Reconstruction of protein form with X-ray solution scattering and a genetic algorithm
Reconstruction of protein form with X-ray solution scattering and a genetic algorithm
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DOI：
10.1006/jmbi.2000.3784
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发表时间：
2000-06-23
影响因子：
5.6
通讯作者：
Andreu, JM
中科院分区：
文献类型：
--
作者：
Chacón, P;Díaz, JF;Andreu, JM
我们已经重建，从实验类似于2 nm分辨率的X射线溶液散射轮廓，相应的形状和大小的肌红蛋白，肌钙蛋白C，精子黏附素PSP-I/PSP-II，胰凝乳蛋白酶原A，超氧化物歧化酶，卵清蛋白，微管蛋白，亚硝酸盐还原酶，过氧化氢酶，肌钙蛋白C的结构变化后，解离的两个高亲和力的Ca 2+，以及在确定其晶体结构之前，整合素α 6 β 4的纤连蛋白III型胞质结构域的串联对的溶液模型结构。为此，我们设计了一种新的遗传算法，逐步探索一个离散的搜索空间，并逐渐收敛的模型，由几百个珠子（下至0.3纳米半径）最适合德拜计算后的散射轮廓，没有几何约束或处罚松散的珠子。这是一个有效的数值变换的一维散射剖面到三维模型结构的过程。模型中的珠子数量与蛋白质分子量相关（有一个例外）。每种蛋白质的形状和近似尺寸已被检索的一组10个解决方案的模型，基本上重叠与现有的晶体结构。(C)北京大学出版社.
We have reconstructed, from experimental similar to 2 nm resolution X-ray solution scattering profiles, the corresponding shapes and sizes of myoglobin, troponin C, spermadhesin PSP-I/PSP-II, chymotrypsinogen A, superoxide dismutase, ovalbumin, tubulin, nitrite reductase, catalase, the structural change of troponin C upon dissociation of the two high affinity Ca2+, and the solution model structure of a tandem pair of fibronectin type III cytoplasmic domains of integrin alpha 6 beta 4 before determination of its crystal structure. To this purpose we have designed a new genetic algorithm which gradually explores a discrete search space and evolves convergent models made of several hundred beads (down to 0.3 nm radius) best fitting the scattering profile upon Debye calculation, without geometrical constraints or penalty for loose beads. This is a procedure of effective numerical transformation of the one-dimensional scattering profiles into three-dimensional model structures. The number of beads in models is correlated with the protein molecular mass (with one exception). The shape and approximate dimensions of each protein have been retrieved by a set of ten solution models, essentially superimposable with the available crystal structures. (C) 2000 Academic Press.