Heparan sulfate (HS) is a sulfated polysaccharide that plays a key role in morphogenesis, physiology and pathogenesis. The biosynthesis of HS takes place in the Golgi apparatus by a group of enzymes that polymerize, epimerize and sulfate the sugar chain. This biosynthetic process introduces varying degrees of sulfate substitution, which are tightly regulated and directly dictate binding specificity to different cytokines, morphogens and growth factors. Here, we report the use of molecular dynamics simulations to investigate the dynamics of substrate recognition of two glycosaminoglycan (GAG) sulfotransferases, N-deacetylase-N-sulfotransferase and 2-O-sulfotransferase to the HS chain during the biosynthetic process. We performed multiple simulations of the binding of the sulfotransferase domains to both the HS oligosaccharide substrate and sulfate donor, 3′-phosphoadenosine-5′-phosphosulfate. Analysis of extended simulations provide detailed and useful insights into the atomic interactions that are at work during oligosaccharide processing. The fast information matching method was used to detect the enzyme global dynamics and to predict the pairwise contact of residues responsible for GAG–enzyme binding and unbinding. The correlation between HS displacement and the location of the modified GAG chain were calculated, indicating a possible route for HS and heparin during sulfotransferase processing. Our data also show sulfotransferases contain a conserved interspaced positively charged amino acid residues that form a patch which controls the protein–GAG binding equilibrium. Together, our findings provide further understanding on the fine-tuned complex mechanism of GAG biosynthesis. Our findings can also be extrapolated to other systems for calculating rates of protein–GAG binding.

中文翻译：

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糖胺聚糖磺基转移酶处理寡糖的结构基础

硫酸乙酰肝素（HS）是一种硫酸化多糖，在形态发生，生理和发病机制中起着关键作用。HS的生物合成是在高尔基体中通过一组使糖链聚合，差向异构化和硫酸化的酶进行的。这种生物合成过程引入了不同程度的硫酸盐取代，硫酸盐取代受到严格调节并直接决定与不同细胞因子，形态发生子和生长因子的结合特异性。在这里，我们报告分子动力学模拟的使用，以调查生物合成过程中两个糖胺聚糖（GAG）磺基转移酶，N-脱乙酰基酶-N-磺基转移酶和2-O-磺基转移酶对HS链的底物识别动力学。我们对磺基转移酶结构域与HS寡糖底物和硫酸盐供体3'-磷酸腺苷-5'-磷酸酯的结合进行了多种模拟。扩展模拟的分析为寡糖加工过程中起作用的原子相互作用提供了详细而有用的见解。快速信息匹配方法用于检测酶的整体动力学，并预测负责GAG-酶结合和解结合的残基的成对接触。计算了HS位移与修饰的GAG链位置之间的相关性，表明在磺基转移酶加工过程中HS和肝素的可能途径。我们的数据还表明，磺基转移酶包含一个保守的，间隔开的带正电荷的氨基酸残基，这些残基形成一个可控制蛋白质与GAG结合平衡的补丁。在一起，我们的发现提供了对GAG生物合成的微调复杂机制的进一步理解。我们的发现也可以外推到其他系统来计算蛋白质与GAG的结合率。