Enhanced visibility of hydrogen atoms by neutron crystallography on fully deuterated myoglobin
Enhanced visibility of hydrogen atoms by neutron crystallography on fully deuterated myoglobin
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DOI：
10.1073/pnas.060024697
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发表时间：
2000-04-11
影响因子：
11.1
通讯作者：
Schoenborn, BP
中科院分区：
文献类型：
--
作者：
Shu, F;Ramakrishnan, V;Schoenborn, BP
尽管氢在蛋白质分子中占了一半的原子，并且在化学和结构上都很重要，但是用晶体学直接可视化它们是很困难的。中子晶体学能够直接揭示氢的位置，但在未标记样品上使用它面临一定的技术困难：氢的大量非相干散射导致背景散射，大大降低了实验的信噪比。此外，C、N和O的散射长度是正的，而氢的散射长度是负的，大约是它们的一半。这导致氢的密度只有原来的一半，接近2.0埃分辨率的探测阈值。此外，由于其符号相反，氢密度与邻近原子的氢密度部分抵消，这可能导致中分辨率解释的模糊性。这些困难可以通过使用氘化蛋白来克服，我们在这里展示了一个完全氘化的肌红蛋白的中子结构，该结构揭示了分子的丰富化学信息，包括氢键的几何形状，组氨酸的质子化状态，以及水分子在蛋白质表面的位置和几何形状。这种结构也应该引起更广泛的兴趣，因为它将作为分子动力学和能量最小化计算的基准，并与核磁共振研究进行比较。
Although hydrogens comprise half of the atoms in a protein molecule and are of great importance chemically and structurally, direct visualization of them by using crystallography is difficult. Neutron crystallography is capable of directly revealing the position of hydrogens, but its use on unlabeled samples faces certain technical difficulties: the large incoherent scattering of hydrogen results in background scattering that greatly reduces the signal to noise of the experiment. Moreover, whereas the scattering lengths of C, N, and O are positive, that of hydrogen is negative and about half the magnitude. This results in density for hydrogens being half as strong and close to the threshold of detection at 2.0-Angstrom resolution. Also, because of its opposite sign, there is a partial cancellation of the hydrogen density with that from neighboring atoms, which can lead to ambiguities in interpretation at medium resolution. These difficulties can be overcome by the use of deuterated protein, and we present here a neutron structure of fully deuterated myoglobin, The structure reveals a wealth of chemical information about the molecule, including the geometry of hydrogen bonding, states of protonation of histidines, and the location and geometry of water molecules at the surface of the protein. The structure also should be of broader interest because it will serve as a benchmark for molecular dynamics and energy minimization calculations and for comparison with NMR studies.