Kogut Małgorzata M, Marcisz Mateusz, Samsonov Sergey A
Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308, Gdańsk, Poland.
Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308, Gdańsk, Poland.
Curr Opin Struct Biol. 2022 Apr;73:102332. doi: 10.1016/j.sbi.2022.102332. Epub 2022 Feb 10.
Glycosaminoglycans are long linear and complex polysaccharides that are fundamental components of the mammalian extracellular matrix. Therefore, it is crucial to appropriately characterize molecular structure, dynamics, and interactions of protein-glycosaminoglycans complexes for improving understanding of molecular mechanisms underlying GAG biological function. Nevertheless, this proved challenging experimentally, and theoretical techniques are beneficial to construct new hypotheses and aid the interpretation of experimental data. The scope of this mini-review is to summarize four specific aspects of the current theoretical approaches for investigating noncovalent protein-glycosaminoglycan complexes such as molecular docking, free binding energy calculations, modeling ion impact, and addressing the phenomena of multipose binding of glycosaminoglycans to proteins.
糖胺聚糖是长链线性且复杂的多糖，是哺乳动物细胞外基质的基本组成部分。因此，准确表征蛋白质 - 糖胺聚糖复合物的分子结构、动力学和相互作用对于增进对糖胺聚糖生物学功能潜在分子机制的理解至关重要。然而，这在实验上被证明具有挑战性，而理论技术有助于构建新的假设并辅助实验数据的解释。本小型综述的范围是总结当前用于研究非共价蛋白质 - 糖胺聚糖复合物的理论方法的四个具体方面，例如分子对接、自由结合能计算、模拟离子影响以及解决糖胺聚糖与蛋白质多姿态结合的现象。
