Large-Scale Structures Group, Institut Laue-Langevin , 71 Avenue des Martyrs, Grenoble 38000, France.
Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool , Liverpool L69 7ZX, UK.
IUCrJ. 2015 Jun 30;2(Pt 4):464-74. doi: 10.1107/S2052252515011239. eCollection 2015 Jul 1.
The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm(3) crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H(+)) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined. New results from two metalloproteins, copper nitrite reductase and cytochrome c', are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.
国际晶体学年见证了蛋白质数据库中大分子结构的数量超过 100000 个,其中超过 90000 个结构是通过 X 射线晶体学获得的。已经确定了超过 600 个亚原子分辨率(即≤1埃)的 X 射线结构,随着 MAX-IV(瑞典)和 Sirius(巴西)等衍射限制同步辐射源的建设,这一数字可能会迅速增长。已经有十几个 X 射线结构被沉积到超高分辨率(即≤0.7埃),对于这些结构,可以利用精确的电子密度来获得电荷密度,并提供关于催化或电子转移位点的键合特性的信息。尽管多年来中子大分子晶体学的发展远不那么显著,其应用也远不那么广泛,但新的和改进的仪器的可用性,加上专用的氘化设施,正开始改变这一领域。在 83 个带有中子衍射数据的大分子结构中,超过一半(49/83,59%)是在 2010 年以后发布的。现在已经可以定期使用亚毫米(3)晶体进行数据收集,已经确定了一些小蛋白质的原子分辨率结构,并且成功地研究了更大的单元系统(晶胞边缘>100埃)。虽然在亚原子分辨率下,X 射线晶体学可以处理与 H 原子位置有关的一些细节,但某些 H 原子的移动性使得它们无法被定位。此外,高度极化的 H 原子和质子(H(+))仍然无法被 X 射线探测到。此外,大多数 X 射线结构都是从 100 K 下的冷冻晶体中确定的,虽然辐射损伤可以得到很好的控制,特别是自从无快门快速探测器出现以来,并且通过使用有限的剂量和晶体在微焦点光束中的平移,可以仍然会发生辐射损伤。因此,中子晶体学仍然是唯一一种可以在没有辐射损伤问题的情况下在室温下收集衍射数据的方法,也是唯一一种可以定位移动或高度极化的 H 原子和质子的方法。本文综述了当前亚原子分辨率 X 射线和中子大分子晶体学的现状,并概述了联合方法的未来前景。还包括来自两种金属蛋白(亚硝酸盐还原酶和细胞色素 c')的新结果,这些结果说明了可以从亚原子分辨率(约 0.8 埃)的 X 射线结构中获得的信息类型,同时也强调了需要进行互补的中子研究,这些研究可以提供 X 射线晶体学无法提供的 H 原子的细节。