proteins (Arps). Herein we report possible interacting residues of actin, Arp1 and Arp2, with Photox. Both actin and Arp1 were predicted to interact with Photox in six main groups across the NAD+ binding surface whereas four interaction groups were proposed between Arp2 and Photox. The possible interactions evaluated included hydrogen bonds, salt bridges, and electrostatic and hydrophobic interactions. Our results suggest that Arp1 is a very likely target of Photox, while Arp2 is also a possible candidate; however, the possible interactions between Photox and Arp2 appear to be weaker than the possible interactions between Photox and Arp1. Understanding the various interactions of Photox and its targets may help to provide insight into its biological action, and may potentially lead to a treatment plan for similar toxin-related diseases.
 
 Keywords: ADP-ribosylating toxins; Photox (Photorhabdus luminescens); actin-related proteins (Arp1, Arp2) (targeting of); in silico modeling of protein interactions
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".