Investigation of The Dimer Interface and Active Site in Pyridoxal 5' Phosphate Enzymes Cystathionine B- Lyase and Cystathionine y- Lyase
Bibliographic record
Abstract
Cystathionine β-lyase (CBL) catalyses the PLP-dependent β-elimination of cystathionine, yielding homocysteine, pyruvate and ammonia, while the γ-elimination of this pseudosymmetric substrate by cystathionine γ-lyase (CGL) produces cysteine, α-ketobutyrate and ammonia.The distinct β versus γ-elimination reaction specificity of the structurally conserved eCBL and yCGL enzymes provides an ideal system to probe the subtle factors that regulate activity and specificity.Studies exploring these factors will enable the continued development of our understanding of the mechanisms whereby PLP-dependent enzymes regulate substrate and reaction specificity, building a framework that will facilitate future studies aiming to engineer these enzymes to harness the power of this catalytically versatile cofactor for use in various industrial processes.Comparison of the structures of Escherichia coli CBL (eCBL) and Saccharomyces cerevisiae CGL (yCGL) identified differences at the dimer interface and within the active site.The effect of substitutions at these positions on enzyme properties is explored in chapters 2 and 3 of this thesis, respectively, as a precursor to studies probing their potential role as determinants of reaction specificity.Charge-reversal substitutions of the four residues involved in the K5-D382 and K17-D37 salt-bridges, which span the dimer interface of eCBL, were constructed and their effect on enzyme stability and activity determined.Single and double charge-reversal substitutions similarly reduce the catalytic efficiency by 11-21-fold, despite the greater effect of the former on the stability of the enzyme.This demonstrates that while even small conformational changes in this region are conveyed to the active site, the distinct dimer interfaces of eCBL and yCGL are unlikely to be a primary determinant of specificity.The potential of active-site residues S50 and S200 of yCGL to influence the positioning of the εamino group of the catalytic base was also explored, via characterization of the S50A, S50G and My journey as a Masters student at Carleton University has been an enlightening, educative and inspirational one, I thank God for allowing me this privilege.As behind every great student there is an even better teacher, special thanks go to my supervisor Dr. Susan M. Aitken, who was my guide through graduate school and a great guide at that.I appreciate her giving me the opportunity to
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.001 |
| 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".