High-pressure room-temperature crystallography reveals catalytic lid dynamics even in the absence of ligands
Bibliographic record
Abstract
Enzymes undergo local and large-scale conformational changes as required to execute each step in their catalytic cycle. Typically, ligand binding and establishment of all protein-ligand interactions generates new protein conformations essential to the chemical transformation. Without the ligand interactions, apo protein crystals often do not have sufficient interactions/bonds to adopt the catalytically “ready” conformation, an obstacle to structural studies when in crystallo binding is not possible. We have explored the use of pressure to perturb interactions and the energy landscape so as to induce active conformations. Using a diamond anvil cell at CHESS crystallography beamline 7B2, we subjected crystals of the metabolic enzyme phosphoenolpyruvate carboxykinase (PEPCK) containing only one of two ligands required for catalysis to pressures up to 4.5 kbar. PEPCK is a well-characterized system with a gating active site loop that must adopt a “closed” conformation for catalysis to occur. We show how high pressure measurements can reveal catalytically active conformations even when all ligands required for closure at ambient pressure and temperature are not present. We will also describe tips and tricks in using the diamond anvil cell to collect high pressure crystallographic data.
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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 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.002 |
| Insufficient payload (model declined to judge) | 0.002 | 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".