title: Transient Interactions of a Cytosolic Protein with Macromolecular and Vesicular Cosolutes: Unspecific and Specific Effects.
abstract: Cytosolic proteins do not occur as isolated but are exposed to many interactions within a crowded cellular environment. We investigated the associations between a test cytosolic protein, human ileal bile acid binding protein (IBABP), and model cosolutes mimicking macromolecular and lipid membrane intracellular components. Using fluorescence spectroscopy, heteronuclear NMR, and molecular dynamics, we found that IBABP associated weakly with anionic lipid vesicles and experienced transient unspecific contacts with albumin. Localized dynamic perturbations were observed even in the case of apparent unspecific binding. IBABP and ubiquitin did not display mutually attractive forces, whereas IBABP associated specifically with lysozyme. A structural model of the IBABP-lysozyme complex was obtained by data-driven docking simulation. Presumably, all the interactions shown here contribute to modulating functional communication of a protein in its native environment.
authors.affiliation: Department of Biotechnology, Biomolecular NMR Laboratory, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
authors.forename: Alberto
authors.initials: A
authors.lastname: Ceccon
authors.affiliation: Department of Biotechnology, Applied Bioinformatics Laboratory, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
authors.forename: Mirko
authors.initials: M
authors.lastname: Busato
authors.affiliation: Department of Biotechnology, Biomolecular NMR Laboratory, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
authors.forename: Silvia
authors.initials: S
authors.lastname: Pérez Santero
authors.affiliation: Department of Biotechnology, Biomolecular NMR Laboratory, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
authors.forename: Mariapina
authors.identifier: http://orcid.org/0000-0002-8699-0847
authors.initials: M
authors.lastname: D'Onofrio
authors.affiliation: Department of Pharmacy and Biotechnology, Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Musiani
authors.affiliation: Department of Biotechnology, Applied Bioinformatics Laboratory, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy. alejandro.giorgetti@univr.it.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Giorgetti
authors.affiliation: Department of Biotechnology, Biomolecular NMR Laboratory, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy. michael.assfalg@univr.it.
authors.forename: Michael
authors.identifier: http://orcid.org/0000-0001-9331-3169
authors.initials: M
authors.lastname: Assfalg
mesh_terms: D001665:Binding Sites; D003600:Cytosol / Q000378:metabolism; D006801:Humans; D006913:Hydroxysteroid Dehydrogenases / Q000737:chemistry / Q000378:metabolism*; D008051:Lipid Bilayers / Q000737:chemistry / Q000378:metabolism; D046911:Macromolecular Substances / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D009113:Muramidase / Q000737:chemistry / Q000378:metabolism; D019906:Nuclear Magnetic Resonance, Biomolecular; D054730:Protein Interaction Domains and Motifs; D013050:Spectrometry, Fluorescence; D025801:Ubiquitin / Q000737:chemistry / Q000378:metabolism; D045002:3-alpha-Hydroxysteroid Dehydrogenase (B-Specific)
chemical_list: D006913:Hydroxysteroid Dehydrogenases; D008051:Lipid Bilayers; D046911:Macromolecular Substances; D009113:Muramidase; D025801:Ubiquitin; C435496:AKR1C2 protein, human; D045002:3-alpha-Hydroxysteroid Dehydrogenase (B-Specific)
keywords: NMR spectroscopy; data-driven docking; intracellular environment; macromolecular crowding; protein-protein interactions