ABSTRACT
We studied the inhibition of mitochondrial malate dehydrogenase (mMDH) by the nucleotides cAMP, AMP, ADP, ATP. The experimental kinetic studies showed that the nucleotides were competitive inhibitors and that cAMP was probably the most potent inhibitor. To explain these observations, we used molecular modeling to determine the location, orientation, and relative binding energy of the nucleotides to mMDH. The order of the calculated binding energies, from lowest (most favorable) to highest, was cAMP, AMP, ADP, and ATP, which corresponded somewhat to the order of the experimentally determined inhibition constants.
Subject(s)
Enzyme Inhibitors/chemistry , Enzyme Inhibitors/metabolism , Malate Dehydrogenase/chemistry , Malate Dehydrogenase/metabolism , Nucleosides/chemistry , Nucleosides/metabolism , Nucleotides/chemistry , Nucleotides/metabolism , Adenosine Monophosphate/chemistry , Adenosine Monophosphate/metabolism , Binding Sites , Cyclic AMP/chemistry , Cyclic AMP/metabolism , Enzyme Inhibitors/pharmacology , Kinetics , Malate Dehydrogenase/antagonists & inhibitors , Models, Molecular , NAD/chemistry , NAD/metabolism , Nucleosides/pharmacology , Nucleotides/pharmacology , Protein ConformationABSTRACT
The purpose of this study was to carry out a thorough search of the conformational space of various adenine-containing nucleotides, applying a previously published searching procedure, known as the representative method. This method, which reduces the number of starting conformations required to explore all the important regions of conformational space, appears to be successful in finding all (or nearly all) the putative low-energy conformations of each molecule.
