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Combining Computational and Experimental approaches to investigate the catalytic mechanism of glyoxysomal Malate Dehydrogenase
Author(s) -
Guterres Hugo,
Hedrick Shan,
Bell Ellis
Publication year - 2011
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.25.1_supplement.536.2
Subject(s) - malate dehydrogenase , active site , histidine , hydride , arginine , in silico , chemistry , stereochemistry , biochemistry , enzyme , amino acid , organic chemistry , gene , hydrogen
Geometry optimization calculations have been used to find the minimum total energy and structure of the transition state during the conversion of malate to oxaloacetate catalysed by the enzyme glyoxysomal Malate Dehydrogenase. The proton abstraction is suggested to precede hydride transfer due to the activity of the arginine residues around the active site. To test this, two truncated models were built; model A included Histidine 220, malate and NAD+, and model B included these three moieties from model A with the addition of three arginine residues around the active site, R124, R130, and R196. Gaussian 03W was used to build the structure of the compounds, arrange their atoms, and run the geometry optimization calculations. For model A, the result shows a single imaginary frequency that vibrates to the hydride transfer. In contrast, for model B there is a single imaginary frequency that vibrates to the proton transfer. The result suggests that the arginine residues around the active site play important roles in facilitating the proton transfer. In silico mutation of these arginine residues is being correlated with the effects of in vitro site directed mutations to ascertain the precise roles of individual arginines in binding and catalysis. This work is supported by NSF Grant MCB 0448905 to EB