蛋白质晶体结构测定通用程序之一——差值帕特逊法确定蛋白质同晶型衍生物中重原子位置

多对同晶置换和反常散射法是目前测定生物大分子晶体结构的主要方法。这一方法可以概括为以下五个步骤; 1.培养出适用于衍射的蛋白质晶体。 2.制备两个以上与蛋白质母体同晶型的重原子衍生物。     

Structure of D-glyceraldehyde-3-phosphate dehydrogenase fromPalinurus versicolor in a tetragonal crystal form

D-glyceraldehyde-3-phosphate dehydrogenase (holo-GAPDH) from Palinurus versicolor was crystallized in a novel crystal form by the method of sitting-drop vapor diffusion. The crystals have space group P4212, cell parameters a=15.49 nm, c=8.03 nm and two subunits per asymmetric unit. The crystal structure at 0.34 nm was determined by the molecular replacement method. The final model has crystallographic Rfree and R factors of 0.274 and 0.262, and r.m.s. deviations of 0.002 nm for bond lengths and 2.33?for bond angles. The two subunits in asymmetric unit are similar to each other not only in the three-dimensional structure, but also in average temperature factors. This result demonstrates that the obvious difference in average temperature factors for the different subunits in C2 crystal form reported previously may be attributed to the different crystallographic environments of the subunits. This further supports that holo-GAPDH has a good 222 molecular symmetry.     

江浙蝮蛇毒溶血毒素晶体培养及初步晶体学研究

从江浙蝮蛇中分离纯化的碱性磷脂酶Ａ２在ｐＨ９．５,０．０５ｍｍｏｌ／ＬＣＨＥＳ缓冲液中,用汽相悬滴扩散的方法,获得了适用于高分辨率Ｘ射线结构分析的单晶．经Ｘ２００Ｂ面探测器分析,表明该晶体属于正交晶系,Ｐ２Ｉ２Ｉ２Ｉ空间群,晶胞参数为ａ＝９７．１３,ｂ＝１０３．６９,ｃ＝２３．２７．并收集了一套衍射数据,独立衍射点数１２００１个,数据完整度为８６．２％,Ｒｍｅｒｇｅ为０．０４５９．最高分辨率达２．０,根据分子量与晶胞体积估算,一个不对称单位含两个分子．     

龙虾甘油醛-3-磷酸脱氢酶结构中的氢键

甘油醛－３－磷酸脱氢酶（ＧＡＰＤＨ）是一种具有别构作用的寡聚酶。根据Ｘ射线晶体学研究得到的中国南海龙虾Ｐ．ｖｅｒｓｉｃｏｌｏｒｈｏｌｏ－ＧＡＰＤＨ高分辩率三维结构显示复杂的氢键结构,对各种类型氢键的分布和几何性质进行了统计分析。这个寡聚蛋白氢键的特性总体上与单体蛋白类似。几乎所有位于亚基间界面的极性侧链都能形成氢键,并满足能量上有利的几何学要求     

Refined structure of basic phospholipase A2 from venom of Agkistrodon halys Pallas in orthorhombic crystal form I at 0.25 nm resolution

The basic phospholipase A2 from the venom of Agkistrodon halys Pallas is a potent hemolytic toxin and anticoagulant. The accurate rotation and translation parameters of the molecules in orthorhombic crystal form I were successfully obtained using the fitting refinement technique. The structure was refined in the resolution range of 0. 6-0.25 nm using least square refinement with non-crystallographic two fold symmetry restraint, and resulted in the final R factor of 20.1 % , and the rms deviations from ideal stereochemistry were 0. 001 3 nm for bond lengths and 1. 32° for bond angles. The overall architecture of the present structure was similar to that of the determined structure of the orthorhombic crystal form Ⅱ, with a few differences in the regions of the β-wing and Ca2 -binding loop. The dimers formed by the two molecules in the asymmetric unit in both crystal forms were also similar. However, one of the monomers showed an orientational difference of 5.5° along the dimer interface in the two cr     

甘油醛-3-磷酸脱氢酶结构的保守性

对中国南海龙虾等五种种属的甘油醛－３－磷酸脱氢酶晶体结构进行了比较,结果显示该酶三维结构的高度保守性。结构类似性包括酶活性中心、与辅酶结合部位、二级结构、结构域组织、亚基排列以及许多有序水结构。位于分子中心的Ｓ－ｌｏｏｐ区存在两种略有差别的构象,分别对应于耐热酶与不耐热酶。对其它细小的结构差别也进行了分析与讨论。     

甘油醛-3-磷酸脱氢酶与辅酶类似物ATP及底物磷酸结合特性的晶体学研究

气相扩散共晶生长法培养出Ｐ．ｖｅｒｓｉｃｏｌｏｒ龙虾肌ＡＴＰ－Ｄ－甘油醛－３－磷酸脱氢酶（ＡＴＰ－ＧＡＰＤＨ）的晶体。用同步辐射Ｘ光源－磷光储屏－Ｗｅｉｓｓｅｎｂｅｒｇ照相机系统收集了一套２．０分辨率的衍射数据。用同晶差值傅立叶法解析了其结构。精化后的结构模型最终Ｒ因子为０．１９７,与标准键长、键角的均方根偏差为０．０１６°和３．２０°。ＰｖＡＴＰ－ＧＡＰＤＨ结构总体上和Ｐｖａｐｏ－ＧＡＰＤＨ相似。ＡＴＰ分子的占有率较低,并表现出一定程度的无序性,提示ＡＴＰ与酶蛋白结合的稳定性较低,表明ＮＡＤ＋的尼克酰胺核苷部分与蛋白质分子的作用在辅酶与蛋白质的稳定结合中起关键作用。ＡＴＰ－ＧＡＰＤＨ中每个亚基只有一个磷酸结合位点（Ｐｉ）。认为无机磷酸结合位点Ｐｉ的形成不依赖于ＮＡＤ＋,而底物磷酸结合位点ＰＳ的形成则依赖于ＮＡＤ＋的存在。