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Abstract：
Protein structures are highly dynamic macromolecules. This dynamics is often analysed through experimental and/or computational methods only for an isolated or a limited number of proteins. Here, we explore large-scale protein dynamics simulation to observe dynamics of local protein conformations using different perspectives. We analysed molecular dynamics to investigate protein flexibility locally, using classical approaches such as RMSf, solvent accessibility, but also innovative approaches such as local entropy. First, we focussed on classical secondary structures and analysed specifically how β-strand, β-turns, and bends evolve during molecular simulations. We underlined interesting specific bias between β-turns and bends, which are considered as the same category, while their dynamics show differences. Second, we used a structural alphabet that is able to approximate every part of the protein structures conformations, namely protein blocks (PBs) to analyse (i) how each initial local protein conformations evolve during dynamics and (ii) if some exchange can exist among these PBs. Interestingly, the results are largely complex than simple regular/rigid and coil/flexible exchange. AbbreviationsNeqnumber of equivalentPBProtein BlocksPDBProtein DataBankRMSfroot mean square fluctuationsCommunicated by Ramaswamy H. Sarma.
摘要：
蛋白质结构是高度动态的大分子。这种动力学通常仅通过实验和/或计算方法对分离的或有限数量的蛋白质进行分析。这里,我们探索了大规模的蛋白质动力学模拟，以使用不同的观点观察局部蛋白质构象的动力学。我们分析了分子动力学来研究蛋白质的局部灵活性，使用经典方法，如RMSf，溶剂可及性,还有创新的方法，如局部熵。首先,我们专注于经典的二级结构，并具体分析了β链，β匝数,和弯曲在分子模拟过程中进化。我们强调了β转角和弯曲之间有趣的特定偏差，它们被认为是同一类别，而他们的动态显示出差异。第二,我们使用了一个结构字母，能够近似蛋白质结构构象的每个部分，即蛋白质块（PBs）来分析（i）每个初始局部蛋白质构象在动力学过程中如何演变，以及（ii）这些PBs之间是否存在一些交换。有趣的是,与简单的常规/刚性和线圈/柔性交换相比，结果在很大程度上是复杂的。等值PBProteinBlocksPDBProteinDataBankRMSf均方根波动的缩写由RamaswamyH.Sarma传播。
