Probing Side-Chain Dynamics in the Proteasome by Relaxation Violated Coherence Transfer NMR Spectroscopy
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Bibliographic record
Abstract
A pair of experiments is presented for measuring intra-methyl 1H-1H dipolar cross-correlated spin relaxation rates in highly deuterated, methyl protonated proteins with significantly improved sensitivity relative to previously developed experiments that measure dynamics via 1H spin relaxation. In applications to proteins with correlation times in the macromolecular limit, these cross-correlation rates are related directly to order parameters, characterizing the amplitude of motion of methyl-containing side-chains. The experimental approach is validated by comparing extracted order parameters with those obtained via 2H and 13C spin relaxation methods for both protein L (7.5 kDa) and malate synthase G (82 kDa), with excellent correlations obtained. The methodology is applied to study Ile, Leu, and Val side-chain dynamics in a 360 kDa "half-proteasome" complex. In particular, order parameters obtained from the WT complex and from a second complex where the proteasome gating residues are deleted establish that the relative levels of dynamics in each of the two molecules are very similar. It thus becomes clear that there is no communication between gating residues and other regions of the molecule involving pico- to nanosecond time-scale dynamics of these methyl-containing side-chains.
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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) | 0.000 | 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 it