UO22+ Uptake by Proteins: Understanding the Binding Features of the Super Uranyl Binding Protein and Design of a Protein with Higher Affinity

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• 作者：Samuel O. Odoh ; Gary D. Bondarevsky ; Jason Karpus ; Qiang Cui ; Chuan He ; Riccardo Spezia ; Laura Gagliardi
• 刊名：Journal of the American Chemical Society
• 出版年：2014
• 出版时间：December 17, 2014
• 年：2014
• 卷：136
• 期：50
• 页码：17484-17494
• 全文大小：636K
• ISSN：1520-5126

文摘

The capture of uranyl, UO₂²⁺, 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 UO₂²⁺ 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 UO₂²⁺ and residues in its second coordination sphere also affects the protein鈥檚 uranyl binding affinity. Free-energy simulations show how UO₂²⁺ 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 UO₂²⁺ to the aqueous protein as well as of the difference between the binding free energies of UO₂²⁺ and other ions (Ca²⁺, Cu²⁺, Mg²⁺, and Zn²⁺), a proxy for the protein鈥檚 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 UO₂²⁺ more strongly than SUP but that is also more selective for UO₂²⁺ over other ions. The predictions from the computations were confirmed experimentally.