Computational methods to study heme proteins

D. A. ESTRIN; M. A. MARTI; CAPECE, L.; BOECHI, L.

Estambul

Conferencia; International Conference on Porphyrins and Phthalocyanines (ICPP); 2014

Society of Porphyrins and Phtalocyanines

p { margin-bottom: 0.25cm; direction: ltr; color: rgb(0, 0, 0); line-height: 120%; text-align: justify; widows: 2; orphans: 2; }p.western { font-family: "Arial",sans-serif; font-size: 12pt; }p.cjk { font-family: "Times New Roman",serif; font-size: 12pt; }p.ctl { font-family: "Arial",sans-serif; font-size: 10pt; }a:visited { color: rgb(128, 0, 128); }a.western:visited { }a.cjk:visited { }a.ctl:visited { } In this work we will present the application of classical and quantum-mechanical atomistic simulation tools to the investigation of several relevant issues in heme protein chemistry: (i) conformational analysis1 and ligand migration2 studied using classical molecular dynamics simulations, in the family of truncated 2/2 hemoglobins, and myoglobin. (ii) interaction of heme proteins with small ligands studied through hybrid quantum-mechanics molecular mechanics (QM-MM) methods, illustrating trends in binding energies3 through a number of selected examples, including truncated hemoglobins, myoglobin, and protoglobin (iii) and finally chemical reactivity and catalysis tackled by a combination of quantum and classical tools, taking as illustrative example the oxygen attack to the substrate reaction mechanism in tryptophan and indoleamine dioxygenases.4 p { margin-bottom: 0.25cm; direction: ltr; color: rgb(0, 0, 0); line-height: 120%; text-align: justify; widows: 2; orphans: 2; }p.western { font-family: "Arial",sans-serif; font-size: 12pt; }p.cjk { font-family: "Times New Roman",serif; font-size: 12pt; }p.ctl { font-family: "Arial",sans-serif; font-size: 10pt; }a:visited { color: rgb(128, 0, 128); }a.western:visited { }a.cjk:visited { }a.ctl:visited { } References E. Droghetti, F. Paolo Nicoletti, A. Bonamore, L. Boechi, P.Arroyo Mañez, D. A. Estrin, A. Boffi, G. Smulevich , and A. Feis, Biochemistry, 49, 10394-10402 (2010). P. Arroyo-Mañez, D.E. Bikiel, L. Boechi, L. Capece, S. Di Lella, D.A. Estrin, M.A. Marti, A.D. Nadra, A.A. Petruk, Biochimica Biophysica Acta, Proteins and Proteomics, 1814, 1054-1064 (2011) ; L. Boechi, M. Arrar, M.A. Marti, J.S. Olson, A.E. Roitberg, D.A. Estrin, J. Biol. Chem 288, 6754-6762 (2013). D.E. Bikiel, L. Boechi, A. Crespo, P.M. de Biase, S. Di Lella, M.C. González Lebrero, M.A. Marti, A.D. Nadra, L.L. Perissinotti, D.A. Scherlis, D.A. Estrin, Physical Chemistry Chemical Physics (2006), 8, 5611-5628; Bikiel, D.E., Forti, F.; Boechi,L., Nardini, M., Luque, F.J., Marti, M.A., Estrin, D.A., J. Phys. Chem. B, 114, 8536-8543 (2010). Capece, L., Arrar, M., Roitberg, A.E., Yeh, SR, Marti, M.A., Estrin, D.A., Proteins, Structure, Function and Bioinformatics, 78, 2961-2972 (2010) ; A. Lewis-Ballester, D. Batabyal, T. Egawa, C. Lu, Y. Lin, M.A. Marti, L. Capece, D. A. Estrin, S. Yeh, Proc. Natl. Acad. Sci. USA, 106, 17376 (2009).