title: Bridging Theory and Experiment to Address Structural Properties of Truncated Haemoglobins: Insights from Thermobifida fusca HbO.
abstract: In this chapter, we will discuss the paradigmatic case of Thermobifida fusca (Tf-trHb) HbO in its ferrous and ferric states and its behaviour towards a battery of possible ligands. This choice was dictated by the fact that it has been one of the most extensively studied truncated haemoglobins, both in terms of spectroscopic and molecular dynamics studies. Tf-trHb typifies the structural properties of group II trHbs, as the active site is characterized by a highly polar distal environment in which TrpG8, TyrCD1, and TyrB10 provide three potential H-bond donors in the distal cavity capable of stabilizing the incoming ligands. The role of these residues in key topological positions, and their interplay with the iron-bound ligands, has been addressed in studies carried out on the CO, F(-), OH(-), CN(-), and HS(-) adducts formed with the wild-type protein and a combinatorial set of mutants, in which the distal polar residues, TrpG8, TyrCD1, and TyrB10, have been singly, doubly, or triply replaced by a Phe residue. In this context, such a complete analysis provides an excellent benchmark for the investigation of the relationship between protein structure and function, allowing one to translate physicochemical properties of the active site into the observed functional behaviour. Tf-trHb will be compared with other members of the group II trHbs and, more generally, with members of the other trHb subgroups.
authors.affiliation: Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentino, Italy.
authors.forename: Barry D
authors.initials: BD
authors.lastname: Howes
authors.affiliation: Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Boechi
authors.affiliation: Dipartimento di Scienze Biochimiche, Università "Sapienza", Rome, Italy.
authors.forename: Alberto
authors.initials: A
authors.lastname: Boffi
authors.affiliation: Departamento de Química Inorgánica, Analítica y Química Física and Inquimae-Conicet, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
authors.forename: Dario E
authors.initials: DE
authors.lastname: Estrin
authors.affiliation: Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentino, Italy. Electronic address: giulietta.smulevich@unifi.it.
authors.forename: Giulietta
authors.initials: G
authors.lastname: Smulevich
mesh_terms: D039903:Actinobacteria / Q000201:enzymology*; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D020134:Catalytic Domain; D006454:Hemoglobins / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding
chemical_list: D001426:Bacterial Proteins; D006454:Hemoglobins
keywords: Computer simulation; Distal residues; Exogenous ligand binding; H-bond; Ligand affinity; Ligand recognition; Molecular dynamics simulation; Resonance Raman; Spectroscopy; Truncated haemoglobins