Computational Modeling of Biological Systems: The LDH Story

  • Silvia Ferrer
  • Sergio Martí
  • Vicent Moliner
  • Iñaki Tuñón
Part of the Challenges and Advances in Computational Chemistry and Physics book series (COCH, volume 12)


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.


Lactate dehydrogenase LDH Enzyme catalysis Molecular mechanisms Molecular modeling of biomolecules Hybrid quantum mechanic/molecular mechanics Hybrid molecular dynamics Potential energy surfaces Transition state characterizations Potential of mean force Statistical simulations 



We thank the Spanish Ministry Ministerio de Ciencia e Inovación for project CTQ2009-14541, Universitat Jaume I - BANCAIXA Foundation for projects P1·1B2005-13, P1·1B2005-15 and P1·1B2005-27, and Generalitat Valenciana for Prometeo/2009/053 project. We are also grateful to Prof. Ian H. Williams and Prof. J. Andrés for fruitful discussions. The authors also acknowledge the Servei d´Informatica, Universitat Jaume I for generous allotment of computer time. V. Moliner would like to thank the Spanish Ministry Ministerio de Ciencia e Innovación for traveling financial support, project PR2009-0539.


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Copyright information

© Springer Netherlands 2010

Authors and Affiliations

  • Silvia Ferrer
    • 1
  • Sergio Martí
    • 1
  • Vicent Moliner
    • 1
    • 2
    • 3
  • Iñaki Tuñón
    • 3
  1. 1.Departament de Química Física i AnalíticaUniversitat Jaume ICastellóSpain
  2. 2.Institute of Applied Radiation ChemistryTechnical University of LodzLodzPoland
  3. 3.Departament de Química FísicaUniversitat de ValènciaBurjasotSpain

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