Predicting Enzyme-Substrate Specificity with QM/MM Methods: A Case Study of the Stereospecificity of D-Glucarate Dehydratase

• The stereospecificity of D-glucarate dehydratase (GlucD) is explored by QM/MM calculations. Both the substrate binding and the chemical steps of GlucD contribute to substrate specificity. Although the identification of transition states remains computationally intensive, we suggest that QM/MM computations on ground states or intermediates can capture aspects of specificity that cannot be obtained using docking or molecular mechanics methods.

Subject headings

MEDICIN OCH HÄLSOVETENSKAP  -- Medicinska och farmaceutiska grundvetenskaper -- Cell- och molekylärbiologi (hsv//swe)

MEDICAL AND HEALTH SCIENCES  -- Basic Medicine -- Cell and Molecular Biology (hsv//eng)

Keyword

MANDELATE RACEMASE ENZYME

D-GALACTONATE DEHYDRATASE

GENERAL ACID

CATALYST

ENOLASE SUPERFAMILY

ESCHERICHIA-COLI

ACTIVE-SITE

COMPUTER-SIMULATIONS

PSEUDOMONAS-PUTIDA

MOLECULAR-DYNAMICS

UNKNOWN

FUNCTION

Publication and Content Type

ref (subject category)

art (subject category)