Aqueous Molecular Dynamics for Understanding Glycosaminoglycan Recognition by Proteins.
Aqueous Molecular Dynamics for Understanding Glycosaminoglycan Recognition by Proteins.
复制标题
用于理解蛋白质识别糖胺聚糖的水分子动力学。
DOI：
10.1007/978-1-0716-1398-6_5
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发表时间：
2022
期刊：
影响因子：
--
通讯作者：
Desai,Umesh
中科院分区：
文献类型：
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作者：
Nagarajan,Balaji;Desai,Umesh
糖胺聚糖（GAGs）是存在于大多数生物体内的生物聚合物。已知gag与数百种蛋白质结合，并参与多种生物过程，如生长、形态发生、炎症、感染等。它们固有的结构异质性和构象变异性给实验研究带来了重大挑战。另一方面，力场发展和计算技术的最新进展为同时研究数千个GAG序列以了解靶蛋白的识别提供了惊人的机会。在这里，我们描述了传统分子动力学模拟GAGs的实验设置，以定位实验生物学家在GAGs的性能，稳定性，特异性和构象特性的分析和解释，同时也阐明了它们在存在水的原子水平上与蛋白质氨基酸残基的相互作用。
Glycosaminoglycans (GAGs) are biopolymers that exist in most organisms. GAGs are known to bind to hundreds of proteins and partake in multiple biological processes such as growth, morphogenesis, inflammation, infection, and others. Their intrinsic structural heterogeneity and conformational variability introduce major challenges in experimental studies. On the other hand, recent advances in force field development and computational technology have yielded phenomenal opportunity to study thousands of GAG sequences simultaneously to understand recognition of target protein(s). Here, we describe experimental setup for conventional molecular dynamics simulations of GAGs to position an experimental biologist favorably in performance, analysis and interpretation of stability, specificity, and conformational properties of GAGs, while also elucidating their interactions with amino acid residues of a protein at an atomistic level in presence of water.