Ligand uptake modulation by internal water molecules and hydrophobic cavities in hemoglobins

Year: 2014

Authors: Bustamante J.P., Abbruzzetti S., Marcelli A., Gauto D., Boechi L., Bonamore A., Boffi A., Bruno S., Feis A., Foggi P., Estrin D.A., Viappiani C.

Autors Affiliation: Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Department of Physics and Earth Sciences Macedonio Melloni, University of Parma, IBF-CNR, Parma, Italy; LENS, European Laboratory for Non-linear Spectroscopy, Florence, Italy; Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Istituto Pasteur, Department of Biochemical Sciences, University of Rome la Sapienza, Rome, Italy; Department of Pharmacy, University of Parma, Parma, Italy; Department of Chemistry Ugo Schiff, University of Florence, Florence, Italy; Department of Chemistry, University of Perugia, Perugia, Italy; INO-CNR, Florence, Italy

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.


Volume: 118 (5)      Pages from: 1234  to: 1245

More Information: This work was supported by CONICET, University of Buenos Aires, and Agenda Nacional de Promocion Cientifica y Tecnologica. J.P.B. and D.G. hold CONICET Ph.D. fellowships. L.B. is a Pew Latin American Fellow. D.A.E. is a member of CONICET. The authors acknowledge Ministero degli Affari Esteri, Direzione generale per la promozione del sistema Paese (Progetti di Grande Rilevanza, Italia-Argentina 2011-2013). University funds C26A139Z23 to A.B. are gratefully acknowledged.
KeyWords: Computational studies; Energetic barriers; Exogenous ligands; Hydrophobic cavities; Molecular dynamics simulations; Positional disorder; Thermobifida fusca; Truncated hemoglobins, Hemoglobin; Hydrophobicity; Molecular dynamics; Molecules; Porphyrins; X ray crystallography, Ligands, carbon monoxide; hemoglobin; ligand; truncated hemoglobin; water, article; chemical phenomena; chemistry; kinetics; metabolism; protein binding; protein tertiary structure; thermodynamics, Carbon Monoxide; Hemoglobins; Hydrophobic and Hydrophilic Interactions; Kinetics; Ligands; Protein Binding; Protein Structure, Tertiary; Thermodynamics; Truncated Hemoglobins; Water
DOI: 10.1021/jp410724z

Citations: 17
data from “WEB OF SCIENCE” (of Thomson Reuters) are update at: 2022-11-27
References taken from IsiWeb of Knowledge: (subscribers only)
Connecting to view paper tab on IsiWeb: Click here
Connecting to view citations from IsiWeb: Click here