title: Ligand uptake modulation by internal water molecules and hydrophobic cavities in hemoglobins.
abstract: Internal water molecules play an active role in ligand uptake regulation, since displacement of retained water molecules from protein surfaces or cavities by incoming ligands can promote favorable or disfavorable effects over the global binding process. Detection of these water molecules by X-ray crystallography is difficult given their positional disorder and low occupancy. In this work, we employ a combination of molecular dynamics simulations and ligand rebinding over a broad time range to shed light into the role of water molecules in ligand migration and binding. Computational studies on the unliganded structure of the thermostable truncated hemoglobin from Thermobifida fusca (Tf-trHbO) show that a water molecule is in the vicinity of the iron heme, stabilized by WG8 with the assistance of YCD1, exerting a steric hindrance for binding of an exogenous ligand. Mutation of WG8 to F results in a significantly lower stabilization of this water molecule and in subtle dynamical structural changes that favor ligand binding, as observed experimentally. Water is absent from the fully hydrophobic distal cavity of the triple mutant YB10F-YCD1F-WG8F (3F), due to the lack of residues capable of stabilizing it nearby the heme. In agreement with these effects on the barriers for ligand rebinding, over 97% of the photodissociated ligands are rebound within a few nanoseconds in the 3F mutant case. Our results demonstrate the specific involvement of water molecules in shaping the energetic barriers for ligand migration and binding.
authors.affiliation: Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , Buenos Aires, Argentina.
authors.forename: Juan P
authors.initials: JP
authors.lastname: Bustamante
authors.forename: Stefania
authors.initials: S
authors.lastname: Abbruzzetti
authors.forename: Agnese
authors.initials: A
authors.lastname: Marcelli
authors.forename: Diego
authors.initials: D
authors.lastname: Gauto
authors.forename: Leonardo
authors.initials: L
authors.lastname: Boechi
authors.forename: Alessandra
authors.initials: A
authors.lastname: Bonamore
authors.forename: Alberto
authors.initials: A
authors.lastname: Boffi
authors.forename: Stefano
authors.initials: S
authors.lastname: Bruno
authors.forename: Alessandro
authors.initials: A
authors.lastname: Feis
authors.forename: Paolo
authors.initials: P
authors.lastname: Foggi
authors.forename: Dario A
authors.initials: DA
authors.lastname: Estrin
authors.forename: Cristiano
authors.initials: C
authors.lastname: Viappiani
mesh_terms: D002248:Carbon Monoxide / Q000737:chemistry / Q000378:metabolism; D006454:Hemoglobins / Q000737:chemistry* / Q000378:metabolism; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D008024:Ligands; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D013816:Thermodynamics; D054793:Truncated Hemoglobins / Q000737:chemistry / Q000378:metabolism; D014867:Water / Q000737:chemistry*
chemical_list: D006454:Hemoglobins; D008024:Ligands; D054793:Truncated Hemoglobins; D014867:Water; D002248:Carbon Monoxide