title: Small ligand-globin interactions: reviewing lessons derived from computer simulation.
abstract: In this work we review the application of classical and quantum-mechanical atomistic computer simulation tools to the investigation of small ligand interaction with globins. In the first part, studies of ligand migration, with its connection to kinetic association rate constants (kon), are presented. In the second part, we review studies for a variety of ligands such as O2, NO, CO, HS(-), F(-), and NO2(-) showing how the heme structure, proximal effects, and the interactions with the distal amino acids can modulate protein ligand binding. The review presents mainly results derived from our previous works on the subject, in the context of other theoretical and experimental studies performed by others. The variety and extent of the presented data yield a clear example of how computer simulation tools have, in the last decade, contributed to our deeper understanding of small ligand interactions with globins. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
authors.affiliation: Departamento de Química Inorgánica, Analítica, y Química Física, Universidad de Buenos Aires, Buenos Aires, Argentina.
authors.forename: Luciana
authors.initials: L
authors.lastname: Capece
authors.forename: Leonardo
authors.initials: L
authors.lastname: Boechi
authors.forename: Laura L
authors.initials: LL
authors.lastname: Perissinotti
authors.forename: Pau
authors.initials: P
authors.lastname: Arroyo-Mañez
authors.forename: Damián E
authors.initials: DE
authors.lastname: Bikiel
authors.forename: Giulietta
authors.initials: G
authors.lastname: Smulevich
authors.forename: Marcelo A
authors.initials: MA
authors.lastname: Marti
authors.forename: Dario A
authors.initials: DA
authors.lastname: Estrin
mesh_terms: D000818:Animals; D003198:Computer Simulation; D005914:Globins / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D008024:Ligands; D011789:Quantum Theory
chemical_list: D008024:Ligands; D005914:Globins
keywords: Computer simulation; Globin; Heme protein; Molecular dynamics; QM/MM