title: Theoretical study of the truncated hemoglobin HbN: exploring the molecular basis of the NO detoxification mechanism.
abstract: Mycobacterium tuberculosis is the causative agent of human tuberculosis. The nitric oxide reaction with oxy-truncated hemoglobin N (trHbN) has been proposed to be responsible for the resistance mechanism by which this microorganism can evade the toxic effects of NO. In this work, we explore the molecular basis of the NO detoxification mechanism using a combination of classical and hybrid quantum-classical (QM-MM) simulation techniques. We have investigated the structural flexibility of the protein, the ligand affinity properties, and the nitric oxide reaction with coordinated O2. The analysis of the classical MD trajectory allowed us to identify Phe62 as the gate of the main channel for ligand diffusion to the active site. Moreover, the opening of the channel stems from the interplay between collective backbone motions and local rearrangements in the side chains of the residues that form the bottleneck of the tunnel. Even though the protein environment is not found to make a significant contribution to the heme moiety catalyzed reaction, the binding site influences the physiological function of the enzyme at three different levels. First, by isolating the intermediates formed in the reaction, it prevents nondesired reactions from proceeding. Second, it modulates the ligand (O2, NO) affinity of the protein, which can be ascribed to both distal and proximal effects. Finally, the stabilization of the Tyr33-Gln58 pair upon O2 binding might alter the essential dynamics of the protein, leading in turn to a mechanism for ligand-induced regulation.
authors.affiliation: Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires (C1428EHA), Argentina.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Crespo
authors.forename: Marcelo A
authors.initials: MA
authors.lastname: Martí
authors.forename: Susana G
authors.initials: SG
authors.lastname: Kalko
authors.forename: Antonio
authors.initials: A
authors.lastname: Morreale
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco
authors.forename: Jose L
authors.initials: JL
authors.lastname: Gelpi
authors.forename: F Javier
authors.initials: FJ
authors.lastname: Luque
authors.forename: Darío A
authors.initials: DA
authors.lastname: Estrin
mesh_terms: D006418:Heme / Q000737:chemistry / Q000378:metabolism; D006454:Hemoglobins / Q000737:chemistry* / Q000378:metabolism*; D008658:Inactivation, Metabolic; D008958:Models, Molecular; D009169:Mycobacterium tuberculosis / Q000737:chemistry / Q000378:metabolism; D009569:Nitric Oxide / Q000737:chemistry* / Q000378:metabolism*; D010084:Oxidation-Reduction; D010100:Oxygen / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D011789:Quantum Theory; D013816:Thermodynamics; D054793:Truncated Hemoglobins
chemical_list: D006454:Hemoglobins; D054793:Truncated Hemoglobins; D009569:Nitric Oxide; D006418:Heme; D010100:Oxygen