title: Nitric oxide reactivity with globins as investigated through computer simulation.
abstract: This chapter reviews the application of classical and quantum-mechanical atomistic simulation tools used in the investigation of several relevant issues in nitric oxide reactivity with globins and presents different simulation strategies based on classical force fields: standard molecular dynamics, essential dynamics, umbrella sampling, multiple steering molecular dynamics, and a novel technique for exploring the protein energy landscape. It also presents hybrid quantum-classical schemes as a tool to obtain relevant information regarding binding energies and chemical reactivity of globins. As illustrative examples, investigations of the structural flexibility, ligand migration profiles, oxygen affinity, and reactivity toward nitric oxide of truncated hemoglobin N of Mycobacterium tuberculosis are presented.
authors.affiliation: Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina.
authors.forename: Marcelo A
authors.initials: MA
authors.lastname: Marti
authors.forename: Luciana
authors.initials: L
authors.lastname: Capece
authors.forename: Axel
authors.initials: A
authors.lastname: Bidon-Chanal
authors.forename: Alejandro
authors.initials: A
authors.lastname: Crespo
authors.forename: Victor
authors.initials: V
authors.lastname: Guallar
authors.forename: F Javier
authors.initials: FJ
authors.lastname: Luque
authors.forename: Dario A
authors.initials: DA
authors.lastname: Estrin
mesh_terms: D001696:Biomechanical Phenomena; D003198:Computer Simulation; D004734:Energy Metabolism; D005914:Globins / Q000737:chemistry* / Q000378:metabolism*; D006418:Heme / Q000737:chemistry; D008658:Inactivation, Metabolic; D007700:Kinetics; D008958:Models, Molecular; D008962:Models, Theoretical; D009169:Mycobacterium tuberculosis; D009211:Myoglobin / Q000737:chemistry / Q000378:metabolism; D009569:Nitric Oxide / Q000737:chemistry* / Q000378:metabolism* / Q000493:pharmacokinetics; D010100:Oxygen / Q000378:metabolism / Q000494:pharmacology; D011485:Protein Binding; D017510:Protein Folding; D011789:Quantum Theory; D015398:Signal Transduction; D013379:Substrate Specificity; D054793:Truncated Hemoglobins / Q000737:chemistry
chemical_list: D009211:Myoglobin; D054793:Truncated Hemoglobins; D009569:Nitric Oxide; D006418:Heme; D005914:Globins; D010100:Oxygen