The DOI matches its Crossref record; 30 of the 30 references it cites were found in a registry or an index.
The Incorporation of Quantum Effects in Enzyme Kinetics Modeling
Abstract
We present an overview of new procedures for including quantum mechanical effects in enzyme kinetics. Quantum effects are included in three ways: (1) The electronic structure of the atoms in the catalytic center is treated quantum mechanically in order to calculate a realistic potential energy surface for the bond rearrangement process. (2) The discrete nature of quantum mechanical vibrational energies is incorporated in the treatment of nuclear motion for computing the potential of mean force. (3) Multidimensional tunneling contributions are included. These procedures are illustrated by applications to proton abstractions catalyzed by enolase and methylamine dehydrogenase and hydride-transfer reactions by alcohol dehydrogenase and xylose isomerase.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Comparison of simple potential functions for simulating liquid water
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983) · The Journal of Chemical Physics · doi:10.1063/1.445869 · Cited by 41,298
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. (1998) · The Journal of Physical Chemistry B · doi:10.1021/jp973084f · Cited by 14,311
Self-citationWarshel, A., & Levitt, M. (1976) · Journal of Molecular Biology · doi:10.1016/0022-2836(76)90311-9 · Cited by 4,479
A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
Field, M. J., Bash, P. A., & Karplus, M. (1990) · Journal of Computational Chemistry · doi:10.1002/jcc.540110605 · Cited by 2,466
Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics
Cramer, C. J., & Truhlar, D. G. (1999) · Chemical Reviews · doi:10.1021/cr960149m · Cited by 2,308
Self-citationVariational transition-state theory
Truhlar, D. G., & Garrett, B. C. (1980) · Accounts of Chemical Research · doi:10.1021/ar50156a002 · Cited by 1,328
Self-citationThe Theory of Chemical Reaction Dynamics
(1986) · Springer eBooks · doi:10.1007/978-94-009-4618-7 · Cited by 1,167
Singh, U. C., & Kollman, P. A. (1986) · Journal of Computational Chemistry · doi:10.1002/jcc.540070604 · Cited by 1,112
Criterion of minimum state density in the transition state theory of bimolecular reactions
Garrett, B. C., & Truhlar, D. G. (1979) · The Journal of Chemical Physics · doi:10.1063/1.437698 · Cited by 551
Self-citationEnergetics and Dynamics of Enzymatic Reactions
Villà, J., & Warshel, A. (2001) · The Journal of Physical Chemistry B · doi:10.1021/jp011048h · Cited by 357
Self-citationActive site dynamics in protein molecules: A stochastic boundary molecular‐dynamics approach
Brooks, C. L., Brünger, A., & Karplus, M. (1985) · Biopolymers · doi:10.1002/bip.360240509 · Cited by 350
Mercury Radar Imaging: Evidence for Polar Ice
Slade, M. A., Butler, B. J., & Muhleman, D. O. (1992) · Science · doi:10.1126/science.258.5082.635 · Cited by 345
Théry, V., Rinaldi, D., Rivail, J., Maigret, B., & Ferenczy, G. G. (1994) · Journal of Computational Chemistry · doi:10.1002/jcc.540150303 · Cited by 322
Molecular dynamics of a model S N 2 reaction in water
Bergsma, J. P., Gertner, B. J., Wilson, K. R., & Hynes, J. T. (1987) · The Journal of Chemical Physics · doi:10.1063/1.452224 · Cited by 318
Aspects of Protein Reaction Dynamics: Deviations from Simple Behavior
Karplus, M. (2000) · The Journal of Physical Chemistry B · doi:10.1021/jp993555t · Cited by 306
From Force Fields to Dynamics: Classical and Quantal Paths
Truhlar, D. G., & Gordon, M. S. (1990) · Science · doi:10.1126/science.249.4968.491 · Cited by 304
Self-citationIncorporation of quantum effects in generalized-transition-state theory
