Interplaying roles of native topology and chain length in marginally cooperative and noncooperative folding of small protein fragments
Bibliographic record
Abstract
Abstract Coarse‐grained chain simulations were used to study fragments of two homologous proteins of the peripheral subunit‐binding domain (PSBD) family, Bacillus stearothermophilus PSBD (E3BD) and Escherichia coli 2‐oxo‐glutarate dehydrogenase PSBD (BBL). To ascertain a robust rank order of folding cooperativity, native‐centric intraprotein interactions were modeled by (i) a common Gō‐like potential, and (ii) native‐centric potentials with desolvation barriers or (iii) many‐body terms. Homologous proteins can possess substantially different folding cooperativity. Consistent with experiment, our calculations indicated that E3BD fragments fold more cooperatively than BBL fragments of approximately the same chain length. For a given fragment, native contacts deduced from Protein Data Bank structures can vary significantly depending on the number of residues that the structure encompasses in addition to those of the fragment itself, resulting in variation in model folding cooperativity predicted using different native contact sets for the same fragment. This observation underscores that folding cooperativity of these fragments can be extremely sensitive to change in chain length. Thus, a ∼40‐residue protein fragment's folding cooperativity, or lack thereof, does not necessarily imply essentially identical behaviors for super‐ or sub‐fragments with only several residues more, or less, than the given fragment. Ramifications for experimental investigations of downhill folding are discussed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
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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 | 0.000 | 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 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".