Exploring chemical reactivity in biomolecules with hybrid QM-MM methods

D.A. ESTRIN

Salta

Conferencia; Workshop: Structural Biology in Latin America; 2010

Centro de Biología Estructural del Mercosur (CeBem)

<!-- @page { margin: 2cm } P { margin-bottom: 0.21cm } --> We present a hybrid Quantum Mechanics Molecular Mechanics (QM/MM) implementation developed to deal with large molecular complexes. It is particularly suited to study relatively large systems in which the environment effects are important, as in the case of an enzyme active site immersed in a protein matrix, or a solute in a condensed phase. In the QM/MM scheme, a region of the system receives a quantum mechanical description, while the environment is treated at the molecular mechanics level using the biomolecules Amber force field. The QM calculations are performed with the SIESTA code, a DFT scheme based on finite basis sets and pseudopotentials, which makes the overall implementation very efficient. We will present results obtained with this scheme for the following problems: NO generation from nitrite catalyzed by deoxy hemoglobin Catalytic mechanism of the enzymes indoleamine and tryptophan dioxygenases.