title: Unraveling the Conformational Landscape of Ligand Binding to Glucose/Galactose-Binding Protein by Paramagnetic NMR and MD Simulations.
abstract: Protein dynamics related to function can nowadays be structurally well characterized (i.e., instances obtained by high resolution structures), but they are still ill-defined energetically, and the energy landscapes are only accessible computationally. This is the case for glucose-galactose binding protein (GGBP), where the crystal structures of the apo and holo states provide structural information for the domain rearrangement upon ligand binding, while the time scale and the energetic determinants for such concerted dynamics have been so far elusive. Here, we use GGBP as a paradigm to define a functional conformational landscape, both structurally and energetically, by using an innovative combination of paramagnetic NMR experiments and MD simulations. Anisotropic NMR parameters induced by self-alignment of paramagnetic metal ions was used to characterize the ensemble of conformations adopted by the protein in solution while the rate of interconversion between conformations was elucidated by long molecular dynamics simulation on two states of GGBP, the closed-liganded (holo_cl) and open-unloaded (apo_op) states. Our results demonstrate that, in its apo state, the protein coexists between open-like (68%) and closed-like (32%) conformations, with an exchange rate around 25 ns. Despite such conformational heterogeneity, the presence of the ligand is the ultimate driving force to unbalance the equilibrium toward the holo_cl form, in a mechanism largely governed by a conformational selection mechanism.
authors.affiliation: Molecular Recognition and Host-Pathogen Interactions, CICbioGUNE , Bizkaia Technology Park, Building 801 A, 48170 Derio, Spain.
authors.forename: Luca
authors.initials: L
authors.lastname: Unione
authors.affiliation: Molecular Recognition and Host-Pathogen Interactions, CICbioGUNE , Bizkaia Technology Park, Building 801 A, 48170 Derio, Spain.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Ortega
authors.affiliation: Institute of Chemistry, Center for Structural and Cell Biology in Medicine (CSCM), University of Luebeck , Ratzeburger Allee 160, 23538 Luebeck, Germany.
authors.forename: Alvaro
authors.initials: A
authors.lastname: Mallagaray
authors.affiliation: Departamento de Química y Centro de Investigación en Síntesis Química, Universidad de La Rioja , 26006 Logroño, La Rioja, Spain.
authors.forename: Francisco
authors.initials: F
authors.lastname: Corzana
authors.affiliation: Facultad de Farmacia, Dpto. Química y Bioquímica, Universidad San Pablo CEU, Urb. Montepríncipe, ctra. , Boadilla km 5,300 Boadilla del Monte, 28668 Madrid, Spain.
authors.forename: Javier
authors.initials: J
authors.lastname: Pérez-Castells
authors.affiliation: Department of Química Orgánica I, Fac. C. C. Químicas, Universidad Complutense de Madrid , Avd. Complutense s/n, 28040 Madrid, Spain.
authors.forename: Angeles
authors.initials: A
authors.lastname: Canales
authors.affiliation: Molecular Recognition and Host-Pathogen Interactions, CICbioGUNE , Bizkaia Technology Park, Building 801 A, 48170 Derio, Spain.|Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, 48009 Bilbao, Spain.|Departament of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country , 48940 Leioa, Bizkaia Spain.
authors.forename: Jesús
authors.initials: J
authors.lastname: Jiménez-Barbero
authors.affiliation: Molecular Recognition and Host-Pathogen Interactions, CICbioGUNE , Bizkaia Technology Park, Building 801 A, 48170 Derio, Spain.
authors.forename: Oscar
authors.initials: O
authors.lastname: Millet
mesh_terms: D002135:Calcium-Binding Proteins / Q000737:chemistry*; D018360:Crystallography, X-Ray; D005947:Glucose / Q000737:chemistry*; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D056004:Molecular Dynamics Simulation; D009004:Monosaccharide Transport Proteins / Q000737:chemistry*; D033902:Periplasmic Binding Proteins / Q000737:chemistry*; D011485:Protein Binding
chemical_list: D002135:Calcium-Binding Proteins; D008024:Ligands; D009004:Monosaccharide Transport Proteins; D033902:Periplasmic Binding Proteins; C023550:galactose-binding protein; D005947:Glucose