Direct Observation of the Ion-Pair Dynamics at a Protein鈥揇NA Interface by NMR Spectroscopy
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- 作者：Kurtis M. Anderson ; Alexandre Esadze ; Mariappan Manoharan ; Rafael Br眉schweiler ; David G. Gorenstein ; Junji Iwahara
- 刊名：The Journal of the American Chemical Society
- 出版年：2013
- 出版时间：March 6, 2013
- 年：2013
- 卷：135
- 期：9
- 页码：3613-3619
- 全文大小：385K
- 年卷期：v.135,no.9(March 6, 2013)
- ISSN：1520-5126
文摘
Ion pairing is one of the most fundamental chemical interactions and is essential for molecular recognition by biological macromolecules. From an experimental standpoint, very little is known to date about ion-pair dynamics in biological macromolecular systems. Absorption, infrared, and Raman spectroscopic methods were previously used to characterize dynamic properties of ion pairs, but these methods can be applied only to small compounds. Here, using NMR 15N relaxation and hydrogen-bond scalar 15N鈥?sup>31P J-couplings (h3JNP), we have investigated the dynamics of the ion pairs between lysine side-chain NH3+ amino groups and DNA phosphate groups at the molecular interface of the HoxD9 homeodomain鈥揇NA complex. We have determined the order parameters and the correlation times for C鈥揘 bond rotation and reorientation of the lysine NH3+ groups. Our data indicate that the NH3+ groups in the intermolecular ion pairs are highly dynamic at the protein鈥揇NA interface, which should lower the entropic costs for protein鈥揇NA association. Judging from the C鈥揘 bond-rotation correlation times along with experimental and quantum-chemically derived h3JNP hydrogen-bond scalar couplings, it seems that breakage of hydrogen bonds in the ion pairs occurs on a sub-nanosecond time scale. Interestingly, the oxygen-to-sulfur substitution in a DNA phosphate group was found to enhance the mobility of the NH3+ group in the intermolecular ion pair. This can partially account for the affinity enhancement of the protein鈥揇NA association by the oxygen-to-sulfur substitution, which is a previously observed but poorly understood phenomenon.