13. Computational Modeling of Biological Systems: The LDH Story

Lactate dehydrogenases, LDH, catalyzed reaction has been used in this chapter as a conductor wire to present the evolution and difficulties on computing methods to model chemical reactions in enzymes, since the early calculations based at semiempirical level carried out in gas phase to the recent sophisticated simulations based on hybrid Quantum Mechanical/Molecular Mechanics Dynamics (QM/MM MD) schemes. LDH catalyzes the reversible transformation of pyruvate into lactate. The chemical step consists in a hydride and a proton transfer from the cofactor (NADH) and a protonated histidine (His195), respectively. This fact has generated a lot of controversy about the timing of both transfers in the active site, as well as the role of the different aminoacids of the active site and problems related with the flexibility of the protein. We herein show how an adequate method within a realistic model, taking into account the pKa of the titratable aminoacids, the flexibility of the protein, the size of the MM and QM region or the level of theory used to describe the QM region, must be used to obtain reliable conclusions. Finally, and keeping in mind the size of the system under study, it has been demonstrated the need of performing statistical simulations to sample the full conformational space of all states involved in the reaction, that allow getting free energies and averaged properties directly compared with experimental data.