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Literature DB >> 11456876

Triosephosphate isomerase: a theoretical comparison of alternative pathways.

Abstract

Three mechanisms proposed for the triosephosphate isomerase (TIM) catalyzed reactions were studied with the QM/MM approach using B3LYP/6-31+G(d,p) as the QM method. The two pathways that involve an enediol species were found to give similar values for the barriers and the calculated rates are in satisfactory agreement with experiment. By contrast, the mechanism that involves intramolecular proton transfer in the enediolate was found to be energetically unfavorable due to electrostatic interactions with His 95, a conserved residue in TIM from different organisms. A perturbation analysis was used to determine the residues that make the major contribution to catalysis.

Entities: Chemical Gene

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Year: 2001 PMID： 11456876 DOI： 10.1021/ja002886c

Source DB: PubMed Journal: J Am Chem Soc ISSN： 0002-7863 Impact factor: 15.419

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Cited

26 in total

1. The missing link between thermodynamics and structure in F1-ATPase.

Authors: W Yang; Y Q Gao; Q Cui; J Ma; M Karplus
Journal: Proc Natl Acad Sci U S A Date: 2003-01-27 Impact factor: 11.205

2. Ab initio quantum chemistry: methodology and applications.

Authors: Richard A Friesner
Journal: Proc Natl Acad Sci U S A Date: 2005-05-03 Impact factor: 11.205

3. Local encoding of computationally designed enzyme activity.

Authors: Malin Allert; Mary A Dwyer; Homme W Hellinga
Journal: J Mol Biol Date: 2006-12-05 Impact factor: 5.469

Review 4. CHARMM: the biomolecular simulation program.

Authors: B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal: J Comput Chem Date: 2009-07-30 Impact factor: 3.376

5. Identification of seven novel virulence genes from Xanthomonas citri subsp. citri by Tn5-based random mutagenesis.

Authors: Xue Song; Jing Guo; Wen-xiu Ma; Zhi-yuan Ji; Li-fang Zou; Gong-you Chen; Hua-song Zou
Journal: J Microbiol Date: 2015-05-03 Impact factor: 3.422

Review 6. Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods.

Authors: Hao Hu; Weitao Yang
Journal: Annu Rev Phys Chem Date: 2008 Impact factor: 12.703

Triosephosphate isomerase: a theoretical comparison of alternative pathways.

1. The missing link between thermodynamics and structure in F1-ATPase.

2. Ab initio quantum chemistry: methodology and applications.

3. Local encoding of computationally designed enzyme activity.

Review 4. CHARMM: the biomolecular simulation program.

5. Identification of seven novel virulence genes from Xanthomonas citri subsp. citri by Tn5-based random mutagenesis.

Review 6. Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods.

7. An analysis of reaction pathways for proton tunnelling in methylamine dehydrogenase.

8. Role of Lys-12 in catalysis by triosephosphate isomerase: a two-part substrate approach.

9. Correct and incorrect nucleotide incorporation pathways in DNA polymerase beta.

10. QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase.