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Record W2093061534 · doi:10.1021/jp030575t

Temperature Dependence of Kinetic Isotope Effects for Enzymatic Carbon−Hydrogen Bond Cleavage

2004· article· en· W2093061534 on OpenAlexaff
Willem Siebrand, Zorka Smedarchina

Bibliographic record

VenueThe Journal of Physical Chemistry B · 2004
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicHemoglobin structure and function
Canadian institutionsSteacie Institute for Molecular Sciences
Fundersnot available
KeywordsChemistryKinetic isotope effectAnharmonicityComputational chemistryProtonElectron transfervan der Waals forcePhysical chemistryAtomic physicsDeuteriumMoleculeOrganic chemistryQuantum mechanics

Abstract

fetched live from OpenAlex

An analysis is reported of the anomalously weak temperature dependence of large kinetic isotope effects (KIEs) observed for enzymes that catalyze carbon−hydrogen bond cleavage. After a critical examination of the experimental data, rate expressions for proton tunneling are used to derive a universal relationship between KIEs and their temperature dependence for a model in which the tunneling coordinate, represented by two crossing Morse potentials or a quartic double-minimum potential, is assisted by a harmonic promoting mode. Since the reactions involve electron transfer to a redox system as well as proton transfer from a CH to an OH bond, both adiabatic and nonadiabatic mechanisms are considered. Model calculations are reported, which show that the derived relationship is valid under a wide range of conditions and depends on a minimum number of model parameters, namely almost exclusively on the proton transfer distance and the tunneling-mode anharmonicity. The results are used to derive proton transfer distances and promoting-mode force constants from the available data on temperature-dependent isotope effects for several enzymatic reactions effecting CH cleavage, including the reactions of linoleic acid catalyzed by soybean lipoxygenase-1 (SLO1), of primary amines catalyzed by methylamine and aromatic amine dehydrogenase (MADH and AADH), and of a dicopper complex that models the active site of monooxygenases and lacks a protein environment. These distances are found to be shorter and the force constants to be larger than those implied by van der Waals radii, but with anharmonicities suitably adjusted, they resemble those encountered in systems with hydrogen bonding. It is proposed that the strong redox system, which is always present in these enzymes, acts so as to withdraw electron density from the C···H···O transfer system. This will tend to shrink the tunneling barrier to a size that allows effective passage of H but not necessarily of D, a condition that may lead to a large KIE. It will also increase the enzyme−substrate force constant, thus reducing the temperature dependence of the KIE. For the reaction catalyzed by SLO1, a transfer distance of 0.9−1.0 Å is found. Similar results are obtained for three artificial mutants from which it is concluded that parts of the protein located outside the reaction site have little influence on the proton transfer. For the reactions catalyzed by MADH and AADH, the corresponding values range from 0.5 to 1.0 Å; however, the values much below 1.0 Å may be unrealistic since they are based on data that show anomalies suggesting that an incomplete kinetic model was used in their derivation. The analysis also yields a transfer distance of about 0.9 Å for the dicopper complex, a value similar to that of SLO1, although no protein is present. Since results for three different systems cluster about the same transfer distance of 0.9−1.0 Å, it is concluded that the large KIEs and their weak temperature dependence are due to a redox-induced C···H···O hydrogen bond.

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 imitation

Not 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.

metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.002
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Bench or experimental · Consensus signal: Bench or experimental
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.002
Threshold uncertainty score0.005

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0000.002
Meta-epidemiology (narrow)0.0000.000
Meta-epidemiology (broad)0.0000.000
Bibliometrics0.0000.000
Science and technology studies0.0000.000
Scholarly communication0.0000.000
Open science0.0000.000
Research integrity0.0000.001
Insufficient payload (model declined to judge)0.0020.000

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.

Opus teacher head0.003
GPT teacher head0.220
Teacher spread0.217 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.

The models applied no category: nothing in the taxonomy fit this work.
Study designBench or experimental
Domainnot available
GenreEmpirical

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".

Quick stats

Citations68
Published2004
Admission routes1
Has abstractyes

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