Dynamic Equilibria of Short-Range Electrostatic Interactions at Molecular Interfaces of Protein鈥揇NA Complexes

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• 作者：Chuanying Chen ; Alexandre Esadze ; Levani Zandarashvili ; Dan Nguyen ; B. Montgomery Pettitt ; Junji Iwahara
• 刊名：The Journal of Physical Chemistry Letters
• 出版年：2015
• 出版时间：July 16, 2015
• 年：2015
• 卷：6
• 期：14
• 页码：2733-2737
• 全文大小：318K
• ISSN：1948-7185

文摘

Intermolecular ion pairs (salt bridges) are crucial for protein鈥揇NA association. For two protein鈥揇NA complexes, we demonstrate that the ion pairs of protein side-chain NHb>3b>⁺ and DNA phosphate groups undergo dynamic transitions between distinct states in which the charged moieties are either in direct contact or separated by water. While the crystal structures of the complexes show only the solvent-separated ion pair (SIP) state for some interfacial lysine side chains, our NMR hydrogen-bond scalar coupling data clearly indicate the presence of the contact ion pair (CIP) state for the same residues. The 0.6-渭s molecular dynamics (MD) simulations confirm dynamic transitions between the CIP and SIP states. This behavior is consistent with our NMR order parameters and scalar coupling data for the lysine side chains. Using the MD trajectories, we also analyze the free energies of the CIP鈥揝IP equilibria. This work illustrates the dynamic nature of short-range electrostatic interactions in DNA recognition by proteins.