Differences and similarities in binding of pyruvate and L-lactate in the active site of M-4 and H-4 isoforms of human lactate dehydrogenase

We present QM/MM calculations that show differences in geometries of active sites of M-4 and H-4 isoforms of human LDH ligated with oxamate, pyruvate or L-lactate. As the consequence of these differences, binding isotope effects of the methyl hydrogen atoms of pyruvate and L-lactate may be used to experimentally distinguish these isoforms. Based on the FEP calculations we argue that L-lactate is a better candidate for the experimental studies. Our calculations of energies of interactions of ligands with the active site residues provide explanation for the observed experimentally sensitivity to inhibition of the M-4 isoenzyme isoform and pinpoint the differences to interactions of the ligand with the histidine residue. We conclude that pyruvate interacts much stronger in the active site of H-4 than M-4 isoform and that the latter interactions are weaker than with water molecules in the aqueous solution. (C) 2010 Elsevier Inc. All rights reserved.