Dioxygen affinity in heme proteins investigated by computer simulation

M.A. MARTI; L. CAPECE; L. BOECHI; D. E. BIKIEL; D. A. ESTRIN

Montevideo

Conferencia; 6th Internacional Conference on Biological Physics; 2007

Society for Biological Physics

   We present an investigation of the molecular basis of the modulation of oxygen affinity in heme proteins using computer simulation.QM-MM calculations are applied to explore distal and proximal effects on O2 binding to the heme, while classical molecular dynamicssimulations are employed to investigate ligand migration across the polypeptide to the active site. Trends in binding energies and in thekinetic constants are illustrated through a number of selected examples highlighting the virtues and the limitations of the applied meth-odologies. These examples cover a wide range of O2-affinities, and include: the truncated-N and truncated-O hemoglobins from Myco-bacterium tuberculosis, the mammalian muscular O2 storage protein: myoglobin, the hemoglobin from the parasitic nematode Ascarislumbricoides, the oxygen transporter in the root of leguminous plants: leghemoglobin, the Cerebratulus lacteus nerve tissue hemoglobin,and the Alcaligenes xyloxidans cytochrome c 0 .