Abstract：
Molecular Dynamics (MD) is a method used to calculate the movement of atoms and molecules broadly applied to several aspects of science. It involves computational simulation, which makes it, at first glance, not easily accessible. The rise of several automated tools to perform molecular simulations has allowed researchers to navigate through the various steps of MD. This enables to elucidate structural properties of proteins that could not be analyzed otherwise, such as the impact of glycosylation. Glycosylation dictates the physicochemical and biological properties of a protein modulating its solubility, stability, resistance to proteolysis, interaction partners, enzymatic activity, binding and recognition. Given the high conformational and compositional diversity of the glycan chains, assessing their influence on the protein structure is challenging using conventional analytical techniques. In this manuscript, we present a step-by-step workflow to build and perform MD analysis of glycoproteins focusing on the SPIKE glycoprotein of SARS-CoV-2 to appraise the impact of glycans in structure stabilization and antibody occlusion.
摘要：
分子动力学（MD）是一种用于计算原子和分子运动的方法，广泛应用于科学的多个方面。它涉及计算模拟，这使得它，乍一看,不容易接近。几种进行分子模拟的自动化工具的兴起使研究人员能够浏览MD的各个步骤。这使得能够阐明蛋白质的结构特性，否则无法分析，如糖基化的影响。糖基化决定了调节其溶解度的蛋白质的物理化学和生物学特性，稳定性,对蛋白水解的抗性，互动伙伴，酶活性，绑定和识别。鉴于聚糖链的高构象和组成多样性，使用常规分析技术评估它们对蛋白质结构的影响是具有挑战性的。在这份手稿中,我们提出了一个循序渐进的工作流程,以构建和执行针对SARS-CoV-2的SPIKE糖蛋白的糖蛋白MD分析,以评估聚糖在结构稳定和抗体闭塞中的影响.
