Using CEST NMR to discover previously unobserved states on the free energy surface of proteins: Application to the L99A cavity mutant of T4 lysozyme
Bibliographic record
Abstract
Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments establish that at room temperature the L99A cavity mutant of T4 lysozyme (L99A T4L) interconverts between two compact folded conformations on the millisecond timescale. These include the native state in which the sidechain of Phe114 is exposed to solvent (E state) and a near native minor state in which the aromatic moiety of Phe114 is buried in the core of the protein (B state, ∼2%). Molecular dynamics simulations that have captured the E to B interconversion in L99A T4L and related mutants suggest that these proteins adopt compact folded conformations other than E and B, yet extensive CPMG studies have not detected such states. In an effort to detect these more elusive conformers experimentally we have recorded Chemical Exchange Saturation Transfer (CEST) experiments, as the widths of minor state dips in the resulting CEST profiles are sensitive to additional, even more sparse, conformers. Analysis of amide 15 N and 13 CH 3 CEST profiles recorded on L99A T4L show that in addition to states E and B, a rare state (I) populated to ∼0.2 % (11.5 o C) exchanges rapidly with state B. CEST-based urea m -values establish that all three states are compact, with interconversion between them proceeding via compact transition states. This study highlights the utility of CEST to characterize the free energy surface of a protein by detecting states with a wide range of lifetimes (100 ms to 100 μs) in ways that are not possible using other relaxation-based NMR techniques.
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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 | 0.001 |
| 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 | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 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".