Truhlar, D. G., Isaacson, A. D., Skodje, R. T., & Garrett, B. C. (1982) · The Journal of Physical Chemistry · doi:10.1021/j100209a021 · Cited by 258
Self-citationEnzymatic H-Transfer Requires Vibration-Driven Extreme Tunneling
Basran, J., Sutcliffe, M. J., & Scrutton, N. S. (1999) · Biochemistry · doi:10.1021/bi982719d · Cited by 246
Garrett, B. C., & Truhlar, D. G. (1983) · The Journal of Chemical Physics · doi:10.1063/1.445586 · Cited by 223
Self-citationAlhambra, C., Corchado, J., Sánchez, M. L., Garcia-Viloca, M., Gao, J., & Truhlar, D. G. (2001) · The Journal of Physical Chemistry B · doi:10.1021/jp0120312 · Cited by 189
Self-citationQuantum Dynamics of Hydride Transfer in Enzyme Catalysis
Alhambra, C., Corchado, J. C., Sánchez, M. L., Gao, J., & Truhlar, D. G. (2000) · Journal of the American Chemical Society · doi:10.1021/ja001476l · Cited by 181
Self-citationRossi, I., & Truhlar, D. G. (1995) · Chemical Physics Letters · doi:10.1016/0009-2614(94)01450-a · Cited by 178
Self-citationBahnson, B. J., Park, D.-H., Kim, K., Plapp, B. V., & Klinman, J. P. (1993) · Biochemistry · doi:10.1021/bi00072a003 · Cited by 138
Quantum Mechanical Dynamical Effects in an Enzyme-Catalyzed Proton Transfer Reaction
Alhambra, C., Gao, J., Corchado, J. C., Villà-Freixa, J., & Truhlar, D. G. (1999) · Journal of the American Chemical Society · doi:10.1021/ja9831655 · Cited by 135
Self-citationMolecular dynamics of an enzyme reaction: proton transfer in TIM
Neria, E., & Kuplus, M. (1997) · Chemical Physics Letters · doi:10.1016/s0009-2614(97)00068-7 · Cited by 101
Inclusion of quantum-mechanical vibrational energy in reactive potentials of mean force
Garcia‐Viloca, M., Alhambra, C., Truhlar, D. G., & Gao, J. (2001) · The Journal of Chemical Physics · doi:10.1063/1.1371497 · Cited by 87
Self-citationPoyner, R. R., Laughlin, L. T., Sowa, G., & Reed, G. H. (1996) · Biochemistry · doi:10.1021/bi952186y · Cited by 64
The Role of Collective Solvent Coordinates and Nonequilibrium Solvation in Charge-Transfer Reactions
Schenter, G. K., Garrett, B. C., & Truhlar, D. G. (2001) · The Journal of Physical Chemistry B · doi:10.1021/jp011981k · Cited by 62
Self-citationQuantum mechanical tunneling in methylamine dehydrogenase
Alhambra, C., Sanchez, M. L., Corchado, J. C., Gao, J., & Truhlar, D. G. (2001) · Chemical Physics Letters · doi:10.1016/s0009-2614(01)00921-6 · Cited by 59
Self-citationAllen, K. N., Lavie, A., Petsko, G. A., & Ringe, D. (1995) · Biochemistry · doi:10.1021/bi00011a032 · Cited by 58
Cited by
Proton-coupled electron transfer
Huynh, M. H. V., & Meyer, T. J. (2007) · Chemical Reviews · doi:10.1021/cr0500030 · Cited by 1,659
P450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by QM/MM Calculations
Shaik, S., Cohen, S., Wang, Y., Chen, H., Kumar, D., & Thiel, W. (2010) · Chemical Reviews · doi:10.1021/cr900121s · Cited by 1,083
Levine, R. D. (2005) · Cambridge University Press eBooks · doi:10.1017/cbo9780511614125 · Cited by 709
Mechanisms and Free Energies of Enzymatic Reactions
Gao, J., Ma, S., Major, D. T., Nam, K., Pu, J., & Truhlar, D. G. (2006) · Chemical Reviews · doi:10.1021/cr050293k · Cited by 401
Self-citationLiu, Y., Yan, Y., Xing, T., & Shi, Q. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.1c02851 · Cited by 23
Metadata
- Authors
- Truhlar, D. G., Gao, J., Alhambra, C., Garcia-Viloca, M., Corchado, J., Sánchez, M. L., & Villà, J.
- Venue
- Accounts of Chemical Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2002-03-03
- Volume
- 35
- Issue
- 6
- Pages
- 341-349
- ISSN
- 0001-4842 (ISSN-L)
- 1520-4898
- OpenAlex
- W1963630470
- Cited by
- 258
- References
- 30
- FWCI
- 17.11
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
