title: Thermodynamic characterization of OsGID1-gibberellin binding using calorimetry and docking simulations.
abstract: Gibberellins (GAs) are phytohormones regulating various developmental processes in plants. In rice, the initial GA-signaling events involve the binding of a GA to the soluble GA receptor protein, GID1. Although X-ray structures for certain GID1/GA complexes have recently been determined, an examination of the complexes does not fully clarify how GID1s discriminate among different GAs. Herein, we present a study aimed at defining the types of forces important to binding via a combination of isothermal titration calorimetry (ITC) and computational docking studies that employed rice GID1 (OsGID1), OsGID1 mutants, which were designed to have a decreased possible number of hydrogen bonds with bound GA, and GA variants. We find that, in general, GA binding is enthalpically driven and that a hydrogen bond between the phenolic hydroxyl of OsGID1 Tyr134 and the C-3 hydroxyl of a GA is a defining structural element. A hydrogen-bond network that involves the C-6 carboxyl of a GA that directly hydrogen bonds the hydroxyl of Ser198 and indirectly, via a two-water-molecule network, the phenolic hydroxyl of Tyr329 and the NH of the amide side-chain of Asn255 is also important for GA binding. The binding of OsGID1 by GA(1) is the most enthalpically driven association found for the biologically active GAs evaluated in this study. This observation might be a consequence of a hydrogen bond formed between the hydroxyl at the C-13 position of GA(1) and the main chain carbonyl of OsGID1 Phe245. Our results demonstrate that by combining ITC experiments and computational methods much can be learned about the thermodynamics of ligand/protein binding.
authors.affiliation: Division of Plant Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
authors.forename: Hongyu
authors.initials: H
authors.lastname: Xiang
authors.forename: Hiromi
authors.initials: H
authors.lastname: Takeuchi
authors.forename: Yuki
authors.initials: Y
authors.lastname: Tsunoda
authors.forename: Masatoshi
authors.initials: M
authors.lastname: Nakajima
authors.forename: Katsuyoshi
authors.initials: K
authors.lastname: Murata
authors.forename: Miyako
authors.initials: M
authors.lastname: Ueguchi-Tanaka
authors.forename: Shun-ichi
authors.initials: S
authors.lastname: Kidokoro
authors.forename: Yuichiro
authors.initials: Y
authors.lastname: Kezuka
authors.forename: Takamasa
authors.initials: T
authors.lastname: Nonaka
authors.forename: Makoto
authors.initials: M
authors.lastname: Matsuoka
authors.forename: Etsuko
authors.initials: E
authors.lastname: Katoh
mesh_terms: D001665:Binding Sites; D002151:Calorimetry / Q000379:methods*; D018360:Crystallography, X-Ray; D005875:Gibberellins / Q000737:chemistry / Q000378:metabolism*; D006860:Hydrogen Bonding; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D010940:Plant Proteins / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D013816:Thermodynamics
chemical_list: D005875:Gibberellins; D010940:Plant Proteins