title: UO₂²⁺ uptake by proteins: understanding the binding features of the super uranyl binding protein and design of a protein with higher affinity.
abstract: The capture of uranyl, UO2(2+), by a recently engineered protein (Zhou et al. Nat. Chem. 2014, 6, 236) with high selectivity and femtomolar sensitivity has been examined by a combination of density functional theory, molecular dynamics, and free-energy simulations. It was found that UO2(2+) is coordinated to five carboxylate oxygen atoms from four amino acid residues of the super uranyl binding protein (SUP). A network of hydrogen bonds between the amino acid residues coordinated to UO2(2+) and residues in its second coordination sphere also affects the protein's uranyl binding affinity. Free-energy simulations show how UO2(2+) capture is governed by the nature of the amino acid residues in the binding site, the integrity and strength of the second-sphere hydrogen bond network, and the number of water molecules in the first coordination sphere. Alteration of any of these three factors through mutations generally results in a reduction of the binding free energy of UO2(2+) to the aqueous protein as well as of the difference between the binding free energies of UO2(2+) and other ions (Ca(2+), Cu(2+), Mg(2+), and Zn(2+)), a proxy for the protein's selectivity over these ions. The results of our free-energy simulations confirmed the previously reported experimental results and allowed us to discover a mutant of SUP, specifically the GLU64ASP mutant, that not only binds UO2(2+) more strongly than SUP but that is also more selective for UO2(2+) over other ions. The predictions from the computations were confirmed experimentally.
authors.affiliation: Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota , Minneapolis, Minnesota 55455-0431, United States.
authors.forename: Samuel O
authors.initials: SO
authors.lastname: Odoh
authors.forename: Gary D
authors.initials: GD
authors.lastname: Bondarevsky
authors.forename: Jason
authors.initials: J
authors.lastname: Karpus
authors.forename: Qiang
authors.initials: Q
authors.lastname: Cui
authors.forename: Chuan
authors.initials: C
authors.lastname: He
authors.forename: Riccardo
authors.initials: R
authors.lastname: Spezia
authors.forename: Laura
authors.initials: L
authors.lastname: Gagliardi
mesh_terms: D015195:Drug Design; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*; D014501:Uranium / Q000737:chemistry*
chemical_list: D011506:Proteins; D014501:Uranium