Calculating binding free energies for protein-carbohydrate complexes.
Calculating binding free energies for protein-carbohydrate complexes.
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DOI：
10.1007/978-1-4939-2343-4_26
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发表时间：
2015-01-01
期刊：
影响因子：
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通讯作者：
Woods, Robert J
中科院分区：
文献类型：
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作者：
Hadden, Jodi A;Tessier, Matthew B;Woods, Robert J
可以应用多种计算技术来计算蛋白质-碳水化合物复合物的理论结合自由能。阐明影响受体结合相对强度的分子间相互作用以及热力学效应可以揭示生物分子识别以及由此引发或抑制的生物过程。这里讨论三种类型的自由能方法，包括 MM-PB/GBSA、热力学积分和利用 SMD 的非平衡替代方法。在本章中，我们采用著名的伴刀豆球蛋白凝集素作为模型系统来演示这些方法在碳水化合物结合的特殊情况下的应用。
A variety of computational techniques may be applied to compute theoretical binding free energies for protein-carbohydrate complexes. Elucidation of the intermolecular interactions, as well as the thermodynamic effects, that contribute to the relative strength of receptor binding can shed light on biomolecular recognition, and the resulting initiation or inhibition of a biological process. Three types of free energy methods are discussed here, including MM-PB/GBSA, thermodynamic integration, and a non-equilibrium alternative utilizing SMD. Throughout this chapter, the well-known concanavalin A lectin is employed as a model system to demonstrate the application of these methods to the special case of carbohydrate binding.