Literature DB >> 21559962

Density-functional study on the equilibria in the ThDP activation.

Eduardo J Delgado1, Joel B Alderete, Gonzalo A Jaña.   

Abstract

The equilibria among the various ionization and tautomeric states involved in the activation of ThDP is addressed using high level density functional theory calculations, X3LYP/6-311++G(d,p)//X3LYP(PB)/6-31++G(d,p). This study provides the first theoretically derived thermodynamic data for the internal equilibria in the activation of ThDP. The role of the medium polarity on the geometry and thermodynamics of the diverse equilibria of ThDP is addressed. The media chosen are cyclohexane and water, as paradigms of apolar and polar media. The results suggest that all ionization and tautomeric states are accessible during the catalytic cycle, even in the absence of substrate, being APH(+) the form required to interconvert the AP and IP tautomers; and the generation of the ylide proceeds via the formation of the IP form. Additionally, the calculated ΔG° values allow to calculate all the equilibrium constants, including the pK(C2) for the thiazolium C2 atom whose ionization is believed to initiate the catalytic cycle.

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Year:  2011        PMID: 21559962     DOI: 10.1007/s00894-011-1076-6

Source DB:  PubMed          Journal:  J Mol Model        ISSN: 0948-5023            Impact factor:   1.810


  8 in total

1.  Kinetic control of thiamin diphosphate activation in enzymes studied by proton-nitrogen correlated NMR spectroscopy.

Authors:  Kai Tittmann; Holger Neef; Ralph Golbik; Gerhard Hübner; Dorothee Kern
Journal:  Biochemistry       Date:  2005-06-21       Impact factor: 3.162

2.  The 1',4'-iminopyrimidine tautomer of thiamin diphosphate is poised for catalysis in asymmetric active centers on enzymes.

Authors:  Natalia Nemeria; Sumit Chakraborty; Ahmet Baykal; Lioubov G Korotchkina; Mulchand S Patel; Frank Jordan
Journal:  Proc Natl Acad Sci U S A       Date:  2006-12-20       Impact factor: 11.205

3.  Very fast empirical prediction and rationalization of protein pKa values.

Authors:  Hui Li; Andrew D Robertson; Jan H Jensen
Journal:  Proteins       Date:  2005-12-01

Review 4.  Thiamin diphosphate catalysis: enzymic and nonenzymic covalent intermediates.

Authors:  Ronald Kluger; Kai Tittmann
Journal:  Chem Rev       Date:  2008-05-21       Impact factor: 60.622

5.  How thiamine diphosphate is activated in enzymes.

Authors:  D Kern; G Kern; H Neef; K Tittmann; M Killenberg-Jabs; C Wikner; G Schneider; G Hübner
Journal:  Science       Date:  1997-01-03       Impact factor: 47.728

Review 6.  Experimental observation of thiamin diphosphate-bound intermediates on enzymes and mechanistic information derived from these observations.

Authors:  Frank Jordan; Natalia S Nemeria
Journal:  Bioorg Chem       Date:  2005-04-01       Impact factor: 5.275

7.  Elucidation of the chemistry of enzyme-bound thiamin diphosphate prior to substrate binding: defining internal equilibria among tautomeric and ionization states.

Authors:  Natalia Nemeria; Lioubov Korotchkina; Michael J McLeish; George L Kenyon; Mulchand S Patel; Frank Jordan
Journal:  Biochemistry       Date:  2007-08-23       Impact factor: 3.162

8.  A DFT study of solvation effects on the tautomeric equilibrium and catalytic ylide generation of thiamin models.

Authors:  Mette Alstrup Lie; Birgit Schiøtt
Journal:  J Comput Chem       Date:  2008-05       Impact factor: 3.376

  8 in total
  1 in total

1.  Computer-assisted study on the reaction between pyruvate and ylide in the pathway leading to lactyl-ThDP.

Authors:  Omar Alvarado; Gonzalo Jaña; Eduardo J Delgado
Journal:  J Comput Aided Mol Des       Date:  2012-07-11       Impact factor: 3.686

  1 in total

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