Differential Role of the Protein Matrix on the Binding of a Catalytic Aspartate to Mg2+ vs Ca2+: Application to Ribonuclease H

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• 作者：C. Satheesan Babu ; Todor Dudev ; Carmay Lim
• 刊名：The Journal of the American Chemical Society
• 出版年：2013
• 出版时间：May 1, 2013
• 年：2013
• 卷：135
• 期：17
• 页码：6541-6548
• 全文大小：448K
• 年卷期：v.135,no.17(May 1, 2013)
• ISSN：1520-5126

文摘

Divalent metal cations are essential cofactors for many enzyme functions. Although Mg²⁺ is the native cofactor in many enzymes such as ribonuclease H, its competitor Ca²⁺ may also bind to the enzyme but inhibit catalysis. Thus, the competition between Mg²⁺ and Ca²⁺ for a given metal-binding site in an enzyme and their effects on enzyme activity are of great interest. Most studies have focused on the interactions between Mg²⁺ or Ca²⁺ and the metal ligands in the first and sometimes second coordination shell. However, no study (to our knowledge) has examined the role of the protein architecture and surrounding aqueous environment on the binding of Mg²⁺ vs Ca²⁺ to a given protein metal-binding site. In this work, the free energy barriers for the binding of a catalytically essential aspartate to Mg²⁺ or Ca²⁺ in ribonuclease H from two organisms were computed using umbrella sampling with a classical force field (鈥渃lassical鈥?model). The corresponding free energy barriers in water were computed using the 鈥渃lassical鈥?model as well as density functional theory combined with a self-consistent reaction field. The results reveal that, relative to water, the protein architecture and coupled protein鈥搘ater interactions raise the free energy barrier for binding of the catalytically essential aspartate to the native Mg²⁺ cofactor more than the respective binding to Ca²⁺. They also reveal the physical basis for the different observed binding modes of Mg²⁺ and Ca²⁺ and highlight limitations of simulations with classical force fields that do not explicitly account for charge transfer and polarization effects.