Glycine Amino Acid Transport inside the Nanopores of Lysozyme Protein Crystal
Bibliographic record
Abstract
Abstract Transport of glycine amino acid molecules inside the fully hydrated nanopores of a lysozyme protein crystal was investigated using molecular dynamics (MD) simulations. Mean square displacement (MSD) analysis of glycine molecules suggested that there are different regimes during glycine transport inside the lysozyme nanopores. Glycine molecules undergo a diffusive behavior along the main pore of the protein crystal with the self-diffusion coefficient of about 1.98 × 10−13 m2 s−1, four orders of magnitude less than that in pure water. This observation is in good agreement with available experimental data. Moreover, analyses based on density and radial distribution functions (RDFs) showed that most interactions of glycine molecules with lysozyme take place on LYS96, ARG14, and ASP87 residues. These interactions are the result of hydrogen-bonding interactions between both amino and carboxylic groups of glycine molecules and active sites of protein residues. These interactions change the effective pore size of the lysozyme crystal.
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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 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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".