Second-Contact Shell Mutation Diminishes Streptavidin鈥揃iotin Binding Affinity through Transmitted Effects on Equilibrium Dynamics

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• 作者：Loren Baugh ; Isolde Le Trong ; David S. Cerutti ; Nital Mehta ; Susanne G眉lich ; Patrick S. Stayton ; Ronald E. Stenkamp ; Terry P. Lybrand
• 刊名：Biochemistry
• 出版年：2012
• 出版时间：January 17, 2012
• 年：2012
• 卷：51
• 期：2
• 页码：597-607
• 全文大小：354K
• 年卷期：v.51,no.2(January 17, 2012)
• ISSN：1520-4995

文摘

We report a point mutation in the second contact shell of the high-affinity streptavidin鈥揵iotin complex that appears to reduce binding affinity through transmitted effects on equilibrium dynamics. The Y54F streptavidin mutation causes a 75-fold loss of binding affinity with 73-fold faster dissociation, a large loss of binding enthalpy (螖螖H = 3.4 kcal/mol at 37 掳C), and a small gain in binding entropy (T螖螖S = 0.7 kcal/mol). The removed Y54 hydroxyl is replaced by a water molecule in the bound structure, but there are no observable changes in structure in the first contact shell and no additional changes surrounding the mutation. Molecular dynamics simulations reveal a large increase in the atomic fluctuation amplitudes for W79, a key biotin contact residue, compared to the fluctuation amplitudes in the wild-type. The increased W79 atomic fluctuation amplitudes are caused by loss of water-mediated hydrogen bonds between the Y54 hydroxyl group and peptide backbone atoms in and near W79. We propose that the increased atomic fluctuation amplitudes diminish the integrity of the W79鈥揵iotin interaction and represents a loosening of the 鈥渢ryptophan collar鈥?that is critical to the slow dissociation and high affinity of streptavidin鈥揵iotin binding. These results illustrate how changes in protein dynamics distal to the ligand binding pocket can have a profound impact on ligand binding, even when equilibrium structure is unperturbed.