Theoretical Studies on the Origin of β-sheet Twisting
Bibliographic record
Abstract
Right-handed twisting is a fundamental structural feature of β-pleated sheets in globular proteins which is critical for their geometry and function. The origin of this twisting is poorly understood and has represented a challenge for theoretical chemistry for almost 30 years. Density functional theory using the B3LYP exchange-correlation functional and the split-valence 6-31G** basis set has been utilized to investigate the structure and conformational transitions of single and double-stranded antiparallel β-sheet models to determine the driving force for the right-handed twisting. Right-handed twisting is found to be an intrinsic property of a peptide main chain because of the difference in rotational potentials around N(sp 2 )−C α (sp 3 ) and C(sp 2 )−C α (sp 3 ) bonds. The difference arises from a tendency of the single C α (sp 3 )−C(sp 2 ) bonds to eclipse the lone pair of atoms N(sp 2 ), which results in decreasing absolute values of dihedral angles φ but not ψ. This tendency is suppressed by hydrogen bonding between adjacent CO and NH groups within single β-strands, and released only when these bonds are disrupted by the interstrand CO···HN hydrogen bonding. The results obtained constitute the following paradigm of the origin of β-sheet twist: although right-handed twisting of β-sheets in globular proteins is an inherent property of the peptide backbone within single β-strands, it is unleashed by the interstrand hydrogen bonding in multistranded β-sheets. The observed pleating, right-handed twisting, skewed mutual orientation of β-strands, and intrinsic conformational variability of double-stranded antiparallel β-sheet motifs in globular proteins are explained from the first principles.
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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) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| 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".