Bibliographic record
Abstract
Obianyo and Thompson assigned a rapid equilibrium random mechanism to PRMT6 in their recent article (1.Obianyo O. Thompson P.R. Kinetic mechanism of protein arginine methyltransferase 6 (PRMT6).J. Biol. Chem. 2012; 287: 6062-6071Abstract Full Text Full Text PDF PubMed Scopus (33) Google Scholar). We disagree with their conclusions and assessment of our work (2.Lakowski T.M. Frankel A. A kinetic study of human protein arginine N-methyltransferase 6 reveals a distributive mechanism.J. Biol. Chem. 2008; 283: 10015-10025Abstract Full Text Full Text PDF PubMed Scopus (69) Google Scholar). PRMT crystal structures solved in complex with substrates and/or substrate analogs contradict their kinetic mechanism and support our sequential ordered mechanism in which S-adenosyl-l-methionine (AdoMet) binds first and S-adenosyl-l-homocysteine (AdoHcy) dissociates last from the enzyme because AdoMet/AdoHcy-binding pockets become buried underneath two α-helical segments when occupied (3.Zhang X. Zhou L. Cheng X. Crystal structure of the conserved core of protein arginine methyltransferase PRMT3.EMBO J. 2000; 19: 3509-3519Crossref PubMed Scopus (268) Google Scholar, 4.Yue W.W. Hassler M. Roe S.M. Thompson-Vale V. Pearl L.H. Insights into histone code syntax from structural and biochemical studies of CARM1 methyltransferase.EMBO J. 2007; 26: 4402-4412Crossref PubMed Scopus (102) Google Scholar, 5.Sack J.S. Thieffine S. Bandiera T. Fasolini M. Duke G.J. Jayaraman L. Kish K.F. Klei H.E. Purandare A.V. Rosettani P. Troiani S. Xie D. Bertrand J.A. Structural basis for CARM1 inhibition by indole and pyrazole inhibitors.Biochem. J. 2011; 436: 331-339Crossref PubMed Scopus (78) Google Scholar). Obianyo and Thompson did not reconcile their kinetic mechanism with any structural or biophysical studies of PRMTs. In our previous work, we used a MS-based assay to measure AdoHcy or methylated peptides where appropriate to directly quantify these products (2.Lakowski T.M. Frankel A. A kinetic study of human protein arginine N-methyltransferase 6 reveals a distributive mechanism.J. Biol. Chem. 2008; 283: 10015-10025Abstract Full Text Full Text PDF PubMed Scopus (69) Google Scholar). Our product inhibition studies for the monomethylated substrate provided solid evidence to support a sequential ordered mechanism. In contrast to our method, Obianyo and Thompson employed a gel-based assay to indirectly measure radioactivity associated with peptide methylation, where phosphorimages or raw densitometry data are not available for scrutiny. Their double-reciprocal plots consistently show line patterns indicative of the type of product inhibition claimed that do not fit with most of the data points displayed. The unfortunate consequence of their interpretation is a proposed kinetic mechanism for PRMT6 unsupported by their own experimental results and what has been reported in the literature (2.Lakowski T.M. Frankel A. A kinetic study of human protein arginine N-methyltransferase 6 reveals a distributive mechanism.J. Biol. Chem. 2008; 283: 10015-10025Abstract Full Text Full Text PDF PubMed Scopus (69) Google Scholar, 3.Zhang X. Zhou L. Cheng X. Crystal structure of the conserved core of protein arginine methyltransferase PRMT3.EMBO J. 2000; 19: 3509-3519Crossref PubMed Scopus (268) Google Scholar, 4.Yue W.W. Hassler M. Roe S.M. Thompson-Vale V. Pearl L.H. Insights into histone code syntax from structural and biochemical studies of CARM1 methyltransferase.EMBO J. 2007; 26: 4402-4412Crossref PubMed Scopus (102) Google Scholar, 5.Sack J.S. Thieffine S. Bandiera T. Fasolini M. Duke G.J. Jayaraman L. Kish K.F. Klei H.E. Purandare A.V. Rosettani P. Troiani S. Xie D. Bertrand J.A. Structural basis for CARM1 inhibition by indole and pyrazole inhibitors.Biochem. J. 2011; 436: 331-339Crossref PubMed Scopus (78) Google Scholar).
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 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) | 0.001 | 0.001 |
| 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 | 0.002 | 0.001 |
| 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".