RNA Binding by the Yeast Slf1 and Sro9 La-motif Domains
Bibliographic record
Abstract
Slf1 and Sro9 are paralogous RNA-binding proteins in Saccharomyces cerevisiae that belong to the LARP1 (La-related protein 1) subgroup of the greater La family. These proteins function as translational regulators during cellular stress, acting through either direct mRNA binding or interactions with ribosomal factors. In this study, we characterized the structural and RNA-binding properties of the La-motif (LaM) domains of Slf1 and Sro9 using a combination of nuclear magnetic resonance (NMR) spectroscopy, calorimetry, and molecular dynamics (MD) simulations. Both LaM domains exhibited micromolar affinity for RNA ligands, including poly(A). Notably, the Sro9 LaM domain displayed a thermal denaturation midpoint of 36 °C suggesting a potential regulatory mechanism for this protein during hyperthermic stress. An NMR analysis of the Slf1 LaM domain revealed that its RNA binding platform undergoes widespread conformational sampling on the micro- to millisecond timescale, even in the presence of RNA. Molecular dynamics simulations corroborated these experimental NMR observations and highlighted the role of transient aromatic stacking during RNA binding. Furthermore, a glutamine substitution mutant (Q278A in Slf1) known to impair RNA binding also destabilized the protein-RNA interaction in molecular simulations. Collectively, our findings confirm that RNA binding by LaM domains is an evolutionarily conserved feature among eukaryotes and provide critical insights into the structural and dynamic mechanisms underlying Slf1 and Sro9 function in yeast.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 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) | 0.000 | 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 source (direct Gemma or distilled Codex), 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".