Simulation of diffusion time of small molecules in protein crystals
Simulation of diffusion time of small molecules in protein crystals
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DOI：
10.1016/j.str.2005.12.007
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发表时间：
2006-03-01
期刊：
影响因子：
5.7
通讯作者：
Johnson, LN
中科院分区：
文献类型：
--
作者：
Geremia, S;Campagnolo, M;Johnson, LN
建立了一个简单的计算小分子在蛋白质晶体中扩散时间的模型，该模型考虑了蛋白质晶体和扩散分子的物理和化学性质。该模型还包括考虑配体与蛋白质的结合和结合亲和力。该模型已被验证的几个例子在文献中发现的实验装置的模拟。这些实验涵盖了广泛的情况：从小到相对较大的扩散分子，晶体具有低，中，高蛋白质密度，和不同的大小。再现的实验包括通过浸泡技术在蛋白质晶体中进行配体交换。尽管简化了模型的假设，但理论和实验数据与现有数据一致，实验扩散时间从几秒到几小时不等。该方法已成功地用于规划中间冷冻捕获实验麦芽糊精磷酸化酶晶体。
A simple model for evaluation of diffusion times of small molecule into protein crystals has been developed, which takes into account the physical and chemical properties both of protein crystal and the diffusing molecules. The model also includes consideration of binding and the binding affinity of a ligand to the protein. The model has been validated by simulation of experimental set-ups of several examples found in the literature. These experiments cover a wide range of situations: from small to relatively large diffusing molecules, crystals having low, medium, or high protein density, and different size. The reproduced experiments include ligand exchange in protein crystals by soaking techniques. Despite the simplifying assumptions of the model, theoretical and experimental data are in agreement with available data, with experimental diffusion times ranging from a few seconds to several hours. The method has been used successfully for planning intermediate cryotrapping experiments in maltodextrin phosphorylase crystals.