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Journal of Molecular Modeling

, Volume 13, Issue 6–7, pp 839–849 | Cite as

Non-empirical study of the phosphorylation reaction catalyzed by 4-methyl-5-β-hydroxyethylthiazole kinase: relevance of the theory of intermolecular interactions

  • Edyta Dyguda-Kazimierowicz
  • W. Andrzej Sokalski
  • Jerzy Leszczyński
Original Paper

Abstract

The subject of this study was an analysis of the role of active site residues in the phosphoryl transfer reaction catalyzed by 4-methyl-5-β-hydroxyethylthiazole kinase (ThiK). The ThiK-catalyzed reaction is of special interest due to the lack of a highly conserved aspartate residue serving as a catalytic base. ONIOM(B3LYP:PM3) models of stationary points along the reaction pathway consisted of reactants, two magnesium ions and several highly conserved ThiK active site residues. The results indicate that an SN2-like mechanism of ThiK, with γ-phosphate acting as an alcohol-activating base is reasonable. Geometries of substrates, transition state and products were utilized in the non-empirical analysis of the physical nature of catalytic interactions taking place in the ThiK active site. The role of particular residues was investigated in terms of their ability to preferentially stabilize the transition state relative to substrates (differential transition state stabilization, DTSS) or products (differential product stabilization, DPS). It seems that Mg2, Glu126 and Cys198 play a major catalytic role, whereas Mg1 and the same Cys198 are responsible for product release. It is remarkable that no dominant role of an electrostatic term in the interactions involved in catalytic activity is observed for product release. Determination of catalytic fields expressing differential electrostatic potential of the transition state with respect to substrates revealed the optimal electrostatic features of an ideal catalyst for the studied reaction. The predicted catalytic environment is in agreement with experimental data showing increased catalytic activity of ThiK upon mutation of Cys198 to aspartate.

Figure

Catalytic fields for ThiK-catalyzed reaction juxtaposed with the positions of active site residues of a model system. Magnesium ions are considered part of the transition state/reactants. The surface of constant electronic density is colored according to differential electrostatic potential of transition state with respect to reactants. The sign of the differential potential reflects the electrostatic properties of a complementary molecular environment. Red (green) color denotes regions where a negative (positive) charge would be optimal for catalytic activity

Keywords

Catalytic fields Enzymatic catalysis Interaction energy Phosphoryl transfer Ribokinase-like kinases 

Notes

Acknowledgments

This work is funded by the British–Polish Young Scientists Programme. The authors are also grateful for financial support from Wrocław University of Technology and Jackson State University subcontract #W912HZ-04-2-0002. Dr. Borys Szefczyk is acknowledged for the software for visualization of catalytic fields. Calculations were performed in Wrocław (WCSS) and Poznań (PCSS) Centers for Supercomputing and Networking as well as the Interdisciplinary Centre for Mathematical and Computational Modeling (ICM) in Warsaw.

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Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Edyta Dyguda-Kazimierowicz
    • 1
  • W. Andrzej Sokalski
    • 1
  • Jerzy Leszczyński
    • 2
  1. 1.Department of ChemistryWrocław University of TechnologyWrocławPoland
  2. 2.Jackson State UniversityJacksonUSA

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