PMID: 9141134Apr 1, 1997

The reaction pathway of the isomerization of D-xylose catalyzed by the enzyme D-xylose isomerase: a theoretical study

Proteins
H HuY Shi

Abstract

Different pathways of the metal-induced isomerization of D-xylose to D-xylulose are investigated and compared in detail using energy minimization and molecular dynamics simulation. Two theoretical models are constructed for the reaction: in vacuum and in the enzyme D-xylose isomerase. The vacuum model is constructed based on the X-ray structure of the active site of D-xylose isomerase. It contains the atoms directly involved in the reaction and is studied using a semi-empirical molecular orbital method (PM3). The model in the enzyme includes the effects of the enzyme environment on the reaction using a combined quantum mechanical and molecular mechanical potential. For both models, the structures of the reactants, products, and intermediate complexes along the isomerization pathway are optimized. The effects of the position of the "catalytic Mg2+ ion" on the energies of the reactions are studied. The results indicate: 1) in vacuum, the isomerization reaction is favored when the catalytic metal cation is at site A, which is remote from the substrate; 2) in the enzyme, the catalytic metal cation, starting from site A, moves and stays at site B, which is close to the substrate; analysis of the charge redistribution of the active s...Continue Reading

References

Jul 1, 1993·Protein Engineering·Y J ZhengG K Farber

Citations

Nov 3, 2010·Acta Crystallographica. Section D, Biological Crystallography·Andrey KovalevskyPaul Langan
May 16, 2012·Protein Engineering, Design & Selection : PEDS·Darshan H PatelHyeun-Jong Bae
Apr 25, 2002·Annual Review of Physical Chemistry·Jiali Gao, Donald G Truhlar
Dec 24, 2002·Journal of Computational Chemistry·Mireia Garcia-VilocaJiali Gao
Mar 27, 2002·Journal of Computational Chemistry·Martin J Field
Apr 19, 2008·Applied Biochemistry and Biotechnology·Kripa RaoSasidhar Varanasi
Jan 1, 2013·Biomolecules·Gábor Náray-SzabóBalázs Krámos

Related Concepts

Glucose isomerase
Carbohydrate Epimerases
Catalysis
In Silico
Magnesium
Molecular Stereochemistry
Thermodynamics
Vacuum (Physical Force)
Xylose
Aldose-Ketose Isomerases

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