Influence of Glycan Agents on Protein Crystallization with Ammonium Sulfate
Influence of Glycan Agents on Protein Crystallization with Ammonium Sulfate
复制标题
聚糖剂对硫酸铵蛋白质结晶的影响
DOI：
10.1021/acs.cgd.2c00901
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发表时间：
2022
期刊：
影响因子：
--
通讯作者：
Hoshino Tyuji
中科院分区：
文献类型：
--
作者：
Guo Yan;Hoshino Tyuji
高分辨率晶体分析的结构信息有利于设计新的药物或工程功能蛋白质。然而，获得高质量的蛋白质晶体是一个障碍。硫酸铵（AS）经常用作调节蛋白质溶解度的沉淀剂。在盐型沉淀剂中包含聚糖有时对于提高蛋白质晶体的X射线衍射的分辨率是有效的。在这项工作中，我们证明了糖苷聚糖剂提高两种蛋白质，流感病毒聚合酶酸性亚基N-末端结构域（PAN）和壳聚糖酶的晶体生长的质量。对聚糖和蛋白质组成的模型体系进行了分子动力学模拟，以阐明它们之间的相互作用。在模拟中观察到蛋白质表面上聚糖的几种结合姿势。均方根偏差和回转半径表明聚糖结合的稳定性。有和没有聚糖的计算模型之间的B-因子的比较证实了在接触区域的蛋白质构象的刚性。主成分分析的模拟轨迹表明，一个显着紧凑的运动的聚糖-蛋白质复合物。结合自由能表明，疏水相互作用主要稳定的复合物。在模拟中仔细检查了蛋白质周围的静电势与聚糖结合之间的关系。大多数聚糖结合位点位于静电势正负区域之间的边界区域，此处静电势的绝对值较低。边界区域与晶体分子堆积中蛋白质之间的接触区域相一致。此外，还在蛋白质数据库中搜索了通过在AS溶液中添加聚糖剂获得的晶体结构。与其他常规化学品相比，在蛋白质结晶条件下包含聚糖的信息仍然有限。添加剂在增加蛋白质稳定性、降低复合物表面柔性、支持蛋白质-蛋白质缔合等方面具有促进蛋白质结晶的优点。本工作的研究结果将有助于利用聚糖试剂进行蛋白质晶体生长。
Structural information from the high-resolution crystal analysis is advantageous for designing novel pharmaceutics or engineering functional proteins. Obtaining high-quality protein crystals is, however, a hurdle. Ammonium sulfate (AS) is frequently used as a precipitant for modulating the solubility of the protein. The inclusion of glycans in salt-type precipitants is sometimes effective for improving the resolution of X-ray diffractions of protein crystals. In this work, we demonstrate that glycoside-glycan agents improve the quality of crystal growth for two kinds of proteins, influenza virus polymerase acidic subunit N-terminal domain (PAN) and chitosanase. Molecular dynamics simulations were performed for the model systems consisting of glycans and proteins to clarify their interaction. Several binding poses of glycans on the protein surface were observed in the simulations. Root mean square deviation and the radius of gyration indicated the stability of the glycan binding. A comparison in B-factors between calculation models with and without glycans confirmed the rigidity of the protein conformations at the contact region. Principal component analysis of the simulation trajectories suggested a significantly compact motion of the glycan–protein complex. The binding free energy showed that hydrophobic interactions primarily stabilize the complexes. The relationship between the electrostatic potential around the proteins and glycan binding was closely examined in the simulations. Most of the glycan-binding sites were at the boundary regions between the positive and negative areas of electrostatic potential, where the absolute values of the electrostatic potential were low. The boundary regions coincide with the contact area among proteins in the molecular packing of crystals. Further, the Protein Data Bank was searched for crystal structures obtained by adding glycan agents in AS solution. The information on the inclusion of glycans was still limited in the protein crystallization condition compared to other conventional chemicals. The additives have merits for protein crystallization in increasing protein stability, decreasing complex surface flexibility, and supporting the protein–protein association. The findings of this work will be helpful in making use of glycan agents in protein crystal growth.
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影响因子：
3.7
作者：
X. Tang;M. Pikal
通讯作者：
X. Tang;M. Pikal
运动蛋白 prestin 胞质部分的结构以及 STAS 结构域在 SLC26/SulP 阴离子转运蛋白中的功能作用。
影响因子：
5.6
作者：
E. Pasqualetto;R. Aiello;L. Gesiot;G. Bonetto;M. Bellanda;R. Battistutta
通讯作者：
R. Battistutta
影响因子：
3.8
作者：
McPherson, A.;Nguyen, C.;Larson, S. B.
通讯作者：
Larson, S. B.
DOI：
10.1073/pnas.0608022103
发表时间：
2006-10-31
影响因子：
11.1
作者：
Salom, David;Lodowski, David T.;Palczewski, Krzysztof
通讯作者：
Palczewski, Krzysztof
影响因子：
5.5
作者：
Nivedha AK;Thieker DF;Makeneni S;Hu H;Woods RJ
通讯作者：
Woods RJ