Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States.
J Phys Chem B. 2011 Jun 9;115(22):7427-32. doi: 10.1021/jp200906y. Epub 2011 May 16.
Motional properties are important for understanding protein function and are accessible to NMR relaxation measurements. The goal of this study is to investigate the internal dynamics occurring in gramicidin A (gA) channels in order to provide benchmark experimental data for comparison with the results of molecular dynamics simulations. We therefore synthesized several (15)N isotope-enriched gA samples, covering all backbone residues as well as the Trp indole side chains for NMR relaxation experiments. On the basis of the (15)N NMR spectra for labeled gA samples incorporated in sodium dodecylsulfate (SDS) micelles, we determined T(1), T(2), and heteronuclear NOE values for backbone and indole (15)NH groups. The results indicate that the SDS-incorporated gA channel is a constrained structure without an especially "floppy" region. The NMR observables, particularly those for backbone groups, are predicted well by the molecular dynamics simulations in the accompanying article (DOI 10.1021/jp200904d ).
动态特性对于理解蛋白质功能非常重要，并且可以通过 NMR 弛豫测量来获得。本研究的目的是研究在格兰菌素 A (gA) 通道中发生的内部动力学，以便为与分子动力学模拟结果的比较提供基准实验数据。因此，我们合成了几种 (15)N 同位素标记的 gA 样品，覆盖了所有的骨架残基以及色氨酸吲哚侧链，用于 NMR 弛豫实验。基于标记的 gA 样品在十二烷基硫酸钠 (SDS) 胶束中的 (15)N NMR 谱，我们确定了骨架和吲哚 (15)NH 基团的 T(1)、T(2)和异核 NOE 值。结果表明，SDS 结合的 gA 通道是一种受限结构，没有特别“柔软”的区域。NMR 观测值，特别是骨架基团的观测值，在随附文章中的分子动力学模拟中得到了很好的预测（DOI 10.1021/jp200904d）。
